Starting phenix.real_space_refine
on Sat Jul  4 01:11:48 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wkd_32565/07_2026/7wkd_32565.map"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5610      2.51       5
     N    1504      2.21       5
     O    1626      1.98       5
     H    8727      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17530
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 3794
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5103
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3479
          Classifications: {'peptide': 230}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 827
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 4279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 4279
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 8, 'TRANS': 254}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 48
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 3.16, per 1000 atoms: 0.18
  Number of scatterers: 17530
  At special positions: 0
  Unit cell: (121.68, 89.44, 123.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     O    1626      8.00
     N    1504      7.00
     C    5610      6.00
     H    8727      1.00
    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: 1.72
  Conformation dependent library (CDL) restraints added in 502.9 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.0% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.782A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 4.454A  pdb=" N   THR A 251 " --> pdb=" O   TRP A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 298 through 318
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 3.584A  pdb=" N   ASP A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 30
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.987A  pdb=" N   ILE B  38 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 55
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.563A  pdb=" N   THR E  90 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 43
      removed outlier: 3.731A  pdb=" N   ALA G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 52
    Processing helix  chain 'R' and resid 58 through 89
      removed outlier: 3.580A  pdb=" N   MET R  73 " --> pdb=" O   VAL R  69 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU R  80 " --> pdb=" O   VAL R  76 " (cutoff:3.500A)
      Proline residue:  R  81  - end of helix
    Processing helix  chain 'R' and resid 93 through 129
      removed outlier: 3.593A  pdb=" N   SER R 113 " --> pdb=" O   ILE R 109 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 137
      removed outlier: 3.669A  pdb=" N   PHE R 135 " --> pdb=" O   ILE R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 158
    Processing helix  chain 'R' and resid 158 through 163
      removed outlier: 4.088A  pdb=" N   PHE R 162 " --> pdb=" O   MET R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 187
    Processing helix  chain 'R' and resid 188 through 198
    Processing helix  chain 'R' and resid 200 through 220
    Processing helix  chain 'R' and resid 263 through 290
      Proline residue:  R 281  - end of helix
      removed outlier: 3.672A  pdb=" N   VAL R 287 " --> pdb=" O   ARG R 283 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 298 through 320
      Proline residue:  R 317  - end of helix
    Processing helix  chain 'R' and resid 324 through 335
      removed outlier: 3.512A  pdb=" N   ARG R 328 " --> pdb=" O   SER R 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.563A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   HIS A 329 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.236A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 341 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 6.463A  pdb=" N   ALA B  78 " --> pdb=" O   TYR B  64 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   MET B  66 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL B  76 " --> pdb=" O   MET B  66 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   TRP B  68 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   LEU B  74 " --> pdb=" O   TRP B  68 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ASP B  88 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.879A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 7.007A  pdb=" N   SER B 165 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   CYS B 154 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   VAL B 163 " --> pdb=" O   CYS B 154 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   PHE B 156 " --> pdb=" O   GLN B 161 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   GLN B 161 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   CYS B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   THR B 184 " --> pdb=" O   CYS B 171 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LEU B 173 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B 180 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 7.095A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.932A  pdb=" N   SER B 250 " --> pdb=" O   THR B 254 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   THR B 254 " --> pdb=" O   SER B 250 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.584A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASN B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.017A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.017A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 4.064A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 165 through 166
      removed outlier: 3.732A  pdb=" N   ASP R 165 " --> pdb=" O   GLY R 180 " (cutoff:3.500A)

    447 hydrogen bonds defined for protein.
