Starting phenix.real_space_refine
on Fri Sep 11 13:17:48 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/3j9s_6272/09_2026/3j9s_6272.cif"
  }
  resolution = 2.6
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Zn      3      6.06       5
     S      45      5.16       5
     Cl      3      4.86       5
     C    6012      2.51       5
     N    1638      2.21       5
     O    2106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9813
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3162
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 397, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 376}
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 109
          Unusual residues: {' CA': 2, ' CL': 1, ' ZN': 1}
          Classifications: {'undetermined': 4, 'water': 105}
          Link IDs: {None: 108}
    Chain: "B"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 105
          Classifications: {'water': 105}
          Link IDs: {None: 104}
    Chain: "C"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 105
          Classifications: {'water': 105}
          Link IDs: {None: 104}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.73, per 1000 atoms: 0.28
  Number of scatterers: 9813
  At special positions: 0
  Unit cell: (87.978, 84.909, 106.392, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      3     29.99
     Ca      6     19.99
     Cl      3     17.00
     S      45     16.00
     O    2106      8.00
     N    1638      7.00
     C    6012      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 336.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 501 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS A 153 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS B 153 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS C 153 "


  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 12 sheets defined
      38.0% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
    Processing helix  chain 'A' and resid 23 through 42
      removed outlier: 3.932A  pdb=" N   VAL A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ASP A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   LEU A  30 " --> pdb=" O   ASN A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.735A  pdb=" N   THR A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL A 101 " --> pdb=" O   MET A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 120
    Processing helix  chain 'A' and resid 122 through 128
      removed outlier: 3.867A  pdb=" N   ARG A 126 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 301 through 308
      removed outlier: 3.636A  pdb=" N   LEU A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 308 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 353
    Processing helix  chain 'A' and resid 362 through 365
    Processing helix  chain 'A' and resid 366 through 373
    Processing helix  chain 'A' and resid 375 through 396
      removed outlier: 3.994A  pdb=" N   LEU A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 18
    Processing helix  chain 'B' and resid 23 through 42
      removed outlier: 3.932A  pdb=" N   VAL B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ASP B  29 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   LEU B  30 " --> pdb=" O   ASN B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.736A  pdb=" N   THR B  84 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B 101 " --> pdb=" O   MET B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 122 through 128
      removed outlier: 3.867A  pdb=" N   ARG B 126 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 144
    Processing helix  chain 'B' and resid 201 through 203
      No H-bonds generated for 'chain 'B' and resid 201 through 203'
    Processing helix  chain 'B' and resid 301 through 308
      removed outlier: 3.637A  pdb=" N   LEU B 307 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE B 308 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 353
    Processing helix  chain 'B' and resid 362 through 365
    Processing helix  chain 'B' and resid 366 through 373
    Processing helix  chain 'B' and resid 375 through 396
      removed outlier: 3.994A  pdb=" N   LEU B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 18
    Processing helix  chain 'C' and resid 23 through 42
      removed outlier: 3.932A  pdb=" N   VAL C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ASP C  29 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   LEU C  30 " --> pdb=" O   ASN C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 101
      removed outlier: 3.735A  pdb=" N   THR C  84 " --> pdb=" O   THR C  80 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL C 101 " --> pdb=" O   MET C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 120
    Processing helix  chain 'C' and resid 122 through 128
      removed outlier: 3.866A  pdb=" N   ARG C 126 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 144
    Processing helix  chain 'C' and resid 201 through 203
      No H-bonds generated for 'chain 'C' and resid 201 through 203'
    Processing helix  chain 'C' and resid 301 through 308
      removed outlier: 3.637A  pdb=" N   LEU C 307 " --> pdb=" O   ALA C 303 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE C 308 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 353
    Processing helix  chain 'C' and resid 362 through 365
    Processing helix  chain 'C' and resid 366 through 373
    Processing helix  chain 'C' and resid 375 through 396
      removed outlier: 3.994A  pdb=" N   LEU C 395 " --> pdb=" O   ILE C 391 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 45 through 48
    Processing sheet with id=2, first strand: chain 'A' and resid 150 through 153
    Processing sheet with id=3, first strand: chain 'A' and resid 158 through 168
      removed outlier: 5.658A  pdb=" N   GLY A 185 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET A 177 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   LEU A 324 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU A 226 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   ILE A 326 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR A 224 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   VAL A 330 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   THR A 220 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASP A 286 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 11.805A  pdb=" N   ARG A 216 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
      removed outlier: 10.296A  pdb=" N   ASN A 284 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU A 218 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ALA A 282 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   THR A 220 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 10.030A  pdb=" N   ILE A 280 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 9.703A  pdb=" N   THR A 222 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 10.859A  pdb=" N   GLY A 278 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU A 264 " --> pdb=" O   ASP A 286 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ILE A 288 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   GLU A 262 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   LEU A 290 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU A 260 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   PHE A 292 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN A 258 " --> pdb=" O   PHE A 292 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL A 259 " --> pdb=" O   GLN A 274 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLN A 274 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE A 261 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR A 272 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE A 263 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'A' and resid 236 through 239
    Processing sheet with id=5, first strand: chain 'B' and resid 45 through 48
    Processing sheet with id=6, first strand: chain 'B' and resid 150 through 153
    Processing sheet with id=7, first strand: chain 'B' and resid 158 through 168
      removed outlier: 5.658A  pdb=" N   GLY B 185 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET B 177 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   LEU B 324 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 226 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   ILE B 326 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR B 224 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   VAL B 330 " --> pdb=" O   THR B 220 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   THR B 220 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASP B 286 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 11.805A  pdb=" N   ARG B 216 " --> pdb=" O   ASN B 284 " (cutoff:3.500A)
      removed outlier: 10.295A  pdb=" N   ASN B 284 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B 282 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ALA B 282 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   THR B 220 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
      removed outlier: 10.029A  pdb=" N   ILE B 280 " --> pdb=" O   THR B 220 " (cutoff:3.500A)
      removed outlier: 9.703A  pdb=" N   THR B 222 " --> pdb=" O   GLY B 278 " (cutoff:3.500A)
      removed outlier: 10.859A  pdb=" N   GLY B 278 " --> pdb=" O   THR B 222 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B 264 " --> pdb=" O   ASP B 286 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ILE B 288 " --> pdb=" O   GLU B 262 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLU B 262 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   LEU B 290 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU B 260 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   PHE B 292 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN B 258 " --> pdb=" O   PHE B 292 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL B 259 " --> pdb=" O   GLN B 274 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLN B 274 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE B 261 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR B 272 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE B 263 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'B' and resid 236 through 239
    Processing sheet with id=9, first strand: chain 'C' and resid 45 through 48
    Processing sheet with id=10, first strand: chain 'C' and resid 150 through 153
    Processing sheet with id=11, first strand: chain 'C' and resid 158 through 168
      removed outlier: 5.658A  pdb=" N   GLY C 185 " --> pdb=" O   PRO C 159 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET C 177 " --> pdb=" O   ASN C 167 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   LEU C 324 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   LEU C 226 " --> pdb=" O   LEU C 324 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   ILE C 326 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR C 224 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   VAL C 330 " --> pdb=" O   THR C 220 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   THR C 220 " --> pdb=" O   VAL C 330 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASP C 286 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
      removed outlier: 11.805A  pdb=" N   ARG C 216 " --> pdb=" O   ASN C 284 " (cutoff:3.500A)
      removed outlier: 10.295A  pdb=" N   ASN C 284 " --> pdb=" O   ARG C 216 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU C 218 " --> pdb=" O   ALA C 282 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   ALA C 282 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   THR C 220 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
      removed outlier: 10.030A  pdb=" N   ILE C 280 " --> pdb=" O   THR C 220 " (cutoff:3.500A)
      removed outlier: 9.703A  pdb=" N   THR C 222 " --> pdb=" O   GLY C 278 " (cutoff:3.500A)
      removed outlier: 10.859A  pdb=" N   GLY C 278 " --> pdb=" O   THR C 222 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU C 264 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ILE C 288 " --> pdb=" O   GLU C 262 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   GLU C 262 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   LEU C 290 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU C 260 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   PHE C 292 " --> pdb=" O   ASN C 258 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN C 258 " --> pdb=" O   PHE C 292 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL C 259 " --> pdb=" O   GLN C 274 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLN C 274 " --> pdb=" O   VAL C 259 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE C 261 " --> pdb=" O   THR C 272 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR C 272 " --> pdb=" O   ILE C 261 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE C 263 " --> pdb=" O   ILE C 270 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'C' and resid 236 through 239

