Starting phenix.real_space_refine
on Thu Feb 13 12:45:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wig_32529/02_2025/7wig_32529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wig_32529/02_2025/7wig_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_32529/02_2025/7wig_32529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wig_32529/02_2025/7wig_32529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wig_32529/02_2025/7wig_32529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wig_32529/02_2025/7wig_32529.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.14, per 1000 atoms: 0.58
  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: 2.08
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.79
  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: 2.47

  Time building geometry restraints manager: 2.39 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:             0.450
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     21.920
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.110
-------------------------------------------------------------------------------
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   9119  Z= 0.433
  Angle     :  0.746  24.373  12350  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 : 6.75
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (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
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.051   0.001   PHE R 127 
 TYR   0.016   0.001   TYR R 211 
 ARG   0.007   0.000   ARG B 251 

*********************** 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  : 0.969 
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: 1.2351
  time to fit residues: 246.0885
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  : 0.955 
-------------------------------------------------------------------------------
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 93 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.137570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117450 restraints weight = 12257.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.89
r_work: 0.3415 rms_B_bonded: 2.29 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: 0.7703
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9119  Z= 0.227
  Angle     :  0.561   7.838  12350  Z= 0.296
  Chirality :  0.044   0.255   1404
  Planarity :  0.004   0.041   1550
  Dihedral  :  5.418  64.483   1266
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.42 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.25), residues: 1123
  helix:  2.03 (0.26), residues: 401
  sheet:  0.93 (0.31), residues: 277
  loop : -0.32 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.022   0.001   PHE R  92 
 TYR   0.030   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 251 

*********************** 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: 12
    poor density    : 183
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: R  119 MET cc_start: 0.6890 (mmm) cc_final: 0.6668 (mpp)
REVERT: A   28 GLU cc_start: 0.7773 (mp0) cc_final: 0.6902 (mp0)
REVERT: A  255 ASN cc_start: 0.8508 (m-40) cc_final: 0.8277 (m-40)
REVERT: B  135 VAL cc_start: 0.8643 (t) cc_final: 0.8315 (p)
REVERT: S  140 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8137 (mtp)
  outliers start: 12
  outliers final: 2
  residues processed: 185
  average time/residue: 1.2634
  time to fit residues: 249.1428
Evaluate side-chains
  182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 179
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
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 58 optimal weight:    0.1980
   chunk 88 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0980
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.138471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.118541 restraints weight = 12434.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.89
r_work: 0.3431 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9119  Z= 0.153
  Angle     :  0.510   7.787  12350  Z= 0.268
  Chirality :  0.042   0.198   1404
  Planarity :  0.003   0.039   1550
  Dihedral  :  4.902  65.285   1264
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.95 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1123
  helix:  2.30 (0.26), residues: 402
  sheet:  0.99 (0.31), residues: 277
  loop : -0.27 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.016   0.001   PHE R  92 
 TYR   0.025   0.001   TYR S 190 
 ARG   0.006   0.000   ARG B 219 

*********************** 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
  202 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7898 (m-30) cc_final: 0.7674 (m-30)
REVERT: A   28 GLU cc_start: 0.7736 (mp0) cc_final: 0.6943 (mp0)
REVERT: A   53 MET cc_start: 0.5367 (mmm) cc_final: 0.5112 (mmp)
REVERT: A  255 ASN cc_start: 0.8442 (m-40) cc_final: 0.8209 (m-40)
REVERT: B  135 VAL cc_start: 0.8603 (t) cc_final: 0.8289 (p)
REVERT: B  217 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7165 (ptp)
REVERT: B  219 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7115 (mpt180)
REVERT: S  140 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (mtp)
REVERT: S  141 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8320 (p)
  outliers start: 20
  outliers final: 5
  residues processed: 186
  average time/residue: 1.2798
  time to fit residues: 253.3647
Evaluate side-chains
  185 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  252 SER
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 79 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0070
   chunk 102 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.7602

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.114869 restraints weight = 12177.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.86
r_work: 0.3373 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9119  Z= 0.362
  Angle     :  0.603   7.580  12350  Z= 0.317
  Chirality :  0.046   0.250   1404
  Planarity :  0.004   0.043   1550
  Dihedral  :  5.226  69.345   1264
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.00 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1123
  helix:  2.18 (0.26), residues: 401
  sheet:  0.94 (0.31), residues: 282
  loop : -0.39 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 108 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.021   0.002   PHE R  92 
 TYR   0.027   0.002   TYR S 190 
 ARG   0.005   0.001   ARG B 219 