    1260 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: 4.04

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8677
        1.03 -     1.23: 55
        1.23 -     1.42: 3814
        1.42 -     1.62: 5072
        1.62 -     1.81: 94
  Bond restraints: 17712
  Sorted by residual:
  bond pdb=" CA  PCA C   1 "
       pdb=" CB  PCA C   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.224  0.306 2.00e-02 2.50e+03 2.33e+02
  bond pdb=" N   LPD C   3 "
       pdb=" CA  LPD C   3 "
    ideal  model  delta    sigma   weight residual
    1.466  1.686 -0.220 1.50e-02 4.44e+03 2.15e+02
  bond pdb=" CG  PCA C   1 "
       pdb=" CD  PCA C   1 "
    ideal  model  delta    sigma   weight residual
    1.517  1.282  0.235 2.00e-02 2.50e+03 1.38e+02
  bond pdb=" C   PCA C   1 "
       pdb=" N   HIS C   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.486 -0.157 1.40e-02 5.10e+03 1.26e+02
  bond pdb=" N   LPD C   3 "
       pdb=" CD  LPD C   3 "
    ideal  model  delta    sigma   weight residual
    1.473  1.322  0.151 1.40e-02 5.10e+03 1.17e+02
  ... (remaining 17707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 31792
        2.67 -     5.35: 60
        5.35 -     8.02: 4
        8.02 -    10.69: 1
       10.69 -    13.37: 1
  Bond angle restraints: 31858
  Sorted by residual:
  angle pdb=" CA  PCA C   1 "
        pdb=" N   PCA C   1 "
        pdb=" H   PCA C   1 "
      ideal   model   delta    sigma   weight residual
     114.00  127.37  -13.37 3.00e+00 1.11e-01 1.99e+01
  angle pdb=" CB  HIS C   2 "
        pdb=" CG  HIS C   2 "
        pdb=" CD2 HIS C   2 "
      ideal   model   delta    sigma   weight residual
     131.20  126.08    5.12 1.30e+00 5.92e-01 1.55e+01
  angle pdb=" N   PCA C   1 "
        pdb=" CA  PCA C   1 "
        pdb=" CB  PCA C   1 "
      ideal   model   delta    sigma   weight residual
     110.50  104.42    6.08 1.70e+00 3.46e-01 1.28e+01
  angle pdb=" CA  PCA C   1 "
        pdb=" N   PCA C   1 "
        pdb=" CD  PCA C   1 "
      ideal   model   delta    sigma   weight residual
     114.17  105.29    8.88 3.00e+00 1.11e-01 8.76e+00
  angle pdb=" N   LPD C   3 "
        pdb=" CA  LPD C   3 "
        pdb=" CB  LPD C   3 "
      ideal   model   delta    sigma   weight residual
     103.00  106.04   -3.04 1.10e+00 8.26e-01 7.62e+00
  ... (remaining 31853 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.31: 7947
       16.31 -    32.61: 267
       32.61 -    48.92: 73
       48.92 -    65.23: 62
       65.23 -    81.53: 6
  Dihedral angle restraints: 8355
    sinusoidal: 4465
      harmonic: 3890
  Sorted by residual:
  dihedral pdb=" N   PCA C   1 "
           pdb=" C   PCA C   1 "
           pdb=" CA  PCA C   1 "
           pdb=" CB  PCA C   1 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.78    8.02     0      2.50e+00 1.60e-01 1.03e+01
  dihedral pdb=" N   PHE B 239 "
           pdb=" CA  PHE B 239 "
           pdb=" CB  PHE B 239 "
           pdb=" CG  PHE B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.43  -59.57     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG B 319 "
           pdb=" CB  ARG B 319 "
           pdb=" CG  ARG B 319 "
           pdb=" CD  ARG B 319 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.24  -56.76     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 8352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 912
       0.028 -    0.055: 302
       0.055 -    0.083: 87
       0.083 -    0.110: 50
       0.110 -    0.138: 30
  Chirality restraints: 1381
  Sorted by residual:
  chirality pdb=" CA  HIS C   2 "
            pdb=" N   HIS C   2 "
            pdb=" C   HIS C   2 "
            pdb=" CB  HIS C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE B  86 "
            pdb=" N   ILE B  86 "
            pdb=" C   ILE B  86 "
            pdb=" CB  ILE B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  VAL E 199 "
            pdb=" N   VAL E 199 "
            pdb=" C   VAL E 199 "
            pdb=" CB  VAL E 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 1378 not shown)

  Planarity restraints: 2612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  73 "   -0.015 5.00e-02 4.00e+02   2.20e-02 7.77e-01
        pdb=" N   PRO E  74 "    0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "    0.014 5.00e-02 4.00e+02   2.06e-02 6.77e-01
        pdb=" N   PRO B 241 "   -0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  98 "   -0.013 5.00e-02 4.00e+02   1.92e-02 5.92e-01
        pdb=" N   PRO B  99 "    0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 2609 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 1498
        2.23 -     2.83: 40190
        2.83 -     3.42: 46760
        3.42 -     4.01: 64054
        4.01 -     4.60: 98630
  Nonbonded interactions: 251132
  Sorted by model distance:
  nonbonded pdb=" O   THR G   5 "
            pdb=" H   ALA G   9 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" HE2 HIS B 316 "
            pdb=" OG1 THR B 334 "
     model   vdw
     1.654 2.450
  nonbonded pdb="HD22 ASN E 169 "
            pdb=" OH  TYR E 173 "
     model   vdw
     1.665 2.450
  nonbonded pdb=" H   ARG E  86 "
            pdb=" OD2 ASP E  89 "
     model   vdw
     1.669 2.450
  nonbonded pdb=" HG  SER B  79 "
            pdb=" OD1 ASP B  81 "
     model   vdw
     1.672 2.450
  ... (remaining 251127 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:             0.570
  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:             0.120
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     18.290
