Starting phenix.real_space_refine
on Tue Mar  3 22:20:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2026/7wig_32529.cif"
  }
  resolution = 2.7
  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=   0.033
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      67      5.16       5
     C    5697      2.51       5
     N    1507      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8931
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2234
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'9FI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.22
  Number of scatterers: 8931
  At special positions: 0
  Unit cell: (106.47, 126.75, 111.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    1660      8.00
     N    1507      7.00
     C    5697      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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: 0.73
  Conformation dependent library (CDL) restraints added in 338.6 milliseconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      38.5% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'R' and resid 41 through 69
    Processing helix  chain 'R' and resid 77 through 96
    Processing helix  chain 'R' and resid 97 through 105
      removed outlier: 3.961A  pdb=" N   MET R 101 " --> pdb=" O   PRO R  97 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLN R 102 " --> pdb=" O   PHE R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 145
      removed outlier: 3.891A  pdb=" N   PHE R 127 " --> pdb=" O   GLY R 123 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE R 130 " --> pdb=" O   GLN R 126 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE R 131 " --> pdb=" O   PHE R 127 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   CYS R 132 " --> pdb=" O   THR R 128 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 148 through 154
      removed outlier: 4.103A  pdb=" N   LYS R 152 " --> pdb=" O   ILE R 148 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   TRP R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 174
      removed outlier: 3.888A  pdb=" N   ILE R 174 " --> pdb=" O   SER R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 180
    Processing helix  chain 'R' and resid 202 through 243
      removed outlier: 5.273A  pdb=" N   VAL R 219 " --> pdb=" O   LEU R 215 " (cutoff:3.500A)
      Proline residue:  R 220  - end of helix
    Processing helix  chain 'R' and resid 246 through 282
      removed outlier: 3.759A  pdb=" N   SER R 250 " --> pdb=" O   LYS R 246 " (cutoff:3.500A)
      Proline residue:  R 271  - end of helix
    Processing helix  chain 'R' and resid 287 through 314
      removed outlier: 3.752A  pdb=" N   SER R 305 " --> pdb=" O   THR R 301 " (cutoff:3.500A)
      Proline residue:  R 309  - end of helix
    Processing helix  chain 'R' and resid 316 through 327
      removed outlier: 3.841A  pdb=" N   SER R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASN R 325 " --> pdb=" O   LYS R 321 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   VAL R 326 " --> pdb=" O   SER R 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.550A  pdb=" N   GLU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 3.733A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.536A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.085A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.569A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.511A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.550A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.617A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.610A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.766A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.537A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 183
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.620A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.736A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.583A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.740A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.641A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.671A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.705A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.725A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.103A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.103A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.777A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    446 hydrogen bonds defined for protein.
    1278 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: 1.32

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1444
        1.30 -     1.43: 2413
        1.43 -     1.56: 5163
        1.56 -     1.69: 1
        1.69 -     1.82: 98
  Bond restraints: 9119
  Sorted by residual:
  bond pdb=" C19 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.369  1.492 -0.123 2.00e-02 2.50e+03 3.78e+01
