Starting phenix.real_space_refine
on Wed Jan 15 16:47:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xoi_38530/01_2025/8xoi_38530.cif"
  }
  resolution = 3.2
  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=   0.008
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      56      5.16       5
     C    5566      2.51       5
     N    1522      2.21       5
     O    1609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8753
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1866
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2554
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "E"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1735
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2162
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
          Chain breaks: 3
  Time building chain proxies: 5.17, per 1000 atoms: 0.59
  Number of scatterers: 8753
  At special positions: 0
  Unit cell: (113.526, 121.023, 109.242, 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      56     16.00
     O    1609      8.00
     N    1522      7.00
     C    5566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.23
  Conformation dependent library (CDL) restraints added in 983.0 milliseconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      39.6% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.603A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 280 through 285
      removed outlier: 3.746A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.540A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.529A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'G' and resid 7 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 53 through 87
      removed outlier: 4.612A  pdb=" N   PHE R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
      removed outlier: 3.518A  pdb=" N   PHE R  87 " --> pdb=" O   VAL R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 91
    Processing helix  chain 'R' and resid 92 through 116
      removed outlier: 3.549A  pdb=" N   LEU R  96 " --> pdb=" O   THR R  92 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR R  97 " --> pdb=" O   ILE R  93 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ILE R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 119 through 124
      removed outlier: 4.308A  pdb=" N   TYR R 123 " --> pdb=" O   LEU R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 161
    Processing helix  chain 'R' and resid 170 through 200
      Proline residue:  R 192  - end of helix
    Processing helix  chain 'R' and resid 211 through 223
    Processing helix  chain 'R' and resid 223 through 247
    Processing helix  chain 'R' and resid 254 through 285
      Proline residue:  R 274  - end of helix
    Processing helix  chain 'R' and resid 302 through 325
      removed outlier: 3.902A  pdb=" N   SER R 317 " --> pdb=" O   ALA R 313 " (cutoff:3.500A)
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 329 through 342
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.418A  pdb=" N   LEU A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.559A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.852A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.576A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.927A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.238A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.910A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.361A  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: 6.384A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.695A  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: 3.792A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.545A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.545A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.470A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 4.174A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1293 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: 2.59

  Time building geometry restraints manager: 2.54 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: 2357
        1.33 -     1.45: 1616
        1.45 -     1.57: 4875
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8930
  Sorted by residual:
  bond pdb=" CA  ASN B 237 "
       pdb=" C   ASN B 237 "
    ideal  model  delta    sigma   weight residual
    1.522  1.552 -0.030 1.39e-02 5.18e+03 4.77e+00
  bond pdb=" C   ASN R  77 "
       pdb=" O   ASN R  77 "
    ideal  model  delta    sigma   weight residual
    1.237  1.213  0.024 1.16e-02 7.43e+03 4.14e+00
  bond pdb=" N   TYR A 391 "
       pdb=" CA  TYR A 391 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.25e-02 6.40e+03 3.68e+00
  bond pdb=" N   THR G   6 "
       pdb=" CA  THR G   6 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.16e+00
  bond pdb=" N   GLU B   3 "