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
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      :  0.007   0.306   8985  Z= 0.410
  Angle     :  0.408   8.882  12171  Z= 0.235
  Chirality :  0.037   0.138   1381
  Planarity :  0.002   0.022   1536
  Dihedral  :  7.824  81.535   3230
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.92 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.23), residues: 1097
  helix:  0.04 (0.25), residues: 385
  sheet: -1.34 (0.30), residues: 251
  loop : -1.95 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  57 
 TYR   0.004   0.000   TYR E 228 
 PHE   0.007   0.001   PHE A 189 
 TRP   0.008   0.001   TRP B  87 
 HIS   0.001   0.000   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00722 /  0.41 ( 8985)
  covalent geometry    : angle       0.40812 /  0.24 (12171)
  hydrogen bonds       : bond        0.13116 /  8.29 (  443)
  hydrogen bonds       : angle       6.31725 /  4.44 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 342
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.7974 (tptt) cc_final: 0.7770 (tptt)
REVERT: A  276 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6779 (tm-30)
REVERT: B   35 LEU cc_start: 0.6859 (tp) cc_final: 0.6623 (tt)
REVERT: B  133 THR cc_start: 0.8063 (p) cc_final: 0.7725 (t)
REVERT: B  203 LEU cc_start: 0.7683 (mt) cc_final: 0.7442 (mp)
REVERT: B  239 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7244 (t80)
REVERT: B  244 ASN cc_start: 0.7569 (m-40) cc_final: 0.7339 (m110)
REVERT: B  251 ASP cc_start: 0.5791 (p0) cc_final: 0.5281 (p0)
REVERT: B  252 ASP cc_start: 0.5060 (t0) cc_final: 0.4729 (t0)
REVERT: E  167 HIS cc_start: 0.7542 (t70) cc_final: 0.7304 (t-90)
REVERT: G   47 ASP cc_start: 0.7390 (t0) cc_final: 0.7088 (t0)
REVERT: R  131 ILE cc_start: 0.7288 (mm) cc_final: 0.7065 (mm)
REVERT: R  263 GLN cc_start: 0.5627 (pm20) cc_final: 0.4815 (pm20)
REVERT: R  319 ILE cc_start: 0.7600 (tp) cc_final: 0.7217 (pt)
  outliers start: 3
  outliers final: 0
  residues processed: 344
  average time/residue: 0.2330
  time to fit residues: 109.5492
Evaluate side-chains
  299 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  239 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.4980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
A 324 HIS
B 273 ASN
B 300 ASN
** R  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 297 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.140583 restraints weight = 36595.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 1.93
r_work: 0.3769 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8985  Z= 0.113
  Angle     :  0.467   5.398  12171  Z= 0.245
  Chirality :  0.038   0.139   1381
  Planarity :  0.004   0.036   1536
  Dihedral  :  3.445  58.185   1227
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.74 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.25), residues: 1097
  helix:  1.40 (0.27), residues: 384
  sheet: -1.13 (0.30), residues: 248
  loop : -1.31 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 224 
 TYR   0.016   0.001   TYR A 306 
 PHE   0.010   0.001   PHE A 330 
 TRP   0.008   0.001   TRP A 248 
 HIS   0.009   0.001   HIS A 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 8985)
  covalent geometry    : angle       0.46711 /  0.24 (12171)
  hydrogen bonds       : bond        0.03086 /  2.05 (  443)
  hydrogen bonds       : angle       4.88318 /  3.39 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  329 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 315
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 VAL cc_start: 0.8430 (t) cc_final: 0.8199 (p)
REVERT: A  193 LYS cc_start: 0.8236 (tptt) cc_final: 0.7921 (tptt)
REVERT: A  198 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8035 (ttm)
REVERT: A  276 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7485 (tm-30)
REVERT: A  309 ARG cc_start: 0.6121 (ttp-170) cc_final: 0.5581 (ttp-170)
REVERT: B   35 LEU cc_start: 0.6773 (tp) cc_final: 0.6555 (tt)
REVERT: B   53 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7805 (mmp80)
REVERT: B   62 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7948 (mtmm)
REVERT: B   81 ASP cc_start: 0.7150 (p0) cc_final: 0.6870 (p0)
REVERT: B   88 ASP cc_start: 0.7685 (t0) cc_final: 0.7337 (t0)
REVERT: B  123 ASP cc_start: 0.7634 (t0) cc_final: 0.7065 (t0)
REVERT: B  129 TYR cc_start: 0.7395 (m-80) cc_final: 0.6600 (m-80)
REVERT: B  194 SER cc_start: 0.8072 (p) cc_final: 0.7834 (t)
REVERT: B  203 LEU cc_start: 0.8030 (mt) cc_final: 0.7821 (mp)
REVERT: B  239 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7197 (t80)
REVERT: B  244 ASN cc_start: 0.8055 (m-40) cc_final: 0.7813 (m110)
REVERT: B  259 ASP cc_start: 0.7315 (t70) cc_final: 0.7061 (t0)
REVERT: E  167 HIS cc_start: 0.7879 (t70) cc_final: 0.7488 (t-90)
REVERT: E  204 SER cc_start: 0.8600 (t) cc_final: 0.8258 (p)
REVERT: G   47 ASP cc_start: 0.7754 (t0) cc_final: 0.7423 (t0)
REVERT: R  263 GLN cc_start: 0.6331 (pm20) cc_final: 0.5419 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 324
  average time/residue: 0.2384
  time to fit residues: 105.0383
Evaluate side-chains
  306 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 294
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  230 HIS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  344 TRP
Chi-restraints excluded: chain E residue   16 SER
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  324 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0030