    441 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1596
        1.29 -     1.42: 2547
        1.42 -     1.55: 5459
        1.55 -     1.68: 13
        1.68 -     1.81: 81
  Bond restraints: 9696
  Sorted by residual:
  bond pdb=" C   ALA C 110 "
       pdb=" N   PRO C 111 "
    ideal  model  delta    sigma   weight residual
    1.333  1.408 -0.076 1.17e-02 7.31e+03 4.20e+01
  bond pdb=" C   ALA A 110 "
       pdb=" N   PRO A 111 "
    ideal  model  delta    sigma   weight residual
    1.333  1.408 -0.076 1.17e-02 7.31e+03 4.18e+01
  bond pdb=" C   ALA B 110 "
       pdb=" N   PRO B 111 "
    ideal  model  delta    sigma   weight residual
    1.333  1.408 -0.076 1.17e-02 7.31e+03 4.17e+01
  bond pdb=" C   PHE B 361 "
       pdb=" N   PRO B 362 "
    ideal  model  delta    sigma   weight residual
    1.335  1.406 -0.071 1.15e-02 7.56e+03 3.82e+01
  bond pdb=" C   PHE A 361 "
       pdb=" N   PRO A 362 "
    ideal  model  delta    sigma   weight residual
    1.335  1.406 -0.071 1.15e-02 7.56e+03 3.82e+01
  ... (remaining 9691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 12519
        3.47 -     6.95: 586
        6.95 -    10.42: 65
       10.42 -    13.90: 3
       13.90 -    17.37: 27
  Bond angle restraints: 13200
  Sorted by residual:
  angle pdb=" C   PHE C 361 "
        pdb=" N   PRO C 362 "
        pdb=" CA  PRO C 362 "
      ideal   model   delta    sigma   weight residual
     119.66  113.23    6.43 7.20e-01 1.93e+00 7.98e+01
  angle pdb=" C   PHE A 361 "
        pdb=" N   PRO A 362 "
        pdb=" CA  PRO A 362 "
      ideal   model   delta    sigma   weight residual
     119.66  113.23    6.43 7.20e-01 1.93e+00 7.98e+01
  angle pdb=" C   PHE B 361 "
        pdb=" N   PRO B 362 "
        pdb=" CA  PRO B 362 "
      ideal   model   delta    sigma   weight residual
     119.66  113.29    6.37 7.20e-01 1.93e+00 7.82e+01
  angle pdb=" N   SER C 339 "
        pdb=" CA  SER C 339 "
        pdb=" C   SER C 339 "
      ideal   model   delta    sigma   weight residual
     111.36  120.50   -9.14 1.09e+00 8.42e-01 7.03e+01
  angle pdb=" N   SER B 339 "
        pdb=" CA  SER B 339 "
        pdb=" C   SER B 339 "
      ideal   model   delta    sigma   weight residual
     111.36  120.49   -9.13 1.09e+00 8.42e-01 7.02e+01
  ... (remaining 13195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4970
       17.94 -    35.87: 583
       35.87 -    53.81: 198
       53.81 -    71.75: 42
       71.75 -    89.68: 21
  Dihedral angle restraints: 5814
    sinusoidal: 2325
      harmonic: 3489
  Sorted by residual:
  dihedral pdb=" CH3 ACE B   0 "
           pdb=" C   ACE B   0 "
           pdb=" N   MET B   1 "
           pdb=" CA  MET B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -160.61  -19.39     1      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CH3 ACE C   0 "
           pdb=" C   ACE C   0 "
           pdb=" N   MET C   1 "
           pdb=" CA  MET C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -160.66  -19.34     1      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CH3 ACE A   0 "
           pdb=" C   ACE A   0 "
           pdb=" N   MET A   1 "
           pdb=" CA  MET A   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -160.68  -19.32     1      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 5811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 965
       0.089 -    0.179: 349
       0.179 -    0.268: 113
       0.268 -    0.357: 37
       0.357 -    0.447: 27
  Chirality restraints: 1491
  Sorted by residual:
  chirality pdb=" CA  LYS B  17 "
            pdb=" N   LYS B  17 "
            pdb=" C   LYS B  17 "
            pdb=" CB  LYS B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.99e+00
  chirality pdb=" CA  LYS C  17 "
            pdb=" N   LYS C  17 "
            pdb=" C   LYS C  17 "
            pdb=" CB  LYS C  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.93e+00
  chirality pdb=" CA  LYS A  17 "
            pdb=" N   LYS A  17 "
            pdb=" C   LYS A  17 "
            pdb=" CB  LYS A  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.93e+00
  ... (remaining 1488 not shown)

  Planarity restraints: 1740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ACE B   0 "   -0.031 2.00e-02 2.50e+03   1.01e-01 1.28e+02
        pdb=" O   ACE B   0 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH3 ACE B   0 "    0.092 2.00e-02 2.50e+03
        pdb=" N   MET B   1 "   -0.161 2.00e-02 2.50e+03
        pdb=" CA  MET B   1 "    0.124 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ACE C   0 "   -0.030 2.00e-02 2.50e+03   1.01e-01 1.28e+02
        pdb=" O   ACE C   0 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH3 ACE C   0 "    0.091 2.00e-02 2.50e+03
        pdb=" N   MET C   1 "   -0.161 2.00e-02 2.50e+03
        pdb=" CA  MET C   1 "    0.124 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ACE A   0 "   -0.030 2.00e-02 2.50e+03   1.01e-01 1.28e+02
        pdb=" O   ACE A   0 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH3 ACE A   0 "    0.091 2.00e-02 2.50e+03
        pdb=" N   MET A   1 "   -0.161 2.00e-02 2.50e+03
        pdb=" CA  MET A   1 "    0.124 2.00e-02 2.50e+03
  ... (remaining 1737 not shown)

