Starting phenix.real_space_refine
on Wed Apr 30 04:17:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jil_36317/04_2025/8jil_36317_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jil_36317/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jil_36317/04_2025/8jil_36317.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jil_36317/04_2025/8jil_36317.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jil_36317/04_2025/8jil_36317_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jil_36317/04_2025/8jil_36317_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.70, per 1000 atoms: 0.63
  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: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.99
  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: 2.51

  Time building geometry restraints manager: 2.76 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:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.440
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.610
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.039   0.003   TRP B 169 
 HIS   0.010   0.002   HIS A 189 
 PHE   0.023   0.002   PHE A 105 
 TYR   0.022   0.002   TYR S  50 
 ARG   0.005   0.001   ARG A 251 

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

*********************** 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  : 0.916 
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: 0.2790
  time to fit residues: 42.7084
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  : 0.956 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 65 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**
A 184 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.145480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.122997 restraints weight = 15362.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.122523 restraints weight = 20183.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123909 restraints weight = 15861.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9229  Z= 0.149
  Angle     :  0.672  10.529  12493  Z= 0.342
  Chirality :  0.045   0.147   1403
  Planarity :  0.005   0.058   1574
  Dihedral  :  6.037  51.988   1300
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.92 %
    Favored  : 92.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1127
  helix:  0.31 (0.29), residues: 335
  sheet: -0.22 (0.30), residues: 281
  loop : -2.26 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 184 
 PHE   0.018   0.002   PHE A  67 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.003   0.000   ARG A  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04770 (  364)
  hydrogen bonds       : angle       5.37234 ( 1017)
  SS BOND              : bond        0.00767 (    4)
  SS BOND              : angle       1.51257 (    8)
  covalent geometry    : bond        0.00336 ( 9225)
  covalent geometry    : angle       0.67112 (12485)

*********************** 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
  113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7303 (mtm180)
  outliers start: 6
  outliers final: 1
  residues processed: 108
  average time/residue: 0.2967
  time to fit residues: 43.0702
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  : 0.980 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0050
   chunk 0 optimal weight:   40.0000
   chunk 21 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0470
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4894

-------------------------------------------------------------------------------
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
A 131 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.147786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.125004 restraints weight = 15310.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.124392 restraints weight = 18565.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.125297 restraints weight = 16680.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9229  Z= 0.120
  Angle     :  0.611  10.221  12493  Z= 0.311
  Chirality :  0.043   0.149   1403
  Planarity :  0.004   0.054   1574
  Dihedral  :  5.687  48.530   1300
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.66 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.24), residues: 1127
  helix:  0.68 (0.30), residues: 341
  sheet: -0.13 (0.30), residues: 282
  loop : -2.11 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.013   0.001   PHE A 105 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.005   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  364)
  hydrogen bonds       : angle       4.97030 ( 1017)
  SS BOND              : bond        0.00524 (    4)
  SS BOND              : angle       2.59665 (    8)
  covalent geometry    : bond        0.00265 ( 9225)
  covalent geometry    : angle       0.60742 (12485)

*********************** 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
  118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  227 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5052 (pp)
  outliers start: 12
  outliers final: 4
  residues processed: 115
  average time/residue: 0.2470
  time to fit residues: 38.3365
Evaluate side-chains
  103 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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 85 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 11 optimal weight:    0.3980
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   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 175 GLN
B 268 ASN
** 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 = 0.4008 r_free = 0.4008 target = 0.146695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124882 restraints weight = 15347.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.125020 restraints weight = 19713.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.126550 restraints weight = 15456.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9229  Z= 0.126
  Angle     :  0.604  10.205  12493  Z= 0.306
  Chirality :  0.043   0.217   1403
  Planarity :  0.004   0.051   1574
  Dihedral  :  5.588  47.715   1300
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.19 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.25), residues: 1127
  helix:  0.81 (0.30), residues: 340
  sheet:  0.01 (0.30), residues: 280
  loop : -2.00 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.015   0.001   PHE A 105 
 TYR   0.012   0.001   TYR B 105 
 ARG   0.005   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  364)
  hydrogen bonds       : angle       4.81563 ( 1017)
  SS BOND              : bond        0.00956 (    4)
  SS BOND              : angle       2.56260 (    8)
  covalent geometry    : bond        0.00291 ( 9225)
  covalent geometry    : angle       0.60042 (12485)

