Starting phenix.real_space_refine
on Thu Mar 13 04:06:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xoi_38530/03_2025/8xoi_38530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xoi_38530/03_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_38530/03_2025/8xoi_38530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xoi_38530/03_2025/8xoi_38530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xoi_38530/03_2025/8xoi_38530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xoi_38530/03_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-5624/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: 5.23, per 1000 atoms: 0.60
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.15
  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: 2.68

  Time building geometry restraints manager: 2.60 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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.640
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.210
-------------------------------------------------------------------------------
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  : 1.030 
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: 0.2463
  time to fit residues: 52.7757
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  : 1.586 
-------------------------------------------------------------------------------
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:    0.9980
   overall best weight:    1.2996

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3801 r_free = 0.3801 target = 0.162386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.112732 restraints weight = 10522.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.31
r_work: 0.3086 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1017

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= 0.224
  Angle     :  0.551   7.943  12092  Z= 0.296
  Chirality :  0.042   0.147   1377
  Planarity :  0.004   0.037   1534
  Dihedral  :  5.016  59.110   1213
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.40 %
    Favored  : 84.18 %
  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:  1.01 (0.25), residues: 1091
  helix:  2.27 (0.25), residues: 409
  sheet: -0.38 (0.31), residues: 257
  loop : -0.14 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 200 
 PHE   0.016   0.002   PHE R 326 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.008   0.001   ARG A  38 

*********************** 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  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8141 (tt0) cc_final: 0.7756 (mt-10)
REVERT: A  386 MET cc_start: 0.8278 (ttp) cc_final: 0.8052 (tmm)
REVERT: B    3 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.4025 (pt0)
REVERT: B  212 ASP cc_start: 0.7977 (t70) cc_final: 0.7684 (t70)
REVERT: B  337 LYS cc_start: 0.9070 (mttm) cc_final: 0.8857 (mttm)
REVERT: E  160 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6277 (mtp85)
  outliers start: 23
  outliers final: 12
  residues processed: 179
  average time/residue: 0.2326
  time to fit residues: 55.7102
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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  160 SER
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 G residue   31 SER
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:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 97 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0770
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.1542

-------------------------------------------------------------------------------
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
** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.163045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.112252 restraints weight = 10681.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.20
r_work: 0.3113 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8930  Z= 0.189
  Angle     :  0.508   6.265  12092  Z= 0.271
  Chirality :  0.041   0.141   1377
  Planarity :  0.004   0.030   1534
  Dihedral  :  4.888  59.807   1211
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.35 %
    Favored  : 83.33 %
  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:  1.05 (0.25), residues: 1091
  helix:  2.37 (0.25), residues: 407
  sheet: -0.37 (0.31), residues: 262
  loop : -0.18 (0.30), residues: 422

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   0.016   0.001   PHE R 269 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.006   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
  175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7781 (p0) cc_final: 0.7503 (p0)
REVERT: A  209 GLU cc_start: 0.8057 (tt0) cc_final: 0.7734 (mt-10)
REVERT: A  265 ARG cc_start: 0.7497 (ptm160) cc_final: 0.7276 (ptm-80)
REVERT: A  386 MET cc_start: 0.8344 (ttp) cc_final: 0.8129 (tmm)
REVERT: B    3 GLU cc_start: 0.4055 (OUTLIER) cc_final: 0.3812 (pt0)
REVERT: B  212 ASP cc_start: 0.7915 (t70) cc_final: 0.7655 (t70)
REVERT: B  217 MET cc_start: 0.8034 (ppp) cc_final: 0.7727 (ppp)
REVERT: E   59 TYR cc_start: 0.8245 (m-80) cc_final: 0.7891 (m-80)
REVERT: E  160 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6292 (mtp85)
REVERT: R   54 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6499 (mp10)
REVERT: R   77 ASN cc_start: 0.8391 (m110) cc_final: 0.7943 (m-40)
REVERT: R  183 MET cc_start: 0.7105 (ttt) cc_final: 0.6341 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 168
  average time/residue: 0.2227
  time to fit residues: 50.5249
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
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  160 SER
Chi-restraints excluded: chain B residue  262 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 G residue   30 VAL
Chi-restraints excluded: chain R residue   54 GLN
Chi-restraints excluded: chain R residue   75 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0170
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.7624

