Starting phenix.real_space_refine
on Mon Apr 28 16:04:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgb_36229/04_2025/8jgb_36229_neut.cif"
  }
  resolution = 2.84
  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=   0.001 sd=   0.020
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      49      5.16       5
     C    4980      2.51       5
     N    1342      2.21       5
     O    1425      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7796
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "L"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 36
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 421
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1612
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 2488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2488
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 68
    Chain: "R"
      Number of atoms: 1529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1529
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 5, 'TRANS': 211}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 207
          Unresolved non-hydrogen angles: 271
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 96
    Chain: "S"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1710
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 5.18, per 1000 atoms: 0.66
  Number of scatterers: 7796
  At special positions: 0
  Unit cell: (102.6, 119.88, 122.04, 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      49     16.00
     O    1425      8.00
     N    1342      7.00
     C    4980      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 158 " - pdb=" SG  CYS S 228 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1982

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      34.2% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'G' and resid 10 through 22
      removed outlier: 3.687A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.692A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA G  39 " --> pdb=" O   ALA G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.742A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.554A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 4.128A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.752A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.902A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 281
      No H-bonds generated for 'chain 'A' and resid 280 through 281'
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.392A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 4.517A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 20
      removed outlier: 3.809A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASP B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'R' and resid 31 through 36
      removed outlier: 3.722A  pdb=" N   CYS R  35 " --> pdb=" O   THR R  31 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 37 through 55
      removed outlier: 3.791A  pdb=" N   THR R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL R  48 " --> pdb=" O   GLY R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 81
      removed outlier: 3.732A  pdb=" N   ILE R  63 " --> pdb=" O   ASN R  59 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   TYR R  64 " --> pdb=" O   ALA R  60 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE R  65 " --> pdb=" O   PHE R  61 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   LEU R  74 " --> pdb=" O   ALA R  70 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE R  75 " --> pdb=" O   ALA R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 84
      No H-bonds generated for 'chain 'R' and resid 82 through 84'
    Processing helix  chain 'R' and resid 97 through 126
      removed outlier: 3.548A  pdb=" N   VAL R 101 " --> pdb=" O   ILE R  97 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   MET R 102 " --> pdb=" O   LEU R  98 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   MET R 103 " --> pdb=" O   TYR R  99 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER R 105 " --> pdb=" O   VAL R 101 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER R 111 " --> pdb=" O   PHE R 107 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER R 114 " --> pdb=" O   LEU R 110 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL R 116 " --> pdb=" O   PHE R 112 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG R 120 " --> pdb=" O   VAL R 116 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   CYS R 121 " --> pdb=" O   SER R 117 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 133
    Processing helix  chain 'R' and resid 137 through 160
      removed outlier: 3.584A  pdb=" N   GLU R 157 " --> pdb=" O   ARG R 153 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 176 through 196
      removed outlier: 3.585A  pdb=" N   LEU R 187 " --> pdb=" O   TRP R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 201
    Processing helix  chain 'R' and resid 212 through 228
      removed outlier: 4.089A  pdb=" N   VAL R 216 " --> pdb=" O   THR R 212 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   THR R 217 " --> pdb=" O   ARG R 213 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU R 219 " --> pdb=" O   TYR R 215 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL R 222 " --> pdb=" O   ILE R 218 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU R 223 " --> pdb=" O   LEU R 219 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   CYS R 228 " --> pdb=" O   VAL R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 231
      No H-bonds generated for 'chain 'R' and resid 229 through 231'
    Processing helix  chain 'R' and resid 232 through 237
      removed outlier: 4.208A  pdb=" N   PHE R 237 " --> pdb=" O   GLY R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 240
      No H-bonds generated for 'chain 'R' and resid 238 through 240'
    Processing helix  chain 'R' and resid 251 through 265
      removed outlier: 4.346A  pdb=" N   LEU R 255 " --> pdb=" O   CYS R 251 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE R 259 " --> pdb=" O   LEU R 255 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER R 265 " --> pdb=" O   SER R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 268 through 273
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.503A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.067A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.658A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.740A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.547A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.616A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.767A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.602A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.658A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.625A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.978A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.305A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 139 through 141
      removed outlier: 4.192A  pdb=" N   ALA S 210 " --> pdb=" O   SER S 207 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 145 through 147
      removed outlier: 3.740A  pdb=" N   GLU S 245 " --> pdb=" O   VAL S 146 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY S 224 " --> pdb=" O   LEU S 244 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU S 173 " --> pdb=" O   TYR S 189 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   TYR S 189 " --> pdb=" O   LEU S 173 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TRP S 175 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 145 through 147
      removed outlier: 3.740A  pdb=" N   GLU S 245 " --> pdb=" O   VAL S 146 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY S 224 " --> pdb=" O   LEU S 244 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   THR S 237 " --> pdb=" O   GLN S 230 " (cutoff:3.500A)

    345 hydrogen bonds defined for protein.