*********************** 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
  117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: D  227 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5056 (pp)
REVERT: A  103 MET cc_start: 0.5797 (ttt) cc_final: 0.5433 (ttt)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 0.2364
  time to fit residues: 37.0029
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  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain D residue  227 LEU
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 107 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:   40.0000
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** 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 = 0.3982 r_free = 0.3982 target = 0.145287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.122344 restraints weight = 15339.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.122493 restraints weight = 18571.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.123356 restraints weight = 16588.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9229  Z= 0.173
  Angle     :  0.639   9.314  12493  Z= 0.328
  Chirality :  0.045   0.185   1403
  Planarity :  0.004   0.051   1574
  Dihedral  :  5.783  51.991   1300
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.70 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.24), residues: 1127
  helix:  0.78 (0.30), residues: 339
  sheet: -0.06 (0.30), residues: 280
  loop : -2.06 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 189 
 PHE   0.025   0.002   PHE S  29 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.006   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04664 (  364)
  hydrogen bonds       : angle       4.87979 ( 1017)
  SS BOND              : bond        0.00814 (    4)
  SS BOND              : angle       2.02406 (    8)
  covalent geometry    : bond        0.00410 ( 9225)
  covalent geometry    : angle       0.63739 (12485)

*********************** 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
  127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  103 MET cc_start: 0.5944 (ttt) cc_final: 0.5571 (ttt)
  outliers start: 21
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2291
  time to fit residues: 37.7846
Evaluate side-chains
  116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  235 VAL
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 9 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:   30.0000
   chunk 23 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 176 GLN
** 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 = 0.3995 r_free = 0.3995 target = 0.146491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126446 restraints weight = 15173.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125538 restraints weight = 23495.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126854 restraints weight = 19343.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9229  Z= 0.145
  Angle     :  0.613  10.502  12493  Z= 0.313
  Chirality :  0.044   0.163   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.669  52.120   1300
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.73 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.24), residues: 1127
  helix:  0.89 (0.30), residues: 338
  sheet: -0.06 (0.30), residues: 281
  loop : -2.00 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 133 
 PHE   0.020   0.002   PHE S  29 
 TYR   0.013   0.001   TYR B 105 
 ARG   0.006   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  364)
  hydrogen bonds       : angle       4.83714 ( 1017)
  SS BOND              : bond        0.00771 (    4)
  SS BOND              : angle       1.77523 (    8)
  covalent geometry    : bond        0.00339 ( 9225)
  covalent geometry    : angle       0.61192 (12485)

*********************** 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
  118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.887 
Fit side-chains
REVERT: S  233 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5440 (tp)
REVERT: A  103 MET cc_start: 0.5750 (ttt) cc_final: 0.5366 (ttt)
  outliers start: 18
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2431
  time to fit residues: 36.3911
Evaluate side-chains
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** 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 = 0.3969 r_free = 0.3969 target = 0.140917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.120786 restraints weight = 15486.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.119975 restraints weight = 21629.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.120737 restraints weight = 19940.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9229  Z= 0.156
  Angle     :  0.621  10.388  12493  Z= 0.318
  Chirality :  0.044   0.160   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.706  53.581   1300
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.14 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.24), residues: 1127
  helix:  0.82 (0.29), residues: 340
  sheet: -0.03 (0.29), residues: 286
  loop : -2.02 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.020   0.002   PHE S  29 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.011   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 (  364)
  hydrogen bonds       : angle       4.80852 ( 1017)
  SS BOND              : bond        0.00706 (    4)
  SS BOND              : angle       1.67303 (    8)
  covalent geometry    : bond        0.00369 ( 9225)
  covalent geometry    : angle       0.62019 (12485)

*********************** 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  : 1.002 
Fit side-chains
  outliers start: 19
  outliers final: 13
  residues processed: 115
  average time/residue: 0.2501
  time to fit residues: 38.8080
Evaluate side-chains
  113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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:    1.9990
   chunk 38 optimal weight:    0.0050
   chunk 103 optimal weight:    1.9990
   chunk 101 optimal weight:    0.3980
   chunk 65 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0770
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   overall best weight:    0.4552