*********************** 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
  203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.836 
Fit side-chains
REVERT: R  119 MET cc_start: 0.6903 (mmm) cc_final: 0.6678 (mpp)
REVERT: A   20 ASP cc_start: 0.7886 (m-30) cc_final: 0.7655 (m-30)
REVERT: A  255 ASN cc_start: 0.8600 (m-40) cc_final: 0.8366 (m-40)
REVERT: B  135 VAL cc_start: 0.8768 (t) cc_final: 0.8521 (p)
REVERT: B  212 ASP cc_start: 0.7683 (p0) cc_final: 0.7464 (p0)
REVERT: B  217 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7281 (ptp)
REVERT: B  219 ARG cc_start: 0.7682 (mpt180) cc_final: 0.7092 (mpt180)
REVERT: S  140 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8132 (mtp)
  outliers start: 21
  outliers final: 10
  residues processed: 187
  average time/residue: 1.2283
  time to fit residues: 244.7458
Evaluate side-chains
  194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  101 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  158 VAL
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 106 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0000
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B 132 ASN
B 220 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 = 0.3796 r_free = 0.3796 target = 0.137043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.117171 restraints weight = 12203.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.88
r_work: 0.3407 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9119  Z= 0.171
  Angle     :  0.506   7.463  12350  Z= 0.268
  Chirality :  0.042   0.200   1404
  Planarity :  0.003   0.040   1550
  Dihedral  :  4.886  68.895   1264
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.79 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1123
  helix:  2.42 (0.27), residues: 401
  sheet:  0.98 (0.30), residues: 284
  loop : -0.30 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.007   0.001   PHE B 199 
 TYR   0.022   0.001   TYR S 190 
 ARG   0.004   0.000   ARG B 214 

*********************** 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
  204 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 1.080 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5708 (OUTLIER) cc_final: 0.5438 (t)
REVERT: R  119 MET cc_start: 0.6863 (mmm) cc_final: 0.6636 (mpp)
REVERT: A   20 ASP cc_start: 0.7899 (m-30) cc_final: 0.7646 (m-30)
REVERT: B   78 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8168 (mttp)
REVERT: B  135 VAL cc_start: 0.8693 (t) cc_final: 0.8415 (p)
REVERT: B  212 ASP cc_start: 0.7667 (p0) cc_final: 0.7444 (p0)
REVERT: B  217 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7218 (ptp)
REVERT: B  219 ARG cc_start: 0.7705 (mpt180) cc_final: 0.7115 (mpt180)
  outliers start: 26
  outliers final: 9
  residues processed: 186
  average time/residue: 1.2206
  time to fit residues: 242.6145
Evaluate side-chains
  188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   78 LYS
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 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 109 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.135117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115217 restraints weight = 12175.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.87
r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.005   0.041   9119  Z= 0.295
  Angle     :  0.572   8.968  12350  Z= 0.300
  Chirality :  0.044   0.235   1404
  Planarity :  0.004   0.041   1550
  Dihedral  :  5.043  71.247   1264
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1123
  helix:  2.28 (0.26), residues: 401
  sheet:  1.06 (0.31), residues: 269
  loop : -0.43 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 108 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.012   0.001   PHE B 234 
 TYR   0.026   0.002   TYR S 190 
 ARG   0.003   0.000   ARG B 251 

*********************** 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
  200 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 0.965 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5714 (OUTLIER) cc_final: 0.5443 (t)
REVERT: A   20 ASP cc_start: 0.7892 (m-30) cc_final: 0.7646 (m-30)
REVERT: A  255 ASN cc_start: 0.8409 (m-40) cc_final: 0.8196 (m-40)
REVERT: A  275 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7420 (mm-30)
REVERT: B  135 VAL cc_start: 0.8680 (t) cc_final: 0.8438 (p)
REVERT: B  212 ASP cc_start: 0.7625 (p0) cc_final: 0.7349 (p0)
REVERT: B  217 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7254 (ptp)
REVERT: B  219 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7079 (mpt180)
  outliers start: 24
  outliers final: 15
  residues processed: 183
  average time/residue: 1.2413
  time to fit residues: 241.8483
Evaluate side-chains
  192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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  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 B residue   96 ARG
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  217 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
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 = 0.3786 r_free = 0.3786 target = 0.136275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.116352 restraints weight = 12338.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.89
r_work: 0.3397 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9119  Z= 0.209
  Angle     :  0.531   8.456  12350  Z= 0.279
  Chirality :  0.043   0.211   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.921  72.068   1264
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.02 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1123
  helix:  2.40 (0.27), residues: 402
  sheet:  1.05 (0.31), residues: 271
  loop : -0.41 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 108 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.009   0.001   PHE B 234 
 TYR   0.021   0.001   TYR S 190 
 ARG   0.003   0.000   ARG B 251 

*********************** 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
  198 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: R   53 VAL cc_start: 0.5714 (OUTLIER) cc_final: 0.5454 (t)
REVERT: A   20 ASP cc_start: 0.7907 (m-30) cc_final: 0.7650 (m-30)
REVERT: A  255 ASN cc_start: 0.8362 (m-40) cc_final: 0.8147 (m-40)
REVERT: A  275 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: B  135 VAL cc_start: 0.8634 (t) cc_final: 0.8381 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 183
  average time/residue: 1.2329
  time to fit residues: 240.2832
Evaluate side-chains
  188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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  252 SER
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  254 ASP
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 51 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 110 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 32 optimal weight:   20.0000
   chunk 88 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
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 = 0.3773 r_free = 0.3773 target = 0.135306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.115445 restraints weight = 12378.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.89
r_work: 0.3383 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9119  Z= 0.265
  Angle     :  0.561   9.255  12350  Z= 0.293
  Chirality :  0.044   0.226   1404
  Planarity :  0.004   0.042   1550
  Dihedral  :  4.991  74.218   1264
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1123
  helix:  2.32 (0.26), residues: 402
  sheet:  1.00 (0.31), residues: 271
  loop : -0.46 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 108 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.011   0.001   PHE B 234 
 TYR   0.023   0.001   TYR S 190 
 ARG   0.002   0.000   ARG B 251 

