Starting phenix.real_space_refine
on Sat Aug 23 02:33:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jil_36317/08_2025/8jil_36317.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.078
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C    5765      2.51       5
     N    1535      2.21       5
     O    1659      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9028
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 1796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1796
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2364
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'CLR': 1, 'NIO': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 2.26, per 1000 atoms: 0.25
  Number of scatterers: 9028
  At special positions: 0
  Unit cell: (109.48, 135.24, 104.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    1659      8.00
     N    1535      7.00
     C    5765      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  19 " - pdb=" SG  CYS A 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 177 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 254.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      34.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 25
      removed outlier: 3.614A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.518A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.525A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 27
    Processing helix  chain 'D' and resid 45 through 53
    Processing helix  chain 'D' and resid 211 through 216
    Processing helix  chain 'D' and resid 241 through 254
      removed outlier: 3.726A  pdb=" N   ALA D 245 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 260
      removed outlier: 6.118A  pdb=" N   TRP D 258 " --> pdb=" O   ASN D 255 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR D 260 " --> pdb=" O   LYS D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 281
      removed outlier: 3.945A  pdb=" N   GLU D 276 " --> pdb=" O   ASP D 272 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LYS D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 309
      removed outlier: 3.691A  pdb=" N   ALA D 299 " --> pdb=" O   THR D 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 351
      removed outlier: 3.816A  pdb=" N   GLN D 333 " --> pdb=" O   THR D 329 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL D 342 " --> pdb=" O   ALA D 338 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS D 351 " --> pdb=" O   ASN D 347 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'A' and resid 25 through 55
      removed outlier: 3.749A  pdb=" N   VAL A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
      Proline residue:  A  31  - end of helix
      removed outlier: 4.211A  pdb=" N   LEU A  43 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 79
      removed outlier: 3.948A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASN A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASP A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   CYS A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 89
      removed outlier: 3.782A  pdb=" N   LEU A  83 " --> pdb=" O   CYS A  79 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG A  89 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 4.251A  pdb=" N   PHE A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A 107 " --> pdb=" O   MET A 103 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.622A  pdb=" N   VAL A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 4.231A  pdb=" N   TYR A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 4.144A  pdb=" N   ILE A 139 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 158
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 187 through 215
      removed outlier: 4.223A  pdb=" N   ALA A 191 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   PHE A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      Proline residue:  A 200  - end of helix
      removed outlier: 4.390A  pdb=" N   PHE A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 261
      removed outlier: 3.740A  pdb=" N   LYS A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      Proline residue:  A 246  - end of helix
      removed outlier: 3.528A  pdb=" N   ARG A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 290
      removed outlier: 3.550A  pdb=" N   MET A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.555A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.860A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.857A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.685A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.563A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.634A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.496A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190
      removed outlier: 3.561A  pdb=" N   PHE D 189 " --> pdb=" O   PHE D 196 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS D  35 " --> pdb=" O   ALA D 220 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ILE D 222 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU D  37 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   CYS D 224 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU D  39 " --> pdb=" O   CYS D 224 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   ALA D 226 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 7.235A  pdb=" N   GLY S  16 " --> pdb=" O   SER S  85 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   SER S  85 " --> pdb=" O   GLY S  16 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.080A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.642A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR S 243 " --> pdb=" O   TYR S 227 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13

    364 hydrogen bonds defined for protein.
