Starting phenix.real_space_refine
on Wed Sep 17 12:48:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yh5_39281/09_2025/8yh5_39281.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   1.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5564      2.51       5
     N    1462      2.21       5
     O    1603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8695
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1700
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2198
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'ZIR%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.23
  Number of scatterers: 8695
  At special positions: 0
  Unit cell: (89.91, 122.1, 124.32, 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      66     16.00
     O    1603      8.00
     N    1462      7.00
     C    5564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 103 " - pdb=" SG  CYS B 114 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  83 " - pdb=" SG  CYS R 165 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 334.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      37.8% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.863A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 33 through 44
      removed outlier: 3.506A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.706A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.576A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.501A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.541A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 275 through 281
      removed outlier: 3.665A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.682A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.544A  pdb=" N   GLY A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 10 through 40
      removed outlier: 3.659A  pdb=" N   LYS R  38 " --> pdb=" O   ILE R  34 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 45 through 64
      removed outlier: 3.637A  pdb=" N   PHE R  50 " --> pdb=" O   THR R  46 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA R  60 " --> pdb=" O   LEU R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 75
    Processing helix  chain 'R' and resid 79 through 115
      removed outlier: 3.613A  pdb=" N   PHE R  93 " --> pdb=" O   LEU R  89 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR R  94 " --> pdb=" O   MET R  90 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR R 115 " --> pdb=" O   ARG R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 122
    Processing helix  chain 'R' and resid 123 through 144
    Processing helix  chain 'R' and resid 145 through 148
      removed outlier: 3.786A  pdb=" N   GLY R 148 " --> pdb=" O   PRO R 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 145 through 148'
    Processing helix  chain 'R' and resid 150 through 154
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.684A  pdb=" N   MET R 171 " --> pdb=" O   PHE R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 4.020A  pdb=" N   MET R 176 " --> pdb=" O   ARG R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 185
    Processing helix  chain 'R' and resid 185 through 207
    Processing helix  chain 'R' and resid 225 through 254
      removed outlier: 3.591A  pdb=" N   CYS R 241 " --> pdb=" O   LEU R 237 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP R 242 " --> pdb=" O   PHE R 238 " (cutoff:3.500A)
      Proline residue:  R 244  - end of helix
      removed outlier: 3.561A  pdb=" N   TYR R 253 " --> pdb=" O   ASN R 249 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE R 254 " --> pdb=" O   CYS R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 282
      removed outlier: 3.517A  pdb=" N   ILE R 267 " --> pdb=" O   LEU R 263 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER R 274 " --> pdb=" O   SER R 270 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   MET R 275 " --> pdb=" O   HIS R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 285 through 295
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.728A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.840A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.974A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.512A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.541A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.303A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.458A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.780A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.123A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 129 through 130
      removed outlier: 3.591A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.049A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   TYR S 216 " --> pdb=" O   PHE S 165 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE S 165 " --> pdb=" O   TYR S 216 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.500A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2733