    954 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: 2.27

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1249
        1.29 -     1.42: 2138
        1.42 -     1.55: 4485
        1.55 -     1.68: 9
        1.68 -     1.81: 68
  Bond restraints: 7949
  Sorted by residual:
  bond pdb=" CA  SER A 263 "
       pdb=" C   SER A 263 "
    ideal  model  delta    sigma   weight residual
    1.524  1.437  0.088 1.31e-02 5.83e+03 4.48e+01
  bond pdb=" C   ILE B 229 "
       pdb=" O   ILE B 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.161  0.073 1.17e-02 7.31e+03 3.85e+01
  bond pdb=" CA  ALA A  11 "
       pdb=" CB  ALA A  11 "
    ideal  model  delta    sigma   weight residual
    1.529  1.429  0.100 1.63e-02 3.76e+03 3.79e+01
  bond pdb=" C   GLY B 244 "
       pdb=" O   GLY B 244 "
    ideal  model  delta    sigma   weight residual
    1.235  1.154  0.081 1.35e-02 5.49e+03 3.61e+01
  bond pdb=" CA  TRP B 211 "
       pdb=" C   TRP B 211 "
    ideal  model  delta    sigma   weight residual
    1.522  1.450  0.072 1.21e-02 6.83e+03 3.53e+01
  ... (remaining 7944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 10363
        2.71 -     5.42: 325
        5.42 -     8.12: 84
        8.12 -    10.83: 22
       10.83 -    13.54: 11
  Bond angle restraints: 10805
  Sorted by residual:
  angle pdb=" N   ALA B  24 "
        pdb=" CA  ALA B  24 "
        pdb=" C   ALA B  24 "
      ideal   model   delta    sigma   weight residual
     111.71   99.25   12.46 1.34e+00 5.57e-01 8.65e+01
  angle pdb=" N   CYS B  25 "
        pdb=" CA  CYS B  25 "
        pdb=" C   CYS B  25 "
      ideal   model   delta    sigma   weight residual
     112.54   99.00   13.54 1.51e+00 4.39e-01 8.04e+01
  angle pdb=" N   ILE R 234 "
        pdb=" CA  ILE R 234 "
        pdb=" C   ILE R 234 "
      ideal   model   delta    sigma   weight residual
     112.80  102.97    9.83 1.15e+00 7.56e-01 7.31e+01
  angle pdb=" N   HIS R 252 "
        pdb=" CA  HIS R 252 "
        pdb=" C   HIS R 252 "
      ideal   model   delta    sigma   weight residual
     113.01  102.77   10.24 1.20e+00 6.94e-01 7.28e+01
  angle pdb=" N   SER R  38 "
        pdb=" CA  SER R  38 "
        pdb=" C   SER R  38 "
      ideal   model   delta    sigma   weight residual
     113.30  101.90   11.40 1.34e+00 5.57e-01 7.24e+01
  ... (remaining 10800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 4107
       17.65 -    35.30: 413
       35.30 -    52.95: 106
       52.95 -    70.60: 21
       70.60 -    88.25: 4
  Dihedral angle restraints: 4651
    sinusoidal: 1587
      harmonic: 3064
  Sorted by residual:
  dihedral pdb=" N   TYR R  99 "
           pdb=" C   TYR R  99 "
           pdb=" CA  TYR R  99 "
           pdb=" CB  TYR R  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.86  -15.06     0      2.50e+00 1.60e-01 3.63e+01
  dihedral pdb=" C   TYR R  99 "
           pdb=" N   TYR R  99 "
           pdb=" CA  TYR R  99 "
           pdb=" CB  TYR R  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.57   13.97     0      2.50e+00 1.60e-01 3.12e+01
  dihedral pdb=" C   LEU R 203 "
           pdb=" N   LEU R 203 "
           pdb=" CA  LEU R 203 "
           pdb=" CB  LEU R 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.82   13.22     0      2.50e+00 1.60e-01 2.79e+01
  ... (remaining 4648 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.146: 1209
       0.146 -    0.292: 49
       0.292 -    0.438: 8
       0.438 -    0.584: 1
       0.584 -    0.730: 1
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  TYR R  99 "
            pdb=" N   TYR R  99 "
            pdb=" C   TYR R  99 "
            pdb=" CB  TYR R  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CA  LEU R 203 "
            pdb=" N   LEU R 203 "
            pdb=" C   LEU R 203 "
            pdb=" CB  LEU R 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.27e+00
  chirality pdb=" CA  SER S  88 "
            pdb=" N   SER S  88 "
            pdb=" C   SER S  88 "
            pdb=" CB  SER S  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  ... (remaining 1265 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  52 "   -0.084 5.00e-02 4.00e+02   1.24e-01 2.45e+01
        pdb=" N   PRO G  53 "    0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 245 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   GLU A 245 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLU A 245 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER A 246 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 210 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.29e+00
        pdb=" C   LEU B 210 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU B 210 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TRP B 211 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1619
