Starting phenix.real_space_refine
on Tue Mar  3 21:04:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6so5_10266/03_2026/6so5_10266.cif"
  }
  resolution = 4.2
  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=   0.000 sd=   0.002
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
     Zn      1      6.06       5
     S      73      5.16       5
     C    5673      2.51       5
     N    1425      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8737
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2464
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 18, 'TRANS': 294}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2301
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 17, 'TRANS': 274}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1160
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1160
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 835
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 816
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4310  SG  CYS B 289      46.170 112.721  80.191  1.00101.14           S
  ATOM   4333  SG  CYS B 292      44.838 111.737  77.378  1.00 91.48           S

  Time building chain proxies: 1.87, per 1000 atoms: 0.21
  Number of scatterers: 8737
  At special positions: 0
  Unit cell: (87.48, 129.6, 106.11, 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)
     Zn      1     29.99
     S      73     16.00
     O    1565      8.00
     N    1425      7.00
     C    5673      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 208 " - pdb=" SG  CYS E 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 208 " - pdb=" SG  CYS F 284 " distance=1.75

  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: 0.70
  Conformation dependent library (CDL) restraints added in 255.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 289 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 292 "


  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 3 sheets defined
      71.4% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 34
      removed outlier: 4.006A  pdb=" N   ILE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 63
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 3.970A  pdb=" N   ASP A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 112
      removed outlier: 4.177A  pdb=" N   LEU A 109 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 125 through 139
      removed outlier: 3.517A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 159
      removed outlier: 4.043A  pdb=" N   VAL A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   MET A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 176
      No H-bonds generated for 'chain 'A' and resid 174 through 176'
    Processing helix  chain 'A' and resid 177 through 203
      removed outlier: 3.838A  pdb=" N   THR A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 182 " --> pdb=" O   ASN A 178 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 192 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ASN A 195 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLN A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      Proline residue:  A 199  - end of helix
    Processing helix  chain 'A' and resid 215 through 238
      removed outlier: 4.053A  pdb=" N   ALA A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 3.543A  pdb=" N   ASP A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
    Processing helix  chain 'A' and resid 289 through 310
      removed outlier: 3.558A  pdb=" N   ASP A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 340
      removed outlier: 4.087A  pdb=" N   LYS A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL A 331 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 49 through 64
    Processing helix  chain 'B' and resid 77 through 84
      removed outlier: 3.586A  pdb=" N   ASP B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 119
      removed outlier: 3.765A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
      Proline residue:  B 115  - end of helix
    Processing helix  chain 'B' and resid 128 through 134
      removed outlier: 4.476A  pdb=" N   GLU B 134 " --> pdb=" O   LYS B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 157
    Processing helix  chain 'B' and resid 175 through 182
      Proline residue:  B 180  - end of helix
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 4.597A  pdb=" N   LEU B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 238
      removed outlier: 3.661A  pdb=" N   THR B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 251 through 268
    Processing helix  chain 'B' and resid 289 through 308
      removed outlier: 3.610A  pdb=" N   ASP B 308 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 338
      removed outlier: 4.217A  pdb=" N   VAL B 331 " --> pdb=" O   GLY B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 27
      removed outlier: 3.740A  pdb=" N   ASN C  22 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 61
      removed outlier: 3.519A  pdb=" N   PHE C  31 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   PHE C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   MET C  35 " --> pdb=" O   PHE C  31 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LYS C  41 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ASP C  42 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 124
    Processing helix  chain 'C' and resid 150 through 171
      removed outlier: 4.457A  pdb=" N   CYS C 157 " --> pdb=" O   VAL C 153 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   CYS C 162 " --> pdb=" O   TRP C 158 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   HIS C 171 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 28
      removed outlier: 3.999A  pdb=" N   TRP D  11 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU D  15 " --> pdb=" O   TRP D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 62
    Processing helix  chain 'D' and resid 64 through 124
      removed outlier: 8.319A  pdb=" N   ALA D  70 " --> pdb=" O   MET D  66 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ARG D  71 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 171
    Processing helix  chain 'E' and resid 190 through 208
      removed outlier: 5.063A  pdb=" N   ALA E 205 " --> pdb=" O   LEU E 201 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE E 206 " --> pdb=" O   GLY E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 231
      removed outlier: 3.951A  pdb=" N   THR E 219 " --> pdb=" O   ALA E 215 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY E 226 " --> pdb=" O   LEU E 222 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU E 227 " --> pdb=" O   ALA E 223 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   TYR E 228 " --> pdb=" O   TYR E 224 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 243 through 251
    Processing helix  chain 'E' and resid 253 through 291
      removed outlier: 4.029A  pdb=" N   MET E 261 " --> pdb=" O   ILE E 257 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU E 288 " --> pdb=" O   CYS E 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 192 through 209
      removed outlier: 3.562A  pdb=" N   LEU F 199 " --> pdb=" O   GLY F 195 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   ALA F 205 " --> pdb=" O   LEU F 201 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   PHE F 206 " --> pdb=" O   GLY F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 215 through 229
      removed outlier: 3.568A  pdb=" N   THR F 219 " --> pdb=" O   ALA F 215 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR F 224 " --> pdb=" O   LEU F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 243 through 251
    Processing helix  chain 'F' and resid 252 through 291
      removed outlier: 3.575A  pdb=" N   VAL F 256 " --> pdb=" O   ILE F 252 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE F 257 " --> pdb=" O   PRO F 253 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ASN F 258 " --> pdb=" O   ALA F 254 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
      removed outlier: 6.859A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 10.376A  pdb=" N   THR A 242 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 9.508A  pdb=" N   ASN A 274 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE A 244 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ILE A 276 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   CYS A 246 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 70
      removed outlier: 6.227A  pdb=" N   LEU B  69 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY B  43 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   THR B 272 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS B 246 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   HIS B 273 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   VAL B 316 " --> pdb=" O   HIS B 273 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ILE B 275 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)

    566 hydrogen bonds defined for protein.
