Starting phenix.real_space_refine
on Wed Mar 12 21:03:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xxz_38766/03_2025/8xxz_38766.cif"
  }
  resolution = 3.3
  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=  -0.000 sd=   1.000
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      59      5.16       5
     C    5289      2.51       5
     N    1433      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8331
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1711
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1791
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1838
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 7, 'TRANS': 229}
          Chain breaks: 3
  Time building chain proxies: 5.20, per 1000 atoms: 0.62
  Number of scatterers: 8331
  At special positions: 0
  Unit cell: (91.3, 120.35, 129.688, 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      59     16.00
     O    1550      8.00
     N    1433      7.00
     C    5289      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 919.5 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1998

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      36.3% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 4.396A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 257
      removed outlier: 4.307A  pdb=" N   HIS A 245 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   GLU A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.078A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 3.514A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 4.137A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.702A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.082A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.647A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'R' and resid 60 through 80
      removed outlier: 3.536A  pdb=" N   LEU R  65 " --> pdb=" O   SER R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 105
      removed outlier: 3.599A  pdb=" N   THR R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 110
    Processing helix  chain 'R' and resid 127 through 154
      removed outlier: 3.511A  pdb=" N   TYR R 136 " --> pdb=" O   ASN R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 168 through 188
      removed outlier: 3.592A  pdb=" N   CYS R 172 " --> pdb=" O   VAL R 168 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE R 182 " --> pdb=" O   LEU R 178 " (cutoff:3.500A)
      Proline residue:  R 185  - end of helix
    Processing helix  chain 'R' and resid 209 through 224
      removed outlier: 3.805A  pdb=" N   PHE R 224 " --> pdb=" O   LEU R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 224 through 244
    Processing helix  chain 'R' and resid 248 through 284
      removed outlier: 4.507A  pdb=" N   ARG R 252 " --> pdb=" O   GLN R 248 " (cutoff:3.500A)
      Proline residue:  R 270  - end of helix
    Processing helix  chain 'R' and resid 289 through 319
      Proline residue:  R 315  - end of helix
    Processing helix  chain 'R' and resid 322 through 332
      removed outlier: 3.650A  pdb=" N   ARG R 326 " --> pdb=" O   GLY R 322 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG R 328 " --> pdb=" O   LYS R 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
      removed outlier: 9.599A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.716A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.827A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.671A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.578A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.811A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.571A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.591A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 5.745A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.664A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.664A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148

    396 hydrogen bonds defined for protein.
    1113 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: 2.35

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2039
        1.33 -     1.45: 1694
        1.45 -     1.57: 4676
        1.57 -     1.69: 0
        1.69 -     1.82: 84
  Bond restraints: 8493
  Sorted by residual:
  bond pdb=" C   GLU A   8 "
       pdb=" O   GLU A   8 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.028 1.16e-02 7.43e+03 5.95e+00
  bond pdb=" C   GLU A  14 "
       pdb=" O   GLU A  14 "
    ideal  model  delta    sigma   weight residual
    1.236  1.211  0.026 1.15e-02 7.56e+03 4.99e+00
  bond pdb=" C   ALA A   7 "
       pdb=" N   GLU A   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.309  0.026 1.33e-02 5.65e+03 3.75e+00
  bond pdb=" N   LEU R  59 "
       pdb=" CA  LEU R  59 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" C   GLU A  14 "
       pdb=" N   ARG A  15 "
    ideal  model  delta    sigma   weight residual
    1.335  1.317  0.018 1.30e-02 5.92e+03 2.02e+00
  ... (remaining 8488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 11114