        2.76 -     3.30: 6786
        3.30 -     3.83: 11942
        3.83 -     4.37: 14820
        4.37 -     4.90: 25741
  Nonbonded interactions: 60908
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OD2 ASP G  48 "
            pdb=" OG  SER B 281 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.334 3.040
  ... (remaining 60903 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.230
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:13.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
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      :  0.010   0.100   7951  Z= 0.707
  Angle     :  1.224  13.540  10809  Z= 0.792
  Chirality :  0.073   0.730   1268
  Planarity :  0.007   0.124   1364
  Dihedral  : 15.632  88.252   2663
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 24.54 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.42 (0.25), residues: 1036
  helix: -2.64 (0.25), residues: 325
  sheet:  0.13 (0.31), residues: 281
  loop : -1.84 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.034   0.003   PHE R 112 
 TYR   0.027   0.002   TYR A 230 
 ARG   0.004   0.000   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27274 (  336)
  hydrogen bonds       : angle       9.38184 (  954)
  SS BOND              : bond        0.00635 (    2)
  SS BOND              : angle       1.43366 (    4)
  covalent geometry    : bond        0.01030 ( 7949)
  covalent geometry    : angle       1.22434 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  270 LYS cc_start: 0.8733 (mptt) cc_final: 0.8510 (mmtp)
REVERT: B   13 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7201 (tm-30)
REVERT: B  111 TYR cc_start: 0.8656 (m-80) cc_final: 0.8312 (m-80)
REVERT: B  258 ASP cc_start: 0.7804 (t0) cc_final: 0.7394 (t0)
REVERT: R   63 ILE cc_start: 0.8662 (mm) cc_final: 0.8140 (mt)
REVERT: R   67 ASN cc_start: 0.8152 (m-40) cc_final: 0.7701 (m110)
REVERT: R  103 MET cc_start: 0.7744 (mmm) cc_final: 0.7507 (mmp)
REVERT: R  186 PHE cc_start: 0.8026 (t80) cc_final: 0.7737 (t80)
REVERT: R  196 LEU cc_start: 0.8101 (pp) cc_final: 0.7895 (pt)
REVERT: R  263 LEU cc_start: 0.8651 (tp) cc_final: 0.8435 (tt)
REVERT: S   80 PHE cc_start: 0.8622 (m-80) cc_final: 0.8359 (m-80)
REVERT: S  148 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7446 (m)
REVERT: S  198 VAL cc_start: 0.8875 (m) cc_final: 0.8629 (p)
  outliers start: 22
  outliers final: 8
  residues processed: 214
  average time/residue: 0.9327
  time to fit residues: 214.0490
Evaluate side-chains
  176 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  105 SER
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue  148 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 81 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0000
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 204 GLN
A 255 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 141 GLN
S 185 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.114523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.099248 restraints weight = 11855.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.00
r_work: 0.3210 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7951  Z= 0.132
  Angle     :  0.587   5.966  10809  Z= 0.317
  Chirality :  0.043   0.147   1268
  Planarity :  0.005   0.070   1364
  Dihedral  :  4.898  50.721   1137
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.80 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.31 (0.26), residues: 1036
  helix: -1.13 (0.28), residues: 322
  sheet:  0.50 (0.32), residues: 286
  loop : -1.54 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.024   0.002   PHE A 274 
 TYR   0.015   0.001   TYR S 189 
 ARG   0.004   0.000   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  336)
  hydrogen bonds       : angle       5.22296 (  954)
  SS BOND              : bond        0.00832 (    2)
  SS BOND              : angle       1.09536 (    4)
  covalent geometry    : bond        0.00293 ( 7949)
  covalent geometry    : angle       0.58632 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A  270 LYS cc_start: 0.8820 (mptt) cc_final: 0.8618 (mmtp)
REVERT: A  296 TYR cc_start: 0.7751 (t80) cc_final: 0.7464 (t80)
REVERT: A  340 THR cc_start: 0.8353 (t) cc_final: 0.7927 (m)
REVERT: A  353 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7994 (tm)
REVERT: B   13 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7407 (tm130)
REVERT: B   46 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7969 (mtt-85)
REVERT: B   70 LEU cc_start: 0.8873 (pt) cc_final: 0.8666 (pt)
REVERT: B  111 TYR cc_start: 0.8773 (m-80) cc_final: 0.8497 (m-80)
REVERT: R   63 ILE cc_start: 0.8771 (mm) cc_final: 0.7945 (mt)