    1689 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: 1.42

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2719
        1.34 -     1.46: 2033
        1.46 -     1.58: 4049
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 8918
  Sorted by residual:
  bond pdb=" N   CYS F 208 "
       pdb=" CA  CYS F 208 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.31e-02 5.83e+03 7.41e+00
  bond pdb=" N   LYS F 209 "
       pdb=" CA  LYS F 209 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.70e+00
  bond pdb=" N   TYR F 210 "
       pdb=" CA  TYR F 210 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.28e-02 6.10e+03 5.44e+00
  bond pdb=" CA  LEU B  28 "
       pdb=" C   LEU B  28 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 1.72e-02 3.38e+03 3.15e+00
  bond pdb=" C   ASP B  74 "
       pdb=" N   PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.337  1.322  0.014 9.80e-03 1.04e+04 2.11e+00
  ... (remaining 8913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 11668
        1.98 -     3.96: 306
        3.96 -     5.94: 62
        5.94 -     7.92: 7
        7.92 -     9.89: 2
  Bond angle restraints: 12045
  Sorted by residual:
  angle pdb=" C   LEU E 274 "
        pdb=" N   CYS E 275 "
        pdb=" CA  CYS E 275 "
      ideal   model   delta    sigma   weight residual
     122.38  112.49    9.89 1.81e+00 3.05e-01 2.99e+01
  angle pdb=" N   ILE E 190 "
        pdb=" CA  ILE E 190 "
        pdb=" C   ILE E 190 "
      ideal   model   delta    sigma   weight residual
     111.91  107.69    4.22 8.90e-01 1.26e+00 2.25e+01
  angle pdb=" CA  CYS E 275 "
        pdb=" CB  CYS E 275 "
        pdb=" SG  CYS E 275 "
      ideal   model   delta    sigma   weight residual
     114.40  123.08   -8.68 2.30e+00 1.89e-01 1.42e+01
  angle pdb=" N   CYS F 208 "
        pdb=" CA  CYS F 208 "
        pdb=" C   CYS F 208 "
      ideal   model   delta    sigma   weight residual
     113.18  108.71    4.47 1.21e+00 6.83e-01 1.36e+01
  angle pdb=" N   ALA C   6 "
        pdb=" CA  ALA C   6 "
        pdb=" C   ALA C   6 "
      ideal   model   delta    sigma   weight residual
     111.82  107.62    4.20 1.16e+00 7.43e-01 1.31e+01
  ... (remaining 12040 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4663
       16.21 -    32.42: 596
       32.42 -    48.62: 124
       48.62 -    64.83: 21
       64.83 -    81.04: 8
  Dihedral angle restraints: 5412
    sinusoidal: 2193
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS F 208 "
           pdb=" SG  CYS F 208 "
           pdb=" SG  CYS F 284 "
           pdb=" CB  CYS F 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.23   69.23     1      1.00e+01 1.00e-02 6.19e+01
  dihedral pdb=" CA  SER F 212 "
           pdb=" C   SER F 212 "
           pdb=" N   ILE F 213 "
           pdb=" CA  ILE F 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  HIS E 285 "
           pdb=" C   HIS E 285 "
           pdb=" N   GLU E 286 "
           pdb=" CA  GLU E 286 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 5409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 933
       0.039 -    0.078: 330
       0.078 -    0.117: 104
       0.117 -    0.156: 15
       0.156 -    0.195: 4
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  CYS E 275 "
            pdb=" N   CYS E 275 "
            pdb=" C   CYS E 275 "
            pdb=" CB  CYS E 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CA  PRO D  29 "
            pdb=" N   PRO D  29 "
            pdb=" C   PRO D  29 "
            pdb=" CB  PRO D  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CB  ILE F 252 "
            pdb=" CA  ILE F 252 "
            pdb=" CG1 ILE F 252 "
            pdb=" CG2 ILE F 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 168 "    0.047 5.00e-02 4.00e+02   7.14e-02 8.17e+00
        pdb=" N   PRO B 169 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 169 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 169 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 207 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.31e+00
        pdb=" C   VAL F 207 "    0.040 2.00e-02 2.50e+03
        pdb=" O   VAL F 207 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS F 208 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 159 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.16e+00
        pdb=" C   ILE D 159 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE D 159 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU D 160 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 130
        2.56 -     3.14: 8344
        3.14 -     3.73: 14458
        3.73 -     4.31: 18665
        4.31 -     4.90: 28255
  Nonbonded interactions: 69852
  Sorted by model distance:
  nonbonded pdb=" CG2 THR E 219 "
            pdb=" CE2 TYR E 277 "
     model   vdw
     1.973 3.760
  nonbonded pdb=" OE1 GLU A 259 "
            pdb=" OH  TYR A 310 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OH  TYR A 256 "
            pdb=" NH2 ARG A 260 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OE2 GLU A 251 "
            pdb=" N   SER A 254 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OE2 GLU C  46 "
            pdb=" NE  ARG C  50 "
     model   vdw
     2.223 3.120
  ... (remaining 69847 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 24 through 190 or resid 220 through 344))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and resid 191 through 291)
  selection = chain 'F'
}

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 group one per residue
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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.710
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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   0.281   8922  Z= 0.320
  Angle     :  0.835  19.298  12049  Z= 0.474
  Chirality :  0.044   0.195   1386
  Planarity :  0.005   0.071   1497
  Dihedral  : 14.990  81.038   3308
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 23.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  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: -4.60 (0.21), residues: 1077
  helix: -2.53 (0.15), residues: 684
  sheet: -4.50 (0.37), residues: 97
  loop : -3.21 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 204 
 TYR   0.014   0.002   TYR E 224 
 PHE   0.016   0.002   PHE F 283 
 TRP   0.012   0.001   TRP D   9 
 HIS   0.012   0.002   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8918)
  covalent geometry    : angle       0.81563 (12045)
  SS BOND              : bond        0.19907 (    2)
  SS BOND              : angle       9.78445 (    4)
  hydrogen bonds       : bond        0.13068 (  566)
  hydrogen bonds       : angle       6.83425 ( 1689)
  metal coordination   : bond        0.19996 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 0.359 
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: A  105 ILE cc_start: 0.9192 (mm) cc_final: 0.8870 (tp)
REVERT: A  124 MET cc_start: 0.2545 (ttp) cc_final: 0.2177 (tpp)
REVERT: A  185 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8448 (tpm170)
REVERT: A  189 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7755 (mmm160)
REVERT: A  221 LYS cc_start: 0.9224 (mttt) cc_final: 0.8955 (mmmt)
REVERT: A  241 GLN cc_start: 0.8011 (pt0) cc_final: 0.7765 (pt0)
REVERT: A  257 GLU cc_start: 0.8290 (tp30) cc_final: 0.8023 (tm-30)
REVERT: B  153 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8712 (mmm-85)
REVERT: B  249 ILE cc_start: 0.9427 (mt) cc_final: 0.9149 (tt)
REVERT: B  288 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.7041 (Cg_exo)
REVERT: C   76 GLU cc_start: 0.8268 (tp30) cc_final: 0.8045 (tp30)
REVERT: C   81 LYS cc_start: 0.9294 (tttt) cc_final: 0.9071 (ttmm)
REVERT: C  155 ILE cc_start: 0.7736 (mt) cc_final: 0.7486 (mt)
REVERT: D   13 LEU cc_start: 0.9003 (tp) cc_final: 0.8549 (tp)
REVERT: D   17 PHE cc_start: 0.8789 (m-80) cc_final: 0.8562 (m-80)
REVERT: D   19 PHE cc_start: 0.8745 (m-80) cc_final: 0.8175 (m-80)
REVERT: D   31 PHE cc_start: 0.6747 (m-80) cc_final: 0.6474 (m-80)
REVERT: D   49 MET cc_start: 0.8686 (mmm) cc_final: 0.8388 (mmm)
REVERT: D   52 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8651 (mt-10)
REVERT: D   53 ILE cc_start: 0.9635 (mt) cc_final: 0.9356 (mt)
REVERT: D   56 MET cc_start: 0.8798 (ptp) cc_final: 0.8494 (mtm)
REVERT: D   57 LYS cc_start: 0.9647 (mttt) cc_final: 0.9290 (mttp)
REVERT: D  101 LYS cc_start: 0.9306 (tmtt) cc_final: 0.9029 (tmtt)
REVERT: D  108 PHE cc_start: 0.8382 (t80) cc_final: 0.8142 (t80)
REVERT: D  123 TYR cc_start: 0.7861 (p90) cc_final: 0.7619 (t80)
REVERT: D  155 ILE cc_start: 0.9369 (mt) cc_final: 0.8812 (mt)
REVERT: E  266 LYS cc_start: 0.8690 (mttt) cc_final: 0.8202 (mtmt)
REVERT: E  273 ASP cc_start: 0.9214 (m-30) cc_final: 0.8807 (m-30)
REVERT: E  274 LEU cc_start: 0.9001 (mm) cc_final: 0.8667 (mm)
REVERT: F  225 MET cc_start: 0.8809 (mmt) cc_final: 0.8543 (mmt)
REVERT: F  227 LEU cc_start: 0.9264 (mt) cc_final: 0.8924 (mm)
REVERT: F  248 LEU cc_start: 0.7080 (pp) cc_final: 0.6838 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 332
  average time/residue: 0.1073
  time to fit residues: 46.7086
Evaluate side-chains
  261 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
B 235 GLN
B 296 HIS
B 332 ASN
C  45 GLN
C  89 HIS