        1.18 -     2.36: 332
        2.36 -     3.55: 44
        3.55 -     4.73: 16
        4.73 -     5.91: 1
  Bond angle restraints: 11507
  Sorted by residual:
  angle pdb=" N   GLU A  14 "
        pdb=" CA  GLU A  14 "
        pdb=" C   GLU A  14 "
      ideal   model   delta    sigma   weight residual
     111.07  106.82    4.25 1.07e+00 8.73e-01 1.58e+01
  angle pdb=" CA  TYR S 178 "
        pdb=" CB  TYR S 178 "
        pdb=" CG  TYR S 178 "
      ideal   model   delta    sigma   weight residual
     113.90  119.81   -5.91 1.80e+00 3.09e-01 1.08e+01
  angle pdb=" C   ALA A   7 "
        pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
      ideal   model   delta    sigma   weight residual
     120.44  116.17    4.27 1.36e+00 5.41e-01 9.85e+00
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     111.14  107.92    3.22 1.08e+00 8.57e-01 8.87e+00
  angle pdb=" C   TYR S 178 "
        pdb=" N   ARG S 179 "
        pdb=" CA  ARG S 179 "
      ideal   model   delta    sigma   weight residual
     122.17  118.25    3.92 1.54e+00 4.22e-01 6.48e+00
  ... (remaining 11502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 4462
       17.16 -    34.32: 447
       34.32 -    51.48: 106
       51.48 -    68.64: 23
       68.64 -    85.80: 5
  Dihedral angle restraints: 5043
    sinusoidal: 1943
      harmonic: 3100
  Sorted by residual:
  dihedral pdb=" CA  SER S 106 "
           pdb=" C   SER S 106 "
           pdb=" N   PRO S 107 "
           pdb=" CA  PRO S 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.60  -18.40     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.80   18.20     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  PHE S 108 "
           pdb=" C   PHE S 108 "
           pdb=" N   ASP S 109 "
           pdb=" CA  ASP S 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.93  -18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 5040 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 934
       0.037 -    0.074: 296
       0.074 -    0.111: 67
       0.111 -    0.148: 25
       0.148 -    0.185: 2
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CA  TYR S 178 "
            pdb=" N   TYR S 178 "
            pdb=" C   TYR S 178 "
            pdb=" CB  TYR S 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  ILE A 222 "
            pdb=" N   ILE A 222 "
            pdb=" C   ILE A 222 "
            pdb=" CB  ILE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 178 "    0.019 2.00e-02 2.50e+03   1.28e-02 3.27e+00
        pdb=" CG  TYR S 178 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 178 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR S 178 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  14 "   -0.006 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C   GLU A  14 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLU A  14 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG A  15 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 184 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.07e+00
        pdb=" N   PRO R 185 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO R 185 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 185 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 529
        2.73 -     3.27: 8354
        3.27 -     3.81: 13017
        3.81 -     4.36: 15552
        4.36 -     4.90: 27955
  Nonbonded interactions: 65407
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" N   THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASP A 252 "
            pdb=" ND2 ASN A 256 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ALA R  96 "
            pdb=" OG1 THR R 100 "
     model   vdw
     2.265 3.040
  ... (remaining 65402 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:             0.970
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.600
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
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      :  0.005   0.047   8493  Z= 0.302
  Angle     :  0.512   5.912  11507  Z= 0.298
  Chirality :  0.040   0.185   1324
  Planarity :  0.003   0.026   1456
  Dihedral  : 14.773  85.795   3039
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 14.38 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1054
  helix:  1.19 (0.27), residues: 336
  sheet:  0.12 (0.31), residues: 281
  loop : -0.65 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE S 108 
 TYR   0.030   0.002   TYR S 178 
 ARG   0.002   0.000   ARG R 149 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8490 (mtmt)
REVERT: A  227 ASP cc_start: 0.7237 (t0) cc_final: 0.6987 (t0)
REVERT: A  299 ASP cc_start: 0.7809 (m-30) cc_final: 0.7308 (m-30)
REVERT: A  322 HIS cc_start: 0.8157 (t-90) cc_final: 0.7571 (t-170)
REVERT: A  323 MET cc_start: 0.7748 (tpp) cc_final: 0.7338 (mmm)
REVERT: B  172 GLU cc_start: 0.7602 (tp30) cc_final: 0.7396 (tp30)
REVERT: B  254 ASP cc_start: 0.6913 (t70) cc_final: 0.6618 (t0)
REVERT: S   34 MET cc_start: 0.8347 (mmm) cc_final: 0.8082 (mmp)