REVERT: R   67 ASN cc_start: 0.8344 (m-40) cc_final: 0.7635 (m110)
REVERT: R  145 LEU cc_start: 0.8185 (tp) cc_final: 0.7901 (tt)
REVERT: R  186 PHE cc_start: 0.8251 (t80) cc_final: 0.7945 (t80)
REVERT: R  226 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8406 (tp)
REVERT: R  258 ILE cc_start: 0.8351 (tt) cc_final: 0.8089 (tp)
REVERT: S  183 SER cc_start: 0.8680 (p) cc_final: 0.8467 (m)
REVERT: S  244 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (mt)
  outliers start: 38
  outliers final: 18
  residues processed: 216
  average time/residue: 1.0831
  time to fit residues: 250.6168
Evaluate side-chains
  195 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  244 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  17 GLN
B  54 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.111792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.096523 restraints weight = 11890.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.02
r_work: 0.3161 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7951  Z= 0.212
  Angle     :  0.633   6.576  10809  Z= 0.337
  Chirality :  0.045   0.147   1268
  Planarity :  0.005   0.063   1364
  Dihedral  :  4.915  54.419   1128
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 25.98 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.91 (0.26), residues: 1036
  helix: -0.52 (0.30), residues: 324
  sheet:  0.63 (0.32), residues: 288
  loop : -1.49 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP S  47 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.023   0.002   PHE A 274 
 TYR   0.014   0.002   TYR A 320 
 ARG   0.005   0.001   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05630 (  336)
  hydrogen bonds       : angle       4.98947 (  954)
  SS BOND              : bond        0.01133 (    2)
  SS BOND              : angle       1.63220 (    4)
  covalent geometry    : bond        0.00501 ( 7949)
  covalent geometry    : angle       0.63194 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 182
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A  252 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8284 (m)
REVERT: A  296 TYR cc_start: 0.7816 (t80) cc_final: 0.7458 (t80)
REVERT: A  340 THR cc_start: 0.8329 (t) cc_final: 0.8025 (m)
REVERT: B   13 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7241 (tm130)
REVERT: B   46 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7947 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8256 (mmt90)
REVERT: B  258 ASP cc_start: 0.7960 (t0) cc_final: 0.7434 (t0)
REVERT: B  291 ASP cc_start: 0.7342 (t0) cc_final: 0.6907 (t0)
REVERT: R   63 ILE cc_start: 0.8849 (mm) cc_final: 0.7998 (mt)
REVERT: R   67 ASN cc_start: 0.8324 (m-40) cc_final: 0.7607 (m110)
REVERT: R  186 PHE cc_start: 0.8269 (t80) cc_final: 0.8017 (t80)
REVERT: R  226 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8397 (tp)
REVERT: R  258 ILE cc_start: 0.8429 (tt) cc_final: 0.8174 (tp)
REVERT: S   59 TYR cc_start: 0.8448 (m-80) cc_final: 0.8103 (m-80)
  outliers start: 38
  outliers final: 15
  residues processed: 204
  average time/residue: 1.0221
  time to fit residues: 222.5115
Evaluate side-chains
  179 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain R residue  271 ILE
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  209 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0020
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.112912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.097652 restraints weight = 11759.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.01
r_work: 0.3181 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7951  Z= 0.151
  Angle     :  0.579   8.379  10809  Z= 0.304
  Chirality :  0.043   0.147   1268
  Planarity :  0.004   0.058   1364
  Dihedral  :  4.454  50.112   1127
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 26.64 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.69 (0.26), residues: 1036
  helix: -0.21 (0.30), residues: 323
  sheet:  0.69 (0.31), residues: 287
  loop : -1.42 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.023   0.002   PHE R 225 
 TYR   0.012   0.002   TYR S 189 
 ARG   0.003   0.000   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  336)
  hydrogen bonds       : angle       4.70535 (  954)
  SS BOND              : bond        0.00935 (    2)
  SS BOND              : angle       1.44311 (    4)
  covalent geometry    : bond        0.00351 ( 7949)
  covalent geometry    : angle       0.57873 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 173
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7875 (mttp)
REVERT: A  296 TYR cc_start: 0.7749 (t80) cc_final: 0.7382 (t80)
REVERT: A  340 THR cc_start: 0.8339 (t) cc_final: 0.8055 (m)