  bond pdb=" C11 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.455  1.571 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" C20 9FI R 401 "
       pdb=" N3  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.444  1.334  0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" C12 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.456  1.347  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C   PHE R 127 "
       pdb=" O   PHE R 127 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.33e-02 5.65e+03 2.53e+01
  ... (remaining 9114 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.87: 12308
        4.87 -     9.75: 37
        9.75 -    14.62: 3
       14.62 -    19.50: 1
       19.50 -    24.37: 1
  Bond angle restraints: 12350
  Sorted by residual:
  angle pdb=" C22 9FI R 401 "
        pdb=" C20 9FI R 401 "
        pdb=" N3  9FI R 401 "
      ideal   model   delta    sigma   weight residual
     110.53   86.16   24.37 3.00e+00 1.11e-01 6.60e+01
  angle pdb=" N   ILE R 124 "
        pdb=" CA  ILE R 124 "
        pdb=" C   ILE R 124 "
      ideal   model   delta    sigma   weight residual
     111.81  105.17    6.64 8.60e-01 1.35e+00 5.96e+01
  angle pdb=" C6  9FI R 401 "
        pdb=" C12 9FI R 401 "
        pdb=" N1  9FI R 401 "
      ideal   model   delta    sigma   weight residual
     111.52  127.12  -15.60 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" N   ALA R 307 "
        pdb=" CA  ALA R 307 "
        pdb=" C   ALA R 307 "
      ideal   model   delta    sigma   weight residual
     111.36  116.61   -5.25 1.09e+00 8.42e-01 2.32e+01
  angle pdb=" C   TYR R 302 "
        pdb=" N   ALA R 303 "
        pdb=" CA  ALA R 303 "
      ideal   model   delta    sigma   weight residual
     120.28  126.19   -5.91 1.34e+00 5.57e-01 1.94e+01
  ... (remaining 12345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4880
       16.36 -    32.72: 432
       32.72 -    49.07: 94
       49.07 -    65.43: 16
       65.43 -    81.79: 7
  Dihedral angle restraints: 5429
    sinusoidal: 2132
      harmonic: 3297
  Sorted by residual:
  dihedral pdb=" CA  LEU R 105 "
           pdb=" C   LEU R 105 "
           pdb=" N   VAL R 106 "
           pdb=" CA  VAL R 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.70  -18.30     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  GLU B 130 "
           pdb=" C   GLU B 130 "
           pdb=" N   GLY B 131 "
           pdb=" CA  GLY B 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5426 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1231
       0.069 -    0.138: 158
       0.138 -    0.207: 6
       0.207 -    0.275: 7
       0.275 -    0.344: 2
  Chirality restraints: 1404
  Sorted by residual:
  chirality pdb=" CA  ASN R 125 "
            pdb=" N   ASN R 125 "
            pdb=" C   ASN R 125 "
            pdb=" CB  ASN R 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  THR R 128 "
            pdb=" N   THR R 128 "
            pdb=" C   THR R 128 "
            pdb=" CB  THR R 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  ILE R 174 "
            pdb=" CA  ILE R 174 "
            pdb=" CG1 ILE R 174 "
            pdb=" CG2 ILE R 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1401 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 127 "    0.035 2.00e-02 2.50e+03   2.61e-02 1.19e+01
        pdb=" CG  PHE R 127 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 127 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 127 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 127 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 127 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C19 9FI R 401 "    0.005 2.00e-02 2.50e+03   2.77e-02 9.56e+00
        pdb=" C20 9FI R 401 "   -0.036 2.00e-02 2.50e+03
        pdb=" N1  9FI R 401 "   -0.023 2.00e-02 2.50e+03
        pdb=" N3  9FI R 401 "    0.043 2.00e-02 2.50e+03
        pdb=" O1  9FI R 401 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 123 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.67e+00
        pdb=" C   GLY R 123 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLY R 123 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE R 124 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 527
        2.73 -     3.27: 8601
        3.27 -     3.82: 14610
        3.82 -     4.36: 17149
        4.36 -     4.90: 30796
  Nonbonded interactions: 71683
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   HIS R 146 "
            pdb=" OG  SER R 150 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NH1 ARG B  48 "
            pdb=" O   ARG G  62 "
     model   vdw
     2.307 3.120
  ... (remaining 71678 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.740
  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:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.123   9122  Z= 0.354
  Angle     :  0.746  24.373  12356  Z= 0.383