D  22 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.114904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.082763 restraints weight = 27429.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.085047 restraints weight = 16847.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.086504 restraints weight = 12355.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.087392 restraints weight = 10194.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.087811 restraints weight = 9047.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8922  Z= 0.188
  Angle     :  0.713   8.720  12049  Z= 0.372
  Chirality :  0.046   0.260   1386
  Planarity :  0.005   0.063   1497
  Dihedral  :  5.266  22.094   1162
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  7.02 %
    Favored  : 92.78 %
  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: -2.56 (0.24), residues: 1077
  helix: -0.85 (0.17), residues: 708
  sheet: -3.71 (0.44), residues: 92
  loop : -2.82 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 260 
 TYR   0.030   0.002   TYR E 277 
 PHE   0.019   0.002   PHE B 160 
 TRP   0.048   0.002   TRP D 158 
 HIS   0.005   0.001   HIS B 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8918)
  covalent geometry    : angle       0.71153 (12045)
  SS BOND              : bond        0.00390 (    2)
  SS BOND              : angle       2.53007 (    4)
  hydrogen bonds       : bond        0.04986 (  566)
  hydrogen bonds       : angle       5.64873 ( 1689)
  metal coordination   : bond        0.00066 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 336
  time to evaluate  : 0.358 
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: A  103 MET cc_start: 0.9079 (tmm) cc_final: 0.8840 (tmm)
REVERT: A  105 ILE cc_start: 0.9247 (mm) cc_final: 0.8885 (tp)
REVERT: A  131 MET cc_start: 0.6922 (mmt) cc_final: 0.6503 (mmm)
REVERT: A  185 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8488 (tpm170)
REVERT: A  189 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7523 (mmm160)
REVERT: A  221 LYS cc_start: 0.9300 (mttt) cc_final: 0.9083 (mmmt)
REVERT: A  257 GLU cc_start: 0.8603 (tp30) cc_final: 0.8212 (tm-30)
REVERT: A  291 MET cc_start: 0.8618 (mtp) cc_final: 0.8313 (pmm)
REVERT: B   69 LEU cc_start: 0.9151 (tp) cc_final: 0.8930 (tp)
REVERT: B   99 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8512 (t0)
REVERT: B  101 PHE cc_start: 0.8168 (m-10) cc_final: 0.7648 (m-10)
REVERT: B  152 MET cc_start: 0.9035 (mmm) cc_final: 0.8717 (mmm)
REVERT: B  153 ARG cc_start: 0.9142 (mtt180) cc_final: 0.8774 (mmm-85)
REVERT: B  241 GLN cc_start: 0.8023 (pt0) cc_final: 0.7789 (pt0)
REVERT: C   82 MET cc_start: 0.8828 (mmm) cc_final: 0.8606 (mpp)
REVERT: C  157 CYS cc_start: 0.9350 (m) cc_final: 0.9122 (p)
REVERT: D   13 LEU cc_start: 0.9029 (tp) cc_final: 0.8585 (tp)
REVERT: D   17 PHE cc_start: 0.8920 (m-10) cc_final: 0.8607 (m-80)
REVERT: D   19 PHE cc_start: 0.8803 (m-80) cc_final: 0.8541 (m-80)
REVERT: D   25 ARG cc_start: 0.8473 (tmt-80) cc_final: 0.8228 (tpt90)
REVERT: D   49 MET cc_start: 0.8643 (mmm) cc_final: 0.8278 (mmm)
REVERT: D   76 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8653 (mm-30)
REVERT: D  101 LYS cc_start: 0.9287 (tmtt) cc_final: 0.9006 (tmtt)
REVERT: D  163 ASN cc_start: 0.8711 (m110) cc_final: 0.8342 (m110)
REVERT: E  273 ASP cc_start: 0.9274 (m-30) cc_final: 0.9029 (m-30)
REVERT: F  225 MET cc_start: 0.8851 (mmt) cc_final: 0.8649 (mmm)
REVERT: F  227 LEU cc_start: 0.8638 (mt) cc_final: 0.8357 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 338
  average time/residue: 0.1017
  time to fit residues: 46.1663
Evaluate side-chains
  267 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0370
   overall best weight:    2.3662

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
B 123 ASN
D  45 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.114906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.082087 restraints weight = 27309.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.084489 restraints weight = 16569.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.086008 restraints weight = 12048.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.086944 restraints weight = 9888.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087326 restraints weight = 8783.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8922  Z= 0.192
  Angle     :  0.711   9.067  12049  Z= 0.371
  Chirality :  0.046   0.248   1386
  Planarity :  0.005   0.053   1497
  Dihedral  :  5.128  19.986   1162
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.75 %
    Favored  : 95.05 %
  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: -1.62 (0.25), residues: 1077
  helix: -0.15 (0.18), residues: 713
  sheet: -3.44 (0.46), residues: 95
  loop : -2.37 (0.41), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.018   0.002   TYR E 277 
