Starting phenix.real_space_refine
on Mon Jun  9 13:16:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w0m_32244/06_2025/7w0m_32244.cif"
  }
  resolution = 3.71
  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=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2101 atoms to isotropic.
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      67      5.16       5
     C    5690      2.51       5
     N    1509      2.21       5
     O    1663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8929
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1758
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2321
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 11, 'TRANS': 278}
    Chain: "S"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'8EH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.90, per 1000 atoms: 0.66
  Number of scatterers: 8929
  At special positions: 0
  Unit cell: (92.65, 119.85, 131.75, 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      67     16.00
     O    1663      8.00
     N    1509      7.00
     C    5690      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      36.1% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.695A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.037A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 3.503A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.883A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.878A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ARG B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.835A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 39 through 55
      removed outlier: 3.562A  pdb=" N   GLN C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ASN C  55 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 74
      removed outlier: 3.561A  pdb=" N   LEU C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 55
    Processing helix  chain 'R' and resid 64 through 81
      removed outlier: 4.494A  pdb=" N   THR R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.020A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR R  89 " --> pdb=" O   TRP R  85 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   TYR R  90 " --> pdb=" O   ALA R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 132
      removed outlier: 3.979A  pdb=" N   LYS R 103 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 148 through 162
      removed outlier: 4.604A  pdb=" N   TRP R 154 " --> pdb=" O   THR R 150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 167
      removed outlier: 3.963A  pdb=" N   VAL R 166 " --> pdb=" O   MET R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 231
      removed outlier: 4.080A  pdb=" N   ALA R 196 " --> pdb=" O   SER R 192 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR R 207 " --> pdb=" O   VAL R 203 " (cutoff:3.500A)
      Proline residue:  R 213  - end of helix
    Processing helix  chain 'R' and resid 238 through 276
      removed outlier: 4.087A  pdb=" N   LYS R 242 " --> pdb=" O   GLU R 238 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL R 254 " --> pdb=" O   ILE R 250 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
      removed outlier: 4.014A  pdb=" N   LEU R 276 " --> pdb=" O   MET R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 291
      removed outlier: 4.361A  pdb=" N   LEU R 285 " --> pdb=" O   CYS R 281 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   PHE R 286 " --> pdb=" O   ASP R 282 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 293 through 304
      removed outlier: 4.244A  pdb=" N   ILE R 297 " --> pdb=" O   TYR R 293 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER R 302 " --> pdb=" O   SER R 298 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 311
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 52 through 56
      removed outlier: 3.781A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.164A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
      removed outlier: 3.577A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.071A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.837A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP B  83 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.039A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.820A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TRP B 169 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.910A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.539A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.163A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 168 through 171
      removed outlier: 3.736A  pdb=" N   GLN R 180 " --> pdb=" O   GLY R 171 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 7
      removed outlier: 3.818A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU S  81 " --> pdb=" O   LEU S  20 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP S  73 " --> pdb=" O   THR S  78 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR S  69 " --> pdb=" O   GLN S  82 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.842A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 147
    Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 160
    Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 187

    352 hydrogen bonds defined for protein.
    1014 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: 2.39

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2854