        1.34 -     1.46: 1661
        1.46 -     1.58: 4386
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 8878
  Sorted by residual:
  bond pdb=" N   ILE R 248 "
       pdb=" CA  ILE R 248 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.16e+00
  bond pdb=" N   ARG S  18 "
       pdb=" CA  ARG S  18 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.16e-02 7.43e+03 8.96e+00
  bond pdb=" N   LYS S  19 "
       pdb=" CA  LYS S  19 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.25e-02 6.40e+03 8.42e+00
  bond pdb=" N   GLN B 259 "
       pdb=" CA  GLN B 259 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.23e-02 6.61e+03 8.39e+00
  bond pdb=" N   ARG S  98 "
       pdb=" CA  ARG S  98 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.15e-02 7.56e+03 7.68e+00
  ... (remaining 8873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 11313
        1.37 -     2.73: 552
        2.73 -     4.10: 131
        4.10 -     5.47: 22
        5.47 -     6.84: 5
  Bond angle restraints: 12023
  Sorted by residual:
  angle pdb=" N   ASN R 249 "
        pdb=" CA  ASN R 249 "
        pdb=" C   ASN R 249 "
      ideal   model   delta    sigma   weight residual
     113.28  107.60    5.68 1.22e+00 6.72e-01 2.17e+01
  angle pdb=" CA  ILE S 100 "
        pdb=" C   ILE S 100 "
        pdb=" O   ILE S 100 "
      ideal   model   delta    sigma   weight residual
     120.36  115.52    4.84 1.06e+00 8.90e-01 2.08e+01
  angle pdb=" N   ILE R 185 "
        pdb=" CA  ILE R 185 "
        pdb=" C   ILE R 185 "
      ideal   model   delta    sigma   weight residual
     112.12  108.39    3.73 8.40e-01 1.42e+00 1.97e+01
  angle pdb=" N   GLU G  22 "
        pdb=" CA  GLU G  22 "
        pdb=" C   GLU G  22 "
      ideal   model   delta    sigma   weight residual
     112.54  107.53    5.01 1.22e+00 6.72e-01 1.69e+01
  angle pdb=" CA  ARG S  18 "
        pdb=" C   ARG S  18 "
        pdb=" O   ARG S  18 "
      ideal   model   delta    sigma   weight residual
     121.89  116.71    5.18 1.27e+00 6.20e-01 1.67e+01
  ... (remaining 12018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.22: 5045
       25.22 -    50.44: 211
       50.44 -    75.67: 17
       75.67 -   100.89: 1
      100.89 -   126.11: 2
  Dihedral angle restraints: 5276
    sinusoidal: 2074
      harmonic: 3202
  Sorted by residual:
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.18  -43.18     1      1.00e+01 1.00e-02 2.60e+01
  dihedral pdb=" CD  ARG S  18 "
           pdb=" NE  ARG S  18 "
           pdb=" CZ  ARG S  18 "
           pdb=" NH1 ARG S  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -41.92   41.92     1      1.00e+01 1.00e-02 2.46e+01
  dihedral pdb=" CA  PHE B 292 "
           pdb=" C   PHE B 292 "
           pdb=" N   ASN B 293 "
           pdb=" CA  ASN B 293 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 5273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 979
       0.039 -    0.078: 276
       0.078 -    0.117: 80
       0.117 -    0.157: 33
       0.157 -    0.196: 8
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  ILE R 248 "
            pdb=" N   ILE R 248 "
            pdb=" C   ILE R 248 "
            pdb=" CB  ILE R 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.57e-01
  chirality pdb=" CA  ILE S 100 "
            pdb=" N   ILE S 100 "
            pdb=" C   ILE S 100 "
            pdb=" CB  ILE S 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CA  LEU B 168 "
            pdb=" N   LEU B 168 "
            pdb=" C   LEU B 168 "
            pdb=" CB  LEU B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.60e-01
  ... (remaining 1373 not shown)

  Planarity restraints: 1499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S  18 "    0.713 9.50e-02 1.11e+02   3.20e-01 6.24e+01
        pdb=" NE  ARG S  18 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  ARG S  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG S  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG S  18 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "   -0.671 9.50e-02 1.11e+02   3.01e-01 5.51e+01
        pdb=" NE  ARG B 219 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  52 "   -0.586 9.50e-02 1.11e+02   2.63e-01 4.23e+01
        pdb=" NE  ARG B  52 "    0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  52 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1496 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 191
        2.66 -     3.22: 8904
        3.22 -     3.78: 13512
        3.78 -     4.34: 18835
        4.34 -     4.90: 30019
  Nonbonded interactions: 71461
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER B 160 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OE1 GLN R 260 "
            pdb=" OH  TYR R 264 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.150 3.040
  ... (remaining 71456 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.340