*********************** 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
  198 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.899 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5735 (OUTLIER) cc_final: 0.5469 (t)
REVERT: R  172 LEU cc_start: 0.7057 (tt) cc_final: 0.6725 (tp)
REVERT: A   20 ASP cc_start: 0.7904 (m-30) cc_final: 0.7652 (m-30)
REVERT: A  255 ASN cc_start: 0.8427 (m-40) cc_final: 0.8196 (m-40)
REVERT: A  275 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7412 (mm-30)
REVERT: B  135 VAL cc_start: 0.8632 (t) cc_final: 0.8394 (p)
REVERT: B  219 ARG cc_start: 0.7754 (tpt170) cc_final: 0.7219 (mpt180)
  outliers start: 23
  outliers final: 14
  residues processed: 183
  average time/residue: 1.2413
  time to fit residues: 242.1003
Evaluate side-chains
  189 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  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  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 33 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0770
   chunk 62 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.138560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.118113 restraints weight = 12194.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.93
r_work: 0.3418 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9119  Z= 0.181
  Angle     :  0.525  10.630  12350  Z= 0.274
  Chirality :  0.042   0.203   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.871  75.000   1264
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.46 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1123
  helix:  2.46 (0.27), residues: 403
  sheet:  1.00 (0.31), residues: 274
  loop : -0.39 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.008   0.001   PHE R  92 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.002   0.000   ARG B 197 

*********************** 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
  196 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 1.001 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5712 (OUTLIER) cc_final: 0.5467 (t)
REVERT: R  172 LEU cc_start: 0.7034 (tt) cc_final: 0.6681 (tp)
REVERT: A   20 ASP cc_start: 0.7902 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  255 ASN cc_start: 0.8317 (m-40) cc_final: 0.8115 (m-40)
REVERT: A  275 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7382 (mm-30)
REVERT: B  135 VAL cc_start: 0.8567 (t) cc_final: 0.8319 (p)
REVERT: B  219 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7218 (mpt180)
REVERT: B  254 ASP cc_start: 0.8004 (t70) cc_final: 0.7644 (p0)
  outliers start: 20
  outliers final: 13
  residues processed: 183
  average time/residue: 1.2518
  time to fit residues: 243.8517
Evaluate side-chains
  190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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  339 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  130 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.138087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.117595 restraints weight = 12141.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.93
r_work: 0.3414 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9119  Z= 0.219
  Angle     :  0.552  11.593  12350  Z= 0.286
  Chirality :  0.043   0.213   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.812  68.009   1264
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.56 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1123
  helix:  2.43 (0.27), residues: 403
  sheet:  1.09 (0.31), residues: 270
  loop : -0.44 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.010   0.001   PHE R  92 
 TYR   0.021   0.001   TYR S 190 
 ARG   0.003   0.000   ARG B 251 

********************** 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
  197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 0.991 
Fit side-chains
REVERT: R   53 VAL cc_start: 0.5714 (OUTLIER) cc_final: 0.5471 (t)
REVERT: R  172 LEU cc_start: 0.7036 (tt) cc_final: 0.6694 (tp)
REVERT: A   20 ASP cc_start: 0.7897 (m-30) cc_final: 0.7644 (m-30)
REVERT: A  255 ASN cc_start: 0.8362 (m-40) cc_final: 0.8136 (m-40)
REVERT: A  275 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7373 (mm-30)
REVERT: B  135 VAL cc_start: 0.8580 (t) cc_final: 0.8334 (p)
REVERT: B  219 ARG cc_start: 0.7748 (tpt170) cc_final: 0.7201 (mpt180)
REVERT: B  254 ASP cc_start: 0.7984 (t70) cc_final: 0.7651 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 186
  average time/residue: 1.2375
  time to fit residues: 245.2724
Evaluate side-chains
  191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
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  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 98 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.138286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117859 restraints weight = 12216.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.93
r_work: 0.3416 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9119  Z= 0.201
  Angle     :  0.545  10.998  12350  Z= 0.283
  Chirality :  0.043   0.215   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  4.716  60.561   1264
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.97 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1123
  helix:  2.43 (0.27), residues: 403
  sheet:  1.07 (0.31), residues: 272
  loop : -0.42 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 108 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE R  92 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.004   0.000   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7488.16 seconds
wall clock time: 132 minutes 42.13 seconds (7962.13 seconds total)