 PHE   0.028   0.002   PHE F 271 
 TRP   0.025   0.001   TRP D 158 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8918)
  covalent geometry    : angle       0.71040 (12045)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       2.17730 (    4)
  hydrogen bonds       : bond        0.04757 (  566)
  hydrogen bonds       : angle       5.46685 ( 1689)
  metal coordination   : bond        0.00399 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 326
  time to evaluate  : 0.338 
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: A  105 ILE cc_start: 0.9213 (mm) cc_final: 0.8832 (tp)
REVERT: A  189 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7444 (mmm160)
REVERT: A  221 LYS cc_start: 0.9262 (mttt) cc_final: 0.9047 (mmmt)
REVERT: A  257 GLU cc_start: 0.8563 (tp30) cc_final: 0.8209 (tm-30)
REVERT: A  291 MET cc_start: 0.8617 (mtp) cc_final: 0.8322 (pmm)
REVERT: B   60 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8103 (mm110)
REVERT: B  101 PHE cc_start: 0.8086 (m-10) cc_final: 0.7471 (m-10)
REVERT: B  152 MET cc_start: 0.9010 (mmm) cc_final: 0.8661 (mmm)
REVERT: B  158 MET cc_start: 0.8795 (tmm) cc_final: 0.8405 (tmm)
REVERT: B  234 GLU cc_start: 0.9196 (pt0) cc_final: 0.8987 (pt0)
REVERT: B  257 GLU cc_start: 0.8630 (tp30) cc_final: 0.8382 (tp30)
REVERT: C   76 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8595 (mm-30)
REVERT: C  157 CYS cc_start: 0.9361 (m) cc_final: 0.9089 (p)
REVERT: D   13 LEU cc_start: 0.9020 (tp) cc_final: 0.8549 (tp)
REVERT: D   17 PHE cc_start: 0.8838 (m-10) cc_final: 0.8550 (m-80)
REVERT: D   19 PHE cc_start: 0.8756 (m-80) cc_final: 0.8519 (m-80)
REVERT: D   49 MET cc_start: 0.8909 (mmm) cc_final: 0.8132 (mmm)
REVERT: D   68 GLU cc_start: 0.7649 (tp30) cc_final: 0.7084 (tp30)
REVERT: D   76 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: D   91 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8784 (mttp)
REVERT: D  155 ILE cc_start: 0.9443 (mt) cc_final: 0.8957 (mt)
REVERT: D  163 ASN cc_start: 0.8771 (m110) cc_final: 0.8252 (m110)
REVERT: E  273 ASP cc_start: 0.9389 (m-30) cc_final: 0.9088 (m-30)
REVERT: E  277 TYR cc_start: 0.8431 (m-80) cc_final: 0.8174 (m-80)
REVERT: F  221 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8686 (tp-100)
REVERT: F  225 MET cc_start: 0.9004 (mmt) cc_final: 0.8374 (mmm)
REVERT: F  227 LEU cc_start: 0.8854 (mt) cc_final: 0.8436 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 327
  average time/residue: 0.0970
  time to fit residues: 43.2581
Evaluate side-chains
  273 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  45 GLN
E 221 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.111430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.079263 restraints weight = 28528.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.081550 restraints weight = 17350.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.083027 restraints weight = 12727.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.083918 restraints weight = 10470.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084343 restraints weight = 9318.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8922  Z= 0.302
  Angle     :  0.789   9.408  12049  Z= 0.418
  Chirality :  0.047   0.285   1386
  Planarity :  0.006   0.060   1497
  Dihedral  :  5.351  23.113   1162
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  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: -1.73 (0.25), residues: 1077
  helix: -0.27 (0.18), residues: 704
  sheet: -3.72 (0.44), residues: 95
  loop : -2.12 (0.41), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 192 
 TYR   0.024   0.002   TYR A 148 
 PHE   0.027   0.002   PHE F 271 
 TRP   0.058   0.002   TRP D 158 
 HIS   0.018   0.002   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 ( 8918)
  covalent geometry    : angle       0.78788 (12045)
  SS BOND              : bond        0.00543 (    2)
  SS BOND              : angle       2.02360 (    4)
  hydrogen bonds       : bond        0.05108 (  566)
  hydrogen bonds       : angle       5.65238 ( 1689)
  metal coordination   : bond        0.00357 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.362 
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: A  103 MET cc_start: 0.9080 (tmm) cc_final: 0.8738 (tmm)
REVERT: A  105 ILE cc_start: 0.9211 (mm) cc_final: 0.8900 (tp)
REVERT: A  175 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7873 (ptt180)
REVERT: A  221 LYS cc_start: 0.9335 (mttt) cc_final: 0.9102 (mmmt)
REVERT: A  257 GLU cc_start: 0.8663 (tp30) cc_final: 0.8451 (tp30)
REVERT: A  264 GLU cc_start: 0.8330 (tt0) cc_final: 0.7906 (tt0)
REVERT: A  291 MET cc_start: 0.8653 (mtp) cc_final: 0.8358 (pmm)