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
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   0.051   8882  Z= 0.263
  Angle     :  0.719   6.835  12031  Z= 0.453
  Chirality :  0.044   0.196   1376
  Planarity :  0.017   0.320   1499
  Dihedral  : 13.520 126.109   3198
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.42 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.26), residues: 1085
  helix:  0.28 (0.27), residues: 375
  sheet: -1.68 (0.30), residues: 290
  loop : -1.51 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 172 
 TYR   0.012   0.001   TYR B 289 
 PHE   0.021   0.001   PHE A 267 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8878)
  covalent geometry    : angle       0.71553 (12023)
  SS BOND              : bond        0.00548 (    4)
  SS BOND              : angle       2.79689 (    8)
  hydrogen bonds       : bond        0.23728 (  392)
  hydrogen bonds       : angle       8.63096 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.8491 (mp0) cc_final: 0.8262 (mp0)
REVERT: B  260 GLU cc_start: 0.5471 (tt0) cc_final: 0.4674 (tm-30)
REVERT: G   58 GLU cc_start: 0.8754 (mp0) cc_final: 0.8537 (mp0)
REVERT: S   46 GLU cc_start: 0.6451 (tp30) cc_final: 0.6006 (tt0)
REVERT: S   93 MET cc_start: 0.6921 (tpt) cc_final: 0.6669 (tpt)
REVERT: S  190 ARG cc_start: 0.4456 (mtp-110) cc_final: 0.4223 (mtp180)
REVERT: S  219 GLN cc_start: 0.3092 (pp30) cc_final: 0.2329 (pp30)
REVERT: A  276 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7803 (mp0)
REVERT: A  322 HIS cc_start: 0.6592 (t70) cc_final: 0.6254 (t-90)
REVERT: A  333 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8132 (mm-40)
REVERT: A  345 LYS cc_start: 0.7926 (mptt) cc_final: 0.7539 (tptp)
REVERT: R  173 MET cc_start: 0.8499 (mmt) cc_final: 0.8139 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1017
  time to fit residues: 31.4963
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 230 ASN
S  82 GLN
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
A 306 GLN
R  30 ASN
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.166267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.137586 restraints weight = 19837.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.141335 restraints weight = 10938.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.144056 restraints weight = 7498.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.145859 restraints weight = 5833.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.146741 restraints weight = 4929.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6208
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8882  Z= 0.147
  Angle     :  0.682  10.900  12031  Z= 0.352
  Chirality :  0.045   0.198   1376
  Planarity :  0.004   0.038   1499
  Dihedral  :  5.928  73.761   1216
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.44 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.26), residues: 1085
  helix:  0.63 (0.27), residues: 386
  sheet: -1.17 (0.32), residues: 276
  loop : -1.41 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 172 
 TYR   0.023   0.002   TYR S 178 
 PHE   0.019   0.002   PHE R 288 
 TRP   0.020   0.002   TRP R  35 
 HIS   0.003   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8878)
  covalent geometry    : angle       0.67991 (12023)
  SS BOND              : bond        0.00609 (    4)
  SS BOND              : angle       2.05452 (    8)
  hydrogen bonds       : bond        0.04411 (  392)
  hydrogen bonds       : angle       5.63900 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 MET cc_start: 0.7165 (tmm) cc_final: 0.6953 (tmm)
REVERT: G   22 GLU cc_start: 0.2665 (tp30) cc_final: 0.2016 (tp30)
REVERT: S   34 MET cc_start: 0.5906 (mmm) cc_final: 0.5642 (mmm)
REVERT: S   43 LYS cc_start: 0.7467 (mmtm) cc_final: 0.7094 (mmtm)
REVERT: S  210 GLU cc_start: 0.6054 (mp0) cc_final: 0.5553 (mp0)
REVERT: A   20 ASP cc_start: 0.6538 (t0) cc_final: 0.6304 (m-30)
REVERT: A  275 GLU cc_start: 0.8155 (pp20) cc_final: 0.7709 (pm20)
REVERT: A  289 GLU cc_start: 0.8632 (tp30) cc_final: 0.7816 (mp0)
REVERT: A  313 ARG cc_start: 0.6721 (mtt180) cc_final: 0.6174 (mmt90)
REVERT: A  333 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8324 (mm-40)
REVERT: A  345 LYS cc_start: 0.7919 (mptt) cc_final: 0.7618 (tptp)
REVERT: R   19 GLU cc_start: 0.6455 (tp30) cc_final: 0.6198 (mm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 212
  average time/residue: 0.0975
  time to fit residues: 28.3661
Evaluate side-chains
  180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  189 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 1 optimal weight:   20.0000
   chunk 103 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0980
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
S 219 GLN
A 213 HIS