       pdb=" CA  GLU B   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  ... (remaining 8925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 11615
        1.21 -     2.41: 393
        2.41 -     3.62: 65
        3.62 -     4.82: 17
        4.82 -     6.03: 2
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
        pdb=" CB  MET E 192 "
      ideal   model   delta    sigma   weight residual
     114.17  109.27    4.90 1.14e+00 7.69e-01 1.85e+01
  angle pdb=" N   TYR B 105 "
        pdb=" CA  TYR B 105 "
        pdb=" C   TYR B 105 "
      ideal   model   delta    sigma   weight residual
     108.76  102.73    6.03 1.69e+00 3.50e-01 1.27e+01
  angle pdb=" C   SER R 325 "
        pdb=" N   PHE R 326 "
        pdb=" CA  PHE R 326 "
      ideal   model   delta    sigma   weight residual
     122.65  117.90    4.75 1.60e+00 3.91e-01 8.80e+00
  angle pdb=" CA  ASN R  77 "
        pdb=" C   ASN R  77 "
        pdb=" O   ASN R  77 "
      ideal   model   delta    sigma   weight residual
     120.70  117.77    2.93 1.03e+00 9.43e-01 8.09e+00
  angle pdb=" N   ILE A 235 "
        pdb=" CA  ILE A 235 "
        pdb=" C   ILE A 235 "
      ideal   model   delta    sigma   weight residual
     112.98  109.45    3.53 1.25e+00 6.40e-01 7.99e+00
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 4680
       17.51 -    35.01: 481
       35.01 -    52.52: 111
       52.52 -    70.03: 19
       70.03 -    87.54: 7
  Dihedral angle restraints: 5298
    sinusoidal: 2063
      harmonic: 3235
  Sorted by residual:
  dihedral pdb=" CA  PHE R 326 "
           pdb=" C   PHE R 326 "
           pdb=" N   LEU R 327 "
           pdb=" CA  LEU R 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.35   18.65     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ASP A 378 "
           pdb=" CB  ASP A 378 "
           pdb=" CG  ASP A 378 "
           pdb=" OD1 ASP A 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.81   59.81     1      2.00e+01 2.50e-03 1.19e+01
  ... (remaining 5295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 943
       0.033 -    0.067: 304
       0.067 -    0.100: 75
       0.100 -    0.133: 50
       0.133 -    0.166: 5
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" CA  TYR B 105 "
            pdb=" N   TYR B 105 "
            pdb=" C   TYR B 105 "
            pdb=" CB  TYR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.92e-01
  chirality pdb=" CA  ILE E 189 "
            pdb=" N   ILE E 189 "
            pdb=" C   ILE E 189 "
            pdb=" CB  ILE E 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" CA  TYR A 391 "
            pdb=" N   TYR A 391 "
            pdb=" C   TYR A 391 "
            pdb=" CB  TYR A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1374 not shown)

  Planarity restraints: 1534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "   -0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO A 321 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 236 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   PRO B 236 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   PRO B 236 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B 237 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 233 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" C   CYS B 233 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   CYS B 233 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE B 234 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1531 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1062
        2.75 -     3.29: 8908
        3.29 -     3.82: 14943
        3.82 -     4.36: 17970
        4.36 -     4.90: 31189
  Nonbonded interactions: 74072
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU A  21 "
            pdb=" OG  SER E  52 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD2 ASP B  76 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.309 3.040
  ... (remaining 74067 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:             0.490
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.060
  Find NCS groups from input model:        0.120
  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:2.760
  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: 0.7784
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      :  0.003   0.034   8930  Z= 0.194
  Angle     :  0.539   6.030  12092  Z= 0.315
  Chirality :  0.040   0.166   1377
  Planarity :  0.004   0.053   1534
  Dihedral  : 15.215  87.536   3202
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 13.19 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1091
  helix:  2.06 (0.25), residues: 417
  sheet: -0.54 (0.31), residues: 262
  loop : -0.20 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.014   0.001   PHE R 326 
 TYR   0.011   0.001   TYR E 103 