REVERT: A  349 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7713 (mttp)
REVERT: B   13 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7254 (tm130)
REVERT: B   46 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7940 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8224 (mmt90)
REVERT: B  258 ASP cc_start: 0.7929 (t0) cc_final: 0.7362 (t0)
REVERT: R   67 ASN cc_start: 0.8334 (m-40) cc_final: 0.7593 (m110)
REVERT: R   74 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (mp)
REVERT: R  153 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7136 (tmt-80)
REVERT: R  179 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (pt)
REVERT: R  226 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: S   59 TYR cc_start: 0.8436 (m-80) cc_final: 0.8100 (m-80)
REVERT: S   83 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7720 (mtp)
  outliers start: 41
  outliers final: 18
  residues processed: 195
  average time/residue: 1.0803
  time to fit residues: 223.9487
Evaluate side-chains
  183 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 158
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  153 ARG
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  203 SER
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0370
   chunk 90 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0020
   chunk 97 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4066

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.114095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098797 restraints weight = 11724.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.01
r_work: 0.3199 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7951  Z= 0.111
  Angle     :  0.556   8.172  10809  Z= 0.285
  Chirality :  0.041   0.143   1268
  Planarity :  0.004   0.053   1364
  Dihedral  :  4.131  44.176   1127
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.30 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.50 (0.26), residues: 1036
  helix:  0.09 (0.31), residues: 323
  sheet:  0.73 (0.31), residues: 287
  loop : -1.38 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.019   0.001   PHE A 274 
 TYR   0.012   0.001   TYR S 189 
 ARG   0.003   0.000   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  336)
  hydrogen bonds       : angle       4.48297 (  954)
  SS BOND              : bond        0.00735 (    2)
  SS BOND              : angle       1.27388 (    4)
  covalent geometry    : bond        0.00246 ( 7949)
  covalent geometry    : angle       0.55509 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 1.786 
Fit side-chains
REVERT: A  296 TYR cc_start: 0.7663 (t80) cc_final: 0.7345 (t80)
REVERT: A  340 THR cc_start: 0.8328 (t) cc_final: 0.8032 (m)
REVERT: A  349 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7717 (mttp)
REVERT: B   13 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7315 (tm-30)
REVERT: B   46 ARG cc_start: 0.8165 (mmt-90) cc_final: 0.7951 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8225 (mmt180)
REVERT: B  258 ASP cc_start: 0.7881 (t0) cc_final: 0.7297 (t0)
REVERT: R   63 ILE cc_start: 0.8808 (mm) cc_final: 0.7940 (mt)
REVERT: R   67 ASN cc_start: 0.8314 (m-40) cc_final: 0.7568 (m110)
REVERT: R   74 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8414 (mp)
REVERT: R  226 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8318 (mp)
REVERT: R  258 ILE cc_start: 0.8308 (tt) cc_final: 0.8087 (tp)
REVERT: S   59 TYR cc_start: 0.8417 (m-80) cc_final: 0.8153 (m-80)
  outliers start: 36
  outliers final: 17
  residues processed: 193
  average time/residue: 1.2149
  time to fit residues: 250.2642
Evaluate side-chains
  187 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  195 SER
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  265 SER
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 70 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
B  44 GLN
B  54 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.114170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098701 restraints weight = 11385.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.96
r_work: 0.3184 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7951  Z= 0.161
  Angle     :  0.584   7.686  10809  Z= 0.305
  Chirality :  0.043   0.142   1268
  Planarity :  0.004   0.052   1364
  Dihedral  :  4.097  15.405   1126
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.30 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.52 (0.26), residues: 1036
  helix:  0.14 (0.31), residues: 323
  sheet:  0.64 (0.31), residues: 288
  loop : -1.39 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.027   0.002   PHE R 225 
 TYR   0.013   0.002   TYR B 111 
 ARG   0.002   0.000   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  336)