        1.35 -     1.47: 2370
        1.47 -     1.60: 3801
        1.60 -     1.72: 1
        1.72 -     1.85: 98
  Bond restraints: 9124
  Sorted by residual:
  bond pdb=" C30 8EH R 401 "
       pdb=" C31 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.472  1.569 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" C30 8EH R 401 "
       pdb=" N29 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.313  1.399 -0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" C10 8EH R 401 "
       pdb=" N11 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.421  1.500 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" C12 8EH R 401 "
       pdb=" N28 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.307  1.386 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C30 8EH R 401 "
       pdb=" N11 8EH R 401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.446 -0.071 2.00e-02 2.50e+03 1.27e+01
  ... (remaining 9119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 12147
        2.46 -     4.91: 180
        4.91 -     7.37: 31
        7.37 -     9.82: 6
        9.82 -    12.28: 1
  Bond angle restraints: 12365
  Sorted by residual:
  angle pdb=" C   LEU R 167 "
        pdb=" N   ARG R 168 "
        pdb=" CA  ARG R 168 "
      ideal   model   delta    sigma   weight residual
     120.75  128.01   -7.26 1.51e+00 4.39e-01 2.31e+01
  angle pdb=" CA  VAL R 166 "
        pdb=" CB  VAL R 166 "
        pdb=" CG2 VAL R 166 "
      ideal   model   delta    sigma   weight residual
     110.40  117.90   -7.50 1.70e+00 3.46e-01 1.94e+01
  angle pdb=" O15 8EH R 401 "
        pdb=" S14 8EH R 401 "
        pdb=" O16 8EH R 401 "
      ideal   model   delta    sigma   weight residual
     119.97  107.69   12.28 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" N   VAL R 148 "
        pdb=" CA  VAL R 148 "
        pdb=" C   VAL R 148 "
      ideal   model   delta    sigma   weight residual
     112.96  108.95    4.01 1.00e+00 1.00e+00 1.61e+01
  angle pdb=" CA  GLU S 234 "
        pdb=" C   GLU S 234 "
        pdb=" O   GLU S 234 "
      ideal   model   delta    sigma   weight residual
     121.16  116.83    4.33 1.12e+00 7.97e-01 1.50e+01
  ... (remaining 12360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4863
       17.87 -    35.74: 444
       35.74 -    53.61: 62
       53.61 -    71.48: 15
       71.48 -    89.35: 12
  Dihedral angle restraints: 5396
    sinusoidal: 2108
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CB  CYS R 102 "
           pdb=" SG  CYS R 102 "
           pdb=" SG  CYS R 181 "
           pdb=" CB  CYS R 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.61  -78.61     1      1.00e+01 1.00e-02 7.70e+01
  dihedral pdb=" CA  TYR S  94 "
           pdb=" C   TYR S  94 "
           pdb=" N   TYR S  95 "
           pdb=" CA  TYR S  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.31   25.69     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  THR B 164 "
           pdb=" C   THR B 164 "
           pdb=" N   THR B 165 "
           pdb=" CA  THR B 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1257
       0.072 -    0.144: 128
       0.144 -    0.217: 4
       0.217 -    0.289: 2
       0.289 -    0.361: 3
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" C19 8EH R 401 "
            pdb=" C17 8EH R 401 "
            pdb=" C21 8EH R 401 "
            pdb=" O20 8EH R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.79    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  LEU S 233 "
            pdb=" N   LEU S 233 "
            pdb=" C   LEU S 233 "
            pdb=" CB  LEU S 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  VAL R 166 "
            pdb=" CA  VAL R 166 "
            pdb=" CG1 VAL R 166 "
            pdb=" CG2 VAL R 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.53e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 147 "    0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO S 148 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO S 148 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 148 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 313 "   -0.040 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO R 314 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO R 314 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 314 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R  95 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO R  96 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R  96 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R  96 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1552 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1558
        2.76 -     3.30: 8547
        3.30 -     3.83: 13975
        3.83 -     4.37: 15727
        4.37 -     4.90: 27291
  Nonbonded interactions: 67098
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" NE  ARG R  91 "
            pdb=" O   ASP R  94 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OE1 GLN B 176 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   THR A 327 "
            pdb=" N   LYS A 330 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" ND2 ASN R  46 "
            pdb=" O   ALA R  72 "
     model   vdw
     2.277 3.120
  ... (remaining 67093 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.550
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