   chunk 107 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.1996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 ASN
A 216 ASN
A 329 HIS
A 344 ASN
B  93 ASN
** R  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.139306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.125694 restraints weight = 37389.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.91
r_work: 0.3583 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8985  Z= 0.193
  Angle     :  0.553   6.025  12171  Z= 0.294
  Chirality :  0.041   0.203   1381
  Planarity :  0.004   0.059   1536
  Dihedral  :  4.053  57.710   1227
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.03 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.26), residues: 1097
  helix:  1.70 (0.27), residues: 382
  sheet: -1.08 (0.30), residues: 258
  loop : -0.85 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 224 
 TYR   0.024   0.002   TYR B 116 
 PHE   0.019   0.002   PHE A 199 
 TRP   0.015   0.002   TRP R 160 
 HIS   0.008   0.002   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.19 ( 8985)
  covalent geometry    : angle       0.55251 /  0.29 (12171)
  hydrogen bonds       : bond        0.03586 /  2.38 (  443)
  hydrogen bonds       : angle       4.91442 /  3.39 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  334 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 305
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7299 (mtm110)
REVERT: A  193 LYS cc_start: 0.8291 (tptt) cc_final: 0.8048 (tptt)
REVERT: A  276 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: B   53 ARG cc_start: 0.8251 (mmt180) cc_final: 0.8038 (mmp80)
REVERT: B  123 ASP cc_start: 0.7601 (t0) cc_final: 0.6996 (t0)
REVERT: B  177 GLU cc_start: 0.7237 (tp30) cc_final: 0.7034 (tp30)
REVERT: B  220 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7445 (mp0)
REVERT: B  224 ARG cc_start: 0.7441 (mtm110) cc_final: 0.7180 (mtp-110)
REVERT: B  244 ASN cc_start: 0.8020 (m-40) cc_final: 0.7771 (m110)
REVERT: B  259 ASP cc_start: 0.7330 (t70) cc_final: 0.7126 (t0)
REVERT: E   66 ARG cc_start: 0.8522 (mtm110) cc_final: 0.8247 (mtm110)
REVERT: E  167 HIS cc_start: 0.8125 (t70) cc_final: 0.7714 (t-90)
REVERT: E  220 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7206 (mm-30)
REVERT: G   47 ASP cc_start: 0.7897 (t0) cc_final: 0.7681 (t0)
REVERT: R   51 MET cc_start: 0.7750 (mmm) cc_final: 0.7451 (mtt)
REVERT: R   56 MET cc_start: 0.7410 (mmm) cc_final: 0.7073 (mmt)
REVERT: R  106 TYR cc_start: 0.7584 (m-10) cc_final: 0.7190 (m-80)
REVERT: R  312 ASN cc_start: 0.8126 (t0) cc_final: 0.7912 (t0)
  outliers start: 29
  outliers final: 16
  residues processed: 315
  average time/residue: 0.2532
  time to fit residues: 106.4833
Evaluate side-chains
  304 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 287
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  230 HIS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  265 THR
Chi-restraints excluded: chain R residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
B 130 ASN
E  12 GLN
E 194 ASN
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.118532 restraints weight = 37065.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.89
r_work: 0.3494 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8985  Z= 0.263
  Angle     :  0.571   5.499  12171  Z= 0.306
  Chirality :  0.042   0.240   1381
  Planarity :  0.004   0.048   1536
  Dihedral  :  4.403  59.148   1227
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.64 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.26), residues: 1097
  helix:  1.71 (0.27), residues: 384
  sheet: -1.00 (0.30), residues: 259
  loop : -0.78 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 139 
 TYR   0.017   0.002   TYR E 190 
 PHE   0.019   0.002   PHE B 240 
 TRP   0.012   0.002   TRP R 160 
 HIS   0.007   0.002   HIS C   2 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.26 ( 8985)
  covalent geometry    : angle       0.57099 /  0.31 (12171)
  hydrogen bonds       : bond        0.03732 /  2.51 (  443)
  hydrogen bonds       : angle       5.00459 /  3.47 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  329 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 301
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7275 (mtm110)
REVERT: A  193 LYS cc_start: 0.8318 (tptt) cc_final: 0.8075 (tptt)
REVERT: A  276 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: A  298 ASP cc_start: 0.7528 (t70) cc_final: 0.7320 (t0)
REVERT: A  341 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7750 (ttm170)
REVERT: B   53 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8052 (mmp80)
REVERT: B  123 ASP cc_start: 0.7660 (t0) cc_final: 0.7069 (t0)
REVERT: B  129 TYR cc_start: 0.8424 (m-80) cc_final: 0.7376 (m-80)
REVERT: B  178 THR cc_start: 0.8136 (m) cc_final: 0.7917 (p)
REVERT: B  244 ASN cc_start: 0.8153 (m-40) cc_final: 0.7891 (m110)
REVERT: B  303 ASP cc_start: 0.7995 (t70) cc_final: 0.7773 (m-30)
REVERT: B  321 SER cc_start: 0.7805 (t) cc_final: 0.7534 (p)
REVERT: E   66 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8126 (mtm110)
REVERT: E  167 HIS cc_start: 0.8216 (t70) cc_final: 0.7812 (t-90)
REVERT: E  220 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7427 (mm-30)
REVERT: R  153 THR cc_start: 0.7834 (m) cc_final: 0.7627 (t)
  outliers start: 28
  outliers final: 21
  residues processed: 312
  average time/residue: 0.2479
  time to fit residues: 103.9046
Evaluate side-chains
  304 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 283