  Histogram of nonbonded interaction distances:
        0.22 -     1.15: 9
        1.15 -     2.09: 8
        2.09 -     3.03: 6267
        3.03 -     3.96: 26695
        3.96 -     4.90: 54752
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 87731
  Sorted by model distance:
  nonbonded pdb="CA    CA A 503 "
            pdb="CA    CA C 503 "
     model   vdw
     0.216 1.980
  nonbonded pdb="CA    CA B 503 "
            pdb="CA    CA C 503 "
     model   vdw
     0.216 1.980
  nonbonded pdb="CA    CA A 503 "
            pdb="CA    CA B 503 "
     model   vdw
     0.217 1.980
  nonbonded pdb="CL    CL B 502 "
            pdb="CL    CL C 502 "
     model   vdw
     0.273 3.340
  nonbonded pdb="CL    CL A 502 "
            pdb="CL    CL B 502 "
     model   vdw
     0.273 3.340
  ... (remaining 87726 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.530
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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      :  0.021   0.358   9699  Z= 1.420
  Angle     :  1.797  17.372  13200  Z= 1.164
  Chirality :  0.120   0.447   1491
  Planarity :  0.009   0.101   1740
  Dihedral  : 18.550  89.683   3546
  Min Nonbonded Distance : 0.216

Molprobity Statistics.
  All-atom Clashscore : 25.10
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  1.27 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 17.71 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.97 (0.24), residues: 1185
  helix:  2.81 (0.23), residues: 387
  sheet:  1.93 (0.30), residues: 315
  loop : -0.44 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 168 
 TYR   0.022   0.005   TYR C 135 
 PHE   0.043   0.004   PHE A 129 
 TRP   0.015   0.003   TRP A 247 
 HIS   0.012   0.004   HIS A 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.02028 /  1.41 ( 9696)
  covalent geometry    : angle       1.79732 /  1.16 (13200)
  hydrogen bonds       : bond        0.24496 / 15.86 (  441)
  hydrogen bonds       : angle       6.87298 /  5.11 ( 1251)
  metal coordination   : bond        0.21303 / 10.65 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 245
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7299 (p90)
  outliers start: 72
  outliers final: 15
  residues processed: 286
  average time/residue: 0.6767
  time to fit residues: 204.8206
Evaluate side-chains
  144 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  239 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
B 128 ASN
B 175 ASN
C 128 ASN
C 175 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.061986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.050562 restraints weight = 16162.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2603 rms_B_bonded: 2.57
r_work: 0.2460 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9699  Z= 0.220
  Angle     :  0.658   7.412  13200  Z= 0.353
  Chirality :  0.044   0.166   1491
  Planarity :  0.005   0.060   1740
  Dihedral  :  8.325  81.009   1334
  Min Nonbonded Distance : 1.261

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 22.38 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.73 (0.24), residues: 1185
  helix:  2.20 (0.24), residues: 393
  sheet:  1.56 (0.30), residues: 318
  loop : -0.02 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 126 
 TYR   0.024   0.002   TYR B 353 
 PHE   0.022   0.002   PHE A 129 
 TRP   0.012   0.001   TRP A  59 
 HIS   0.005   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.22 ( 9696)
  covalent geometry    : angle       0.65837 /  0.35 (13200)
  hydrogen bonds       : bond        0.05622 /  3.56 (  441)
  hydrogen bonds       : angle       4.61336 /  3.35 ( 1251)
  metal coordination   : bond        0.01260 /  0.63 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ASN cc_start: 0.9256 (t0) cc_final: 0.8928 (m-40)
REVERT: A  154 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8942 (mtmm)
REVERT: A  170 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8231 (pm20)
REVERT: A  187 GLU cc_start: 0.9269 (tt0) cc_final: 0.8955 (tt0)
REVERT: A  209 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7458 (tt0)
REVERT: A  289 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7820 (ptm-80)
REVERT: A  327 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8251 (mm-30)
REVERT: A  332 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9086 (mt-10)
REVERT: A  396 VAL cc_start: 0.9442 (t) cc_final: 0.9203 (p)
REVERT: B    9 LYS cc_start: 0.9259 (tptm) cc_final: 0.9038 (tppp)
REVERT: B   45 GLU cc_start: 0.8306 (tp30) cc_final: 0.8042 (mm-30)
REVERT: B   60 ASN cc_start: 0.9278 (t0) cc_final: 0.8884 (t0)
REVERT: B  154 LYS cc_start: 0.8689 (mtmm) cc_final: 0.7834 (mttp)
REVERT: B  187 GLU cc_start: 0.9186 (tt0) cc_final: 0.8851 (tt0)
REVERT: B  209 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7883 (tt0)
REVERT: B  213 GLN cc_start: 0.9168 (tt0) cc_final: 0.8947 (tp40)
REVERT: B  342 MET cc_start: 0.9438 (mpp) cc_final: 0.9226 (mpp)
REVERT: C   20 GLU cc_start: 0.9257 (tt0) cc_final: 0.8906 (tt0)
REVERT: C  154 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8590 (mmmm)
REVERT: C  209 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8199 (tt0)
REVERT: C  352 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9276 (tt0)
REVERT: C  396 VAL cc_start: 0.9426 (t) cc_final: 0.9226 (p)
  outliers start: 42
  outliers final: 8
  residues processed: 194
  average time/residue: 0.6785
  time to fit residues: 139.4645
Evaluate side-chains
  154 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  352 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 34 optimal weight:   20.0000
   chunk 116 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 110 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    7.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 128 ASN
B 366 ASN
C 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.062619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.051489 restraints weight = 14409.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2596 rms_B_bonded: 2.36
r_work: 0.2457 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2325 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8994
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9699  Z= 0.205
  Angle     :  0.566   6.491  13200  Z= 0.300
  Chirality :  0.041   0.144   1491
  Planarity :  0.004   0.043   1740
  Dihedral  :  6.526  80.561   1315
  Min Nonbonded Distance : 1.034