 ARG   0.009   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.7991 (ttp) cc_final: 0.7719 (tmm)
REVERT: B  212 ASP cc_start: 0.7801 (t70) cc_final: 0.7341 (t70)
REVERT: B  217 MET cc_start: 0.7918 (ppp) cc_final: 0.7660 (ppp)
REVERT: B  337 LYS cc_start: 0.9066 (mttm) cc_final: 0.8783 (mttm)
REVERT: G   20 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7363 (ptmt)
REVERT: R   64 LEU cc_start: 0.7654 (tp) cc_final: 0.7434 (mt)
REVERT: R  314 PHE cc_start: 0.7976 (m-80) cc_final: 0.7551 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 162
  average time/residue: 0.2659
  time to fit residues: 56.9719
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain R residue   99 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0050
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.4998

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 227 GLN
B 259 GLN
R 200 HIS
R 282 HIS
R 341 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.161724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.110843 restraints weight = 10524.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.17
r_work: 0.3008 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8930  Z= 0.233
  Angle     :  0.557   8.161  12092  Z= 0.298
  Chirality :  0.042   0.147   1377
  Planarity :  0.004   0.039   1534
  Dihedral  :  5.078  59.524   1213
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.71 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1091
  helix:  2.23 (0.25), residues: 409
  sheet: -0.38 (0.32), residues: 252
  loop : -0.18 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 200 
 PHE   0.016   0.002   PHE R 326 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.005   0.001   ARG A 265 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8071 (mtp-110) cc_final: 0.7817 (mtp-110)
REVERT: A  209 GLU cc_start: 0.8185 (tt0) cc_final: 0.7726 (mt-10)
REVERT: A  386 MET cc_start: 0.8267 (ttp) cc_final: 0.7981 (tmm)
REVERT: B    3 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3997 (pt0)
REVERT: B  212 ASP cc_start: 0.7927 (t70) cc_final: 0.7609 (t70)
REVERT: B  337 LYS cc_start: 0.9080 (mttm) cc_final: 0.8860 (mttm)
REVERT: E  160 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6146 (mtp85)
  outliers start: 23
  outliers final: 10
  residues processed: 179
  average time/residue: 0.2379
  time to fit residues: 57.1506
Evaluate side-chains
  154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  197 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 66 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 73 optimal weight:    0.1980
   chunk 97 optimal weight:    7.9990
   chunk 70 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
E 179 GLN
R  54 GLN
** R  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 200 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.164244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119043 restraints weight = 10684.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.15
r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8930  Z= 0.151
  Angle     :  0.495   5.676  12092  Z= 0.265
  Chirality :  0.041   0.185   1377
  Planarity :  0.003   0.030   1534
  Dihedral  :  4.821  59.620   1211
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.77 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1091
  helix:  2.42 (0.25), residues: 407
  sheet: -0.40 (0.30), residues: 271
  loop : -0.18 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 245 
 PHE   0.017   0.001   PHE R 269 
 TYR   0.008   0.001   TYR E  59 
 ARG   0.005   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8017 (tt0) cc_final: 0.7682 (mt-10)
REVERT: A  265 ARG cc_start: 0.7530 (ptm160) cc_final: 0.7218 (ptm-80)
REVERT: A  386 MET cc_start: 0.8262 (ttp) cc_final: 0.8038 (tmm)
REVERT: B    3 GLU cc_start: 0.4395 (OUTLIER) cc_final: 0.3984 (pt0)
REVERT: B  212 ASP cc_start: 0.7874 (t70) cc_final: 0.7635 (t70)
REVERT: E   59 TYR cc_start: 0.8176 (m-80) cc_final: 0.7846 (m-80)
REVERT: E  160 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6270 (mtp85)
REVERT: E  192 MET cc_start: 0.8738 (ttp) cc_final: 0.8499 (tmm)
REVERT: R   72 ILE cc_start: 0.8326 (mm) cc_final: 0.8112 (mt)
REVERT: R   77 ASN cc_start: 0.8377 (m110) cc_final: 0.7930 (m110)
REVERT: R  183 MET cc_start: 0.7090 (ttt) cc_final: 0.6353 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 173
  average time/residue: 0.2268
  time to fit residues: 53.0352
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0050
   chunk 60 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 30 optimal weight:    0.1980
   chunk 74 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
** R  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 245 HIS
R 247 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.164987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.126028 restraints weight = 10655.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.83