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      :  0.004   0.100   9125  Z= 0.224
  Angle     :  0.761  12.279  12367  Z= 0.405
  Chirality :  0.047   0.361   1394
  Planarity :  0.005   0.076   1555
  Dihedral  : 14.112  89.348   3275
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -1.90 (0.25), residues: 1118
  helix:  0.51 (0.29), residues: 352
  sheet: -1.72 (0.32), residues: 256
  loop : -2.30 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.027   0.001   PHE S  27 
 TYR   0.022   0.002   TYR S 235 
 ARG   0.005   0.000   ARG R 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16688 (  352)
  hydrogen bonds       : angle       5.91827 ( 1014)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       1.33790 (    2)
  covalent geometry    : bond        0.00447 ( 9124)
  covalent geometry    : angle       0.76062 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: A  191 PHE cc_start: 0.8395 (t80) cc_final: 0.8183 (t80)
REVERT: A  193 ASP cc_start: 0.7955 (m-30) cc_final: 0.7741 (m-30)
REVERT: A  245 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7718 (mm-30)
REVERT: A  271 LYS cc_start: 0.8171 (tptp) cc_final: 0.7911 (tptt)
REVERT: A  344 ILE cc_start: 0.7883 (tt) cc_final: 0.7677 (tt)
REVERT: A  348 LEU cc_start: 0.7514 (tp) cc_final: 0.7254 (tt)
REVERT: B   25 CYS cc_start: 0.8399 (m) cc_final: 0.7912 (t)
REVERT: B   61 MET cc_start: 0.6892 (tmm) cc_final: 0.6578 (tmm)
REVERT: B  124 TYR cc_start: 0.8294 (m-80) cc_final: 0.7711 (m-80)
REVERT: B  197 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7578 (mtp85)
REVERT: B  199 PHE cc_start: 0.8189 (p90) cc_final: 0.7933 (p90)
REVERT: B  212 ASP cc_start: 0.7593 (t0) cc_final: 0.7318 (t70)
REVERT: B  220 GLN cc_start: 0.7811 (mt0) cc_final: 0.7520 (mt0)
REVERT: B  233 CYS cc_start: 0.7497 (t) cc_final: 0.7115 (t)
REVERT: B  247 ASP cc_start: 0.7413 (t0) cc_final: 0.7060 (t0)
REVERT: B  314 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7216 (ptm160)
REVERT: R   97 PHE cc_start: 0.7240 (m-10) cc_final: 0.7018 (m-10)
REVERT: R  162 MET cc_start: 0.5536 (mmp) cc_final: 0.5175 (mmp)
REVERT: R  165 MET cc_start: 0.7280 (tpt) cc_final: 0.6920 (tpt)
REVERT: R  166 VAL cc_start: 0.7767 (t) cc_final: 0.7111 (t)
REVERT: R  183 MET cc_start: 0.4866 (tmm) cc_final: 0.4437 (tmm)
REVERT: R  268 LYS cc_start: 0.8837 (mttt) cc_final: 0.8499 (mttt)
REVERT: R  284 ASP cc_start: 0.8074 (t0) cc_final: 0.7810 (t0)
REVERT: R  301 ASN cc_start: 0.7790 (t0) cc_final: 0.7429 (t0)
REVERT: S   34 MET cc_start: 0.7776 (mmm) cc_final: 0.7165 (mmm)
REVERT: S   85 SER cc_start: 0.7950 (p) cc_final: 0.7679 (m)
REVERT: S   89 GLU cc_start: 0.7756 (tp30) cc_final: 0.7500 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.2180
  time to fit residues: 90.7368
Evaluate side-chains
  279 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.0870
   chunk 84 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 175 GLN
B 259 GLN
** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.142631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.117018 restraints weight = 15326.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.120441 restraints weight = 8191.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.122766 restraints weight = 5291.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9125  Z= 0.136
  Angle     :  0.641   8.640  12367  Z= 0.327
  Chirality :  0.043   0.223   1394
  Planarity :  0.004   0.048   1555
  Dihedral  :  8.631  73.840   1261
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.58 %
    Favored  : 86.39 %
  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: -1.71 (0.25), residues: 1118
  helix:  0.68 (0.29), residues: 352
  sheet: -1.41 (0.32), residues: 255
  loop : -2.32 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 261 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.013   0.001   PHE R 291 
 TYR   0.030   0.002   TYR S 235 
 ARG   0.003   0.000   ARG R 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  352)
  hydrogen bonds       : angle       4.77484 ( 1014)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.92198 (    2)
  covalent geometry    : bond        0.00299 ( 9124)
  covalent geometry    : angle       0.64070 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 278
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: A   26 ASP cc_start: 0.7897 (t0) cc_final: 0.7439 (t0)
REVERT: A  205 ARG cc_start: 0.7176 (mmp80) cc_final: 0.6917 (mmp80)
REVERT: A  216 GLU cc_start: 0.7695 (tp30) cc_final: 0.7463 (tp30)
REVERT: A  245 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  344 ILE cc_start: 0.8068 (tt) cc_final: 0.7845 (tt)
REVERT: A  348 LEU cc_start: 0.7846 (tp) cc_final: 0.7609 (tp)
REVERT: B   25 CYS cc_start: 0.8169 (m) cc_final: 0.7889 (t)
REVERT: B   59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7988 (m-80)
REVERT: B   61 MET cc_start: 0.6911 (tmm) cc_final: 0.6422 (tmm)
REVERT: B  102 THR cc_start: 0.8465 (t) cc_final: 0.8098 (m)
REVERT: B  197 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7544 (mtp85)
REVERT: B  212 ASP cc_start: 0.7632 (t0) cc_final: 0.7359 (t70)
REVERT: B  220 GLN cc_start: 0.7680 (mt0) cc_final: 0.7439 (mt0)
REVERT: B  233 CYS cc_start: 0.7531 (t) cc_final: 0.7119 (t)
REVERT: R   71 LEU cc_start: 0.7417 (tp) cc_final: 0.6798 (mm)
REVERT: R  162 MET cc_start: 0.5054 (mmp) cc_final: 0.4719 (mmp)
REVERT: R  183 MET cc_start: 0.4876 (tmm) cc_final: 0.4254 (tmm)