    1017 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: 1.11

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2903
        1.34 -     1.47: 2302
        1.47 -     1.60: 3920
        1.60 -     1.72: 0
        1.72 -     1.85: 100
  Bond restraints: 9225
  Sorted by residual:
  bond pdb=" CA  SER A 179 "
       pdb=" CB  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.537  1.480  0.057 1.38e-02 5.25e+03 1.70e+01
  bond pdb=" N   CYS A 183 "
       pdb=" CA  CYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.453  1.496 -0.043 1.39e-02 5.18e+03 9.61e+00
  bond pdb=" N   PHE A 186 "
       pdb=" CA  PHE A 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.22e-02 6.72e+03 9.25e+00
  bond pdb=" N   ILE A  77 "
       pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.18e-02 7.18e+03 7.87e+00
  bond pdb=" N   SER A 179 "
       pdb=" CA  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.31e-02 5.83e+03 7.82e+00
  ... (remaining 9220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 12292
        2.83 -     5.67: 172
        5.67 -     8.50: 17
        8.50 -    11.34: 3
       11.34 -    14.17: 1
  Bond angle restraints: 12485
  Sorted by residual:
  angle pdb=" CB  MET S 230 "
        pdb=" CG  MET S 230 "
        pdb=" SD  MET S 230 "
      ideal   model   delta    sigma   weight residual
     112.70  126.87  -14.17 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" N   SER A 178 "
        pdb=" CA  SER A 178 "
        pdb=" C   SER A 178 "
      ideal   model   delta    sigma   weight residual
     108.96  114.78   -5.82 1.49e+00 4.50e-01 1.53e+01
  angle pdb=" N   SER A 179 "
        pdb=" CA  SER A 179 "
        pdb=" C   SER A 179 "
      ideal   model   delta    sigma   weight residual
     114.31  109.31    5.00 1.29e+00 6.01e-01 1.50e+01
  angle pdb=" CA  MET C  21 "
        pdb=" CB  MET C  21 "
        pdb=" CG  MET C  21 "
      ideal   model   delta    sigma   weight residual
     114.10  121.68   -7.58 2.00e+00 2.50e-01 1.44e+01
  angle pdb=" C   CYS A 183 "
        pdb=" CA  CYS A 183 "
        pdb=" CB  CYS A 183 "
      ideal   model   delta    sigma   weight residual
     112.43  105.21    7.22 1.91e+00 2.74e-01 1.43e+01
  ... (remaining 12480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 4887
       16.33 -    32.67: 506
       32.67 -    49.00: 100
       49.00 -    65.34: 10
       65.34 -    81.67: 8
  Dihedral angle restraints: 5511
    sinusoidal: 2208
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" CA  PHE S 239 "
           pdb=" C   PHE S 239 "
           pdb=" N   GLY S 240 "
           pdb=" CA  GLY S 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.39   25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  ASP A  14 "
           pdb=" C   ASP A  14 "
           pdb=" N   LYS A  15 "
           pdb=" CA  LYS A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.94   23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  GLU D   8 "
           pdb=" C   GLU D   8 "
           pdb=" N   ASP D   9 "
           pdb=" CA  ASP D   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 837
       0.037 -    0.075: 371
       0.075 -    0.112: 146
       0.112 -    0.150: 39
       0.150 -    0.187: 10
  Chirality restraints: 1403
  Sorted by residual:
  chirality pdb=" CA  VAL S  37 "
            pdb=" N   VAL S  37 "
            pdb=" C   VAL S  37 "
            pdb=" CB  VAL S  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.76e-01
  chirality pdb=" CA  LEU A  76 "
            pdb=" N   LEU A  76 "
            pdb=" C   LEU A  76 "
            pdb=" CB  LEU A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" CA  CYS A 177 "
            pdb=" N   CYS A 177 "
            pdb=" C   CYS A 177 "
            pdb=" CB  CYS A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.28e-01
  ... (remaining 1400 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 182 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.57e+00
        pdb=" C   ILE A 182 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A 182 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   CYS A 183 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "   -0.045 5.00e-02 4.00e+02   6.91e-02 7.63e+00
        pdb=" N   PRO C  49 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.038 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO S  75 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1058
        2.75 -     3.29: 8595
        3.29 -     3.82: 14216
        3.82 -     4.36: 17102
        4.36 -     4.90: 30046
  Nonbonded interactions: 71017
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  56 "
            pdb=" NH1 ARG C  62 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE C  61 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH2 ARG B  22 "
            pdb=" O   THR B 221 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OG  SER S  30 "
            pdb=" OD1 ASP S  74 "
     model   vdw
     2.279 3.040
  ... (remaining 71012 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
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      :  0.006   0.061   9229  Z= 0.274
  Angle     :  0.879  14.172  12493  Z= 0.503
  Chirality :  0.050   0.187   1403
  Planarity :  0.005   0.069   1574
  Dihedral  : 13.683  81.670   3365
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.41 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.24), residues: 1127
  helix: -0.21 (0.29), residues: 325
  sheet: -0.34 (0.30), residues: 273
  loop : -2.35 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 251 
 TYR   0.022   0.002   TYR S  50 
 PHE   0.023   0.002   PHE A 105 
 TRP   0.039   0.003   TRP B 169 
 HIS   0.010   0.002   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 9225)
  covalent geometry    : angle       0.87625 (12485)
  SS BOND              : bond        0.01057 (    4)
  SS BOND              : angle       2.80672 (    8)
  hydrogen bonds       : bond        0.16112 (  364)
  hydrogen bonds       : angle       6.81685 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  167 MET cc_start: 0.5256 (tpt) cc_final: 0.5011 (tpp)