-------------------------------------------------------------------------------
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  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 200 HIS
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 = 0.3788 r_free = 0.3788 target = 0.161147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113964 restraints weight = 10682.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.18
r_work: 0.3040 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8930  Z= 0.241
  Angle     :  0.522   7.018  12092  Z= 0.278
  Chirality :  0.041   0.145   1377
  Planarity :  0.004   0.031   1534
  Dihedral  :  4.977  59.520   1211
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.77 %
    Favored  : 82.28 %
  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:  0.96 (0.25), residues: 1091
  helix:  2.23 (0.25), residues: 413
  sheet: -0.35 (0.31), residues: 258
  loop : -0.23 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.017   0.001   PHE R 326 
 TYR   0.011   0.001   TYR R 156 
 ARG   0.006   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
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8064 (tt0) cc_final: 0.7703 (mt-10)
REVERT: A  213 GLN cc_start: 0.8235 (tt0) cc_final: 0.7851 (tt0)
REVERT: A  230 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6514 (tm-30)
REVERT: A  386 MET cc_start: 0.8358 (ttp) cc_final: 0.8150 (tmm)
REVERT: B    3 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.4013 (pt0)
REVERT: B  212 ASP cc_start: 0.7897 (t70) cc_final: 0.7655 (t70)
REVERT: B  217 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7817 (ppp)
REVERT: B  266 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6757 (t-170)
REVERT: E   59 TYR cc_start: 0.8242 (m-80) cc_final: 0.7892 (m-80)
REVERT: E  160 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6310 (mtp85)
REVERT: R   77 ASN cc_start: 0.8406 (m110) cc_final: 0.7910 (m-40)
REVERT: R  183 MET cc_start: 0.6968 (ttt) cc_final: 0.6232 (tpp)
REVERT: R  190 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7129 (mp)
  outliers start: 28
  outliers final: 16
  residues processed: 159
  average time/residue: 0.2217
  time to fit residues: 48.4538
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
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   65 THR
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  215 THR
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   75 VAL
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  190 LEU
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  220 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 11 optimal weight:    0.1980
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R  54 GLN
R  77 ASN
R 247 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.164854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.125486 restraints weight = 10585.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.71
r_work: 0.3056 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8930  Z= 0.155
  Angle     :  0.475   5.630  12092  Z= 0.253
  Chirality :  0.040   0.136   1377
  Planarity :  0.003   0.032   1534
  Dihedral  :  4.683  59.636   1211
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.61 %
    Favored  : 81.43 %
  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:  1.17 (0.26), residues: 1091
  helix:  2.54 (0.25), residues: 407
  sheet: -0.22 (0.31), residues: 253
  loop : -0.26 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.008   0.001   TYR E 190 
 ARG   0.005   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: 28
    poor density    : 144
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.8353 (tt0) cc_final: 0.8148 (tt0)
REVERT: A  209 GLU cc_start: 0.7817 (tt0) cc_final: 0.7580 (mt-10)
REVERT: A  213 GLN cc_start: 0.8065 (tt0) cc_final: 0.7659 (tt0)
REVERT: A  230 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6405 (tm-30)
REVERT: A  265 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7410 (ptm-80)
REVERT: A  386 MET cc_start: 0.8193 (ttp) cc_final: 0.7979 (tmm)
REVERT: B    3 GLU cc_start: 0.4404 (OUTLIER) cc_final: 0.4063 (pt0)
REVERT: B  212 ASP cc_start: 0.7782 (t70) cc_final: 0.7562 (t70)
REVERT: B  217 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7831 (ppp)
REVERT: B  266 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6689 (t-170)
REVERT: E   59 TYR cc_start: 0.8109 (m-80) cc_final: 0.7773 (m-80)
REVERT: E  160 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6340 (mtp85)
REVERT: R   77 ASN cc_start: 0.8354 (m-40) cc_final: 0.7813 (m110)
REVERT: R  183 MET cc_start: 0.7034 (ttt) cc_final: 0.6209 (tpp)
  outliers start: 28
  outliers final: 13
  residues processed: 166
  average time/residue: 0.2083
  time to fit residues: 47.5049
Evaluate side-chains
  154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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  289 LEU
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  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  229 CYS
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   99 ILE