REVERT: S   42 GLU cc_start: 0.7152 (pm20) cc_final: 0.6913 (mp0)
REVERT: S  127 VAL cc_start: 0.9094 (t) cc_final: 0.8796 (p)
REVERT: S  189 ASP cc_start: 0.8258 (p0) cc_final: 0.7991 (t0)
REVERT: R  135 PHE cc_start: 0.8129 (t80) cc_final: 0.7231 (t80)
REVERT: R  146 SER cc_start: 0.8951 (m) cc_final: 0.8719 (p)
REVERT: R  268 TRP cc_start: 0.7322 (m100) cc_final: 0.6765 (m100)
REVERT: R  313 LEU cc_start: 0.8957 (mt) cc_final: 0.8689 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 277
  average time/residue: 0.2539
  time to fit residues: 89.9820
Evaluate side-chains
  172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   89 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 31 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
B  91 HIS
B 259 GLN
S  13 GLN
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099286 restraints weight = 15501.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.84
r_work: 0.3163 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8493  Z= 0.185
  Angle     :  0.561   7.412  11507  Z= 0.299
  Chirality :  0.042   0.173   1324
  Planarity :  0.004   0.055   1456
  Dihedral  :  4.032  29.769   1166
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.92 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1054
  helix:  2.02 (0.27), residues: 348
  sheet:  0.34 (0.31), residues: 285
  loop : -0.66 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  94 
 PHE   0.015   0.001   PHE R 131 
 TYR   0.027   0.002   TYR S 178 
 ARG   0.006   0.000   ARG G  13 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9018 (tp) cc_final: 0.8780 (tp)
REVERT: A  291 TYR cc_start: 0.7012 (t80) cc_final: 0.5920 (t80)
REVERT: A  322 HIS cc_start: 0.8438 (t-90) cc_final: 0.8147 (t-90)
REVERT: A  323 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7397 (mtp)
REVERT: B  325 MET cc_start: 0.8614 (tpp) cc_final: 0.8373 (tpp)
REVERT: G   19 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8236 (mm)
REVERT: G   22 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7288 (tp30)
REVERT: S   34 MET cc_start: 0.8691 (mmm) cc_final: 0.8398 (mmp)
REVERT: S   42 GLU cc_start: 0.7541 (pm20) cc_final: 0.7202 (mp0)
REVERT: S  127 VAL cc_start: 0.9066 (t) cc_final: 0.8799 (p)
REVERT: S  208 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7822 (mp0)
REVERT: S  232 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8794 (ttpt)
REVERT: R  135 PHE cc_start: 0.8217 (t80) cc_final: 0.7428 (t80)
REVERT: R  136 TYR cc_start: 0.6247 (m-10) cc_final: 0.6009 (m-10)
REVERT: R  268 TRP cc_start: 0.7221 (m100) cc_final: 0.6649 (m100)
REVERT: R  271 TYR cc_start: 0.7482 (t80) cc_final: 0.6955 (t80)
REVERT: R  281 MET cc_start: 0.5318 (tpt) cc_final: 0.4640 (tpt)
REVERT: R  313 LEU cc_start: 0.8949 (mt) cc_final: 0.8607 (mt)
  outliers start: 22
  outliers final: 11
  residues processed: 215
  average time/residue: 0.2092
  time to fit residues: 60.8309
Evaluate side-chains
  180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  258 VAL
Chi-restraints excluded: chain R residue  306 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0270
   chunk 10 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
S  13 GLN
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.123286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.096047 restraints weight = 15882.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.99
r_work: 0.3070 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8493  Z= 0.332
  Angle     :  0.613   9.833  11507  Z= 0.325
  Chirality :  0.044   0.221   1324
  Planarity :  0.004   0.043   1456
  Dihedral  :  4.521  39.035   1164
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 17.92 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1054
  helix:  1.84 (0.27), residues: 347
  sheet:  0.07 (0.30), residues: 296
  loop : -0.86 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.004   0.001   HIS R 237 
 PHE   0.014   0.002   PHE S 108 
 TYR   0.034   0.002   TYR S 178 
 ARG   0.004   0.001   ARG R 288 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 178
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 LEU cc_start: 0.9095 (tp) cc_final: 0.8875 (tp)
REVERT: A  299 ASP cc_start: 0.7356 (t0) cc_final: 0.6904 (t0)
REVERT: B   10 GLU cc_start: 0.8824 (tp30) cc_final: 0.8567 (tp30)
REVERT: B   15 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8609 (mmmt)
REVERT: B   96 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7501 (ttp-170)
REVERT: G   22 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7242 (tm-30)
REVERT: G   47 GLU cc_start: 0.8720 (mp0) cc_final: 0.8484 (mp0)
REVERT: S   34 MET cc_start: 0.8810 (mmm) cc_final: 0.8578 (mmt)
REVERT: S  208 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7955 (mp0)
REVERT: R  313 LEU cc_start: 0.9068 (mt) cc_final: 0.8856 (mt)
  outliers start: 44
  outliers final: 24
  residues processed: 208
  average time/residue: 0.2137
  time to fit residues: 60.2070
Evaluate side-chains
  192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   65 LYS