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

Flipped N/Q/H residues before XYZ refinement:
B 175 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 = 0.4003 r_free = 0.4003 target = 0.143349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.123607 restraints weight = 15508.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.122611 restraints weight = 22081.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.123510 restraints weight = 20140.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9229  Z= 0.110
  Angle     :  0.577  10.685  12493  Z= 0.296
  Chirality :  0.043   0.142   1403
  Planarity :  0.004   0.052   1574
  Dihedral  :  5.390  49.012   1300
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.85 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.25), residues: 1127
  helix:  1.00 (0.30), residues: 339
  sheet:  0.06 (0.30), residues: 275
  loop : -1.91 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 133 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.009   0.001   TYR S  95 
 ARG   0.004   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  364)
  hydrogen bonds       : angle       4.65370 ( 1017)
  SS BOND              : bond        0.00661 (    4)
  SS BOND              : angle       1.51779 (    8)
  covalent geometry    : bond        0.00240 ( 9225)
  covalent geometry    : angle       0.57560 (12485)

*********************** 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
  120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.875 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 116
  average time/residue: 0.2378
  time to fit residues: 37.2363
Evaluate side-chains
  107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  227 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    0.0170
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0170
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** 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 = 0.4012 r_free = 0.4012 target = 0.147721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.128005 restraints weight = 15285.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.127369 restraints weight = 21005.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.128127 restraints weight = 18839.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9229  Z= 0.125
  Angle     :  0.582  10.819  12493  Z= 0.300
  Chirality :  0.043   0.138   1403
  Planarity :  0.004   0.050   1574
  Dihedral  :  5.366  42.368   1300
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.06 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1127
  helix:  1.01 (0.30), residues: 339
  sheet:  0.07 (0.30), residues: 275
  loop : -1.92 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.011   0.001   TYR S  50 
 ARG   0.006   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  364)
  hydrogen bonds       : angle       4.64156 ( 1017)
  SS BOND              : bond        0.00606 (    4)
  SS BOND              : angle       1.52062 (    8)
  covalent geometry    : bond        0.00287 ( 9225)
  covalent geometry    : angle       0.58089 (12485)

*********************** 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
  111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 107
  average time/residue: 0.2387
  time to fit residues: 35.1420
Evaluate side-chains
  103 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
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 49 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** 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 = 0.4019 r_free = 0.4019 target = 0.148194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.128642 restraints weight = 15324.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.128185 restraints weight = 20385.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.128756 restraints weight = 18006.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9229  Z= 0.119
  Angle     :  0.578  10.657  12493  Z= 0.298
  Chirality :  0.043   0.165   1403
  Planarity :  0.004   0.051   1574
  Dihedral  :  5.309  40.161   1300
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.36 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1127
  helix:  1.06 (0.30), residues: 339
  sheet:  0.12 (0.30), residues: 274
  loop : -1.90 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.010   0.001   TYR S  50 
 ARG   0.004   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  364)
  hydrogen bonds       : angle       4.57706 ( 1017)
  SS BOND              : bond        0.00590 (    4)
  SS BOND              : angle       1.49028 (    8)
  covalent geometry    : bond        0.00270 ( 9225)
  covalent geometry    : angle       0.57659 (12485)

********************** 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
  110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.091 
Fit side-chains
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.2611
  time to fit residues: 37.3611
Evaluate side-chains
  107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
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 20 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** 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 = 0.3999 r_free = 0.3999 target = 0.146687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.126960 restraints weight = 15231.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.125808 restraints weight = 20454.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.126620 restraints weight = 19398.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9229  Z= 0.148
  Angle     :  0.619  10.526  12493  Z= 0.319
  Chirality :  0.044   0.197   1403
  Planarity :  0.004   0.050   1574
  Dihedral  :  5.490  42.323   1300
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.77 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.25), residues: 1127
  helix:  0.97 (0.30), residues: 339
  sheet:  0.04 (0.30), residues: 276
  loop : -1.88 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.018   0.002   PHE S  29 
 TYR   0.013   0.001   TYR S  50 
 ARG   0.010   0.000   ARG A 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  364)
  hydrogen bonds       : angle       4.65339 ( 1017)
  SS BOND              : bond        0.00606 (    4)
  SS BOND              : angle       1.54520 (    8)
  covalent geometry    : bond        0.00348 ( 9225)
  covalent geometry    : angle       0.61759 (12485)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2973.60 seconds
wall clock time: 53 minutes 19.34 seconds (3199.34 seconds total)