  hydrogen bonds       : angle       4.56178 (  954)
  SS BOND              : bond        0.00911 (    2)
  SS BOND              : angle       1.54875 (    4)
  covalent geometry    : bond        0.00380 ( 7949)
  covalent geometry    : angle       0.58296 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 1.506 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8285 (mtmm) cc_final: 0.7977 (mttp)
REVERT: A  252 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8302 (m)
REVERT: A  296 TYR cc_start: 0.7723 (t80) cc_final: 0.7342 (t80)
REVERT: A  340 THR cc_start: 0.8340 (t) cc_final: 0.8057 (m)
REVERT: A  349 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7795 (mttp)
REVERT: B   13 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: B   46 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7908 (mtt-85)
REVERT: B  134 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7993 (mtm-85)
REVERT: B  150 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8202 (mmt90)
REVERT: B  258 ASP cc_start: 0.7935 (t0) cc_final: 0.7418 (t0)
REVERT: R   63 ILE cc_start: 0.8866 (mm) cc_final: 0.8004 (mt)
REVERT: R   67 ASN cc_start: 0.8333 (m-40) cc_final: 0.7602 (m110)
REVERT: R   74 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8440 (mp)
REVERT: R   81 ILE cc_start: 0.8096 (tt) cc_final: 0.7664 (pt)
REVERT: R  223 LEU cc_start: 0.8275 (tp) cc_final: 0.8056 (tp)
REVERT: R  226 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8343 (mp)
REVERT: R  258 ILE cc_start: 0.8356 (tt) cc_final: 0.8132 (tp)
REVERT: S   59 TYR cc_start: 0.8411 (m-80) cc_final: 0.8136 (m-80)
  outliers start: 36
  outliers final: 21
  residues processed: 190
  average time/residue: 1.3238
  time to fit residues: 268.6407
Evaluate side-chains
  190 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  203 SER
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.113042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.097531 restraints weight = 11534.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.97
r_work: 0.3171 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7951  Z= 0.204
  Angle     :  0.623   8.274  10809  Z= 0.325
  Chirality :  0.045   0.144   1268
  Planarity :  0.004   0.052   1364
  Dihedral  :  4.268  15.660   1126
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.74 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.53 (0.26), residues: 1036
  helix:  0.14 (0.30), residues: 324
  sheet:  0.64 (0.31), residues: 288
  loop : -1.41 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP S  47 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.022   0.002   PHE R 104 
 TYR   0.018   0.002   TYR B 111 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04936 (  336)
  hydrogen bonds       : angle       4.63694 (  954)
  SS BOND              : bond        0.01001 (    2)
  SS BOND              : angle       1.69707 (    4)
  covalent geometry    : bond        0.00484 ( 7949)
  covalent geometry    : angle       0.62222 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.799 
Fit side-chains
REVERT: G   27 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8261 (mtt90)
REVERT: A   10 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8030 (mttp)
REVERT: A  252 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8311 (m)
REVERT: A  266 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8430 (tp)
REVERT: A  296 TYR cc_start: 0.7691 (t80) cc_final: 0.7281 (t80)
REVERT: A  340 THR cc_start: 0.8304 (t) cc_final: 0.8038 (m)
REVERT: B   13 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7360 (tm-30)
REVERT: B   46 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7897 (mtt-85)
REVERT: B  134 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7997 (mtm-85)
REVERT: B  150 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8165 (mmt90)
REVERT: B  219 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7626 (mtp85)
REVERT: B  258 ASP cc_start: 0.7938 (t0) cc_final: 0.7367 (t0)
REVERT: R   63 ILE cc_start: 0.8885 (mm) cc_final: 0.8023 (mt)
REVERT: R   67 ASN cc_start: 0.8343 (m-40) cc_final: 0.7622 (m110)
REVERT: R   81 ILE cc_start: 0.8073 (tt) cc_final: 0.7669 (pt)
REVERT: R  223 LEU cc_start: 0.8327 (tp) cc_final: 0.8110 (tp)
REVERT: R  226 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: R  258 ILE cc_start: 0.8393 (tt) cc_final: 0.8162 (tp)
REVERT: S   59 TYR cc_start: 0.8432 (m-80) cc_final: 0.8160 (m-80)
  outliers start: 31
  outliers final: 16
  residues processed: 192
  average time/residue: 1.2938
  time to fit residues: 265.1540
Evaluate side-chains
  200 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   27 ARG
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  203 SER