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 273 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.157761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.128699 restraints weight = 20124.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.132217 restraints weight = 11692.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.134734 restraints weight = 8280.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.136402 restraints weight = 6588.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.137272 restraints weight = 5647.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6555
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8882  Z= 0.224
  Angle     :  0.741   9.867  12031  Z= 0.389
  Chirality :  0.047   0.207   1376
  Planarity :  0.005   0.045   1499
  Dihedral  :  5.840  45.612   1216
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.99 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.84 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.26), residues: 1085
  helix:  0.62 (0.26), residues: 379
  sheet: -1.26 (0.32), residues: 259
  loop : -1.16 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S 190 
 TYR   0.022   0.003   TYR S 178 
 PHE   0.023   0.002   PHE R  48 
 TRP   0.023   0.002   TRP B 297 
 HIS   0.012   0.002   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 8878)
  covalent geometry    : angle       0.73664 (12023)
  SS BOND              : bond        0.00705 (    4)
  SS BOND              : angle       3.09195 (    8)
  hydrogen bonds       : bond        0.04849 (  392)
  hydrogen bonds       : angle       5.49065 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8248 (m100) cc_final: 0.7993 (m100)
REVERT: B  101 MET cc_start: 0.7752 (mpp) cc_final: 0.7349 (mpp)
REVERT: B  117 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (tp)
REVERT: B  217 MET cc_start: 0.7717 (tmm) cc_final: 0.7509 (tmm)
REVERT: S  220 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.4515 (t-90)
REVERT: A  275 GLU cc_start: 0.8164 (pp20) cc_final: 0.7697 (pm20)
REVERT: A  313 ARG cc_start: 0.6645 (mtt180) cc_final: 0.6234 (mmt90)
REVERT: A  318 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6859 (mm-30)
REVERT: A  333 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8362 (mm-40)
REVERT: R  171 MET cc_start: 0.8658 (tpp) cc_final: 0.8317 (tpp)
REVERT: R  173 MET cc_start: 0.7962 (mmt) cc_final: 0.7760 (mmt)
  outliers start: 32
  outliers final: 17
  residues processed: 195
  average time/residue: 0.0973
  time to fit residues: 26.3366
Evaluate side-chains
  178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.162621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.133973 restraints weight = 20054.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.137633 restraints weight = 11352.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.140284 restraints weight = 7896.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.141890 restraints weight = 6204.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.143191 restraints weight = 5303.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8882  Z= 0.126
  Angle     :  0.649   9.228  12031  Z= 0.336
  Chirality :  0.043   0.215   1376
  Planarity :  0.004   0.038   1499
  Dihedral  :  5.408  51.811   1216
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.15 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.36 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.26), residues: 1085
  helix:  0.69 (0.26), residues: 386
  sheet: -1.08 (0.31), residues: 276
  loop : -1.09 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 117 
 TYR   0.021   0.002   TYR S 178 
 PHE   0.015   0.001   PHE S 200 
 TRP   0.021   0.001   TRP R 184 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8878)
  covalent geometry    : angle       0.64398 (12023)
  SS BOND              : bond        0.00617 (    4)
  SS BOND              : angle       3.14767 (    8)
  hydrogen bonds       : bond        0.03705 (  392)
  hydrogen bonds       : angle       5.10239 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 180
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8012 (m100) cc_final: 0.7747 (m100)
REVERT: B  101 MET cc_start: 0.7621 (mpp) cc_final: 0.7264 (mpp)
REVERT: B  130 GLU cc_start: 0.8615 (mp0) cc_final: 0.8408 (mp0)
REVERT: B  256 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.7252 (mmp80)
REVERT: G   21 MET cc_start: 0.7528 (ppp) cc_final: 0.6970 (ppp)
REVERT: G   22 GLU cc_start: 0.3711 (tp30) cc_final: 0.3000 (tp30)
REVERT: S  148 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7985 (mmm-85)
REVERT: S  176 LEU cc_start: 0.7732 (mp) cc_final: 0.7278 (mp)
REVERT: A  275 GLU cc_start: 0.8076 (pp20) cc_final: 0.7624 (pm20)
REVERT: A  287 TYR cc_start: 0.7413 (m-80) cc_final: 0.7184 (m-80)
REVERT: A  313 ARG cc_start: 0.6563 (mtt180) cc_final: 0.6120 (mmt90)
REVERT: R   37 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6984 (p)
  outliers start: 33
  outliers final: 16
  residues processed: 198
  average time/residue: 0.1000
  time to fit residues: 27.0874