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  230 HIS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue   82 ASN
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0470
   chunk 22 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.1682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 329 HIS
** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN
R  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.132710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.118913 restraints weight = 37130.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.87
r_work: 0.3491 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8985  Z= 0.182
  Angle     :  0.511   5.219  12171  Z= 0.273
  Chirality :  0.039   0.215   1381
  Planarity :  0.004   0.051   1536
  Dihedral  :  4.305  59.087   1227
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.67 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.26), residues: 1097
  helix:  1.76 (0.27), residues: 384
  sheet: -1.01 (0.29), residues: 261
  loop : -0.61 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 139 
 TYR   0.017   0.002   TYR B 116 
 PHE   0.015   0.001   PHE R 296 
 TRP   0.009   0.001   TRP B 104 
 HIS   0.005   0.001   HIS B 271 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 8985)
  covalent geometry    : angle       0.51141 /  0.27 (12171)
  hydrogen bonds       : bond        0.03448 /  2.31 (  443)
  hydrogen bonds       : angle       4.86803 /  3.37 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  317 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 294
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 VAL cc_start: 0.8403 (t) cc_final: 0.8149 (p)
REVERT: A   31 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7233 (mtm110)
REVERT: A  193 LYS cc_start: 0.8267 (tptt) cc_final: 0.8042 (tptt)
REVERT: A  248 TRP cc_start: 0.8516 (m100) cc_final: 0.8285 (m100)
REVERT: A  276 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  338 ASN cc_start: 0.8320 (t0) cc_final: 0.8095 (m-40)
REVERT: A  341 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7627 (tpp80)
REVERT: B   53 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8077 (mmp80)
REVERT: B  123 ASP cc_start: 0.7707 (t0) cc_final: 0.7117 (t0)
REVERT: B  129 TYR cc_start: 0.8413 (m-80) cc_final: 0.7456 (m-80)
REVERT: B  244 ASN cc_start: 0.8127 (m-40) cc_final: 0.7883 (m-40)
REVERT: B  321 SER cc_start: 0.7744 (t) cc_final: 0.7468 (p)
REVERT: E   66 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8266 (mtm110)
REVERT: E  220 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7479 (mm-30)
REVERT: G   26 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7489 (mtt-85)
REVERT: R  106 TYR cc_start: 0.7682 (m-80) cc_final: 0.7429 (m-10)
REVERT: R  267 MET cc_start: 0.7841 (tpt) cc_final: 0.7453 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 303
  average time/residue: 0.2550
  time to fit residues: 103.2113
Evaluate side-chains
  306 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 289
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  217 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115827 restraints weight = 36458.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.84
r_work: 0.3455 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.6027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8985  Z= 0.264
  Angle     :  0.560   5.142  12171  Z= 0.304
  Chirality :  0.041   0.227   1381
  Planarity :  0.004   0.051   1536
  Dihedral  :  4.639  59.372   1227
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.35 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.26), residues: 1097
  helix:  1.50 (0.27), residues: 384
  sheet: -0.85 (0.30), residues: 257
  loop : -0.58 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 134 
 TYR   0.017   0.002   TYR E 190 
 PHE   0.023   0.002   PHE B 240 
 TRP   0.011   0.002   TRP E 110 
 HIS   0.006   0.002   HIS C   2 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00581 /  0.26 ( 8985)
  covalent geometry    : angle       0.56023 /  0.30 (12171)
  hydrogen bonds       : bond        0.03904 /  2.58 (  443)
  hydrogen bonds       : angle       5.04762 /  3.51 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 308
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7610 (t)
REVERT: A    9 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7421 (m-30)
REVERT: A   10 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7926 (mtmm)
REVERT: A   29 VAL cc_start: 0.8359 (t) cc_final: 0.8111 (p)
REVERT: A  185 PHE cc_start: 0.7653 (t80) cc_final: 0.7274 (t80)
REVERT: A  193 LYS cc_start: 0.8298 (tptt) cc_final: 0.8069 (tptt)
REVERT: A  276 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: A  298 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7450 (t0)
REVERT: A  341 ARG cc_start: 0.8069 (tpp-160) cc_final: 0.7638 (tpp80)
REVERT: B   49 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6950 (tm-30)
REVERT: B   53 ARG cc_start: 0.8391 (mmt180) cc_final: 0.8122 (mmt-90)
REVERT: B  102 SER cc_start: 0.8228 (t) cc_final: 0.7770 (p)
REVERT: B  123 ASP cc_start: 0.7890 (t0) cc_final: 0.7277 (t0)
REVERT: B  129 TYR cc_start: 0.8514 (m-80) cc_final: 0.7908 (m-80)
REVERT: B  142 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7640 (tpp-160)
REVERT: B  244 ASN cc_start: 0.8103 (m-40) cc_final: 0.7852 (m-40)
REVERT: B  321 SER cc_start: 0.7831 (t) cc_final: 0.7513 (p)
REVERT: E   86 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7866 (mtm-85)
REVERT: E  220 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7523 (mm-30)