REVERT: B   60 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8331 (mm110)
REVERT: B   69 LEU cc_start: 0.9149 (tp) cc_final: 0.8800 (tp)
REVERT: B  101 PHE cc_start: 0.8063 (m-10) cc_final: 0.7725 (m-10)
REVERT: B  152 MET cc_start: 0.9081 (mmm) cc_final: 0.8723 (mmm)
REVERT: B  234 GLU cc_start: 0.9260 (pt0) cc_final: 0.9037 (pt0)
REVERT: B  241 GLN cc_start: 0.8211 (pt0) cc_final: 0.7859 (pt0)
REVERT: B  257 GLU cc_start: 0.8720 (tp30) cc_final: 0.8468 (tp30)
REVERT: B  315 ILE cc_start: 0.8919 (mp) cc_final: 0.8685 (mp)
REVERT: C   48 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8675 (tm-30)
REVERT: C   76 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: C   82 MET cc_start: 0.9112 (mpp) cc_final: 0.8625 (mpp)
REVERT: D   13 LEU cc_start: 0.9094 (tp) cc_final: 0.8591 (tp)
REVERT: D   17 PHE cc_start: 0.8939 (m-10) cc_final: 0.8609 (m-80)
REVERT: D   19 PHE cc_start: 0.8828 (m-80) cc_final: 0.8607 (m-80)
REVERT: D   49 MET cc_start: 0.8757 (mmm) cc_final: 0.8131 (mmm)
REVERT: D   55 ASP cc_start: 0.8659 (t70) cc_final: 0.8292 (t70)
REVERT: D   76 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8680 (mm-30)
REVERT: D   91 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8849 (mtpp)
REVERT: D  155 ILE cc_start: 0.9447 (mt) cc_final: 0.9207 (mt)
REVERT: D  163 ASN cc_start: 0.8834 (m110) cc_final: 0.8355 (m110)
REVERT: E  204 ARG cc_start: 0.8752 (ppt170) cc_final: 0.8478 (ppt170)
REVERT: E  266 LYS cc_start: 0.8563 (mttt) cc_final: 0.8199 (mtmt)
REVERT: E  273 ASP cc_start: 0.9451 (m-30) cc_final: 0.9183 (m-30)
REVERT: E  277 TYR cc_start: 0.8559 (m-80) cc_final: 0.8119 (m-80)
REVERT: F  221 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8597 (tp-100)
REVERT: F  225 MET cc_start: 0.9073 (mmt) cc_final: 0.8404 (mmm)
REVERT: F  227 LEU cc_start: 0.8818 (mt) cc_final: 0.8420 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.0966
  time to fit residues: 39.8955
Evaluate side-chains
  252 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 89 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 274 ASN
D  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.112796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.080857 restraints weight = 28568.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.083130 restraints weight = 17691.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.084582 restraints weight = 13030.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.085468 restraints weight = 10813.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.085829 restraints weight = 9665.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8922  Z= 0.234
  Angle     :  0.739   9.533  12049  Z= 0.388
  Chirality :  0.046   0.271   1386
  Planarity :  0.005   0.063   1497
  Dihedral  :  5.300  22.561   1162
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.20 %
    Favored  : 96.70 %
  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: -1.45 (0.26), residues: 1077
  helix: -0.07 (0.19), residues: 711
  sheet: -3.52 (0.47), residues: 95
  loop : -2.07 (0.42), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 192 
 TYR   0.017   0.002   TYR B 302 
 PHE   0.030   0.002   PHE A 165 
 TRP   0.064   0.002   TRP D 158 
 HIS   0.007   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 8918)
  covalent geometry    : angle       0.73870 (12045)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       1.97410 (    4)
  hydrogen bonds       : bond        0.04852 (  566)
  hydrogen bonds       : angle       5.48519 ( 1689)
  metal coordination   : bond        0.00296 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 300
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.9253 (mm) cc_final: 0.8896 (tp)
REVERT: A  148 TYR cc_start: 0.8732 (t80) cc_final: 0.8501 (t80)
REVERT: A  221 LYS cc_start: 0.9328 (mttt) cc_final: 0.9049 (mmmt)
REVERT: A  257 GLU cc_start: 0.8508 (tp30) cc_final: 0.8175 (tm-30)
REVERT: A  264 GLU cc_start: 0.8241 (tt0) cc_final: 0.8032 (tt0)
REVERT: A  291 MET cc_start: 0.8556 (mtp) cc_final: 0.8326 (pmm)
REVERT: B   69 LEU cc_start: 0.9006 (tp) cc_final: 0.8759 (tp)
REVERT: B  101 PHE cc_start: 0.8178 (m-10) cc_final: 0.7599 (m-10)
REVERT: B  152 MET cc_start: 0.9062 (mmm) cc_final: 0.8698 (mmm)
REVERT: B  234 GLU cc_start: 0.9235 (pt0) cc_final: 0.8994 (pt0)
REVERT: B  241 GLN cc_start: 0.7977 (pt0) cc_final: 0.7640 (pt0)
REVERT: B  257 GLU cc_start: 0.8626 (tp30) cc_final: 0.8416 (tp30)
REVERT: B  293 GLU cc_start: 0.8574 (pp20) cc_final: 0.7980 (tm-30)
REVERT: B  315 ILE cc_start: 0.8961 (mp) cc_final: 0.8730 (mp)
REVERT: C   49 MET cc_start: 0.9377 (ttt) cc_final: 0.9146 (ttm)
REVERT: C   76 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: C   82 MET cc_start: 0.8934 (mpp) cc_final: 0.8653 (mpp)