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:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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  44 GLN
E 179 GLN
R 247 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.162118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.122554 restraints weight = 10413.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 3.23
r_work: 0.2955 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8930  Z= 0.282
  Angle     :  0.546   8.179  12092  Z= 0.288
  Chirality :  0.042   0.147   1377
  Planarity :  0.004   0.033   1534
  Dihedral  :  4.792  59.580   1211
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.98 %
    Favored  : 81.86 %
  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:  1.01 (0.26), residues: 1091
  helix:  2.31 (0.25), residues: 413
  sheet: -0.20 (0.31), residues: 249
  loop : -0.37 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.023   0.002   PHE R 269 
 TYR   0.014   0.002   TYR R 156 
 ARG   0.004   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
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.8511 (tt0) cc_final: 0.8258 (tt0)
REVERT: A  230 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6439 (tm-30)
REVERT: A  386 MET cc_start: 0.8160 (ttp) cc_final: 0.7870 (tmm)
REVERT: B    3 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4134 (pt0)
REVERT: B  217 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7754 (ppp)
REVERT: B  266 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6604 (t-170)
REVERT: E   59 TYR cc_start: 0.8184 (m-80) cc_final: 0.7788 (m-80)
REVERT: E  160 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.6204 (mtp85)
REVERT: R   64 LEU cc_start: 0.8044 (tt) cc_final: 0.7738 (mt)
REVERT: R   77 ASN cc_start: 0.8489 (m-40) cc_final: 0.8111 (m-40)
REVERT: R  183 MET cc_start: 0.6830 (ttt) cc_final: 0.5990 (tpp)
  outliers start: 30
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2127
  time to fit residues: 47.4750
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
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   75 VAL
Chi-restraints excluded: chain R residue   92 THR
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
Chi-restraints excluded: chain R residue  220 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 67 optimal weight:   10.0000
   chunk 86 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0980
   chunk 101 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.165273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126272 restraints weight = 10666.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.79
r_work: 0.3063 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8930  Z= 0.137
  Angle     :  0.479   7.736  12092  Z= 0.253
  Chirality :  0.039   0.136   1377
  Planarity :  0.003   0.035   1534
  Dihedral  :  4.349  59.793   1210
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.82 %
    Favored  : 81.86 %
  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:  1.21 (0.26), residues: 1091
  helix:  2.58 (0.25), residues: 407
  sheet: -0.23 (0.30), residues: 264
  loop : -0.22 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.021   0.001   PHE R 269 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.006   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
  173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7732 (tt0) cc_final: 0.7411 (mt-10)
REVERT: A  213 GLN cc_start: 0.8078 (tt0) cc_final: 0.7735 (tt0)
REVERT: A  230 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6394 (tm-30)
REVERT: A  386 MET cc_start: 0.8211 (ttp) cc_final: 0.7999 (tmm)
REVERT: B    3 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.4121 (pt0)
REVERT: B  217 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7862 (ppp)
REVERT: B  266 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6752 (t-170)
REVERT: E   59 TYR cc_start: 0.8111 (m-80) cc_final: 0.7799 (m-80)
REVERT: R   64 LEU cc_start: 0.8101 (tt) cc_final: 0.7736 (mt)
REVERT: R   79 LEU cc_start: 0.7561 (mt) cc_final: 0.7331 (mp)
REVERT: R  183 MET cc_start: 0.6899 (ttt) cc_final: 0.6091 (tpp)
REVERT: R  269 PHE cc_start: 0.8422 (t80) cc_final: 0.8055 (t80)
REVERT: R  284 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6413 (mm)
REVERT: R  315 SER cc_start: 0.8844 (m) cc_final: 0.8568 (p)
  outliers start: 22
  outliers final: 10
  residues processed: 167
  average time/residue: 0.2165
  time to fit residues: 49.4089
Evaluate side-chains
  156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
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  215 THR
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0970
   chunk 2 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 83 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
E 142 GLN
E 179 GLN
R 247 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.163713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124792 restraints weight = 10770.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.78
r_work: 0.3028 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2267