Evaluate side-chains
  179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   37 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 96 optimal weight:    0.3980
   chunk 84 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 88 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  54 HIS
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.157201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.127903 restraints weight = 20391.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.131524 restraints weight = 11896.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.133704 restraints weight = 8463.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.135569 restraints weight = 6813.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.136367 restraints weight = 5846.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8882  Z= 0.177
  Angle     :  0.703  11.208  12031  Z= 0.361
  Chirality :  0.045   0.257   1376
  Planarity :  0.004   0.045   1499
  Dihedral  :  5.427  46.049   1216
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 18.89 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.26), residues: 1085
  helix:  0.76 (0.26), residues: 388
  sheet: -0.99 (0.31), residues: 264
  loop : -1.10 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  15 
 TYR   0.020   0.002   TYR S 178 
 PHE   0.015   0.002   PHE S 200 
 TRP   0.018   0.002   TRP R 184 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8878)
  covalent geometry    : angle       0.69881 (12023)
  SS BOND              : bond        0.00634 (    4)
  SS BOND              : angle       3.16442 (    8)
  hydrogen bonds       : bond        0.04144 (  392)
  hydrogen bonds       : angle       5.03827 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8193 (m100) cc_final: 0.7861 (m100)
REVERT: B  130 GLU cc_start: 0.8717 (mp0) cc_final: 0.8428 (mp0)
REVERT: B  256 ARG cc_start: 0.7636 (mmp-170) cc_final: 0.7007 (mmp80)
REVERT: G   21 MET cc_start: 0.7668 (ppp) cc_final: 0.7154 (ppp)
REVERT: G   22 GLU cc_start: 0.4041 (tp30) cc_final: 0.3285 (tp30)
REVERT: S  179 ARG cc_start: 0.5714 (mtm-85) cc_final: 0.5458 (mtm-85)
REVERT: S  183 LEU cc_start: 0.8951 (mm) cc_final: 0.8750 (mm)
REVERT: S  206 ARG cc_start: 0.8784 (mpp80) cc_final: 0.8352 (mpp80)
REVERT: S  220 HIS cc_start: 0.5651 (OUTLIER) cc_final: 0.4521 (t-90)
REVERT: A  249 LEU cc_start: 0.8038 (tp) cc_final: 0.7831 (tp)
REVERT: A  276 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: A  287 TYR cc_start: 0.7439 (m-80) cc_final: 0.7211 (m-80)
REVERT: A  313 ARG cc_start: 0.6538 (mtt180) cc_final: 0.6200 (mmt90)
REVERT: A  318 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6711 (mm-30)
REVERT: R  173 MET cc_start: 0.8048 (mmt) cc_final: 0.7725 (mmt)
  outliers start: 45
  outliers final: 31
  residues processed: 198
  average time/residue: 0.1001
  time to fit residues: 27.0014
Evaluate side-chains
  192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  248 ILE
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.156543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.127362 restraints weight = 20121.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.130762 restraints weight = 11896.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.133163 restraints weight = 8512.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.134449 restraints weight = 6837.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.135813 restraints weight = 5980.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.5809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8882  Z= 0.173
  Angle     :  0.741  13.518  12031  Z= 0.376
  Chirality :  0.046   0.239   1376
  Planarity :  0.004   0.046   1499
  Dihedral  :  5.476  46.611   1216
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.62 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 20.78 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.26), residues: 1085
  helix:  0.85 (0.26), residues: 382
  sheet: -0.83 (0.32), residues: 258
  loop : -1.07 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  15 
 TYR   0.018   0.002   TYR S 178 
 PHE   0.014   0.002   PHE R  48 
 TRP   0.020   0.002   TRP R 184 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8878)
  covalent geometry    : angle       0.73017 (12023)
  SS BOND              : bond        0.00130 (    4)
  SS BOND              : angle       4.90789 (    8)
  hydrogen bonds       : bond        0.04052 (  392)
  hydrogen bonds       : angle       5.03147 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 166
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8183 (m100) cc_final: 0.7839 (m100)
REVERT: B  101 MET cc_start: 0.7286 (mpp) cc_final: 0.6921 (mpp)
REVERT: B  130 GLU cc_start: 0.8744 (mp0) cc_final: 0.8384 (mp0)
REVERT: B  234 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7003 (m-80)
REVERT: B  256 ARG cc_start: 0.7800 (mmp-170) cc_final: 0.7024 (mmp80)