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.00 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.64 (0.25), residues: 1185
  helix:  2.29 (0.24), residues: 393
  sheet:  1.16 (0.31), residues: 303
  loop :  0.11 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.012   0.001   TYR C 160 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.005   0.001   TRP C  59 
 HIS   0.004   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.20 ( 9696)
  covalent geometry    : angle       0.56628 /  0.30 (13200)
  hydrogen bonds       : bond        0.04866 /  3.07 (  441)
  hydrogen bonds       : angle       4.25489 /  3.07 ( 1251)
  metal coordination   : bond        0.00569 /  0.28 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8726 (tp30) cc_final: 0.7953 (mm-30)
REVERT: A   60 ASN cc_start: 0.9326 (t0) cc_final: 0.8929 (m-40)
REVERT: A  130 ASP cc_start: 0.9541 (t0) cc_final: 0.9169 (t0)
REVERT: A  154 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8692 (mtmm)
REVERT: A  187 GLU cc_start: 0.9384 (tt0) cc_final: 0.9123 (tt0)
REVERT: A  209 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.7501 (tp30)
REVERT: A  289 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8107 (ptm-80)
REVERT: A  327 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8492 (mm-30)
REVERT: A  352 GLU cc_start: 0.9524 (OUTLIER) cc_final: 0.9311 (tm-30)
REVERT: A  396 VAL cc_start: 0.9388 (t) cc_final: 0.9183 (p)
REVERT: B    9 LYS cc_start: 0.9289 (tptm) cc_final: 0.9050 (tppp)
REVERT: B   20 GLU cc_start: 0.9429 (tt0) cc_final: 0.8885 (tt0)
REVERT: B   45 GLU cc_start: 0.8724 (tp30) cc_final: 0.8144 (mm-30)
REVERT: B   60 ASN cc_start: 0.9373 (t0) cc_final: 0.8831 (t0)
REVERT: B   62 ASP cc_start: 0.9620 (t0) cc_final: 0.9418 (t0)
REVERT: B  154 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8097 (mtmm)
REVERT: B  187 GLU cc_start: 0.9318 (tt0) cc_final: 0.9049 (tt0)
REVERT: B  209 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8662 (tp30)
REVERT: C    9 LYS cc_start: 0.9172 (tptm) cc_final: 0.8955 (tptm)
REVERT: C   20 GLU cc_start: 0.9395 (tt0) cc_final: 0.9069 (tt0)
REVERT: C   79 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8683 (mm-30)
REVERT: C   86 ASP cc_start: 0.9290 (m-30) cc_final: 0.9035 (m-30)
REVERT: C  130 ASP cc_start: 0.9561 (t0) cc_final: 0.8942 (t0)
REVERT: C  154 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8684 (mmmm)
REVERT: C  209 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (mt-10)
REVERT: C  325 ARG cc_start: 0.9253 (ttp-170) cc_final: 0.8825 (ttm110)
REVERT: C  327 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.9026 (mt-10)
  outliers start: 36
  outliers final: 10
  residues processed: 185
  average time/residue: 0.6627
  time to fit residues: 130.0758
Evaluate side-chains
  151 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:   40.0000
   chunk 65 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 74 optimal weight:    7.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 366 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.062625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.051547 restraints weight = 15123.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.2597 rms_B_bonded: 2.42
r_work: 0.2454 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8965
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9699  Z= 0.167
  Angle     :  0.527   5.308  13200  Z= 0.278
  Chirality :  0.039   0.140   1491
  Planarity :  0.004   0.034   1740
  Dihedral  :  5.243  59.950   1308
  Min Nonbonded Distance : 1.121

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.29 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.52 (0.25), residues: 1185
  helix:  2.21 (0.25), residues: 396
  sheet:  0.90 (0.31), residues: 303
  loop :  0.16 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.011   0.001   TYR C 160 
 PHE   0.014   0.001   PHE C 129 
 TRP   0.005   0.001   TRP C  59 
 HIS   0.003   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.17 ( 9696)
  covalent geometry    : angle       0.52737 /  0.28 (13200)
  hydrogen bonds       : bond        0.04423 /  2.81 (  441)
  hydrogen bonds       : angle       4.09029 /  2.95 ( 1251)
  metal coordination   : bond        0.00361 /  0.18 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8687 (tp30) cc_final: 0.7564 (mm-30)
REVERT: A   60 ASN cc_start: 0.9165 (t0) cc_final: 0.8841 (m-40)
REVERT: A  130 ASP cc_start: 0.9501 (t0) cc_final: 0.9085 (t0)
REVERT: A  137 GLU cc_start: 0.9309 (tt0) cc_final: 0.9028 (tt0)
REVERT: A  154 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8700 (mtmm)
REVERT: A  187 GLU cc_start: 0.9310 (tt0) cc_final: 0.9044 (tt0)
REVERT: A  209 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7223 (tp30)
REVERT: A  289 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8016 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9432 (OUTLIER) cc_final: 0.9142 (tm-30)
REVERT: B    9 LYS cc_start: 0.9290 (tptm) cc_final: 0.9083 (tppp)
REVERT: B   16 ASP cc_start: 0.9145 (m-30) cc_final: 0.8920 (m-30)
REVERT: B   20 GLU cc_start: 0.9229 (tt0) cc_final: 0.8760 (tp30)
REVERT: B   45 GLU cc_start: 0.8655 (tp30) cc_final: 0.7882 (mm-30)
REVERT: B   60 ASN cc_start: 0.9235 (t0) cc_final: 0.8635 (t0)
REVERT: B   79 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8481 (mm-30)
REVERT: B  154 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7664 (mtmm)
REVERT: B  187 GLU cc_start: 0.9185 (tt0) cc_final: 0.8954 (tt0)
REVERT: B  209 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8352 (tp30)
REVERT: B  352 GLU cc_start: 0.9492 (tt0) cc_final: 0.9203 (tt0)
REVERT: B  394 MET cc_start: 0.9356 (mtp) cc_final: 0.9003 (ttm)
REVERT: C    9 LYS cc_start: 0.9182 (tptm) cc_final: 0.8928 (tptm)
REVERT: C   45 GLU cc_start: 0.8689 (tp30) cc_final: 0.8404 (mm-30)
REVERT: C   79 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: C   86 ASP cc_start: 0.9165 (m-30) cc_final: 0.8844 (m-30)
REVERT: C  130 ASP cc_start: 0.9535 (t0) cc_final: 0.8824 (t0)
REVERT: C  137 GLU cc_start: 0.9270 (tt0) cc_final: 0.9032 (tt0)
REVERT: C  154 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8596 (mmmm)
REVERT: C  209 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8428 (mt-10)
REVERT: C  325 ARG cc_start: 0.9177 (ttp-170) cc_final: 0.8837 (ttm110)
REVERT: C  327 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (mt-10)
  outliers start: 31
  outliers final: 11
  residues processed: 171
  average time/residue: 0.6805
  time to fit residues: 123.2331
Evaluate side-chains
  159 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  137 GLU
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain C residue    8 SER
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 104 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 106 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 44 optimal weight:   30.0000
   overall best weight:    6.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.062390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.051377 restraints weight = 14684.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2591 rms_B_bonded: 2.38
r_work: 0.2453 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2323 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9699  Z= 0.169
  Angle     :  0.516   5.516  13200  Z= 0.270
  Chirality :  0.039   0.137   1491
  Planarity :  0.003   0.029   1740
  Dihedral  :  4.823  49.453   1306
  Min Nonbonded Distance : 1.100