r_work: 0.3053 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8930  Z= 0.157
  Angle     :  0.478   5.438  12092  Z= 0.255
  Chirality :  0.040   0.136   1377
  Planarity :  0.003   0.031   1534
  Dihedral  :  4.713  59.905   1211
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.87 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1091
  helix:  2.53 (0.25), residues: 407
  sheet: -0.22 (0.31), residues: 252
  loop : -0.18 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.009   0.001   HIS R 245 
 PHE   0.012   0.001   PHE R 326 
 TYR   0.008   0.001   TYR E 190 
 ARG   0.007   0.000   ARG E  87 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7839 (tt0) cc_final: 0.7580 (mt-10)
REVERT: A  213 GLN cc_start: 0.8112 (tt0) cc_final: 0.7719 (tt0)
REVERT: A  230 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6489 (tm-30)
REVERT: A  386 MET cc_start: 0.8221 (ttp) cc_final: 0.8007 (tmm)
REVERT: B    3 GLU cc_start: 0.4261 (OUTLIER) cc_final: 0.4007 (pt0)
REVERT: B  212 ASP cc_start: 0.7736 (t70) cc_final: 0.7489 (t70)
REVERT: B  217 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7643 (ppp)
REVERT: E   59 TYR cc_start: 0.8098 (m-80) cc_final: 0.7773 (m-80)
REVERT: E  160 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6282 (mtp85)
REVERT: E  192 MET cc_start: 0.8565 (ttp) cc_final: 0.8356 (tmm)
REVERT: R   77 ASN cc_start: 0.8312 (m110) cc_final: 0.7912 (m110)
REVERT: R  183 MET cc_start: 0.6997 (ttt) cc_final: 0.6248 (tpp)
  outliers start: 28
  outliers final: 16
  residues processed: 166
  average time/residue: 0.2324
  time to fit residues: 52.5049
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    0.2980
   chunk 85 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R  77 ASN
R 247 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.165182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.126018 restraints weight = 10600.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.74
r_work: 0.3056 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8930  Z= 0.157
  Angle     :  0.482   7.951  12092  Z= 0.254
  Chirality :  0.040   0.135   1377
  Planarity :  0.003   0.032   1534
  Dihedral  :  4.488  59.910   1211
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.82 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1091
  helix:  2.63 (0.25), residues: 406
  sheet: -0.10 (0.31), residues: 252
  loop : -0.19 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.016   0.001   PHE R  70 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7813 (tt0) cc_final: 0.7563 (mt-10)
REVERT: A  230 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6476 (tm-30)
REVERT: A  386 MET cc_start: 0.8217 (ttp) cc_final: 0.8012 (tmm)
REVERT: B    3 GLU cc_start: 0.4257 (OUTLIER) cc_final: 0.4014 (pt0)
REVERT: B  212 ASP cc_start: 0.7720 (t70) cc_final: 0.7486 (t70)
REVERT: B  217 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7741 (ppp)
REVERT: B  266 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6659 (t-170)
REVERT: E   59 TYR cc_start: 0.8103 (m-80) cc_final: 0.7797 (m-80)
REVERT: E  160 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6332 (mtp85)
REVERT: R   64 LEU cc_start: 0.8084 (tt) cc_final: 0.7821 (mt)
REVERT: R   77 ASN cc_start: 0.8454 (m-40) cc_final: 0.8174 (m-40)
REVERT: R   79 LEU cc_start: 0.7518 (mt) cc_final: 0.7302 (mp)
REVERT: R  183 MET cc_start: 0.7085 (ttt) cc_final: 0.6264 (tpp)
REVERT: R  269 PHE cc_start: 0.8407 (t80) cc_final: 0.8097 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 166
  average time/residue: 0.2260
  time to fit residues: 50.8046
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
E 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.165131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125883 restraints weight = 10562.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.67
r_work: 0.3058 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8930  Z= 0.158
  Angle     :  0.478   6.616  12092  Z= 0.253
  Chirality :  0.040   0.135   1377
  Planarity :  0.003   0.033   1534
  Dihedral  :  4.331  59.907   1211
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.61 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1091
  helix:  2.67 (0.25), residues: 406
  sheet: -0.06 (0.31), residues: 253
  loop : -0.18 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.014   0.001   PHE R  70 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.006   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7777 (tt0) cc_final: 0.7548 (mt-10)
REVERT: A  213 GLN cc_start: 0.8087 (tt0) cc_final: 0.7739 (tt0)
REVERT: A  230 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6394 (tm-30)
REVERT: A  386 MET cc_start: 0.8181 (ttp) cc_final: 0.7976 (tmm)