  Chirality :  0.048   0.344   1404
  Planarity :  0.004   0.064   1550
  Dihedral  : 13.302  81.791   3294
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.11 (0.26), residues: 1123
  helix:  1.86 (0.27), residues: 398
  sheet:  0.93 (0.32), residues: 282
  loop : -0.39 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 251 
 TYR   0.016   0.001   TYR R 211 
 PHE   0.051   0.001   PHE R 127 
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 9119)
  covalent geometry    : angle       0.74647 (12350)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       0.79614 (    6)
  hydrogen bonds       : bond        0.18215 (  442)
  hydrogen bonds       : angle       6.46646 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7294 (mp0) cc_final: 0.6651 (mp0)
REVERT: B  135 VAL cc_start: 0.8506 (t) cc_final: 0.8177 (p)
REVERT: B  217 MET cc_start: 0.6505 (ppp) cc_final: 0.6131 (ppp)
  outliers start: 0
  outliers final: 1
  residues processed: 187
  average time/residue: 0.5265
  time to fit residues: 104.6564
Evaluate side-chains
  176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
R 125 ASN
A 188 HIS
A 195 HIS
B 176 GLN
B 220 GLN
B 239 ASN
B 259 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118381 restraints weight = 12392.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.90
r_work: 0.3426 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9122  Z= 0.129
  Angle     :  0.546   7.751  12356  Z= 0.288
  Chirality :  0.043   0.257   1404
  Planarity :  0.004   0.041   1550
  Dihedral  :  5.359  63.138   1266
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.52 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.29 (0.25), residues: 1123
  helix:  2.07 (0.26), residues: 401
  sheet:  0.99 (0.31), residues: 276
  loop : -0.33 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 251 
 TYR   0.029   0.001   TYR S 190 
 PHE   0.021   0.001   PHE R  92 
 TRP   0.015   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9119)
  covalent geometry    : angle       0.54605 (12350)
  SS BOND              : bond        0.00639 (    3)
  SS BOND              : angle       0.93203 (    6)
  hydrogen bonds       : bond        0.04281 (  442)
  hydrogen bonds       : angle       4.62385 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: R  119 MET cc_start: 0.6882 (mmm) cc_final: 0.6670 (mpp)
REVERT: A   20 ASP cc_start: 0.7959 (m-30) cc_final: 0.7755 (m-30)
REVERT: A   28 GLU cc_start: 0.7793 (mp0) cc_final: 0.6912 (mp0)
REVERT: A  255 ASN cc_start: 0.8483 (m-40) cc_final: 0.8250 (m-40)
REVERT: B  135 VAL cc_start: 0.8602 (t) cc_final: 0.8274 (p)
REVERT: S  140 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8112 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 187
  average time/residue: 0.5340
  time to fit residues: 106.3356
Evaluate side-chains
  181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  140 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 220 GLN
B 259 GLN
B 340 ASN
S 142 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.116359 restraints weight = 12133.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.87
r_work: 0.3402 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9122  Z= 0.163
  Angle     :  0.555   7.777  12356  Z= 0.292
  Chirality :  0.044   0.226   1404
  Planarity :  0.004   0.039   1550
  Dihedral  :  5.092  66.701   1264
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.05 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.33 (0.26), residues: 1123
  helix:  2.23 (0.26), residues: 401
  sheet:  0.93 (0.31), residues: 273
  loop : -0.37 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.028   0.001   TYR S 190 
 PHE   0.020   0.001   PHE R  92 
 TRP   0.015   0.001   TRP R 108 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9119)
  covalent geometry    : angle       0.55410 (12350)
  SS BOND              : bond        0.00749 (    3)
  SS BOND              : angle       1.37132 (    6)
  hydrogen bonds       : bond        0.04448 (  442)
  hydrogen bonds       : angle       4.48121 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 177
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: A   20 ASP cc_start: 0.7952 (m-30) cc_final: 0.7722 (m-30)
REVERT: A   53 MET cc_start: 0.5428 (mmm) cc_final: 0.5178 (mmp)
REVERT: A  255 ASN cc_start: 0.8543 (m-40) cc_final: 0.8315 (m-40)
REVERT: A  330 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7567 (mmmm)
REVERT: B  135 VAL cc_start: 0.8710 (t) cc_final: 0.8410 (p)
REVERT: B  217 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7224 (ptp)
REVERT: B  219 ARG cc_start: 0.7638 (mpt180) cc_final: 0.7053 (mpt180)
REVERT: S  140 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8104 (mtp)
REVERT: S  141 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8342 (p)
  outliers start: 24
  outliers final: 6
  residues processed: 184
  average time/residue: 0.5610