REVERT: R  187 TYR cc_start: 0.7099 (m-80) cc_final: 0.6863 (m-80)
REVERT: R  267 MET cc_start: 0.7853 (tpt) cc_final: 0.7482 (tpp)
REVERT: R  327 PHE cc_start: 0.8021 (t80) cc_final: 0.7725 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 317
  average time/residue: 0.2556
  time to fit residues: 108.2467
Evaluate side-chains
  335 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 306
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  193 MET
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain G residue   20 MET
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.3980
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.130971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.117071 restraints weight = 37075.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.89
r_work: 0.3472 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.6112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8985  Z= 0.156
  Angle     :  0.513   4.984  12171  Z= 0.274
  Chirality :  0.040   0.205   1381
  Planarity :  0.004   0.039   1536
  Dihedral  :  4.445  59.592   1227
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.13 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.26), residues: 1097
  helix:  1.80 (0.27), residues: 383
  sheet: -0.86 (0.30), residues: 258
  loop : -0.47 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.015   0.002   TYR B 150 
 PHE   0.012   0.001   PHE B 240 
 TRP   0.009   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.16 ( 8985)
  covalent geometry    : angle       0.51323 /  0.27 (12171)
  hydrogen bonds       : bond        0.03479 /  2.33 (  443)
  hydrogen bonds       : angle       4.87417 /  3.39 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  322 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 296
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7591 (t)
REVERT: A   29 VAL cc_start: 0.8380 (t) cc_final: 0.8103 (p)
REVERT: A   31 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7315 (mtm110)
REVERT: A   33 THR cc_start: 0.8593 (t) cc_final: 0.8216 (p)
REVERT: A  185 PHE cc_start: 0.7575 (t80) cc_final: 0.7154 (t80)
REVERT: A  188 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7652 (ttpp)
REVERT: A  193 LYS cc_start: 0.8264 (tptt) cc_final: 0.8056 (tptt)
REVERT: A  276 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: A  341 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7748 (tpp80)
REVERT: B   49 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6938 (tm-30)
REVERT: B   53 ARG cc_start: 0.8387 (mmt180) cc_final: 0.8146 (mmp80)
REVERT: B  102 SER cc_start: 0.8233 (t) cc_final: 0.7770 (p)
REVERT: B  123 ASP cc_start: 0.7774 (t0) cc_final: 0.7197 (t0)
REVERT: B  129 TYR cc_start: 0.8407 (m-80) cc_final: 0.7751 (m-80)
REVERT: B  142 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7644 (tpp-160)
REVERT: B  244 ASN cc_start: 0.8088 (m-40) cc_final: 0.7840 (m-40)
REVERT: B  321 SER cc_start: 0.7758 (t) cc_final: 0.7462 (p)
REVERT: E   86 ARG cc_start: 0.8172 (ptp-170) cc_final: 0.7936 (mtm-85)
REVERT: E  220 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7503 (mm-30)
REVERT: R  106 TYR cc_start: 0.7683 (m-80) cc_final: 0.7420 (m-10)
REVERT: R  187 TYR cc_start: 0.7080 (m-80) cc_final: 0.6814 (m-80)
REVERT: R  267 MET cc_start: 0.7858 (tpt) cc_final: 0.7506 (tpp)
REVERT: R  327 PHE cc_start: 0.8027 (t80) cc_final: 0.7748 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 305
  average time/residue: 0.2500
  time to fit residues: 102.0354
Evaluate side-chains
  314 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 293
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  193 MET
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  217 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 246 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.131520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.117801 restraints weight = 36746.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.85
r_work: 0.3467 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.6291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8985  Z= 0.180
  Angle     :  0.520   5.080  12171  Z= 0.278
  Chirality :  0.040   0.209   1381
  Planarity :  0.004   0.041   1536
  Dihedral  :  4.442  59.971   1227
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.33 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.26), residues: 1097
  helix:  1.82 (0.27), residues: 384
  sheet: -0.81 (0.30), residues: 257
  loop : -0.46 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 134 
 TYR   0.014   0.002   TYR E 235 
 PHE   0.014   0.002   PHE B 240 
 TRP   0.009   0.001   TRP B 302 
 HIS   0.006   0.001   HIS C   2 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 8985)
  covalent geometry    : angle       0.51959 /  0.28 (12171)
  hydrogen bonds       : bond        0.03516 /  2.35 (  443)
  hydrogen bonds       : angle       4.88073 /  3.39 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  325 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 301
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7577 (t)
REVERT: A   10 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7849 (mtmm)
REVERT: A   29 VAL cc_start: 0.8340 (t) cc_final: 0.8098 (p)
REVERT: A   31 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7310 (mtm110)
REVERT: A  185 PHE cc_start: 0.7547 (t80) cc_final: 0.7190 (t80)
REVERT: A  193 LYS cc_start: 0.8287 (tptt) cc_final: 0.8063 (tptt)
REVERT: A  276 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: A  341 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7723 (tpp80)