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 94 optimal weight:    0.4980
   chunk 53 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.112812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.097500 restraints weight = 11841.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.02
r_work: 0.3180 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7951  Z= 0.154
  Angle     :  0.590   8.813  10809  Z= 0.306
  Chirality :  0.043   0.147   1268
  Planarity :  0.004   0.050   1364
  Dihedral  :  4.085  15.428   1126
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 28.87 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.26), residues: 1036
  helix:  0.29 (0.30), residues: 324
  sheet:  0.66 (0.31), residues: 288
  loop : -1.37 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.028   0.002   PHE R 225 
 TYR   0.018   0.002   TYR B 111 
 ARG   0.006   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  336)
  hydrogen bonds       : angle       4.51621 (  954)
  SS BOND              : bond        0.00915 (    2)
  SS BOND              : angle       1.60924 (    4)
  covalent geometry    : bond        0.00361 ( 7949)
  covalent geometry    : angle       0.58897 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.922 
Fit side-chains
REVERT: G   27 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8258 (mtt90)
REVERT: A  252 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8306 (m)
REVERT: A  266 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8404 (tp)
REVERT: A  340 THR cc_start: 0.8304 (t) cc_final: 0.8056 (m)
REVERT: B   13 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7339 (tm-30)
REVERT: B   46 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7943 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8130 (mmt90)
REVERT: B  219 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7818 (mtt90)
REVERT: B  258 ASP cc_start: 0.7951 (t0) cc_final: 0.7384 (t0)
REVERT: R   63 ILE cc_start: 0.8872 (mm) cc_final: 0.8032 (mt)
REVERT: R   67 ASN cc_start: 0.8339 (m-40) cc_final: 0.7616 (m110)
REVERT: R  155 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6778 (tp)
REVERT: R  223 LEU cc_start: 0.8297 (tp) cc_final: 0.8074 (tp)
REVERT: R  226 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8325 (mp)
REVERT: R  258 ILE cc_start: 0.8361 (tt) cc_final: 0.8116 (tp)
REVERT: S   59 TYR cc_start: 0.8422 (m-80) cc_final: 0.8149 (m-80)
  outliers start: 29
  outliers final: 19
  residues processed: 192
  average time/residue: 1.1682
  time to fit residues: 238.3830
Evaluate side-chains
  200 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   27 ARG
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  211 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  203 SER
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0870
   chunk 6 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 81 optimal weight:    0.3980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.113475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.098026 restraints weight = 12027.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.05
r_work: 0.3188 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7951  Z= 0.134
  Angle     :  0.577   8.947  10809  Z= 0.299
  Chirality :  0.042   0.144   1268
  Planarity :  0.004   0.049   1364
  Dihedral  :  3.953  15.436   1126
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 30.05 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.29 (0.26), residues: 1036
  helix:  0.47 (0.31), residues: 322
  sheet:  0.71 (0.31), residues: 288
  loop : -1.32 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.020   0.001   PHE R 104 
 TYR   0.017   0.001   TYR B 111 
 ARG   0.007   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04010 (  336)
  hydrogen bonds       : angle       4.42722 (  954)
  SS BOND              : bond        0.00831 (    2)
  SS BOND              : angle       1.60266 (    4)
  covalent geometry    : bond        0.00310 ( 7949)
  covalent geometry    : angle       0.57636 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A  252 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8284 (m)
REVERT: A  266 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8381 (tp)
REVERT: A  340 THR cc_start: 0.8288 (t) cc_final: 0.8057 (m)
REVERT: B   13 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7365 (tm-30)
REVERT: B   46 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7984 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8158 (mmt180)
REVERT: B  219 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7833 (mtt90)
REVERT: B  258 ASP cc_start: 0.7934 (t0) cc_final: 0.7408 (t0)
REVERT: R   63 ILE cc_start: 0.8859 (mm) cc_final: 0.7999 (mt)
REVERT: R   67 ASN cc_start: 0.8323 (m-40) cc_final: 0.7570 (m110)