REVERT: G   21 MET cc_start: 0.7697 (ppp) cc_final: 0.7202 (ppp)
REVERT: G   22 GLU cc_start: 0.4301 (tp30) cc_final: 0.3544 (tp30)
REVERT: S  168 ARG cc_start: 0.8667 (tpm170) cc_final: 0.8394 (tpm170)
REVERT: S  206 ARG cc_start: 0.8807 (mpp80) cc_final: 0.8351 (mpp80)
REVERT: S  220 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.4594 (t-90)
REVERT: A  313 ARG cc_start: 0.6475 (mtt180) cc_final: 0.6196 (mmt90)
REVERT: A  315 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7828 (p0)
REVERT: A  318 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6831 (mm-30)
  outliers start: 47
  outliers final: 32
  residues processed: 196
  average time/residue: 0.0948
  time to fit residues: 25.5287
Evaluate side-chains
  192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Chi-restraints excluded: chain R residue  285 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0470
   chunk 98 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  44 GLN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.160149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.131750 restraints weight = 20147.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.135247 restraints weight = 11465.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.137884 restraints weight = 8093.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.139506 restraints weight = 6398.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.140572 restraints weight = 5477.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8882  Z= 0.131
  Angle     :  0.715  10.229  12031  Z= 0.363
  Chirality :  0.045   0.253   1376
  Planarity :  0.004   0.043   1499
  Dihedral  :  5.162  39.715   1216
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 23.61 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.26), residues: 1085
  helix:  1.03 (0.26), residues: 385
  sheet: -0.77 (0.32), residues: 264
  loop : -0.93 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG S 190 
 TYR   0.021   0.001   TYR S 178 
 PHE   0.012   0.001   PHE R  48 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8878)
  covalent geometry    : angle       0.70767 (12023)
  SS BOND              : bond        0.00346 (    4)
  SS BOND              : angle       4.05157 (    8)
  hydrogen bonds       : bond        0.03676 (  392)
  hydrogen bonds       : angle       4.90660 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7489 (t0) cc_final: 0.7186 (t0)
REVERT: B   82 TRP cc_start: 0.8089 (m100) cc_final: 0.7720 (m100)
REVERT: B  101 MET cc_start: 0.7136 (mpp) cc_final: 0.6789 (mpp)
REVERT: B  130 GLU cc_start: 0.8714 (mp0) cc_final: 0.8365 (mp0)
REVERT: B  234 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6921 (m-80)
REVERT: B  256 ARG cc_start: 0.7773 (mmp-170) cc_final: 0.6975 (mmp80)
REVERT: G   21 MET cc_start: 0.7753 (ppp) cc_final: 0.7298 (ppp)
REVERT: G   22 GLU cc_start: 0.4164 (tp30) cc_final: 0.3510 (tp30)
REVERT: S  168 ARG cc_start: 0.8595 (tpm170) cc_final: 0.8380 (tpm170)
REVERT: S  206 ARG cc_start: 0.8871 (mpp80) cc_final: 0.8628 (mpp80)
REVERT: A  216 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7587 (mm-30)
REVERT: A  243 MET cc_start: 0.5128 (pmm) cc_final: 0.4907 (pmm)
REVERT: A  313 ARG cc_start: 0.6378 (mtt180) cc_final: 0.6075 (mmt90)
REVERT: A  315 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7761 (p0)
REVERT: A  318 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: R   40 ASN cc_start: 0.7643 (t0) cc_final: 0.7192 (m-40)
REVERT: R  152 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8285 (mmmt)
REVERT: R  173 MET cc_start: 0.7988 (mmt) cc_final: 0.7679 (mmt)
REVERT: R  276 MET cc_start: 0.7618 (ttp) cc_final: 0.7411 (ttt)
  outliers start: 33
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1043
  time to fit residues: 27.5059
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.159940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.131385 restraints weight = 20052.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.134888 restraints weight = 11583.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.137478 restraints weight = 8164.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.139177 restraints weight = 6460.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.140067 restraints weight = 5525.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.6262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8882  Z= 0.138
  Angle     :  0.739  12.652  12031  Z= 0.368
  Chirality :  0.046   0.268   1376
  Planarity :  0.004   0.042   1499
  Dihedral  :  5.189  38.223   1216
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 22.98 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.26), residues: 1085
  helix:  1.02 (0.26), residues: 384
  sheet: -0.71 (0.32), residues: 258
  loop : -0.97 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG S 190 
 TYR   0.021   0.001   TYR S 178 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8878)