REVERT: R  268 LYS cc_start: 0.8768 (mttt) cc_final: 0.8408 (mttt)
REVERT: R  284 ASP cc_start: 0.7826 (t0) cc_final: 0.7584 (t0)
REVERT: S   34 MET cc_start: 0.7670 (mmm) cc_final: 0.6957 (mmm)
REVERT: S   85 SER cc_start: 0.7938 (p) cc_final: 0.7725 (m)
  outliers start: 10
  outliers final: 4
  residues processed: 280
  average time/residue: 0.2073
  time to fit residues: 79.1826
Evaluate side-chains
  275 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 271
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 100 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0070
   chunk 88 optimal weight:    0.0170
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0030
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.1646

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  75 GLN
R 112 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.146291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120720 restraints weight = 15506.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.124285 restraints weight = 7897.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.126717 restraints weight = 4914.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9125  Z= 0.110
  Angle     :  0.590   7.567  12367  Z= 0.300
  Chirality :  0.041   0.243   1394
  Planarity :  0.004   0.040   1555
  Dihedral  :  8.323  72.143   1261
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.19 %
    Favored  : 82.47 %
  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: -1.51 (0.24), residues: 1118
  helix:  0.74 (0.29), residues: 353
  sheet: -1.07 (0.32), residues: 247
  loop : -2.25 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 261 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.018   0.001   PHE S  27 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  352)
  hydrogen bonds       : angle       4.48494 ( 1014)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       0.72924 (    2)
  covalent geometry    : bond        0.00233 ( 9124)
  covalent geometry    : angle       0.58954 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 276
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7458 (tm-30)
REVERT: A   26 ASP cc_start: 0.7848 (t0) cc_final: 0.7392 (t0)
REVERT: A  190 THR cc_start: 0.8873 (t) cc_final: 0.8625 (m)
REVERT: A  197 LYS cc_start: 0.8068 (tttp) cc_final: 0.7689 (tptt)
REVERT: A  205 ARG cc_start: 0.7230 (mmp80) cc_final: 0.6974 (mmp80)
REVERT: A  216 GLU cc_start: 0.7709 (tp30) cc_final: 0.7462 (tp30)
REVERT: A  245 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7442 (mm-30)
REVERT: A  248 LYS cc_start: 0.8694 (mttt) cc_final: 0.8455 (tttt)
REVERT: A  333 GLN cc_start: 0.7942 (tp40) cc_final: 0.7444 (tp40)
REVERT: A  344 ILE cc_start: 0.8072 (tt) cc_final: 0.7834 (tt)
REVERT: A  348 LEU cc_start: 0.7881 (tp) cc_final: 0.7611 (tp)
REVERT: B   59 TYR cc_start: 0.8317 (m-80) cc_final: 0.8101 (m-80)
REVERT: B   61 MET cc_start: 0.6895 (tmm) cc_final: 0.6428 (tmm)
REVERT: B  102 THR cc_start: 0.8487 (t) cc_final: 0.8040 (m)
REVERT: B  188 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7349 (mmt)
REVERT: B  191 SER cc_start: 0.8449 (t) cc_final: 0.7910 (t)
REVERT: B  197 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7505 (mtp85)
REVERT: B  212 ASP cc_start: 0.7590 (t0) cc_final: 0.7352 (t0)
REVERT: B  233 CYS cc_start: 0.7445 (t) cc_final: 0.7095 (t)
REVERT: B  291 ASP cc_start: 0.6572 (p0) cc_final: 0.6349 (p0)
REVERT: R   36 MET cc_start: 0.6262 (mmp) cc_final: 0.5951 (mmp)
REVERT: R   78 PHE cc_start: 0.6675 (t80) cc_final: 0.6330 (t80)
REVERT: R  162 MET cc_start: 0.5099 (mmp) cc_final: 0.4736 (mmp)
REVERT: R  183 MET cc_start: 0.4963 (tmm) cc_final: 0.4272 (tmm)
REVERT: R  268 LYS cc_start: 0.8755 (mttt) cc_final: 0.8437 (mttt)
REVERT: S   89 GLU cc_start: 0.7614 (tp30) cc_final: 0.7409 (tp30)
REVERT: S  231 GLN cc_start: 0.8131 (pp30) cc_final: 0.7724 (pp30)
  outliers start: 13
  outliers final: 8
  residues processed: 279
  average time/residue: 0.2141
  time to fit residues: 82.0649
Evaluate side-chains
  283 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 274
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain S residue   25 SER
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.142600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.116501 restraints weight = 15418.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.120070 restraints weight = 8049.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122400 restraints weight = 5105.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9125  Z= 0.146
  Angle     :  0.600   7.745  12367  Z= 0.309
  Chirality :  0.042   0.266   1394
  Planarity :  0.004   0.036   1555
  Dihedral  :  8.429  69.607   1261
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.22 %
    Favored  : 80.72 %
  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: -1.52 (0.24), residues: 1118
  helix:  0.68 (0.28), residues: 359
  sheet: -0.99 (0.32), residues: 247
  loop : -2.29 (0.24), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.022   0.001   PHE S  27 
 TYR   0.024   0.002   TYR S 235 
 ARG   0.006   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  352)
  hydrogen bonds       : angle       4.45609 ( 1014)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.82905 (    2)
  covalent geometry    : bond        0.00326 ( 9124)
  covalent geometry    : angle       0.60020 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 281