REVERT: R  155 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6802 (tp)
REVERT: R  223 LEU cc_start: 0.8299 (tp) cc_final: 0.8075 (tp)
REVERT: R  258 ILE cc_start: 0.8339 (tt) cc_final: 0.8095 (tp)
REVERT: S   59 TYR cc_start: 0.8406 (m-80) cc_final: 0.8124 (m-80)
  outliers start: 25
  outliers final: 16
  residues processed: 195
  average time/residue: 1.1779
  time to fit residues: 242.9123
Evaluate side-chains
  196 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 93 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0170
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.099465 restraints weight = 11584.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.97
r_work: 0.3200 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7951  Z= 0.132
  Angle     :  0.579   9.100  10809  Z= 0.299
  Chirality :  0.042   0.146   1268
  Planarity :  0.004   0.049   1364
  Dihedral  :  3.934  15.453   1126
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 30.45 %
    Favored  : 66.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.21 (0.26), residues: 1036
  helix:  0.54 (0.31), residues: 323
  sheet:  0.69 (0.31), residues: 288
  loop : -1.24 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.031   0.002   PHE R 225 
 TYR   0.017   0.001   TYR B 111 
 ARG   0.006   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  336)
  hydrogen bonds       : angle       4.40041 (  954)
  SS BOND              : bond        0.00812 (    2)
  SS BOND              : angle       1.56173 (    4)
  covalent geometry    : bond        0.00305 ( 7949)
  covalent geometry    : angle       0.57835 (10805)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.831 
Fit side-chains
REVERT: G   27 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8292 (mtt90)
REVERT: A  252 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8300 (m)
REVERT: A  266 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8393 (tp)
REVERT: A  340 THR cc_start: 0.8279 (t) cc_final: 0.8049 (m)
REVERT: B   13 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: B   46 ARG cc_start: 0.8217 (mmt-90) cc_final: 0.7997 (mtt-85)
REVERT: B  150 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8193 (mmt180)
REVERT: B  219 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7839 (mtt90)
REVERT: B  258 ASP cc_start: 0.7931 (t0) cc_final: 0.7357 (t0)
REVERT: B  325 MET cc_start: 0.8708 (tpp) cc_final: 0.8417 (mmt)
REVERT: R   63 ILE cc_start: 0.8845 (mm) cc_final: 0.7979 (mt)
REVERT: R   67 ASN cc_start: 0.8315 (m-40) cc_final: 0.7566 (m110)
REVERT: R  155 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6781 (tp)
REVERT: R  223 LEU cc_start: 0.8362 (tp) cc_final: 0.8148 (tp)
REVERT: R  258 ILE cc_start: 0.8320 (tt) cc_final: 0.8083 (tp)
REVERT: S   59 TYR cc_start: 0.8408 (m-80) cc_final: 0.8130 (m-80)
REVERT: S  119 VAL cc_start: 0.8125 (m) cc_final: 0.7855 (t)
  outliers start: 24
  outliers final: 16
  residues processed: 189
  average time/residue: 1.1810
  time to fit residues: 235.9516
Evaluate side-chains
  193 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   27 ARG
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue  132 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  201 ARG
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  209 THR
Chi-restraints excluded: chain S residue  218 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    0.2980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  54 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.114441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.099058 restraints weight = 11616.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.98
r_work: 0.3196 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7951  Z= 0.148
  Angle     :  0.592   9.072  10809  Z= 0.305
  Chirality :  0.043   0.143   1268
  Planarity :  0.004   0.049   1364
  Dihedral  :  3.990  17.130   1126
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 30.18 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.22 (0.26), residues: 1036
  helix:  0.53 (0.30), residues: 323
  sheet:  0.68 (0.31), residues: 288
  loop : -1.23 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.019   0.002   PHE R 104 
 TYR   0.017   0.002   TYR B 111 
 ARG   0.006   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  336)
  hydrogen bonds       : angle       4.42641 (  954)
  SS BOND              : bond        0.00878 (    2)
  SS BOND              : angle       1.69546 (    4)
  covalent geometry    : bond        0.00346 ( 7949)
  covalent geometry    : angle       0.59135 (10805)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7513.65 seconds
wall clock time: 132 minutes 20.46 seconds (7940.46 seconds total)