REVERT: B    3 GLU cc_start: 0.4384 (OUTLIER) cc_final: 0.4066 (pt0)
REVERT: B  212 ASP cc_start: 0.7693 (t70) cc_final: 0.7414 (t70)
REVERT: B  217 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (ppp)
REVERT: B  266 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6654 (t-170)
REVERT: E   59 TYR cc_start: 0.8104 (m-80) cc_final: 0.7800 (m-80)
REVERT: E  160 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6356 (mtp85)
REVERT: R   64 LEU cc_start: 0.8045 (tt) cc_final: 0.7717 (mt)
REVERT: R   77 ASN cc_start: 0.8457 (m-40) cc_final: 0.7874 (m110)
REVERT: R  183 MET cc_start: 0.7012 (ttt) cc_final: 0.6196 (tpp)
REVERT: R  269 PHE cc_start: 0.8433 (t80) cc_final: 0.7990 (t80)
REVERT: R  315 SER cc_start: 0.8860 (m) cc_final: 0.8542 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2182
  time to fit residues: 49.1895
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 11 optimal weight:    0.3980
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R 247 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.165565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126915 restraints weight = 10745.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.75
r_work: 0.3050 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8930  Z= 0.145
  Angle     :  0.470   6.593  12092  Z= 0.248
  Chirality :  0.039   0.133   1377
  Planarity :  0.003   0.035   1534
  Dihedral  :  4.228  59.920   1210
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.98 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1091
  helix:  2.70 (0.25), residues: 406
  sheet: -0.01 (0.31), residues: 252
  loop : -0.16 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.018   0.001   PHE R  70 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.005   0.000   ARG E  87 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.8035 (tt0) cc_final: 0.7674 (tt0)
REVERT: B    3 GLU cc_start: 0.4394 (OUTLIER) cc_final: 0.4094 (pt0)
REVERT: B  212 ASP cc_start: 0.7666 (t70) cc_final: 0.7396 (t70)
REVERT: B  217 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (ppp)
REVERT: B  266 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6691 (t-170)
REVERT: E   59 TYR cc_start: 0.8108 (m-80) cc_final: 0.7821 (m-80)
REVERT: G   32 LYS cc_start: 0.7772 (tptp) cc_final: 0.7169 (tptt)
REVERT: R   64 LEU cc_start: 0.8091 (tt) cc_final: 0.7729 (mt)
REVERT: R   77 ASN cc_start: 0.8379 (m-40) cc_final: 0.7441 (m110)
REVERT: R  183 MET cc_start: 0.6949 (ttt) cc_final: 0.6188 (tpp)
REVERT: R  269 PHE cc_start: 0.8400 (t80) cc_final: 0.7997 (t80)
REVERT: R  315 SER cc_start: 0.8852 (m) cc_final: 0.8571 (p)
REVERT: R  332 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7441 (ttm-80)
  outliers start: 27
  outliers final: 15
  residues processed: 175
  average time/residue: 0.2157
  time to fit residues: 51.7410
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  197 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
** R 320 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 = 0.3800 r_free = 0.3800 target = 0.161548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.122477 restraints weight = 10833.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.97
r_work: 0.2995 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8930  Z= 0.305
  Angle     :  0.545   6.364  12092  Z= 0.288
  Chirality :  0.043   0.219   1377
  Planarity :  0.004   0.037   1534
  Dihedral  :  4.636  59.965   1210
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.08 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1091
  helix:  2.46 (0.25), residues: 407
  sheet: -0.11 (0.31), residues: 263
  loop : -0.30 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 234 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.018   0.002   PHE R 326 
 TYR   0.016   0.002   TYR R 156 
 ARG   0.005   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6493 (tm-30)
REVERT: B    3 GLU cc_start: 0.4569 (OUTLIER) cc_final: 0.4205 (pt0)
REVERT: B  217 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7805 (ppp)
REVERT: B  266 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6905 (t-90)
REVERT: E   59 TYR cc_start: 0.8153 (m-80) cc_final: 0.7850 (m-80)
REVERT: G   32 LYS cc_start: 0.7905 (tptp) cc_final: 0.7597 (tptp)
REVERT: G   58 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6819 (tp30)
REVERT: R   64 LEU cc_start: 0.8065 (tt) cc_final: 0.7607 (mt)
REVERT: R  183 MET cc_start: 0.6876 (ttt) cc_final: 0.6110 (tpp)
REVERT: R  315 SER cc_start: 0.8814 (m) cc_final: 0.8579 (p)
  outliers start: 27
  outliers final: 19
  residues processed: 167
  average time/residue: 0.2184
  time to fit residues: 50.2847
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  197 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.162860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.123603 restraints weight = 10744.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 3.09