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= 0.208
  Angle     :  0.514   9.025  12092  Z= 0.268
  Chirality :  0.040   0.143   1377
  Planarity :  0.003   0.037   1534
  Dihedral  :  4.464  59.516   1210
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.03 %
    Favored  : 81.01 %
  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:  1.23 (0.26), residues: 1091
  helix:  2.55 (0.25), residues: 407
  sheet: -0.04 (0.31), residues: 249
  loop : -0.29 (0.30), residues: 435

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   0.020   0.002   PHE R 314 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.005   0.000   ARG E  87 

*********************** 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
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7735 (tt0) cc_final: 0.7408 (mt-10)
REVERT: A  213 GLN cc_start: 0.8120 (tt0) cc_final: 0.7709 (tt0)
REVERT: A  230 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6394 (tm-30)
REVERT: A  386 MET cc_start: 0.8235 (ttp) cc_final: 0.8027 (tmm)
REVERT: B    3 GLU cc_start: 0.4553 (OUTLIER) cc_final: 0.4198 (pt0)
REVERT: B   42 ARG cc_start: 0.7053 (ttt90) cc_final: 0.6845 (ttt90)
REVERT: B  217 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (ppp)
REVERT: B  266 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6774 (t-170)
REVERT: E   59 TYR cc_start: 0.8139 (m-80) cc_final: 0.7809 (m-80)
REVERT: R   64 LEU cc_start: 0.8111 (tt) cc_final: 0.7688 (mt)
REVERT: R   77 ASN cc_start: 0.8297 (m-40) cc_final: 0.8041 (m-40)
REVERT: R  183 MET cc_start: 0.6886 (ttt) cc_final: 0.6134 (tpp)
REVERT: R  269 PHE cc_start: 0.8438 (t80) cc_final: 0.8125 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2133
  time to fit residues: 46.7121
Evaluate side-chains
  157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
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 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0170
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3832 r_free = 0.3832 target = 0.164522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125558 restraints weight = 10716.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.87
r_work: 0.3010 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8930  Z= 0.153
  Angle     :  0.493   8.715  12092  Z= 0.258
  Chirality :  0.040   0.136   1377
  Planarity :  0.003   0.036   1534
  Dihedral  :  4.382  59.673   1210
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.46 %
    Favored  : 81.22 %
  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:  1.27 (0.26), residues: 1091
  helix:  2.57 (0.25), residues: 407
  sheet: -0.03 (0.31), residues: 254
  loop : -0.25 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 282 
 PHE   0.018   0.001   PHE R 269 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.006   0.000   ARG R 246 