REVERT: B   22 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7035 (tm-30)
REVERT: B   53 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8146 (mmp80)
REVERT: B  102 SER cc_start: 0.8220 (t) cc_final: 0.7759 (p)
REVERT: B  123 ASP cc_start: 0.7859 (t0) cc_final: 0.7265 (t0)
REVERT: B  129 TYR cc_start: 0.8413 (m-80) cc_final: 0.7780 (m-80)
REVERT: B  244 ASN cc_start: 0.8087 (m-40) cc_final: 0.7830 (m-40)
REVERT: B  321 SER cc_start: 0.7771 (t) cc_final: 0.7466 (p)
REVERT: E   86 ARG cc_start: 0.8206 (ptp-170) cc_final: 0.7913 (mtm-85)
REVERT: E  220 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7496 (mm-30)
REVERT: R  187 TYR cc_start: 0.7110 (m-80) cc_final: 0.6819 (m-80)
REVERT: R  267 MET cc_start: 0.7860 (tpt) cc_final: 0.7482 (tpp)
REVERT: R  327 PHE cc_start: 0.8019 (t80) cc_final: 0.7742 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 309
  average time/residue: 0.2539
  time to fit residues: 104.8473
Evaluate side-chains
  314 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 294
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 HIS
A 246 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.131283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.117175 restraints weight = 36805.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.89
r_work: 0.3469 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.6400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8985  Z= 0.176
  Angle     :  0.519   5.688  12171  Z= 0.277
  Chirality :  0.040   0.209   1381
  Planarity :  0.004   0.085   1536
  Dihedral  :  4.482  59.928   1227
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.33 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.26), residues: 1097
  helix:  1.86 (0.26), residues: 384
  sheet: -0.78 (0.30), residues: 253
  loop : -0.43 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 139 
 TYR   0.012   0.002   TYR E 235 
 PHE   0.014   0.001   PHE B 240 
 TRP   0.010   0.001   TRP B 302 
 HIS   0.005   0.001   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 ( 8985)
  covalent geometry    : angle       0.51929 /  0.28 (12171)
  hydrogen bonds       : bond        0.03476 /  2.31 (  443)
  hydrogen bonds       : angle       4.86510 /  3.38 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  330 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 306
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7642 (t)
REVERT: A   10 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7850 (mtmm)
REVERT: A   29 VAL cc_start: 0.8339 (t) cc_final: 0.8095 (p)
REVERT: A   31 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7324 (mtm110)
REVERT: A   39 LEU cc_start: 0.7789 (mt) cc_final: 0.7539 (mt)
REVERT: A  185 PHE cc_start: 0.7527 (t80) cc_final: 0.7142 (t80)
REVERT: A  193 LYS cc_start: 0.8293 (tptt) cc_final: 0.8066 (tptt)
REVERT: A  276 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7754 (tm-30)
REVERT: A  341 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7712 (tpp80)
REVERT: B   22 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: B   53 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8143 (mmp80)
REVERT: B  102 SER cc_start: 0.8237 (t) cc_final: 0.7776 (p)
REVERT: B  123 ASP cc_start: 0.7880 (t0) cc_final: 0.7284 (t0)
REVERT: B  129 TYR cc_start: 0.8424 (m-80) cc_final: 0.7734 (m-80)
REVERT: B  244 ASN cc_start: 0.8058 (m-40) cc_final: 0.7793 (m110)
REVERT: B  321 SER cc_start: 0.7805 (t) cc_final: 0.7451 (p)
REVERT: B  322 CYS cc_start: 0.7851 (p) cc_final: 0.7605 (p)
REVERT: E   86 ARG cc_start: 0.8183 (ptp-170) cc_final: 0.7914 (mtm-85)
REVERT: E  220 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7517 (mm-30)
REVERT: R  187 TYR cc_start: 0.7167 (m-80) cc_final: 0.6818 (m-80)
REVERT: R  267 MET cc_start: 0.7860 (tpt) cc_final: 0.7492 (tpp)
REVERT: R  327 PHE cc_start: 0.8024 (t80) cc_final: 0.7750 (t80)
  outliers start: 24
  outliers final: 22
  residues processed: 315
  average time/residue: 0.2509
  time to fit residues: 105.5649
Evaluate side-chains
  334 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 311
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  217 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
E 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.128786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.115026 restraints weight = 36801.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.84
r_work: 0.3447 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.6654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8985  Z= 0.262
  Angle     :  0.565   5.237  12171  Z= 0.305
  Chirality :  0.042   0.226   1381
  Planarity :  0.004   0.064   1536
  Dihedral  :  4.707  59.446   1227
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.44 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.26), residues: 1097
  helix:  1.65 (0.26), residues: 383
  sheet: -0.79 (0.30), residues: 259
  loop : -0.46 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 139 
 TYR   0.023   0.002   TYR B 116 
 PHE   0.020   0.002   PHE B 240 
 TRP   0.015   0.002   TRP R  91 
 HIS   0.009   0.002   HIS A 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00578 /  0.26 ( 8985)
  covalent geometry    : angle       0.56513 /  0.31 (12171)
  hydrogen bonds       : bond        0.03829 /  2.55 (  443)
  hydrogen bonds       : angle       5.07075 /  3.53 ( 1260)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue THR   60 is missing expected H atoms. Skipping.