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7476 (tm-30)
REVERT: A   26 ASP cc_start: 0.7872 (t0) cc_final: 0.7368 (t0)
REVERT: A  216 GLU cc_start: 0.7695 (tp30) cc_final: 0.7458 (tp30)
REVERT: A  245 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  248 LYS cc_start: 0.8729 (mttt) cc_final: 0.8510 (tttt)
REVERT: A  348 LEU cc_start: 0.7907 (tp) cc_final: 0.7615 (tt)
REVERT: B   59 TYR cc_start: 0.8327 (m-80) cc_final: 0.8105 (m-80)
REVERT: B   61 MET cc_start: 0.6876 (tmm) cc_final: 0.6387 (tmm)
REVERT: B   82 TRP cc_start: 0.8342 (m100) cc_final: 0.8065 (m100)
REVERT: B  180 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6763 (p90)
REVERT: B  188 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7354 (mmt)
REVERT: B  191 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8106 (t)
REVERT: B  233 CYS cc_start: 0.7535 (t) cc_final: 0.7255 (t)
REVERT: B  291 ASP cc_start: 0.6775 (p0) cc_final: 0.6498 (p0)
REVERT: R   78 PHE cc_start: 0.6677 (t80) cc_final: 0.6425 (t80)
REVERT: R  162 MET cc_start: 0.5161 (mmp) cc_final: 0.4810 (mmp)
REVERT: R  180 GLN cc_start: 0.4280 (pm20) cc_final: 0.3993 (pm20)
REVERT: R  183 MET cc_start: 0.5008 (tmm) cc_final: 0.4306 (tmm)
REVERT: S  231 GLN cc_start: 0.8119 (pp30) cc_final: 0.7696 (pp30)
  outliers start: 20
  outliers final: 12
  residues processed: 290
  average time/residue: 0.2007
  time to fit residues: 80.5117
Evaluate side-chains
  291 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 276
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0370
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.142739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116597 restraints weight = 15474.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.120144 restraints weight = 8116.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.122480 restraints weight = 5166.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9125  Z= 0.142
  Angle     :  0.605   8.018  12367  Z= 0.311
  Chirality :  0.043   0.275   1394
  Planarity :  0.004   0.035   1555
  Dihedral  :  8.423  63.933   1261
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.45 %
    Favored  : 78.35 %
  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: -1.45 (0.24), residues: 1118
  helix:  0.74 (0.28), residues: 357
  sheet: -0.98 (0.32), residues: 261
  loop : -2.25 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 261 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.022   0.001   PHE S  27 
 TYR   0.024   0.002   TYR S 235 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  352)
  hydrogen bonds       : angle       4.42626 ( 1014)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.85678 (    2)
  covalent geometry    : bond        0.00315 ( 9124)
  covalent geometry    : angle       0.60454 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 281
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: A   26 ASP cc_start: 0.7880 (t0) cc_final: 0.7404 (t0)
REVERT: A  205 ARG cc_start: 0.7255 (mmp80) cc_final: 0.7037 (mmp80)
REVERT: A  216 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (tp30)
REVERT: A  245 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7533 (mm-30)
REVERT: A  248 LYS cc_start: 0.8740 (mttt) cc_final: 0.8497 (tttt)
REVERT: A  271 LYS cc_start: 0.8181 (tptp) cc_final: 0.7879 (tptt)
REVERT: A  348 LEU cc_start: 0.7856 (tp) cc_final: 0.7590 (tt)
REVERT: B   61 MET cc_start: 0.6938 (tmm) cc_final: 0.6362 (tmm)
REVERT: B   82 TRP cc_start: 0.8316 (m100) cc_final: 0.8035 (m100)
REVERT: B  180 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6853 (p90)
REVERT: B  188 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (mmt)
REVERT: B  191 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8091 (t)
REVERT: B  233 CYS cc_start: 0.7643 (t) cc_final: 0.7356 (t)
REVERT: B  243 THR cc_start: 0.8048 (p) cc_final: 0.7804 (p)
REVERT: B  291 ASP cc_start: 0.6667 (p0) cc_final: 0.6417 (p0)
REVERT: B  317 CYS cc_start: 0.7625 (p) cc_final: 0.7294 (p)
REVERT: R   36 MET cc_start: 0.6455 (mmp) cc_final: 0.6199 (mmp)
REVERT: R   78 PHE cc_start: 0.6691 (t80) cc_final: 0.6489 (t80)
REVERT: R  162 MET cc_start: 0.5249 (mmp) cc_final: 0.4892 (mmp)
REVERT: R  268 LYS cc_start: 0.8810 (mttt) cc_final: 0.8480 (mttt)
REVERT: S   34 MET cc_start: 0.7681 (mmm) cc_final: 0.6964 (mmm)
REVERT: S  231 GLN cc_start: 0.8153 (pp30) cc_final: 0.7648 (pp30)
  outliers start: 31
  outliers final: 19
  residues processed: 297
  average time/residue: 0.1947
  time to fit residues: 80.1110
Evaluate side-chains
  302 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 279
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 259 GLN
** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.115661 restraints weight = 15289.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.119186 restraints weight = 8080.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.121487 restraints weight = 5164.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9125  Z= 0.162
  Angle     :  0.621   7.992  12367  Z= 0.321
  Chirality :  0.043   0.277   1394
  Planarity :  0.004   0.036   1555
  Dihedral  :  8.479  61.529   1261
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.25 %
    Favored  : 77.73 %
  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: -1.44 (0.25), residues: 1118
  helix:  0.75 (0.28), residues: 357
  sheet: -0.93 (0.32), residues: 263