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue  157 THR
Chi-restraints excluded: chain R residue  169 THR
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  258 VAL
Chi-restraints excluded: chain R residue  306 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0020
   chunk 69 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5126

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
S  13 GLN
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.126947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.098261 restraints weight = 15785.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.74
r_work: 0.3170 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8493  Z= 0.146
  Angle     :  0.543  13.292  11507  Z= 0.277
  Chirality :  0.041   0.163   1324
  Planarity :  0.003   0.037   1456
  Dihedral  :  4.091  29.255   1164
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.35 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1054
  helix:  1.99 (0.28), residues: 353
  sheet:  0.25 (0.31), residues: 282
  loop : -0.83 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 272 
 PHE   0.017   0.001   PHE R 131 
 TYR   0.023   0.001   TYR S 178 
 ARG   0.005   0.000   ARG A 209 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7899 (tmtt) cc_final: 0.7373 (mtpp)
REVERT: A   53 MET cc_start: 0.5588 (mmt) cc_final: 0.5305 (mtt)
REVERT: A   55 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6535 (mt)
REVERT: A  250 LEU cc_start: 0.9012 (tp) cc_final: 0.8761 (tp)
REVERT: A  299 ASP cc_start: 0.7002 (t0) cc_final: 0.6747 (t0)
REVERT: B   10 GLU cc_start: 0.8801 (tp30) cc_final: 0.8557 (tp30)
REVERT: B   15 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8625 (mmmt)
REVERT: B  118 ASP cc_start: 0.8647 (t0) cc_final: 0.8409 (t0)
REVERT: B  134 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.8286 (ptt-90)
REVERT: G   19 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8286 (mm)
REVERT: G   22 GLU cc_start: 0.7286 (tm-30) cc_final: 0.7005 (tm-30)
REVERT: S   42 GLU cc_start: 0.7562 (pm20) cc_final: 0.7146 (mp0)
REVERT: S  208 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8122 (mp0)
REVERT: S  232 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8791 (ttpp)
REVERT: R  218 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7496 (pp)
REVERT: R  226 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7736 (tt)
  outliers start: 27
  outliers final: 21
  residues processed: 197
  average time/residue: 0.2203
  time to fit residues: 57.9676
Evaluate side-chains
  192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  297 ASP
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0470
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.9680

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
B 340 ASN
S  13 GLN
S 171 GLN
R 134 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.125665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098146 restraints weight = 15597.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.76
r_work: 0.3158 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8493  Z= 0.182
  Angle     :  0.541   9.586  11507  Z= 0.281
  Chirality :  0.041   0.185   1324
  Planarity :  0.003   0.035   1456
  Dihedral  :  4.087  30.207   1164
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.68 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1054
  helix:  2.12 (0.28), residues: 348
  sheet:  0.15 (0.30), residues: 284
  loop : -0.79 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 272 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.004   0.000   ARG A 209 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6705 (mt)
REVERT: A  250 LEU cc_start: 0.9023 (tp) cc_final: 0.8767 (tp)
REVERT: A  299 ASP cc_start: 0.7080 (t0) cc_final: 0.6854 (t0)
REVERT: B   10 GLU cc_start: 0.8826 (tp30) cc_final: 0.8617 (tp30)
REVERT: B   15 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8645 (mmmt)
REVERT: B  118 ASP cc_start: 0.8668 (t0) cc_final: 0.8434 (t0)
REVERT: G   19 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8331 (mm)
REVERT: G   22 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7017 (tm-30)
REVERT: R  226 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7777 (tt)
  outliers start: 36
  outliers final: 27
  residues processed: 191
  average time/residue: 0.2109
  time to fit residues: 54.7194
Evaluate side-chains
  193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  297 ASP
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0010
   chunk 103 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
S  13 GLN
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.125489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097861 restraints weight = 15564.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.78
r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8493  Z= 0.201
  Angle     :  0.565  12.351  11507  Z= 0.287
  Chirality :  0.042   0.241   1324
  Planarity :  0.003   0.037   1456
  Dihedral  :  4.166  31.942   1164