Residue VAL   74 is missing expected H atoms. Skipping.
Residue ILE  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  334 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 312
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7887 (mtmm)
REVERT: A   29 VAL cc_start: 0.8381 (t) cc_final: 0.8118 (p)
REVERT: A   31 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7395 (mtm110)
REVERT: A   33 THR cc_start: 0.8557 (t) cc_final: 0.8275 (p)
REVERT: A  185 PHE cc_start: 0.7515 (t80) cc_final: 0.7129 (t80)
REVERT: A  186 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6776 (tm-30)
REVERT: A  193 LYS cc_start: 0.8281 (tptt) cc_final: 0.8074 (tptt)
REVERT: A  247 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7869 (ttm110)
REVERT: A  276 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: A  306 TYR cc_start: 0.7751 (m-80) cc_final: 0.7406 (m-10)
REVERT: A  341 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7697 (tpp80)
REVERT: B   53 ARG cc_start: 0.8404 (mmt180) cc_final: 0.8158 (mmt-90)
REVERT: B   56 LEU cc_start: 0.8485 (mt) cc_final: 0.8231 (mp)
REVERT: B  102 SER cc_start: 0.8234 (t) cc_final: 0.7801 (p)
REVERT: B  123 ASP cc_start: 0.7875 (t0) cc_final: 0.7301 (t0)
REVERT: B  129 TYR cc_start: 0.8534 (m-80) cc_final: 0.7833 (m-80)
REVERT: B  160 ASN cc_start: 0.7980 (t0) cc_final: 0.7669 (t0)
REVERT: B  244 ASN cc_start: 0.8029 (m-40) cc_final: 0.7774 (m-40)
REVERT: B  321 SER cc_start: 0.7867 (t) cc_final: 0.7519 (p)
REVERT: E   86 ARG cc_start: 0.8140 (ptp-170) cc_final: 0.7878 (mtm-85)
REVERT: E   92 MET cc_start: 0.8205 (ttm) cc_final: 0.7922 (tpp)
REVERT: E  215 THR cc_start: 0.8085 (m) cc_final: 0.7677 (p)
REVERT: E  220 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7503 (mm-30)
REVERT: R   99 LEU cc_start: 0.7627 (mt) cc_final: 0.7386 (mm)
REVERT: R  187 TYR cc_start: 0.7174 (m-80) cc_final: 0.6808 (m-80)
REVERT: R  267 MET cc_start: 0.7871 (tpt) cc_final: 0.7533 (tpp)
REVERT: R  312 ASN cc_start: 0.8260 (t0) cc_final: 0.7831 (t0)
REVERT: R  327 PHE cc_start: 0.8049 (t80) cc_final: 0.7762 (t80)
  outliers start: 22
  outliers final: 19
  residues processed: 318
  average time/residue: 0.2525
  time to fit residues: 107.6909
Evaluate side-chains
  326 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 307
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain R residue   28 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   66 SER
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  217 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 73 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN
R 297 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.131670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.118035 restraints weight = 36707.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.85
r_work: 0.3485 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.6629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8985  Z= 0.118
  Angle     :  0.514   5.156  12171  Z= 0.272
  Chirality :  0.040   0.199   1381
  Planarity :  0.004   0.069   1536
  Dihedral  :  4.457  58.062   1227
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.27 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.26), residues: 1097
  helix:  1.97 (0.26), residues: 383
  sheet: -0.69 (0.30), residues: 249
  loop : -0.40 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 139 
 TYR   0.016   0.002   TYR B 269 
 PHE   0.012   0.001   PHE R 296 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.007   0.001   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 8985)
  covalent geometry    : angle       0.51404 /  0.27 (12171)
  hydrogen bonds       : bond        0.03368 /  2.23 (  443)
  hydrogen bonds       : angle       4.81986 /  3.36 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5282.14 seconds
wall clock time: 90 minutes 39.10 seconds (5439.10 seconds total)