  covalent geometry    : angle       0.73389 (12023)
  SS BOND              : bond        0.00250 (    4)
  SS BOND              : angle       3.59425 (    8)
  hydrogen bonds       : bond        0.03759 (  392)
  hydrogen bonds       : angle       4.86102 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 171
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8041 (m100) cc_final: 0.7622 (m100)
REVERT: B  101 MET cc_start: 0.7007 (mpp) cc_final: 0.6804 (mpp)
REVERT: B  130 GLU cc_start: 0.8720 (mp0) cc_final: 0.8362 (mp0)
REVERT: B  234 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.6943 (m-80)
REVERT: B  256 ARG cc_start: 0.7862 (mmp-170) cc_final: 0.6981 (mmp80)
REVERT: G   21 MET cc_start: 0.7833 (ppp) cc_final: 0.7413 (ppp)
REVERT: G   22 GLU cc_start: 0.4266 (tp30) cc_final: 0.3581 (tp30)
REVERT: S  168 ARG cc_start: 0.8598 (tpm170) cc_final: 0.8243 (tpm170)
REVERT: S  220 HIS cc_start: 0.4971 (OUTLIER) cc_final: 0.3964 (t-90)
REVERT: A  216 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7608 (mm-30)
REVERT: A  276 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: A  313 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6171 (mmt90)
REVERT: A  315 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7845 (p0)
REVERT: A  318 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6892 (mm-30)
REVERT: R   40 ASN cc_start: 0.7527 (t0) cc_final: 0.7142 (m-40)
REVERT: R   49 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.5521 (m-10)
REVERT: R  152 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8409 (mmmt)
REVERT: R  173 MET cc_start: 0.7939 (mmt) cc_final: 0.7667 (mmt)
  outliers start: 39
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1005
  time to fit residues: 27.1685
Evaluate side-chains
  196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   49 TYR
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 107 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.155585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.126451 restraints weight = 20310.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.129754 restraints weight = 11981.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.132189 restraints weight = 8611.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.133586 restraints weight = 6921.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.134834 restraints weight = 6010.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.6513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8882  Z= 0.198
  Angle     :  0.802  11.769  12031  Z= 0.402
  Chirality :  0.047   0.279   1376
  Planarity :  0.004   0.048   1499
  Dihedral  :  5.666  38.592   1216
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.36 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.08 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.26), residues: 1085
  helix:  0.82 (0.26), residues: 386
  sheet: -0.93 (0.32), residues: 255
  loop : -0.97 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S 190 
 TYR   0.017   0.002   TYR S 178 
 PHE   0.032   0.002   PHE R 181 
 TRP   0.029   0.002   TRP R 184 
 HIS   0.012   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8878)
  covalent geometry    : angle       0.79605 (12023)
  SS BOND              : bond        0.00307 (    4)
  SS BOND              : angle       3.74565 (    8)
  hydrogen bonds       : bond        0.04395 (  392)
  hydrogen bonds       : angle       5.06518 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 166
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8175 (m100) cc_final: 0.7898 (m100)
REVERT: B  130 GLU cc_start: 0.8802 (mp0) cc_final: 0.8404 (mp0)
REVERT: B  188 MET cc_start: 0.7076 (ppp) cc_final: 0.6745 (ppp)
REVERT: B  234 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7191 (m-80)
REVERT: G   21 MET cc_start: 0.7915 (ppp) cc_final: 0.7517 (ppp)
REVERT: G   22 GLU cc_start: 0.4416 (tp30) cc_final: 0.3687 (tp30)
REVERT: G   48 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6309 (m-30)
REVERT: S  168 ARG cc_start: 0.8728 (tpm170) cc_final: 0.8346 (tpm170)
REVERT: S  190 ARG cc_start: 0.6102 (mtp180) cc_final: 0.5745 (mtp180)
REVERT: S  220 HIS cc_start: 0.5800 (OUTLIER) cc_final: 0.5265 (t-90)
REVERT: A  313 ARG cc_start: 0.6559 (mtt180) cc_final: 0.6156 (mmt90)
REVERT: A  315 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8055 (p0)
REVERT: A  318 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7044 (mm-30)
REVERT: A  336 PHE cc_start: 0.8848 (t80) cc_final: 0.8599 (t80)
REVERT: R   40 ASN cc_start: 0.7479 (t0) cc_final: 0.7109 (m-40)
REVERT: R  151 MET cc_start: 0.8366 (mmm) cc_final: 0.8086 (mmm)
  outliers start: 39
  outliers final: 26
  residues processed: 189
  average time/residue: 0.1044
  time to fit residues: 26.8377
Evaluate side-chains
  192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   48 ASP
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain R residue   49 TYR