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.79 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1054
  helix:  2.14 (0.28), residues: 348
  sheet:  0.14 (0.30), residues: 279
  loop : -0.81 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 272 
 PHE   0.014   0.001   PHE R 131 
 TYR   0.028   0.001   TYR S 178 
 ARG   0.006   0.000   ARG S 206 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6742 (mt)
REVERT: A  250 LEU cc_start: 0.9029 (tp) cc_final: 0.8799 (tp)
REVERT: A  299 ASP cc_start: 0.7145 (t0) cc_final: 0.6886 (t0)
REVERT: B   10 GLU cc_start: 0.8869 (tp30) cc_final: 0.8557 (tp30)
REVERT: B   15 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8628 (mmmt)
REVERT: B  118 ASP cc_start: 0.8687 (t0) cc_final: 0.8469 (t0)
REVERT: G   19 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: S  127 VAL cc_start: 0.9186 (t) cc_final: 0.8953 (p)
REVERT: S  208 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8134 (mp0)
REVERT: R  226 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7866 (tt)
  outliers start: 36
  outliers final: 27
  residues processed: 191
  average time/residue: 0.2027
  time to fit residues: 52.4821
Evaluate side-chains
  193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  297 ASP
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  13 GLN
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.126026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098723 restraints weight = 15708.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.92
r_work: 0.3164 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8493  Z= 0.177
  Angle     :  0.540   9.522  11507  Z= 0.279
  Chirality :  0.041   0.180   1324
  Planarity :  0.003   0.037   1456
  Dihedral  :  4.077  30.793   1164
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 21.24 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.26), residues: 1054
  helix:  2.20 (0.28), residues: 348
  sheet:  0.19 (0.31), residues: 273
  loop : -0.78 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 272 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.027   0.001   TYR S 178 
 ARG   0.005   0.000   ARG S 206 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 168
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6913 (mt)
REVERT: A  250 LEU cc_start: 0.9038 (tp) cc_final: 0.8806 (tp)
REVERT: A  299 ASP cc_start: 0.7213 (t0) cc_final: 0.6956 (t0)
REVERT: B   10 GLU cc_start: 0.8830 (tp30) cc_final: 0.8623 (tp30)
REVERT: B   15 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8617 (mmmt)
REVERT: B  118 ASP cc_start: 0.8688 (t0) cc_final: 0.8473 (t0)
REVERT: G   19 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8286 (mm)
REVERT: S  127 VAL cc_start: 0.9187 (t) cc_final: 0.8950 (p)
REVERT: S  208 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8127 (mp0)
REVERT: R  226 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7815 (tt)
  outliers start: 35
  outliers final: 28
  residues processed: 192
  average time/residue: 0.2025
  time to fit residues: 52.8526
Evaluate side-chains
  195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  258 VAL
Chi-restraints excluded: chain R residue  297 ASP
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 98 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  13 GLN
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.126451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100369 restraints weight = 16015.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.64
r_work: 0.3159 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8493  Z= 0.175
  Angle     :  0.555  10.954  11507  Z= 0.284
  Chirality :  0.041   0.222   1324
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.050  30.391   1164
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 21.35 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1054
  helix:  2.24 (0.28), residues: 347
  sheet:  0.11 (0.30), residues: 279
  loop : -0.70 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 272 
 PHE   0.014   0.001   PHE R 131 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.007   0.000   ARG S 206 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 166
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7108 (mt)
REVERT: A  250 LEU cc_start: 0.8958 (tp) cc_final: 0.8740 (tp)
REVERT: A  299 ASP cc_start: 0.7071 (t0) cc_final: 0.6790 (t0)
REVERT: B   10 GLU cc_start: 0.8810 (tp30) cc_final: 0.8586 (tp30)
REVERT: B   15 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8605 (mmmt)
REVERT: B  118 ASP cc_start: 0.8681 (t0) cc_final: 0.8472 (t0)
REVERT: G   19 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8346 (mm)
REVERT: S  127 VAL cc_start: 0.9172 (t) cc_final: 0.8945 (p)
REVERT: S  208 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8129 (mp0)
REVERT: R  184 LEU cc_start: 0.8793 (mm) cc_final: 0.8590 (pp)
REVERT: R  226 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7747 (tt)
  outliers start: 35
  outliers final: 30
  residues processed: 191
  average time/residue: 0.2154
  time to fit residues: 55.7241