  loop : -2.27 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 261 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.020   0.001   PHE S  27 
 TYR   0.023   0.002   TYR S 235 
 ARG   0.006   0.000   ARG R 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  352)
  hydrogen bonds       : angle       4.43523 ( 1014)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       0.84631 (    2)
  covalent geometry    : bond        0.00364 ( 9124)
  covalent geometry    : angle       0.62069 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 276
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A   26 ASP cc_start: 0.7871 (t0) cc_final: 0.7397 (t0)
REVERT: A  200 ASP cc_start: 0.8408 (t0) cc_final: 0.8166 (t0)
REVERT: A  216 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7464 (tp30)
REVERT: A  243 MET cc_start: 0.7415 (mtp) cc_final: 0.7127 (ttp)
REVERT: A  245 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: A  271 LYS cc_start: 0.8197 (tptp) cc_final: 0.7887 (tptt)
REVERT: A  306 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7102 (tt0)
REVERT: A  348 LEU cc_start: 0.7880 (tp) cc_final: 0.7618 (tt)
REVERT: B   61 MET cc_start: 0.6944 (tmm) cc_final: 0.6388 (tmm)
REVERT: B   82 TRP cc_start: 0.8323 (m100) cc_final: 0.8037 (m100)
REVERT: B  180 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6840 (p90)
REVERT: B  188 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (mmt)
REVERT: B  191 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8141 (t)
REVERT: B  220 GLN cc_start: 0.7723 (mt0) cc_final: 0.7461 (mt0)
REVERT: B  233 CYS cc_start: 0.7674 (t) cc_final: 0.7397 (t)
REVERT: B  243 THR cc_start: 0.8099 (p) cc_final: 0.7891 (p)
REVERT: B  317 CYS cc_start: 0.7625 (p) cc_final: 0.7252 (p)
REVERT: R   36 MET cc_start: 0.6513 (mmp) cc_final: 0.6271 (mmp)
REVERT: R  162 MET cc_start: 0.5438 (mmp) cc_final: 0.5059 (mmp)
REVERT: R  268 LYS cc_start: 0.8805 (mttt) cc_final: 0.8463 (mttt)
REVERT: S   11 LEU cc_start: 0.8070 (mp) cc_final: 0.7800 (mm)
  outliers start: 39
  outliers final: 27
  residues processed: 291
  average time/residue: 0.2021
  time to fit residues: 81.6084
Evaluate side-chains
  305 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 273
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
S 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.115753 restraints weight = 15526.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.119363 restraints weight = 8091.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.121746 restraints weight = 5113.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9125  Z= 0.149
  Angle     :  0.634   8.162  12367  Z= 0.327
  Chirality :  0.043   0.277   1394
  Planarity :  0.004   0.048   1555
  Dihedral  :  8.458  60.003   1261
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.72 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.39 (0.25), residues: 1118
  helix:  0.76 (0.29), residues: 357
  sheet: -0.78 (0.33), residues: 254
  loop : -2.28 (0.24), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.021   0.001   PHE S  27 
 TYR   0.020   0.002   TYR S 235 
 ARG   0.009   0.000   ARG R 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  352)
  hydrogen bonds       : angle       4.39951 ( 1014)
  SS BOND              : bond        0.00428 (    1)
  SS BOND              : angle       0.63301 (    2)
  covalent geometry    : bond        0.00337 ( 9124)
  covalent geometry    : angle       0.63444 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 264
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A   26 ASP cc_start: 0.7854 (t0) cc_final: 0.7378 (t0)
REVERT: A  216 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7461 (tp30)
REVERT: A  245 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7504 (mm-30)
REVERT: A  271 LYS cc_start: 0.8197 (tptp) cc_final: 0.7878 (tptt)
REVERT: A  309 ASP cc_start: 0.7669 (t0) cc_final: 0.7463 (t0)
REVERT: A  348 LEU cc_start: 0.7882 (tp) cc_final: 0.7623 (tt)
REVERT: B   47 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8171 (m)
REVERT: B   61 MET cc_start: 0.6936 (tmm) cc_final: 0.6460 (tmm)
REVERT: B   82 TRP cc_start: 0.8324 (m100) cc_final: 0.8039 (m100)
REVERT: B  180 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6888 (p90)
REVERT: B  188 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7374 (mmt)
REVERT: B  191 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8145 (t)
REVERT: B  233 CYS cc_start: 0.7682 (t) cc_final: 0.7444 (t)
REVERT: B  243 THR cc_start: 0.8155 (p) cc_final: 0.7928 (p)
REVERT: B  247 ASP cc_start: 0.7448 (t0) cc_final: 0.7084 (t0)
REVERT: R   36 MET cc_start: 0.6499 (mmp) cc_final: 0.6269 (mmp)
REVERT: R  162 MET cc_start: 0.5461 (mmp) cc_final: 0.5081 (mmp)
REVERT: R  268 LYS cc_start: 0.8777 (mttt) cc_final: 0.8422 (mttt)
REVERT: S   11 LEU cc_start: 0.8066 (mp) cc_final: 0.7822 (mm)
REVERT: S   34 MET cc_start: 0.7663 (mmm) cc_final: 0.6995 (mmm)
  outliers start: 37
  outliers final: 26
  residues processed: 280
  average time/residue: 0.2063
  time to fit residues: 80.0419
Evaluate side-chains
  295 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  168 ARG
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0670
   chunk 32 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 259 GLN