  time to fit residues: 109.6896
Evaluate side-chains
  187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.116773 restraints weight = 12390.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.89
r_work: 0.3404 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9122  Z= 0.145
  Angle     :  0.534   9.837  12356  Z= 0.280
  Chirality :  0.043   0.217   1404
  Planarity :  0.003   0.040   1550
  Dihedral  :  4.964  67.878   1264
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.18 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.46 (0.26), residues: 1123
  helix:  2.35 (0.26), residues: 401
  sheet:  1.05 (0.31), residues: 276
  loop : -0.36 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.014   0.001   PHE R  92 
 TRP   0.014   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9119)
  covalent geometry    : angle       0.53333 (12350)
  SS BOND              : bond        0.00676 (    3)
  SS BOND              : angle       1.29218 (    6)
  hydrogen bonds       : bond        0.04156 (  442)
  hydrogen bonds       : angle       4.37523 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.318 
Fit side-chains
REVERT: R  119 MET cc_start: 0.6944 (mmm) cc_final: 0.6712 (mpp)
REVERT: A   20 ASP cc_start: 0.7963 (m-30) cc_final: 0.7737 (m-30)
REVERT: A   53 MET cc_start: 0.5495 (mmm) cc_final: 0.5212 (mmp)
REVERT: A  255 ASN cc_start: 0.8528 (m-40) cc_final: 0.8298 (m-40)
REVERT: B  135 VAL cc_start: 0.8687 (t) cc_final: 0.8390 (p)
REVERT: B  217 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7294 (ptp)
REVERT: B  219 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7124 (mpt180)
REVERT: S  140 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (mtp)
  outliers start: 20
  outliers final: 10
  residues processed: 184
  average time/residue: 0.5615
  time to fit residues: 109.9720
Evaluate side-chains
  190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0980
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
S 142 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117513 restraints weight = 12344.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.89
r_work: 0.3414 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9122  Z= 0.116
  Angle     :  0.510   8.664  12356  Z= 0.267
  Chirality :  0.042   0.202   1404
  Planarity :  0.003   0.039   1550
  Dihedral  :  4.772  67.196   1264
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.41 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.56 (0.26), residues: 1123
  helix:  2.47 (0.27), residues: 402
  sheet:  1.03 (0.31), residues: 281
  loop : -0.31 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.022   0.001   TYR S 190 
 PHE   0.011   0.001   PHE R  92 
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9119)
  covalent geometry    : angle       0.50907 (12350)
  SS BOND              : bond        0.00541 (    3)
  SS BOND              : angle       1.13726 (    6)
  hydrogen bonds       : bond        0.03724 (  442)
  hydrogen bonds       : angle       4.26855 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.333 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5567 (OUTLIER) cc_final: 0.5331 (t)
REVERT: R  119 MET cc_start: 0.6836 (mmm) cc_final: 0.6596 (mpp)
REVERT: A   20 ASP cc_start: 0.7953 (m-30) cc_final: 0.7723 (m-30)
REVERT: A  255 ASN cc_start: 0.8480 (m-40) cc_final: 0.8247 (m-40)
REVERT: A  314 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8336 (mttm)
REVERT: B  129 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7808 (mmm-85)
REVERT: B  135 VAL cc_start: 0.8620 (t) cc_final: 0.8342 (p)
REVERT: B  217 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7269 (ptp)
REVERT: B  219 ARG cc_start: 0.7693 (mpt180) cc_final: 0.7097 (mpt180)
REVERT: S  141 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8273 (p)
  outliers start: 24
  outliers final: 9
  residues processed: 182
  average time/residue: 0.5270
  time to fit residues: 102.1542
Evaluate side-chains
  187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.135608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.115782 restraints weight = 12235.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.87
r_work: 0.3390 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9122  Z= 0.176
  Angle     :  0.567  10.245  12356  Z= 0.296
  Chirality :  0.044   0.227   1404
  Planarity :  0.004   0.040   1550
  Dihedral  :  4.928  67.990   1264
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.51 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.46 (0.26), residues: 1123
  helix:  2.36 (0.26), residues: 401
  sheet:  1.06 (0.31), residues: 273
  loop : -0.36 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.025   0.002   TYR S 190 
 PHE   0.015   0.001   PHE R  92 
 TRP   0.017   0.001   TRP R 108 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 9119)
  covalent geometry    : angle       0.56664 (12350)