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.81 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.44 (0.25), residues: 1185
  helix:  2.17 (0.25), residues: 396
  sheet:  0.76 (0.31), residues: 303
  loop :  0.14 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 289 
 TYR   0.010   0.001   TYR C 160 
 PHE   0.015   0.001   PHE C 129 
 TRP   0.005   0.001   TRP B 139 
 HIS   0.002   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.17 ( 9696)
  covalent geometry    : angle       0.51551 /  0.27 (13200)
  hydrogen bonds       : bond        0.04294 /  2.73 (  441)
  hydrogen bonds       : angle       4.02697 /  2.90 ( 1251)
  metal coordination   : bond        0.00360 /  0.18 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8953 (tp30) cc_final: 0.7883 (mm-30)
REVERT: A   60 ASN cc_start: 0.9291 (t0) cc_final: 0.9015 (m-40)
REVERT: A  130 ASP cc_start: 0.9555 (t0) cc_final: 0.9185 (t0)
REVERT: A  154 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8742 (mttp)
REVERT: A  187 GLU cc_start: 0.9416 (tt0) cc_final: 0.9192 (tt0)
REVERT: A  209 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.7659 (tp30)
REVERT: A  289 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8140 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9260 (tm-30)
REVERT: B   20 GLU cc_start: 0.9353 (tt0) cc_final: 0.8847 (tp30)
REVERT: B   45 GLU cc_start: 0.8915 (tp30) cc_final: 0.8166 (mm-30)
REVERT: B   60 ASN cc_start: 0.9329 (t0) cc_final: 0.8819 (t0)
REVERT: B   79 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8627 (mm-30)
REVERT: B  154 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8021 (mtmm)
REVERT: B  209 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8406 (tp30)
REVERT: B  325 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8497 (ttm-80)
REVERT: B  394 MET cc_start: 0.9386 (mtp) cc_final: 0.9124 (ttm)
REVERT: C   20 GLU cc_start: 0.9412 (tt0) cc_final: 0.8696 (tp30)
REVERT: C   45 GLU cc_start: 0.8951 (tp30) cc_final: 0.8602 (mm-30)
REVERT: C   68 THR cc_start: 0.9538 (p) cc_final: 0.9111 (m)
REVERT: C   79 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: C   86 ASP cc_start: 0.9291 (m-30) cc_final: 0.8961 (m-30)
REVERT: C  130 ASP cc_start: 0.9636 (t0) cc_final: 0.8980 (t0)
REVERT: C  137 GLU cc_start: 0.9387 (tt0) cc_final: 0.9185 (tt0)
REVERT: C  148 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8650 (t)
REVERT: C  154 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8700 (mmmm)
REVERT: C  209 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8576 (mt-10)
REVERT: C  325 ARG cc_start: 0.9245 (ttp-170) cc_final: 0.8968 (ttm110)
REVERT: C  327 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8937 (mt-10)
  outliers start: 31
  outliers final: 9
  residues processed: 167
  average time/residue: 0.7351
  time to fit residues: 129.8769
Evaluate side-chains
  153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain C residue    8 SER
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 70 optimal weight:   30.0000
   chunk 74 optimal weight:    7.9990
   chunk 17 optimal weight:   50.0000
   chunk 50 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 21 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 96 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    5.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.062279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.051240 restraints weight = 15185.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2553 rms_B_bonded: 2.43
r_work: 0.2414 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9699  Z= 0.154
  Angle     :  0.518   7.643  13200  Z= 0.269
  Chirality :  0.039   0.137   1491
  Planarity :  0.003   0.027   1740
  Dihedral  :  4.743  49.877   1306
  Min Nonbonded Distance : 1.120

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.81 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.40 (0.25), residues: 1185
  helix:  2.19 (0.25), residues: 396
  sheet:  0.64 (0.31), residues: 303
  loop :  0.16 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.010   0.001   TYR C  77 
 PHE   0.014   0.001   PHE A 129 
 TRP   0.004   0.001   TRP C 247 
 HIS   0.002   0.000   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 9696)
  covalent geometry    : angle       0.51755 /  0.27 (13200)
  hydrogen bonds       : bond        0.04164 /  2.64 (  441)
  hydrogen bonds       : angle       3.98411 /  2.87 ( 1251)
  metal coordination   : bond        0.00310 /  0.16 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8855 (tp30) cc_final: 0.7796 (mm-30)
REVERT: A   60 ASN cc_start: 0.9149 (t0) cc_final: 0.8923 (m-40)
REVERT: A  130 ASP cc_start: 0.9464 (t0) cc_final: 0.9052 (t0)
REVERT: A  154 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8543 (mttp)
REVERT: A  187 GLU cc_start: 0.9284 (tt0) cc_final: 0.9045 (tt0)
REVERT: A  209 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.7229 (tp30)
REVERT: A  289 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7967 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9119 (tm-30)
REVERT: B   20 GLU cc_start: 0.9228 (tt0) cc_final: 0.8676 (tp30)
REVERT: B   45 GLU cc_start: 0.8765 (tp30) cc_final: 0.7918 (mm-30)
REVERT: B   60 ASN cc_start: 0.9196 (t0) cc_final: 0.8651 (t0)
REVERT: B  130 ASP cc_start: 0.9399 (t0) cc_final: 0.8909 (t0)
REVERT: B  137 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8846 (tt0)
REVERT: B  154 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7367 (mtmm)
REVERT: B  177 MET cc_start: 0.9087 (tmm) cc_final: 0.8000 (tmm)
REVERT: B  187 GLU cc_start: 0.9039 (tt0) cc_final: 0.8628 (tp30)
REVERT: B  209 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8216 (tp30)
REVERT: B  230 GLU cc_start: 0.9088 (mp0) cc_final: 0.8830 (mp0)
REVERT: B  325 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8536 (ttm110)
REVERT: B  352 GLU cc_start: 0.9481 (tt0) cc_final: 0.9070 (tm-30)
REVERT: B  394 MET cc_start: 0.9190 (mtp) cc_final: 0.8911 (ttm)
REVERT: C    9 LYS cc_start: 0.8876 (tptm) cc_final: 0.8478 (tppp)
REVERT: C   20 GLU cc_start: 0.9274 (tt0) cc_final: 0.8497 (tp30)
REVERT: C   45 GLU cc_start: 0.8885 (tp30) cc_final: 0.8528 (mm-30)
REVERT: C   68 THR cc_start: 0.9490 (p) cc_final: 0.9031 (m)
REVERT: C   79 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8527 (mm-30)
REVERT: C   86 ASP cc_start: 0.9134 (m-30) cc_final: 0.8799 (m-30)
REVERT: C  130 ASP cc_start: 0.9507 (t0) cc_final: 0.8640 (t0)
REVERT: C  137 GLU cc_start: 0.9261 (tt0) cc_final: 0.9054 (tt0)
REVERT: C  148 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8528 (t)
REVERT: C  154 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8410 (mmmm)
REVERT: C  187 GLU cc_start: 0.9176 (tt0) cc_final: 0.8659 (tp30)
REVERT: C  209 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8548 (mt-10)
REVERT: C  325 ARG cc_start: 0.9034 (ttp-170) cc_final: 0.8631 (ttm110)
REVERT: C  327 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8672 (mt-10)
REVERT: C  352 GLU cc_start: 0.9408 (tt0) cc_final: 0.9152 (tm-30)
REVERT: C  365 MET cc_start: 0.9583 (mmm) cc_final: 0.9339 (tpp)
  outliers start: 32
  outliers final: 10
  residues processed: 179
  average time/residue: 0.7350
  time to fit residues: 139.0517
Evaluate side-chains
  161 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  137 GLU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain C residue    8 SER
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 87 optimal weight:   10.0000
   chunk 97 optimal weight:   30.0000
   chunk 71 optimal weight:   30.0000
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    6.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.061966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.050944 restraints weight = 14837.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.2543 rms_B_bonded: 2.40
r_work: 0.2406 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2284 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9699  Z= 0.176
  Angle     :  0.527   5.822  13200  Z= 0.275
  Chirality :  0.039   0.138   1491
  Planarity :  0.003   0.027   1740
  Dihedral  :  4.743  50.310   1306
  Min Nonbonded Distance : 1.095