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.116716 restraints weight = 15663.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.120267 restraints weight = 8158.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.122674 restraints weight = 5190.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9125  Z= 0.123
  Angle     :  0.621   8.107  12367  Z= 0.317
  Chirality :  0.043   0.271   1394
  Planarity :  0.004   0.046   1555
  Dihedral  :  8.229  58.736   1261
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.24 %
    Favored  : 74.74 %
  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: -1.30 (0.25), residues: 1118
  helix:  0.84 (0.29), residues: 357
  sheet: -0.76 (0.33), residues: 255
  loop : -2.21 (0.24), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS R 265 
 PHE   0.018   0.001   PHE R  97 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.008   0.000   ARG R 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  352)
  hydrogen bonds       : angle       4.30182 ( 1014)
  SS BOND              : bond        0.00452 (    1)
  SS BOND              : angle       0.50366 (    2)
  covalent geometry    : bond        0.00273 ( 9124)
  covalent geometry    : angle       0.62147 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 264
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7493 (tm-30)
REVERT: A   26 ASP cc_start: 0.7846 (t0) cc_final: 0.7385 (t0)
REVERT: A  216 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7462 (tp30)
REVERT: A  245 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7469 (mm-30)
REVERT: A  271 LYS cc_start: 0.8180 (tptp) cc_final: 0.7866 (tptt)
REVERT: A  348 LEU cc_start: 0.7898 (tp) cc_final: 0.7625 (tt)
REVERT: B   45 MET cc_start: 0.7756 (mtt) cc_final: 0.7517 (mtm)
REVERT: B   61 MET cc_start: 0.6959 (tmm) cc_final: 0.6496 (tmm)
REVERT: B   82 TRP cc_start: 0.8335 (m100) cc_final: 0.8065 (m100)
REVERT: B  180 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6890 (p90)
REVERT: B  188 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7349 (mmt)
REVERT: B  191 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8076 (t)
REVERT: B  233 CYS cc_start: 0.7663 (t) cc_final: 0.7445 (t)
REVERT: B  243 THR cc_start: 0.8167 (p) cc_final: 0.7951 (p)
REVERT: C   48 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: R  162 MET cc_start: 0.5434 (mmp) cc_final: 0.5050 (mmp)
REVERT: R  268 LYS cc_start: 0.8765 (mttt) cc_final: 0.8398 (mttt)
REVERT: S   34 MET cc_start: 0.7660 (mmm) cc_final: 0.6975 (mmm)
REVERT: S  231 GLN cc_start: 0.8088 (pp30) cc_final: 0.7621 (pp30)
  outliers start: 39
  outliers final: 25
  residues processed: 280
  average time/residue: 0.2050
  time to fit residues: 78.8196
Evaluate side-chains
  291 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 261
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  168 ARG
Chi-restraints excluded: chain R residue  183 MET
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  175 TYR
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 58 optimal weight:    0.0010
   chunk 16 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0980
   chunk 110 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0010
   chunk 98 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
S  39 GLN
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.145233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.119023 restraints weight = 15449.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.122491 restraints weight = 8151.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.124832 restraints weight = 5223.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9125  Z= 0.114
  Angle     :  0.618   8.777  12367  Z= 0.313
  Chirality :  0.042   0.269   1394
  Planarity :  0.004   0.048   1555
  Dihedral  :  7.855  59.952   1261
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.37 %
    Favored  : 74.43 %
  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: -1.19 (0.25), residues: 1118
  helix:  0.89 (0.29), residues: 357
  sheet: -0.63 (0.33), residues: 253
  loop : -2.16 (0.24), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 265 
 PHE   0.017   0.001   PHE S  27 
 TYR   0.019   0.001   TYR S 235 
 ARG   0.007   0.000   ARG R 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  352)
  hydrogen bonds       : angle       4.23183 ( 1014)
  SS BOND              : bond        0.00464 (    1)
  SS BOND              : angle       0.35524 (    2)
  covalent geometry    : bond        0.00243 ( 9124)
  covalent geometry    : angle       0.61753 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 270
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: A   26 ASP cc_start: 0.7851 (t0) cc_final: 0.7362 (t0)
REVERT: A  216 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7485 (tp30)
REVERT: A  245 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: A  271 LYS cc_start: 0.8136 (tptp) cc_final: 0.7862 (tptt)
REVERT: A  307 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7965 (m-80)
REVERT: A  333 GLN cc_start: 0.7984 (tp40) cc_final: 0.7554 (tp40)
REVERT: A  348 LEU cc_start: 0.7878 (tp) cc_final: 0.7602 (tt)
REVERT: B   61 MET cc_start: 0.6979 (tmm) cc_final: 0.6458 (tmm)
REVERT: B   82 TRP cc_start: 0.8327 (m100) cc_final: 0.8057 (m100)
REVERT: B  180 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6839 (p90)
REVERT: B  188 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7284 (mmt)
REVERT: B  191 SER cc_start: 0.8474 (t) cc_final: 0.7948 (t)
REVERT: B  243 THR cc_start: 0.8010 (p) cc_final: 0.7757 (p)