  SS BOND              : bond        0.00778 (    3)
  SS BOND              : angle       1.40682 (    6)
  hydrogen bonds       : bond        0.04373 (  442)
  hydrogen bonds       : angle       4.37378 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: R   53 VAL cc_start: 0.5718 (OUTLIER) cc_final: 0.5436 (t)
REVERT: A   20 ASP cc_start: 0.7948 (m-30) cc_final: 0.7724 (m-30)
REVERT: A  255 ASN cc_start: 0.8557 (m-40) cc_final: 0.8322 (m-40)
REVERT: A  275 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7414 (mm-30)
REVERT: B   78 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8135 (mttm)
REVERT: B  135 VAL cc_start: 0.8659 (t) cc_final: 0.8415 (p)
REVERT: S  141 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (p)
  outliers start: 27
  outliers final: 14
  residues processed: 183
  average time/residue: 0.5312
  time to fit residues: 103.7751
Evaluate side-chains
  190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN
B 340 ASN
S 142 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.136283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.116386 restraints weight = 12428.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.89
r_work: 0.3398 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9122  Z= 0.144
  Angle     :  0.542   9.481  12356  Z= 0.283
  Chirality :  0.043   0.214   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.859  68.465   1264
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.51 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.49 (0.26), residues: 1123
  helix:  2.43 (0.26), residues: 401
  sheet:  1.08 (0.31), residues: 270
  loop : -0.39 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.021   0.001   TYR S 190 
 PHE   0.009   0.001   PHE R  92 
 TRP   0.015   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9119)
  covalent geometry    : angle       0.54169 (12350)
  SS BOND              : bond        0.00642 (    3)
  SS BOND              : angle       1.27152 (    6)
  hydrogen bonds       : bond        0.04022 (  442)
  hydrogen bonds       : angle       4.32526 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.281 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5719 (OUTLIER) cc_final: 0.5453 (t)
REVERT: A   20 ASP cc_start: 0.7956 (m-30) cc_final: 0.7728 (m-30)
REVERT: A  275 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7431 (mm-30)
REVERT: B   78 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8153 (mttm)
REVERT: B  135 VAL cc_start: 0.8624 (t) cc_final: 0.8382 (p)
REVERT: B  219 ARG cc_start: 0.7727 (tpt170) cc_final: 0.7168 (mpt180)
  outliers start: 29
  outliers final: 14
  residues processed: 185
  average time/residue: 0.5341
  time to fit residues: 105.4769
Evaluate side-chains
  189 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 THR
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.116521 restraints weight = 12312.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.89
r_work: 0.3399 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9122  Z= 0.140
  Angle     :  0.549   9.492  12356  Z= 0.285
  Chirality :  0.043   0.212   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.822  68.194   1264
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.64 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.47 (0.26), residues: 1123
  helix:  2.42 (0.26), residues: 403
  sheet:  1.01 (0.31), residues: 273
  loop : -0.39 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.021   0.001   TYR S 190 
 PHE   0.009   0.001   PHE B 234 
 TRP   0.014   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9119)
  covalent geometry    : angle       0.54887 (12350)
  SS BOND              : bond        0.00636 (    3)
  SS BOND              : angle       1.26994 (    6)
  hydrogen bonds       : bond        0.04001 (  442)
  hydrogen bonds       : angle       4.32354 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.319 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5706 (OUTLIER) cc_final: 0.5460 (t)
REVERT: A   20 ASP cc_start: 0.7952 (m-30) cc_final: 0.7721 (m-30)
REVERT: A  197 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8087 (mttm)
REVERT: A  275 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7428 (mm-30)
REVERT: B   78 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8136 (mttm)
REVERT: B  135 VAL cc_start: 0.8603 (t) cc_final: 0.8361 (p)
REVERT: B  219 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7147 (mpt180)
  outliers start: 24
  outliers final: 14
  residues processed: 185
  average time/residue: 0.5465
  time to fit residues: 107.6109
Evaluate side-chains
  193 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 THR
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0470
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.118260 restraints weight = 12140.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.93
r_work: 0.3424 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9122  Z= 0.119