Evaluate side-chains
  194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  297 ASP
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
** B   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  13 GLN
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.125071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.099018 restraints weight = 16006.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.82
r_work: 0.3136 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8493  Z= 0.228
  Angle     :  0.577   9.797  11507  Z= 0.297
  Chirality :  0.042   0.221   1324
  Planarity :  0.004   0.039   1456
  Dihedral  :  4.191  34.069   1164
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 21.46 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1054
  helix:  2.15 (0.28), residues: 348
  sheet:  0.02 (0.30), residues: 281
  loop : -0.72 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 272 
 PHE   0.010   0.001   PHE B 151 
 TYR   0.029   0.002   TYR S 178 
 ARG   0.007   0.000   ARG S 206 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7219 (mt)
REVERT: A  299 ASP cc_start: 0.7147 (t0) cc_final: 0.6901 (t0)
REVERT: B   15 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8608 (mmmt)
REVERT: G   19 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8330 (mm)
REVERT: S  127 VAL cc_start: 0.9190 (t) cc_final: 0.8956 (p)
REVERT: S  208 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8106 (mp0)
REVERT: R  226 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7894 (tt)
  outliers start: 37
  outliers final: 29
  residues processed: 193
  average time/residue: 0.2280
  time to fit residues: 59.8618
Evaluate side-chains
  191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  157 THR
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
S  13 GLN
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.097995 restraints weight = 15715.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.62
r_work: 0.3169 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8493  Z= 0.182
  Angle     :  0.570   9.583  11507  Z= 0.292
  Chirality :  0.041   0.179   1324
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.116  32.227   1164
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.35 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1054
  helix:  2.16 (0.28), residues: 348
  sheet:  0.09 (0.31), residues: 279
  loop : -0.73 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 272 
 PHE   0.014   0.001   PHE S  80 
 TYR   0.027   0.001   TYR S 178 
 ARG   0.008   0.000   ARG S 206 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7413 (tttm)
REVERT: A   55 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7200 (mt)
REVERT: A  299 ASP cc_start: 0.7132 (t0) cc_final: 0.6884 (t0)
REVERT: A  333 GLN cc_start: 0.8156 (tp40) cc_final: 0.7946 (tp40)
REVERT: B   15 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8597 (mmmt)
REVERT: B  130 GLU cc_start: 0.8665 (mp0) cc_final: 0.8403 (mp0)
REVERT: G   19 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8342 (mm)
REVERT: G   22 GLU cc_start: 0.7420 (tp30) cc_final: 0.7149 (tp30)
REVERT: S  127 VAL cc_start: 0.9198 (t) cc_final: 0.8960 (p)
REVERT: R  226 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7795 (tt)
  outliers start: 31
  outliers final: 26
  residues processed: 192
  average time/residue: 0.2562
  time to fit residues: 65.9917
Evaluate side-chains
  194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 2.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain B residue    5 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  147 CYS
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  178 TYR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain R residue   64 PHE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  151 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  258 VAL
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain R residue  324 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 23 optimal weight:    0.0270
   chunk 3 optimal weight:    0.0170
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.127382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.100324 restraints weight = 15895.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.81
r_work: 0.3181 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8493  Z= 0.153
  Angle     :  0.569  12.569  11507  Z= 0.287
  Chirality :  0.041   0.299   1324
  Planarity :  0.003   0.039   1456
  Dihedral  :  3.967  28.807   1164
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.23 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 1054
  helix:  2.24 (0.28), residues: 348
  sheet:  0.19 (0.31), residues: 276
  loop : -0.71 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 268 
 HIS   0.003   0.001   HIS R 272 
 PHE   0.015   0.001   PHE R 131 
 TYR   0.024   0.001   TYR S 178 
 ARG   0.008   0.000   ARG S 206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4144.84 seconds
wall clock time: 72 minutes 55.08 seconds (4375.08 seconds total)