REVERT: B  317 CYS cc_start: 0.7570 (p) cc_final: 0.7227 (p)
REVERT: C   48 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7621 (mp0)
REVERT: R  162 MET cc_start: 0.5488 (mmp) cc_final: 0.5045 (mmp)
REVERT: R  167 LEU cc_start: 0.7673 (tp) cc_final: 0.6888 (mp)
REVERT: R  264 TYR cc_start: 0.7189 (t80) cc_final: 0.6063 (t80)
REVERT: R  268 LYS cc_start: 0.8774 (mttt) cc_final: 0.8288 (mttt)
REVERT: S   89 GLU cc_start: 0.7627 (tp30) cc_final: 0.7426 (tp30)
  outliers start: 31
  outliers final: 21
  residues processed: 282
  average time/residue: 0.2079
  time to fit residues: 80.6328
Evaluate side-chains
  290 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 264
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  183 MET
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 92 optimal weight:    0.4980
   chunk 94 optimal weight:    0.0570
   chunk 59 optimal weight:    0.2980
   chunk 64 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 259 GLN
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.143346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.117521 restraints weight = 15389.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121081 restraints weight = 8076.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123425 restraints weight = 5111.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9125  Z= 0.119
  Angle     :  0.633   9.361  12367  Z= 0.319
  Chirality :  0.043   0.302   1394
  Planarity :  0.004   0.047   1555
  Dihedral  :  7.767  58.860   1261
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.20 %
    Favored  : 73.92 %
  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: -1.17 (0.25), residues: 1118
  helix:  0.93 (0.29), residues: 357
  sheet: -0.65 (0.32), residues: 263
  loop : -2.16 (0.24), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.019   0.001   PHE S  27 
 TYR   0.016   0.001   TYR S 235 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  352)
  hydrogen bonds       : angle       4.20190 ( 1014)
  SS BOND              : bond        0.00459 (    1)
  SS BOND              : angle       0.55347 (    2)
  covalent geometry    : bond        0.00264 ( 9124)
  covalent geometry    : angle       0.63288 (12365)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 269
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: A   26 ASP cc_start: 0.7850 (t0) cc_final: 0.7347 (t0)
REVERT: A  245 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7406 (mm-30)
REVERT: A  271 LYS cc_start: 0.8098 (tptp) cc_final: 0.7834 (tptt)
REVERT: A  333 GLN cc_start: 0.7951 (tp40) cc_final: 0.7542 (tp40)
REVERT: A  348 LEU cc_start: 0.7933 (tp) cc_final: 0.7653 (tt)
REVERT: B   61 MET cc_start: 0.6932 (tmm) cc_final: 0.6418 (tmm)
REVERT: B   82 TRP cc_start: 0.8334 (m100) cc_final: 0.8066 (m100)
REVERT: B  180 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6873 (p90)
REVERT: B  188 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7304 (mmt)
REVERT: B  191 SER cc_start: 0.8556 (t) cc_final: 0.8022 (t)
REVERT: B  243 THR cc_start: 0.8009 (p) cc_final: 0.7780 (p)
REVERT: B  317 CYS cc_start: 0.7579 (p) cc_final: 0.7223 (p)
REVERT: C   48 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: R  162 MET cc_start: 0.5438 (mmp) cc_final: 0.5014 (mmp)
REVERT: R  167 LEU cc_start: 0.7689 (tp) cc_final: 0.6909 (mp)
REVERT: R  264 TYR cc_start: 0.7156 (t80) cc_final: 0.6026 (t80)
REVERT: R  268 LYS cc_start: 0.8727 (mttt) cc_final: 0.8239 (mttt)
REVERT: S   89 GLU cc_start: 0.7640 (tp30) cc_final: 0.7437 (tp30)
  outliers start: 28
  outliers final: 21
  residues processed: 279
  average time/residue: 0.2113
  time to fit residues: 81.6490
Evaluate side-chains
  289 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 265
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   48 GLU
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue   84 LEU
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  183 MET
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0270
   chunk 92 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
R 265 HIS
S 169 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.115192 restraints weight = 15303.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118770 restraints weight = 8149.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.121155 restraints weight = 5175.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9125  Z= 0.156
  Angle     :  0.672  10.401  12367  Z= 0.341
  Chirality :  0.044   0.291   1394
  Planarity :  0.004   0.048   1555
  Dihedral  :  8.081  64.281   1261
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.30 %
    Favored  : 73.71 %
  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: -1.22 (0.25), residues: 1118
  helix:  0.87 (0.29), residues: 357
  sheet: -0.53 (0.34), residues: 246
  loop : -2.23 (0.24), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.004   0.001   HIS R 265 
 PHE   0.021   0.002   PHE S  27 
 TYR   0.017   0.002   TYR S 235 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  352)
  hydrogen bonds       : angle       4.31783 ( 1014)
  SS BOND              : bond        0.00558 (    1)
  SS BOND              : angle       0.65897 (    2)
  covalent geometry    : bond        0.00352 ( 9124)
  covalent geometry    : angle       0.67209 (12365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3468.56 seconds
wall clock time: 60 minutes 52.87 seconds (3652.87 seconds total)