  Angle     :  0.533  10.788  12356  Z= 0.275
  Chirality :  0.042   0.201   1404
  Planarity :  0.003   0.040   1550
  Dihedral  :  4.749  67.629   1264
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.64 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.56 (0.26), residues: 1123
  helix:  2.54 (0.27), residues: 402
  sheet:  1.06 (0.31), residues: 274
  loop : -0.38 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.019   0.001   TYR S 190 
 PHE   0.009   0.001   PHE B 234 
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9119)
  covalent geometry    : angle       0.53273 (12350)
  SS BOND              : bond        0.00521 (    3)
  SS BOND              : angle       1.12581 (    6)
  hydrogen bonds       : bond        0.03737 (  442)
  hydrogen bonds       : angle       4.26043 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: R   53 VAL cc_start: 0.5734 (OUTLIER) cc_final: 0.5469 (t)
REVERT: A   20 ASP cc_start: 0.7931 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  275 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: B  135 VAL cc_start: 0.8573 (t) cc_final: 0.8331 (p)
REVERT: B  219 ARG cc_start: 0.7717 (tpt170) cc_final: 0.7183 (mpt180)
  outliers start: 23
  outliers final: 16
  residues processed: 190
  average time/residue: 0.5292
  time to fit residues: 107.1898
Evaluate side-chains
  199 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 THR
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  211 TYR
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 22 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.118434 restraints weight = 12195.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.93
r_work: 0.3425 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9122  Z= 0.124
  Angle     :  0.543  11.407  12356  Z= 0.282
  Chirality :  0.043   0.211   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.725  67.016   1264
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.56 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.54 (0.26), residues: 1123
  helix:  2.46 (0.27), residues: 403
  sheet:  1.02 (0.31), residues: 276
  loop : -0.32 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.020   0.001   TYR S 190 
 PHE   0.010   0.001   PHE R  92 
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9119)
  covalent geometry    : angle       0.54274 (12350)
  SS BOND              : bond        0.00535 (    3)
  SS BOND              : angle       1.11403 (    6)
  hydrogen bonds       : bond        0.03769 (  442)
  hydrogen bonds       : angle       4.31017 ( 1278)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: R   53 VAL cc_start: 0.5702 (OUTLIER) cc_final: 0.5442 (t)
REVERT: R  178 MET cc_start: 0.5266 (mmm) cc_final: 0.5000 (mmm)
REVERT: A   20 ASP cc_start: 0.7934 (m-30) cc_final: 0.7694 (m-30)
REVERT: A  275 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7367 (mm-30)
REVERT: B  135 VAL cc_start: 0.8574 (t) cc_final: 0.8341 (p)
REVERT: B  212 ASP cc_start: 0.7778 (p0) cc_final: 0.7514 (p0)
REVERT: B  219 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7030 (mpt180)
REVERT: B  254 ASP cc_start: 0.7952 (t70) cc_final: 0.7635 (p0)
  outliers start: 16
  outliers final: 14
  residues processed: 185
  average time/residue: 0.5481
  time to fit residues: 107.9142
Evaluate side-chains
  195 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 THR
Chi-restraints excluded: chain R residue   53 VAL
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0030
   chunk 110 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN
S 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.139368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118929 restraints weight = 12014.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.92
r_work: 0.3432 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9122  Z= 0.116
  Angle     :  0.539  11.002  12356  Z= 0.278
  Chirality :  0.042   0.221   1404
  Planarity :  0.003   0.040   1550
  Dihedral  :  4.683  65.803   1264
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.35 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 are not related in a simple way.
  whole:  1.55 (0.26), residues: 1123
  helix:  2.46 (0.27), residues: 404
  sheet:  1.01 (0.31), residues: 276
  loop : -0.30 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.019   0.001   TYR S 190 
 PHE   0.010   0.001   PHE R  92 
 TRP   0.015   0.001   TRP R 269 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9119)
  covalent geometry    : angle       0.53883 (12350)
  SS BOND              : bond        0.00469 (    3)
  SS BOND              : angle       1.04385 (    6)
  hydrogen bonds       : bond        0.03605 (  442)
  hydrogen bonds       : angle       4.30752 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3486.59 seconds
wall clock time: 59 minutes 59.68 seconds (3599.68 seconds total)