REVERT: A  217 GLN cc_start: 0.7802 (pp30) cc_final: 0.7594 (pp30)
  outliers start: 1
  outliers final: 1
  residues processed: 116
  average time/residue: 0.0908
  time to fit residues: 13.9641
Evaluate side-chains
  98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0010
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
C  18 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.146322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124026 restraints weight = 15513.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123579 restraints weight = 19439.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124687 restraints weight = 16569.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.125123 restraints weight = 12499.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.125214 restraints weight = 11103.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9229  Z= 0.138
  Angle     :  0.658  10.832  12493  Z= 0.335
  Chirality :  0.045   0.147   1403
  Planarity :  0.005   0.057   1574
  Dihedral  :  5.950  50.728   1300
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.61 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.24), residues: 1127
  helix:  0.38 (0.29), residues: 335
  sheet: -0.22 (0.30), residues: 282
  loop : -2.22 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S  38 
 TYR   0.012   0.001   TYR S  95 
 PHE   0.017   0.002   PHE A  67 
 TRP   0.030   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9225)
  covalent geometry    : angle       0.65678 (12485)
  SS BOND              : bond        0.00703 (    4)
  SS BOND              : angle       1.52192 (    8)
  hydrogen bonds       : bond        0.04499 (  364)
  hydrogen bonds       : angle       5.30794 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.7248 (mtm180)
  outliers start: 6
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1322
  time to fit residues: 19.4650
Evaluate side-chains
  99 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
D 188 HIS
S 167 HIS
A 131 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.146932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124087 restraints weight = 15366.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.124163 restraints weight = 18822.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124836 restraints weight = 15710.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.125207 restraints weight = 13403.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.125769 restraints weight = 11040.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9229  Z= 0.135
  Angle     :  0.622  10.025  12493  Z= 0.317
  Chirality :  0.044   0.229   1403
  Planarity :  0.004   0.053   1574
  Dihedral  :  5.735  49.499   1300
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.07 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.24), residues: 1127
  helix:  0.65 (0.29), residues: 341
  sheet: -0.15 (0.29), residues: 282
  loop : -2.12 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 222 
 TYR   0.013   0.001   TYR B 105 
 PHE   0.016   0.001   PHE A 105 
 TRP   0.023   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9225)
  covalent geometry    : angle       0.61922 (12485)
  SS BOND              : bond        0.01168 (    4)
  SS BOND              : angle       2.49914 (    8)
  hydrogen bonds       : bond        0.04250 (  364)
  hydrogen bonds       : angle       4.97812 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  227 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5118 (pp)
  outliers start: 11
  outliers final: 4
  residues processed: 111
  average time/residue: 0.1177
  time to fit residues: 17.5904
Evaluate side-chains
  102 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  278 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 99 optimal weight:    0.3980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 268 ASN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.146551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.124814 restraints weight = 15570.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.123746 restraints weight = 19803.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.124910 restraints weight = 17961.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.125227 restraints weight = 12297.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.125501 restraints weight = 11760.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9229  Z= 0.125
  Angle     :  0.603  10.175  12493  Z= 0.306
  Chirality :  0.043   0.192   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.589  48.403   1300
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.78 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.24), residues: 1127
  helix:  0.81 (0.30), residues: 340
  sheet: -0.04 (0.30), residues: 281
  loop : -2.03 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 222 
 TYR   0.012   0.001   TYR B 105 
 PHE   0.015   0.001   PHE A 105 
 TRP   0.020   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9225)
  covalent geometry    : angle       0.59897 (12485)
  SS BOND              : bond        0.01146 (    4)
  SS BOND              : angle       2.73988 (    8)
  hydrogen bonds       : bond        0.03963 (  364)
  hydrogen bonds       : angle       4.81165 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: B  332 TRP cc_start: 0.8206 (m-10) cc_final: 0.7960 (m-10)
REVERT: A  103 MET cc_start: 0.5814 (ttt) cc_final: 0.5434 (ttt)
REVERT: A  167 MET cc_start: 0.4988 (tpp) cc_final: 0.4754 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1170
  time to fit residues: 17.9354
Evaluate side-chains
  106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  242 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 11 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  45 ASN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.144797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125302 restraints weight = 15387.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.124767 restraints weight = 20647.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.125225 restraints weight = 18973.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.125076 restraints weight = 15106.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.125149 restraints weight = 13539.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9229  Z= 0.200