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0370
   chunk 7 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 142 HIS
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.159962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.131210 restraints weight = 19889.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.134753 restraints weight = 11563.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.137254 restraints weight = 8134.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.139015 restraints weight = 6461.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.140089 restraints weight = 5510.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.6702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8882  Z= 0.142
  Angle     :  0.777  12.350  12031  Z= 0.390
  Chirality :  0.046   0.275   1376
  Planarity :  0.004   0.045   1499
  Dihedral  :  5.384  44.923   1216
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 24.66 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.26), residues: 1085
  helix:  0.90 (0.26), residues: 384
  sheet: -0.84 (0.33), residues: 252
  loop : -0.94 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 190 
 TYR   0.021   0.001   TYR S 178 
 PHE   0.016   0.001   PHE S 200 
 TRP   0.023   0.001   TRP R 184 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8878)
  covalent geometry    : angle       0.77229 (12023)
  SS BOND              : bond        0.00245 (    4)
  SS BOND              : angle       3.39185 (    8)
  hydrogen bonds       : bond        0.03868 (  392)
  hydrogen bonds       : angle       4.93139 ( 1107)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.8047 (m100) cc_final: 0.7750 (m100)
REVERT: B  101 MET cc_start: 0.6447 (mpp) cc_final: 0.6105 (mpp)
REVERT: B  130 GLU cc_start: 0.8744 (mp0) cc_final: 0.8382 (mp0)
REVERT: B  188 MET cc_start: 0.6844 (ppp) cc_final: 0.6545 (ppp)
REVERT: B  234 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7073 (m-80)
REVERT: B  256 ARG cc_start: 0.7212 (mmp-170) cc_final: 0.6043 (mmm160)
REVERT: G   21 MET cc_start: 0.7861 (ppp) cc_final: 0.7492 (ppp)
REVERT: G   22 GLU cc_start: 0.4399 (tp30) cc_final: 0.3774 (tp30)
REVERT: S   18 ARG cc_start: 0.6986 (tpt-90) cc_final: 0.6657 (tpt-90)
REVERT: S  168 ARG cc_start: 0.8688 (tpm170) cc_final: 0.8342 (tpm170)
REVERT: S  220 HIS cc_start: 0.4872 (OUTLIER) cc_final: 0.4333 (t-90)
REVERT: A  216 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7693 (mm-30)
REVERT: A  276 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: A  313 ARG cc_start: 0.6579 (mtt180) cc_final: 0.6198 (mmt90)
REVERT: A  315 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8001 (p0)
REVERT: A  336 PHE cc_start: 0.8831 (t80) cc_final: 0.8525 (t80)
REVERT: R  151 MET cc_start: 0.8339 (mmm) cc_final: 0.8043 (mmm)
REVERT: R  173 MET cc_start: 0.8072 (mmt) cc_final: 0.7566 (mmt)
  outliers start: 32
  outliers final: 23
  residues processed: 189
  average time/residue: 0.1091
  time to fit residues: 28.0403
Evaluate side-chains
  190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain R residue   49 TYR
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  279 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 142 HIS
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 269 ASN
A 322 HIS
A 331 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.159055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.131394 restraints weight = 20088.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.134683 restraints weight = 11906.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.137087 restraints weight = 8505.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.138626 restraints weight = 6784.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.139434 restraints weight = 5832.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.6817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8882  Z= 0.153
  Angle     :  0.770  12.522  12031  Z= 0.386
  Chirality :  0.046   0.277   1376
  Planarity :  0.004   0.043   1499
  Dihedral  :  5.434  48.177   1216
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 24.13 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.26), residues: 1085
  helix:  0.80 (0.26), residues: 383
  sheet: -0.83 (0.33), residues: 252
  loop : -0.90 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 190 
 TYR   0.019   0.001   TYR S 178 
 PHE   0.037   0.002   PHE R 181 
 TRP   0.024   0.002   TRP R 184 
 HIS   0.002   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8878)
  covalent geometry    : angle       0.76534 (12023)
  SS BOND              : bond        0.00157 (    4)
  SS BOND              : angle       3.40859 (    8)
  hydrogen bonds       : bond        0.03993 (  392)
  hydrogen bonds       : angle       4.94483 ( 1107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1930.30 seconds
wall clock time: 34 minutes 9.02 seconds (2049.02 seconds total)