r_work: 0.3002 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8930  Z= 0.196
  Angle     :  0.497   6.890  12092  Z= 0.264
  Chirality :  0.040   0.142   1377
  Planarity :  0.003   0.037   1534
  Dihedral  :  4.493  59.973   1210
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.61 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1091
  helix:  2.52 (0.25), residues: 407
  sheet: -0.07 (0.31), residues: 253
  loop : -0.29 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.023   0.002   PHE R 269 
 TYR   0.014   0.001   TYR R 156 
 ARG   0.005   0.000   ARG E  87 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6484 (tm-30)
REVERT: B    3 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.4218 (pt0)
REVERT: B  195 ASP cc_start: 0.7645 (p0) cc_final: 0.7336 (p0)
REVERT: B  217 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7809 (ppp)
REVERT: B  266 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6779 (t-170)
REVERT: E   59 TYR cc_start: 0.8156 (m-80) cc_final: 0.7859 (m-80)
REVERT: G   32 LYS cc_start: 0.7936 (tptp) cc_final: 0.7600 (tptp)
REVERT: G   58 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6810 (tp30)
REVERT: R   77 ASN cc_start: 0.8294 (m-40) cc_final: 0.8037 (m-40)
REVERT: R  183 MET cc_start: 0.6875 (ttt) cc_final: 0.6105 (tpp)
REVERT: R  269 PHE cc_start: 0.8429 (t80) cc_final: 0.8063 (t80)
REVERT: R  315 SER cc_start: 0.8818 (m) cc_final: 0.8601 (p)
  outliers start: 27
  outliers final: 20
  residues processed: 160
  average time/residue: 0.2270
  time to fit residues: 49.5189
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  197 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  260 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0170
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 31 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 247 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.126492 restraints weight = 10685.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.82
r_work: 0.3059 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8930  Z= 0.143
  Angle     :  0.472   8.679  12092  Z= 0.249
  Chirality :  0.040   0.138   1377
  Planarity :  0.003   0.038   1534
  Dihedral  :  4.258  59.653   1210
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.82 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1091
  helix:  2.67 (0.25), residues: 407
  sheet:  0.00 (0.31), residues: 256
  loop : -0.26 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 282 
 PHE   0.023   0.001   PHE R 269 
 TYR   0.008   0.001   TYR R 156 
 ARG   0.006   0.000   ARG B  42 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.8071 (tt0) cc_final: 0.7696 (tt0)
REVERT: A  230 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6368 (tm-30)
REVERT: B    3 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4152 (pt0)
REVERT: B  195 ASP cc_start: 0.7651 (p0) cc_final: 0.7349 (p0)
REVERT: B  198 LEU cc_start: 0.8861 (mt) cc_final: 0.8628 (mt)
REVERT: B  217 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7810 (ppp)
REVERT: B  266 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6830 (t-170)
REVERT: E   59 TYR cc_start: 0.8137 (m-80) cc_final: 0.7841 (m-80)
REVERT: G   32 LYS cc_start: 0.7920 (tptp) cc_final: 0.7596 (tptp)
REVERT: G   58 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6669 (tp30)
REVERT: R   77 ASN cc_start: 0.8359 (m-40) cc_final: 0.7214 (m110)
REVERT: R  183 MET cc_start: 0.6873 (ttt) cc_final: 0.6104 (tpp)
REVERT: R  269 PHE cc_start: 0.8369 (t80) cc_final: 0.7967 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 174
  average time/residue: 0.2160
  time to fit residues: 51.5535
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain E residue  197 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  247 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
R 247 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.161837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124581 restraints weight = 10795.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.91
r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8930  Z= 0.184
  Angle     :  0.487   8.429  12092  Z= 0.257
  Chirality :  0.040   0.149   1377
  Planarity :  0.003   0.040   1534
  Dihedral  :  4.318  59.778   1210
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.56 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1091
  helix:  2.63 (0.25), residues: 407
  sheet:  0.06 (0.31), residues: 263
  loop : -0.31 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 247 
 PHE   0.023   0.001   PHE R 269 
 TYR   0.012   0.001   TYR R 156 
 ARG   0.005   0.000   ARG E  87 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4893.78 seconds
wall clock time: 87 minutes 19.17 seconds (5239.17 seconds total)