  Angle     :  0.681   9.293  12493  Z= 0.347
  Chirality :  0.047   0.193   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.989  55.292   1300
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.51 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.24), residues: 1127
  helix:  0.66 (0.29), residues: 339
  sheet: -0.17 (0.29), residues: 282
  loop : -2.13 (0.24), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S  67 
 TYR   0.021   0.002   TYR B 105 
 PHE   0.020   0.002   PHE A 105 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.009   0.002   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 9225)
  covalent geometry    : angle       0.67893 (12485)
  SS BOND              : bond        0.00859 (    4)
  SS BOND              : angle       2.16008 (    8)
  hydrogen bonds       : bond        0.05138 (  364)
  hydrogen bonds       : angle       4.98981 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.5886 (ttt) cc_final: 0.5430 (ttt)
REVERT: A  167 MET cc_start: 0.4941 (tpp) cc_final: 0.4724 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 121
  average time/residue: 0.1086
  time to fit residues: 18.0253
Evaluate side-chains
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.145383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.126066 restraints weight = 15461.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.125511 restraints weight = 20588.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.125970 restraints weight = 18548.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.125021 restraints weight = 14944.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.125398 restraints weight = 13837.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9229  Z= 0.173
  Angle     :  0.643   9.278  12493  Z= 0.329
  Chirality :  0.045   0.178   1403
  Planarity :  0.004   0.054   1574
  Dihedral  :  5.893  55.396   1300
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.43 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.24), residues: 1127
  helix:  0.70 (0.29), residues: 339
  sheet: -0.14 (0.29), residues: 283
  loop : -2.10 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 222 
 TYR   0.015   0.002   TYR B 105 
 PHE   0.019   0.002   PHE A 105 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9225)
  covalent geometry    : angle       0.64096 (12485)
  SS BOND              : bond        0.00807 (    4)
  SS BOND              : angle       1.93284 (    8)
  hydrogen bonds       : bond        0.04721 (  364)
  hydrogen bonds       : angle       4.95794 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.384 
Fit side-chains
REVERT: S  233 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5495 (tp)
REVERT: A  103 MET cc_start: 0.5581 (ttt) cc_final: 0.5366 (ttt)
  outliers start: 19
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1114
  time to fit residues: 18.1439
Evaluate side-chains
  114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0570
   chunk 39 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 3 optimal weight:   30.0000
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.5904

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 311 HIS
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.145073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.122503 restraints weight = 15511.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.121489 restraints weight = 15251.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121856 restraints weight = 13755.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.122245 restraints weight = 11852.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.122448 restraints weight = 11006.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9229  Z= 0.191
  Angle     :  0.664  10.581  12493  Z= 0.338
  Chirality :  0.046   0.175   1403
  Planarity :  0.004   0.055   1574
  Dihedral  :  5.969  57.040   1300
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.26 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.24), residues: 1127
  helix:  0.62 (0.29), residues: 341
  sheet: -0.18 (0.29), residues: 284
  loop : -2.11 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S  67 
 TYR   0.017   0.002   TYR S  50 
 PHE   0.020   0.002   PHE A 105 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9225)
  covalent geometry    : angle       0.66253 (12485)
  SS BOND              : bond        0.00731 (    4)
  SS BOND              : angle       1.75983 (    8)
  hydrogen bonds       : bond        0.04949 (  364)
  hydrogen bonds       : angle       4.96075 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.331 
Fit side-chains
REVERT: S  233 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5545 (tp)
REVERT: A  103 MET cc_start: 0.5771 (ttt) cc_final: 0.5562 (ttt)
  outliers start: 19
  outliers final: 14
  residues processed: 116
  average time/residue: 0.1131
  time to fit residues: 17.8725
Evaluate side-chains
  118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0670
   chunk 24 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.140577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.121806 restraints weight = 15482.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.122207 restraints weight = 22044.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121529 restraints weight = 17886.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.121455 restraints weight = 17950.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121618 restraints weight = 13468.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9229  Z= 0.149
  Angle     :  0.617  10.499  12493  Z= 0.316
  Chirality :  0.044   0.161   1403
  Planarity :  0.004   0.056   1574
  Dihedral  :  5.746  54.575   1300
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.67 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.24), residues: 1127
  helix:  0.81 (0.29), residues: 339
  sheet: -0.14 (0.29), residues: 293