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.52 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.41 (0.25), residues: 1185
  helix:  2.15 (0.25), residues: 396
  sheet:  0.78 (0.31), residues: 294
  loop :  0.10 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 126 
 TYR   0.011   0.001   TYR B 353 
 PHE   0.014   0.001   PHE C 129 
 TRP   0.004   0.001   TRP C 247 
 HIS   0.002   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.18 ( 9696)
  covalent geometry    : angle       0.52653 /  0.27 (13200)
  hydrogen bonds       : bond        0.04212 /  2.67 (  441)
  hydrogen bonds       : angle       3.99803 /  2.88 ( 1251)
  metal coordination   : bond        0.00371 /  0.19 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9039 (tp30) cc_final: 0.8053 (mm-30)
REVERT: A   60 ASN cc_start: 0.9233 (t0) cc_final: 0.9031 (m-40)
REVERT: A  130 ASP cc_start: 0.9462 (t0) cc_final: 0.9089 (t0)
REVERT: A  137 GLU cc_start: 0.9322 (tt0) cc_final: 0.9058 (tt0)
REVERT: A  154 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8611 (mttp)
REVERT: A  187 GLU cc_start: 0.9339 (tt0) cc_final: 0.9127 (tt0)
REVERT: A  209 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.7452 (tp30)
REVERT: A  289 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8246 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9483 (OUTLIER) cc_final: 0.9234 (tm-30)
REVERT: B   20 GLU cc_start: 0.9328 (tt0) cc_final: 0.8733 (tp30)
REVERT: B   45 GLU cc_start: 0.8952 (tp30) cc_final: 0.8136 (mm-30)
REVERT: B   60 ASN cc_start: 0.9270 (t0) cc_final: 0.8808 (t0)
REVERT: B  130 ASP cc_start: 0.9457 (t0) cc_final: 0.9067 (t0)
REVERT: B  137 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9035 (tt0)
REVERT: B  154 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7440 (mtmm)
REVERT: B  187 GLU cc_start: 0.9142 (tt0) cc_final: 0.8729 (tp30)
REVERT: B  209 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8296 (tp30)
REVERT: B  230 GLU cc_start: 0.9193 (mp0) cc_final: 0.8943 (mp0)
REVERT: B  325 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8545 (ttm110)
REVERT: B  352 GLU cc_start: 0.9546 (tt0) cc_final: 0.9140 (tm-30)
REVERT: B  394 MET cc_start: 0.9185 (mtp) cc_final: 0.8958 (ttm)
REVERT: C    9 LYS cc_start: 0.8917 (tptm) cc_final: 0.8702 (tppp)
REVERT: C   20 GLU cc_start: 0.9354 (tt0) cc_final: 0.8587 (tp30)
REVERT: C   45 GLU cc_start: 0.9036 (tp30) cc_final: 0.8663 (mm-30)
REVERT: C   68 THR cc_start: 0.9517 (p) cc_final: 0.9074 (m)
REVERT: C   79 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8665 (mm-30)
REVERT: C   86 ASP cc_start: 0.9217 (m-30) cc_final: 0.8913 (m-30)
REVERT: C  130 ASP cc_start: 0.9519 (t0) cc_final: 0.9087 (t0)
REVERT: C  148 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (t)
REVERT: C  154 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8360 (mttp)
REVERT: C  187 GLU cc_start: 0.9257 (tt0) cc_final: 0.8793 (tp30)
REVERT: C  325 ARG cc_start: 0.9092 (ttp-170) cc_final: 0.8676 (ttm110)
REVERT: C  327 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8851 (mt-10)
REVERT: C  352 GLU cc_start: 0.9482 (tt0) cc_final: 0.9244 (tm-30)
REVERT: C  365 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.9347 (tpp)
  outliers start: 32
  outliers final: 9
  residues processed: 177
  average time/residue: 0.7714
  time to fit residues: 144.4156
Evaluate side-chains
  159 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  137 GLU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 102 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   chunk 89 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 92 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 317 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.061889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.050945 restraints weight = 14968.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2541 rms_B_bonded: 2.40
r_work: 0.2403 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2275 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9699  Z= 0.178
  Angle     :  0.540   9.152  13200  Z= 0.280
  Chirality :  0.039   0.138   1491
  Planarity :  0.003   0.026   1740
  Dihedral  :  4.757  51.227   1306
  Min Nonbonded Distance : 1.098