*********************** 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
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7733 (tt0) cc_final: 0.7419 (mt-10)
REVERT: A  213 GLN cc_start: 0.8075 (tt0) cc_final: 0.7668 (tt0)
REVERT: A  230 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6372 (tm-30)
REVERT: A  378 ASP cc_start: 0.8221 (m-30) cc_final: 0.8012 (m-30)
REVERT: A  386 MET cc_start: 0.8235 (ttp) cc_final: 0.8028 (tmm)
REVERT: B    3 GLU cc_start: 0.4535 (OUTLIER) cc_final: 0.4178 (pt0)
REVERT: B   42 ARG cc_start: 0.6999 (ttt90) cc_final: 0.6797 (ttt90)
REVERT: B  217 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7836 (ppp)
REVERT: B  266 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6710 (t-170)
REVERT: E   59 TYR cc_start: 0.8145 (m-80) cc_final: 0.7830 (m-80)
REVERT: G   32 LYS cc_start: 0.7750 (tptp) cc_final: 0.7506 (tptp)
REVERT: R   64 LEU cc_start: 0.8107 (tt) cc_final: 0.7663 (mt)
REVERT: R   77 ASN cc_start: 0.8237 (m-40) cc_final: 0.7972 (m-40)
REVERT: R  183 MET cc_start: 0.6888 (ttt) cc_final: 0.6125 (tpp)
REVERT: R  269 PHE cc_start: 0.8438 (t80) cc_final: 0.8133 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2072
  time to fit residues: 44.4288
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 GLU
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  143 SER
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  247 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:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 73 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0770
   chunk 9 optimal weight:    0.0970
   chunk 105 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R 247 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127317 restraints weight = 10746.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.91
r_work: 0.3028 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8930  Z= 0.140
  Angle     :  0.486   8.722  12092  Z= 0.254
  Chirality :  0.040   0.134   1377
  Planarity :  0.003   0.037   1534
  Dihedral  :  4.296  59.947   1210
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.56 %
    Favored  : 81.01 %
  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:  2.66 (0.25), residues: 406
  sheet: -0.10 (0.30), residues: 267
  loop : -0.15 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 247 
 PHE   0.018   0.001   PHE R 269 
 TYR   0.008   0.001   TYR E 190 
 ARG   0.006   0.000   ARG R 246 

********************** 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
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.7659 (tt0) cc_final: 0.7415 (mt-10)
REVERT: A  213 GLN cc_start: 0.8019 (tt0) cc_final: 0.7607 (tt0)
REVERT: A  230 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6366 (tm-30)
REVERT: A  386 MET cc_start: 0.8160 (ttp) cc_final: 0.7958 (tmm)
REVERT: B    3 GLU cc_start: 0.4506 (OUTLIER) cc_final: 0.4188 (pt0)
REVERT: B   42 ARG cc_start: 0.7006 (ttt90) cc_final: 0.6802 (ttt90)
REVERT: B  217 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7818 (ppp)
REVERT: E   59 TYR cc_start: 0.8133 (m-80) cc_final: 0.7821 (m-80)
REVERT: G   32 LYS cc_start: 0.7784 (tptp) cc_final: 0.7523 (tptp)
REVERT: R   64 LEU cc_start: 0.8088 (tt) cc_final: 0.7621 (mt)
REVERT: R   77 ASN cc_start: 0.8304 (m-40) cc_final: 0.7230 (m110)
REVERT: R  183 MET cc_start: 0.6865 (ttt) cc_final: 0.6087 (tpp)
REVERT: R  269 PHE cc_start: 0.8405 (t80) cc_final: 0.7994 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 161
  average time/residue: 0.2126
  time to fit residues: 47.3605
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  230 GLU
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  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  143 SER
Chi-restraints excluded: chain R residue  196 VAL
Chi-restraints excluded: chain R residue  197 HIS
Chi-restraints excluded: chain R residue  247 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 54 optimal weight:   10.0000
   chunk 31 optimal weight:    0.1980
   chunk 69 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.165842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.127711 restraints weight = 10844.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.89
r_work: 0.3028 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   8930  Z= 0.244
  Angle     :  0.944  59.200  12092  Z= 0.594
  Chirality :  0.050   0.838   1377
  Planarity :  0.005   0.162   1534
  Dihedral  :  4.330  59.909   1210
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.88 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.19 %
  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:  1.32 (0.26), residues: 1091
  helix:  2.64 (0.25), residues: 406
  sheet: -0.09 (0.30), residues: 268
  loop : -0.18 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.222   0.006   HIS R 247 
 PHE   0.017   0.001   PHE R 269 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.004   0.000   ARG E  87 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5135.87 seconds
wall clock time: 88 minutes 34.89 seconds (5314.89 seconds total)