  loop : -2.09 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG S  67 
 TYR   0.013   0.001   TYR S  50 
 PHE   0.017   0.002   PHE A 105 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9225)
  covalent geometry    : angle       0.61528 (12485)
  SS BOND              : bond        0.00702 (    4)
  SS BOND              : angle       1.66182 (    8)
  hydrogen bonds       : bond        0.04406 (  364)
  hydrogen bonds       : angle       4.86211 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.371 
Fit side-chains
REVERT: S    6 GLU cc_start: 0.5981 (pt0) cc_final: 0.5689 (pt0)
REVERT: A   40 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6830 (m-10)
  outliers start: 20
  outliers final: 16
  residues processed: 118
  average time/residue: 0.1189
  time to fit residues: 18.6461
Evaluate side-chains
  117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 25 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0040
   chunk 106 optimal weight:    0.9980
   chunk 111 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.146599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.127161 restraints weight = 15309.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126750 restraints weight = 21676.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.127411 restraints weight = 18610.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.126959 restraints weight = 13759.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.127255 restraints weight = 14049.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9229  Z= 0.123
  Angle     :  0.603  10.947  12493  Z= 0.309
  Chirality :  0.044   0.167   1403
  Planarity :  0.004   0.055   1574
  Dihedral  :  5.556  51.421   1300
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.38 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.24), residues: 1127
  helix:  0.92 (0.29), residues: 339
  sheet: -0.09 (0.29), residues: 281
  loop : -2.01 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  32 
 TYR   0.011   0.001   TYR S  50 
 PHE   0.016   0.001   PHE S  68 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9225)
  covalent geometry    : angle       0.60208 (12485)
  SS BOND              : bond        0.00668 (    4)
  SS BOND              : angle       1.57976 (    8)
  hydrogen bonds       : bond        0.03970 (  364)
  hydrogen bonds       : angle       4.77982 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   40 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6813 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1084
  time to fit residues: 16.5170
Evaluate side-chains
  109 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0070
   chunk 66 optimal weight:    0.0060
   chunk 13 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0170
   overall best weight:    0.1790

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.149562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.128001 restraints weight = 15316.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.127398 restraints weight = 18787.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.129422 restraints weight = 14834.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.129056 restraints weight = 10590.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129377 restraints weight = 10137.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9229  Z= 0.102
  Angle     :  0.559  11.268  12493  Z= 0.289
  Chirality :  0.042   0.152   1403
  Planarity :  0.004   0.056   1574
  Dihedral  :  5.097  38.201   1300
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.19 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1127
  helix:  1.28 (0.30), residues: 336
  sheet:  0.06 (0.30), residues: 277
  loop : -1.85 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 222 
 TYR   0.011   0.001   TYR S  95 
 PHE   0.025   0.001   PHE S  29 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9225)
  covalent geometry    : angle       0.55834 (12485)
  SS BOND              : bond        0.00642 (    4)
  SS BOND              : angle       1.46478 (    8)
  hydrogen bonds       : bond        0.03226 (  364)
  hydrogen bonds       : angle       4.52663 ( 1017)

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S    6 GLU cc_start: 0.5833 (pt0) cc_final: 0.5339 (mt-10)
REVERT: S   83 MET cc_start: 0.6463 (tpt) cc_final: 0.6096 (tpt)
REVERT: S  233 LEU cc_start: 0.5211 (tp) cc_final: 0.4962 (tp)
  outliers start: 11
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1030
  time to fit residues: 16.5595
Evaluate side-chains
  108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  235 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.148302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.126814 restraints weight = 15067.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.126282 restraints weight = 18931.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.127444 restraints weight = 17150.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.127313 restraints weight = 13394.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.127780 restraints weight = 11818.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9229  Z= 0.122
  Angle     :  0.579  10.702  12493  Z= 0.299
  Chirality :  0.043   0.141   1403
  Planarity :  0.004   0.054   1574
  Dihedral  :  5.168  38.450   1300
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.99 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.25), residues: 1127
  helix:  1.25 (0.30), residues: 336
  sheet:  0.10 (0.30), residues: 276
  loop : -1.82 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 222 
 TYR   0.012   0.001   TYR S  50 
 PHE   0.023   0.002   PHE S  29 
 TRP   0.012   0.001   TRP S  47 
 HIS   0.018   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9225)
  covalent geometry    : angle       0.57787 (12485)
  SS BOND              : bond        0.00609 (    4)
  SS BOND              : angle       1.45531 (    8)
  hydrogen bonds       : bond        0.03740 (  364)
  hydrogen bonds       : angle       4.50044 ( 1017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1495.50 seconds
wall clock time: 26 minutes 41.72 seconds (1601.72 seconds total)