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.10 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.36 (0.25), residues: 1185
  helix:  2.10 (0.25), residues: 396
  sheet:  0.67 (0.31), residues: 297
  loop :  0.16 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 126 
 TYR   0.010   0.002   TYR B 353 
 PHE   0.014   0.001   PHE C 129 
 TRP   0.004   0.001   TRP C 247 
 HIS   0.002   0.001   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.18 ( 9696)
  covalent geometry    : angle       0.53968 /  0.28 (13200)
  hydrogen bonds       : bond        0.04187 /  2.66 (  441)
  hydrogen bonds       : angle       4.00372 /  2.89 ( 1251)
  metal coordination   : bond        0.00361 /  0.18 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9096 (tp30) cc_final: 0.8156 (mm-30)
REVERT: A   60 ASN cc_start: 0.9246 (t0) cc_final: 0.9045 (m-40)
REVERT: A  130 ASP cc_start: 0.9476 (t0) cc_final: 0.9072 (t0)
REVERT: A  137 GLU cc_start: 0.9342 (tt0) cc_final: 0.9130 (tt0)
REVERT: A  154 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8642 (mttp)
REVERT: A  187 GLU cc_start: 0.9351 (tt0) cc_final: 0.9145 (tt0)
REVERT: A  209 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.7387 (tp30)
REVERT: A  289 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8306 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9241 (tm-30)
REVERT: B   20 GLU cc_start: 0.9326 (tt0) cc_final: 0.9029 (tt0)
REVERT: B   45 GLU cc_start: 0.8972 (tp30) cc_final: 0.8122 (mm-30)
REVERT: B   60 ASN cc_start: 0.9266 (t0) cc_final: 0.8796 (t0)
REVERT: B  130 ASP cc_start: 0.9518 (t0) cc_final: 0.8949 (t0)
REVERT: B  137 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8997 (tt0)
REVERT: B  154 LYS cc_start: 0.8510 (mtmm) cc_final: 0.7414 (mtmm)
REVERT: B  177 MET cc_start: 0.9107 (tmm) cc_final: 0.8004 (tmm)
REVERT: B  187 GLU cc_start: 0.9157 (tt0) cc_final: 0.8737 (tp30)
REVERT: B  209 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8336 (tp30)
REVERT: B  230 GLU cc_start: 0.9197 (mp0) cc_final: 0.8940 (mp0)
REVERT: B  325 ARG cc_start: 0.8870 (mtm-85) cc_final: 0.8532 (ttm110)
REVERT: B  352 GLU cc_start: 0.9560 (tt0) cc_final: 0.9164 (tm-30)
REVERT: B  374 TYR cc_start: 0.9416 (OUTLIER) cc_final: 0.9045 (t80)
REVERT: B  394 MET cc_start: 0.9196 (mtp) cc_final: 0.8977 (ttm)
REVERT: C   45 GLU cc_start: 0.9102 (tp30) cc_final: 0.8743 (mm-30)
REVERT: C   86 ASP cc_start: 0.9219 (m-30) cc_final: 0.8916 (m-30)
REVERT: C  130 ASP cc_start: 0.9516 (t0) cc_final: 0.9082 (t0)
REVERT: C  148 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8317 (t)
REVERT: C  154 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8353 (mttt)
REVERT: C  187 GLU cc_start: 0.9266 (tt0) cc_final: 0.8773 (tp30)
REVERT: C  230 GLU cc_start: 0.9162 (mp0) cc_final: 0.8832 (mp0)
REVERT: C  260 GLU cc_start: 0.7819 (pp20) cc_final: 0.7522 (pp20)
REVERT: C  325 ARG cc_start: 0.9094 (ttp-170) cc_final: 0.8756 (ttm-80)
REVERT: C  327 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8860 (mt-10)
REVERT: C  352 GLU cc_start: 0.9489 (tt0) cc_final: 0.9167 (tm-30)
REVERT: C  379 GLU cc_start: 0.9352 (tt0) cc_final: 0.9062 (tt0)
  outliers start: 28
  outliers final: 10
  residues processed: 181
  average time/residue: 0.8048
  time to fit residues: 153.8107
Evaluate side-chains
  172 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  137 GLU
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  374 TYR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 83 optimal weight:   30.0000
   chunk 75 optimal weight:    0.0870
   chunk 98 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    4.6166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 317 HIS
B 317 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.062686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.051616 restraints weight = 15522.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.2558 rms_B_bonded: 2.48
r_work: 0.2420 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9699  Z= 0.136
  Angle     :  0.530   7.206  13200  Z= 0.276
  Chirality :  0.039   0.141   1491
  Planarity :  0.003   0.032   1740
  Dihedral  :  4.715  51.687   1306
  Min Nonbonded Distance : 1.150

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.90 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.34 (0.25), residues: 1185
  helix:  2.06 (0.25), residues: 396
  sheet:  0.63 (0.31), residues: 297
  loop :  0.19 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 126 
 TYR   0.010   0.001   TYR B 135 
 PHE   0.013   0.001   PHE C 129 
 TRP   0.005   0.001   TRP B 139 
 HIS   0.002   0.000   HIS C 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 9696)
  covalent geometry    : angle       0.52959 /  0.28 (13200)
  hydrogen bonds       : bond        0.03999 /  2.54 (  441)
  hydrogen bonds       : angle       3.99241 /  2.88 ( 1251)
  metal coordination   : bond        0.00251 /  0.13 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8970 (tp30) cc_final: 0.7860 (mm-30)
REVERT: A   60 ASN cc_start: 0.9122 (t0) cc_final: 0.8890 (m-40)
REVERT: A  130 ASP cc_start: 0.9443 (t0) cc_final: 0.9033 (t0)
REVERT: A  137 GLU cc_start: 0.9255 (tt0) cc_final: 0.9028 (tt0)
REVERT: A  154 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8563 (mttp)
REVERT: A  187 GLU cc_start: 0.9270 (tt0) cc_final: 0.9056 (tt0)
REVERT: A  209 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.7127 (tp30)
REVERT: A  289 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8417 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9103 (tm-30)
REVERT: B   20 GLU cc_start: 0.9179 (tt0) cc_final: 0.8638 (tp30)
REVERT: B   45 GLU cc_start: 0.8838 (tp30) cc_final: 0.7989 (mm-30)
REVERT: B   60 ASN cc_start: 0.9155 (t0) cc_final: 0.8652 (m-40)
REVERT: B  130 ASP cc_start: 0.9497 (t0) cc_final: 0.8792 (t0)
REVERT: B  135 TYR cc_start: 0.9152 (m-80) cc_final: 0.8890 (m-80)
REVERT: B  154 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7102 (mtmm)
REVERT: B  187 GLU cc_start: 0.9075 (tt0) cc_final: 0.8593 (tp30)
REVERT: B  209 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8246 (tp30)
REVERT: B  230 GLU cc_start: 0.9099 (mp0) cc_final: 0.8825 (mp0)
REVERT: B  262 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8812 (tt0)
REVERT: B  315 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9014 (pt0)
REVERT: B  325 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8350 (ttm110)
REVERT: B  352 GLU cc_start: 0.9492 (tt0) cc_final: 0.9069 (tm-30)
REVERT: B  374 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8967 (t80)
REVERT: B  379 GLU cc_start: 0.9277 (tt0) cc_final: 0.8988 (tt0)
REVERT: C   20 GLU cc_start: 0.9251 (tt0) cc_final: 0.8588 (tt0)
REVERT: C   45 GLU cc_start: 0.8947 (tp30) cc_final: 0.8586 (mm-30)
REVERT: C   68 THR cc_start: 0.9463 (p) cc_final: 0.9033 (m)
REVERT: C   79 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8504 (mm-30)
REVERT: C   86 ASP cc_start: 0.9134 (m-30) cc_final: 0.8796 (m-30)
REVERT: C  130 ASP cc_start: 0.9461 (t0) cc_final: 0.9055 (t0)
REVERT: C  148 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8414 (t)
REVERT: C  154 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8328 (mttp)
REVERT: C  187 GLU cc_start: 0.9143 (tt0) cc_final: 0.8678 (tp30)
REVERT: C  262 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8698 (mt-10)
REVERT: C  289 ARG cc_start: 0.9066 (ptm-80) cc_final: 0.8294 (ptm-80)
REVERT: C  295 MET cc_start: 0.9123 (ttm) cc_final: 0.8612 (tpp)
REVERT: C  325 ARG cc_start: 0.9035 (ttp-170) cc_final: 0.8572 (ttm110)
REVERT: C  327 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8616 (mt-10)
REVERT: C  352 GLU cc_start: 0.9409 (tt0) cc_final: 0.9142 (tm-30)
REVERT: C  365 MET cc_start: 0.9250 (tpp) cc_final: 0.8876 (tpp)
  outliers start: 27
  outliers final: 11
  residues processed: 181
  average time/residue: 0.7306
  time to fit residues: 139.9206
Evaluate side-chains
  178 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  374 TYR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 317 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.062328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.051588 restraints weight = 15062.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2559 rms_B_bonded: 2.37
r_work: 0.2425 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2301 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9699  Z= 0.150
  Angle     :  0.541   8.781  13200  Z= 0.280
  Chirality :  0.039   0.140   1491
  Planarity :  0.003   0.039   1740
  Dihedral  :  4.690  51.549   1306
  Min Nonbonded Distance : 1.119