REVERT: D   13 LEU cc_start: 0.9056 (tp) cc_final: 0.8541 (tp)
REVERT: D   17 PHE cc_start: 0.8893 (m-10) cc_final: 0.8582 (m-80)
REVERT: D   49 MET cc_start: 0.8810 (mmm) cc_final: 0.8078 (mmm)
REVERT: D   55 ASP cc_start: 0.8592 (t70) cc_final: 0.8181 (t70)
REVERT: D   59 GLU cc_start: 0.8817 (pt0) cc_final: 0.8295 (pt0)
REVERT: D   76 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8718 (mm-30)
REVERT: D  155 ILE cc_start: 0.9404 (mt) cc_final: 0.9200 (mt)
REVERT: D  163 ASN cc_start: 0.8823 (m110) cc_final: 0.8329 (m110)
REVERT: E  204 ARG cc_start: 0.8690 (ppt170) cc_final: 0.8464 (ppt170)
REVERT: E  266 LYS cc_start: 0.8554 (mttt) cc_final: 0.8192 (mtmt)
REVERT: E  273 ASP cc_start: 0.9449 (m-30) cc_final: 0.9194 (m-30)
REVERT: E  277 TYR cc_start: 0.8577 (m-80) cc_final: 0.8167 (m-80)
REVERT: F  221 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8482 (tp-100)
REVERT: F  225 MET cc_start: 0.9071 (mmt) cc_final: 0.8132 (mmm)
REVERT: F  227 LEU cc_start: 0.8802 (mt) cc_final: 0.8457 (tp)
REVERT: F  229 LYS cc_start: 0.8511 (mppt) cc_final: 0.8126 (tptt)
REVERT: F  261 MET cc_start: 0.8630 (tpp) cc_final: 0.8084 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 301
  average time/residue: 0.0931
  time to fit residues: 38.6701
Evaluate side-chains
  254 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.115929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.083885 restraints weight = 27854.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.086285 restraints weight = 17002.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.087818 restraints weight = 12415.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.088734 restraints weight = 10201.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.089220 restraints weight = 9067.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8922  Z= 0.165
  Angle     :  0.692   9.762  12049  Z= 0.359
  Chirality :  0.045   0.313   1386
  Planarity :  0.005   0.068   1497
  Dihedral  :  5.052  19.296   1162
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  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: -1.03 (0.26), residues: 1077
  helix:  0.32 (0.19), residues: 720
  sheet: -3.07 (0.50), residues: 92
  loop : -2.37 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 192 
 TYR   0.015   0.001   TYR C  72 
 PHE   0.037   0.002   PHE D  19 
 TRP   0.078   0.002   TRP D 158 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8918)
  covalent geometry    : angle       0.69159 (12045)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       1.57060 (    4)
  hydrogen bonds       : bond        0.04580 (  566)
  hydrogen bonds       : angle       5.21005 ( 1689)
  metal coordination   : bond        0.00122 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.365 
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: A  103 MET cc_start: 0.9000 (tmm) cc_final: 0.8546 (tmm)
REVERT: A  105 ILE cc_start: 0.9177 (mm) cc_final: 0.8946 (tp)
REVERT: A  221 LYS cc_start: 0.9273 (mttt) cc_final: 0.8927 (mmmt)
REVERT: A  257 GLU cc_start: 0.8466 (tp30) cc_final: 0.8184 (tm-30)
REVERT: B   60 GLN cc_start: 0.8332 (mm110) cc_final: 0.7593 (mm110)
REVERT: B   69 LEU cc_start: 0.8902 (tp) cc_final: 0.8685 (tp)
REVERT: B  101 PHE cc_start: 0.8085 (m-10) cc_final: 0.7599 (m-10)
REVERT: B  152 MET cc_start: 0.9072 (mmm) cc_final: 0.8775 (mmm)
REVERT: B  162 VAL cc_start: 0.8730 (t) cc_final: 0.8518 (m)
REVERT: B  241 GLN cc_start: 0.8047 (pt0) cc_final: 0.7655 (pt0)
REVERT: B  257 GLU cc_start: 0.8576 (tp30) cc_final: 0.8330 (tp30)
REVERT: B  293 GLU cc_start: 0.8462 (pp20) cc_final: 0.8033 (tm-30)
REVERT: B  315 ILE cc_start: 0.8939 (mp) cc_final: 0.8698 (mp)
REVERT: C   49 MET cc_start: 0.9403 (ttt) cc_final: 0.9146 (ttm)
REVERT: C   52 GLU cc_start: 0.8794 (pt0) cc_final: 0.8509 (pt0)
REVERT: C   60 LEU cc_start: 0.9293 (tt) cc_final: 0.8942 (tt)
REVERT: C   72 TYR cc_start: 0.8708 (t80) cc_final: 0.8415 (t80)
REVERT: D   17 PHE cc_start: 0.8826 (m-10) cc_final: 0.8601 (m-80)
REVERT: D   19 PHE cc_start: 0.8699 (m-80) cc_final: 0.8288 (m-80)
REVERT: D   49 MET cc_start: 0.8835 (mmm) cc_final: 0.7957 (mmm)
REVERT: D   55 ASP cc_start: 0.8560 (t70) cc_final: 0.8190 (t70)
REVERT: D   59 GLU cc_start: 0.8861 (pt0) cc_final: 0.8326 (pt0)
REVERT: D   76 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: D   91 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8735 (mttp)
REVERT: D  155 ILE cc_start: 0.9421 (mt) cc_final: 0.9179 (mt)
REVERT: D  163 ASN cc_start: 0.8765 (m110) cc_final: 0.8204 (m110)
REVERT: E  273 ASP cc_start: 0.9418 (m-30) cc_final: 0.9062 (m-30)
REVERT: E  277 TYR cc_start: 0.8529 (m-80) cc_final: 0.8227 (m-80)