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 22.95 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.36 (0.25), residues: 1185
  helix:  2.07 (0.25), residues: 396
  sheet:  0.63 (0.31), residues: 297
  loop :  0.21 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 126 
 TYR   0.011   0.002   TYR B 195 
 PHE   0.014   0.001   PHE C 129 
 TRP   0.004   0.001   TRP B 139 
 HIS   0.005   0.001   HIS B 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 9696)
  covalent geometry    : angle       0.54095 /  0.28 (13200)
  hydrogen bonds       : bond        0.04043 /  2.56 (  441)
  hydrogen bonds       : angle       3.99595 /  2.89 ( 1251)
  metal coordination   : bond        0.00301 /  0.15 (    3)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9111 (tp30) cc_final: 0.8127 (mm-30)
REVERT: A   60 ASN cc_start: 0.9214 (t0) cc_final: 0.9003 (m-40)
REVERT: A   90 ASP cc_start: 0.9326 (t0) cc_final: 0.8967 (t0)
REVERT: A  130 ASP cc_start: 0.9469 (t0) cc_final: 0.9093 (t0)
REVERT: A  154 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8658 (mttp)
REVERT: A  209 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7344 (tp30)
REVERT: A  289 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8364 (ptm-80)
REVERT: A  352 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9226 (tm-30)
REVERT: B   20 GLU cc_start: 0.9297 (tt0) cc_final: 0.8722 (tp30)
REVERT: B   45 GLU cc_start: 0.8987 (tp30) cc_final: 0.8236 (mm-30)
REVERT: B   60 ASN cc_start: 0.9264 (t0) cc_final: 0.8798 (m-40)
REVERT: B  130 ASP cc_start: 0.9487 (t0) cc_final: 0.8854 (t0)
REVERT: B  135 TYR cc_start: 0.9198 (m-80) cc_final: 0.8982 (m-80)
REVERT: B  154 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7461 (mtmm)
REVERT: B  187 GLU cc_start: 0.9146 (tt0) cc_final: 0.8720 (tp30)
REVERT: B  209 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8390 (tp30)
REVERT: B  230 GLU cc_start: 0.9218 (mp0) cc_final: 0.8948 (mp0)
REVERT: B  262 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8867 (tt0)
REVERT: B  325 ARG cc_start: 0.8818 (mtm-85) cc_final: 0.8453 (ttm110)
REVERT: B  352 GLU cc_start: 0.9564 (tt0) cc_final: 0.9163 (tm-30)
REVERT: B  374 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.9019 (t80)
REVERT: C   20 GLU cc_start: 0.9344 (tt0) cc_final: 0.8698 (tt0)
REVERT: C   45 GLU cc_start: 0.9110 (tp30) cc_final: 0.8758 (mm-30)
REVERT: C   68 THR cc_start: 0.9510 (p) cc_final: 0.9094 (m)
REVERT: C   79 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: C   86 ASP cc_start: 0.9217 (m-30) cc_final: 0.8923 (m-30)
REVERT: C  130 ASP cc_start: 0.9486 (t0) cc_final: 0.9117 (t0)
REVERT: C  148 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8385 (t)
REVERT: C  154 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8481 (mttp)
REVERT: C  177 MET cc_start: 0.8885 (tmt) cc_final: 0.8346 (ttp)
REVERT: C  187 GLU cc_start: 0.9222 (tt0) cc_final: 0.8812 (tp30)
REVERT: C  262 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8869 (mt-10)
REVERT: C  295 MET cc_start: 0.9170 (ttm) cc_final: 0.8663 (tpp)
REVERT: C  327 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (mt-10)
REVERT: C  352 GLU cc_start: 0.9489 (tt0) cc_final: 0.9252 (tm-30)
  outliers start: 21
  outliers final: 9
  residues processed: 183
  average time/residue: 0.7533
  time to fit residues: 145.7619
Evaluate side-chains
  183 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  374 TYR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  327 GLU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    0.0570
   chunk 62 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 75 optimal weight:    0.0050
   chunk 109 optimal weight:    2.9990
   chunk 17 optimal weight:   30.0000
   chunk 54 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.2118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.063401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.052295 restraints weight = 15820.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2573 rms_B_bonded: 2.52
r_work: 0.2434 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9699  Z= 0.117
  Angle     :  0.527   6.872  13200  Z= 0.274
  Chirality :  0.039   0.141   1491
  Planarity :  0.003   0.034   1740
  Dihedral  :  4.661  50.827   1306
  Min Nonbonded Distance : 1.182

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 22.76 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.28 (0.25), residues: 1185
  helix:  1.94 (0.25), residues: 396
  sheet:  0.59 (0.31), residues: 297
  loop :  0.23 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 126 
 TYR   0.010   0.002   TYR A 195 
 PHE   0.012   0.001   PHE C 129 
 TRP   0.005   0.001   TRP B 139 
 HIS   0.010   0.001   HIS A 317 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 9696)
  covalent geometry    : angle       0.52680 /  0.27 (13200)
  hydrogen bonds       : bond        0.03896 /  2.49 (  441)
  hydrogen bonds       : angle       3.97830 /  2.88 ( 1251)
  metal coordination   : bond        0.00180 /  0.09 (    3)

===============================================================================
Job complete
usr+sys time: 3443.71 seconds
wall clock time: 59 minutes 27.39 seconds (3567.39 seconds total)