REVERT: F  221 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8426 (tp-100)
REVERT: F  225 MET cc_start: 0.9035 (mmt) cc_final: 0.8514 (mmm)
REVERT: F  261 MET cc_start: 0.8614 (tpp) cc_final: 0.8119 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 320
  average time/residue: 0.0915
  time to fit residues: 40.3461
Evaluate side-chains
  256 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 98 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.113697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.081703 restraints weight = 28181.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084119 restraints weight = 16858.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.085664 restraints weight = 12138.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.086586 restraints weight = 9889.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.086976 restraints weight = 8747.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8922  Z= 0.211
  Angle     :  0.751   9.951  12049  Z= 0.391
  Chirality :  0.046   0.311   1386
  Planarity :  0.005   0.071   1497
  Dihedral  :  5.147  23.591   1162
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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: -1.13 (0.26), residues: 1077
  helix:  0.21 (0.19), residues: 705
  sheet: -3.42 (0.46), residues: 95
  loop : -2.00 (0.41), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 326 
 TYR   0.018   0.002   TYR E 277 
 PHE   0.033   0.002   PHE D  19 
 TRP   0.083   0.003   TRP D 158 
 HIS   0.007   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8918)
  covalent geometry    : angle       0.75069 (12045)
  SS BOND              : bond        0.00365 (    2)
  SS BOND              : angle       1.64831 (    4)
  hydrogen bonds       : bond        0.04750 (  566)
  hydrogen bonds       : angle       5.40530 ( 1689)
  metal coordination   : bond        0.00170 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.435 
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: A  103 MET cc_start: 0.9077 (tmm) cc_final: 0.8650 (tmm)
REVERT: A  105 ILE cc_start: 0.9198 (mm) cc_final: 0.8998 (tp)
REVERT: A  257 GLU cc_start: 0.8537 (tp30) cc_final: 0.8219 (tm-30)
REVERT: A  326 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7479 (mmm-85)
REVERT: B  152 MET cc_start: 0.9084 (mmm) cc_final: 0.8786 (mmm)
REVERT: B  158 MET cc_start: 0.8825 (tmm) cc_final: 0.8588 (tmm)
REVERT: B  241 GLN cc_start: 0.8162 (pt0) cc_final: 0.7743 (pt0)
REVERT: B  293 GLU cc_start: 0.8505 (pp20) cc_final: 0.7866 (tm-30)
REVERT: C   49 MET cc_start: 0.9425 (ttt) cc_final: 0.9166 (ttm)
REVERT: C   52 GLU cc_start: 0.8840 (pt0) cc_final: 0.8519 (pt0)
REVERT: C   60 LEU cc_start: 0.9336 (tt) cc_final: 0.9099 (tp)
REVERT: C   82 MET cc_start: 0.8967 (mpp) cc_final: 0.8671 (mpp)
REVERT: D   17 PHE cc_start: 0.8815 (m-10) cc_final: 0.8610 (m-80)
REVERT: D   19 PHE cc_start: 0.8745 (m-80) cc_final: 0.8453 (m-80)
REVERT: D   49 MET cc_start: 0.8836 (mmm) cc_final: 0.8019 (mmm)
REVERT: D   55 ASP cc_start: 0.8636 (t70) cc_final: 0.8212 (t70)
REVERT: D   59 GLU cc_start: 0.8845 (pt0) cc_final: 0.8272 (pt0)
REVERT: D   91 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8786 (mtpp)
REVERT: D  163 ASN cc_start: 0.8743 (m110) cc_final: 0.8174 (m110)
REVERT: E  255 GLU cc_start: 0.8594 (pm20) cc_final: 0.8313 (pm20)
REVERT: E  277 TYR cc_start: 0.8585 (m-80) cc_final: 0.8171 (m-80)
REVERT: F  221 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8280 (tp-100)
REVERT: F  225 MET cc_start: 0.9040 (mmt) cc_final: 0.8225 (mmm)
REVERT: F  261 MET cc_start: 0.8608 (tpp) cc_final: 0.8104 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.0890
  time to fit residues: 36.6729
Evaluate side-chains
  242 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:   30.0000
   chunk 22 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 59 optimal weight:    0.0370
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    0.4980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS
A 273 HIS
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.118236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.085832 restraints weight = 27847.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.088481 restraints weight = 16383.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.090179 restraints weight = 11621.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.091214 restraints weight = 9364.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.091850 restraints weight = 8235.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8922  Z= 0.148
  Angle     :  0.714   9.732  12049  Z= 0.365
  Chirality :  0.046   0.313   1386
  Planarity :  0.005   0.074   1497
  Dihedral  :  4.866  18.545   1162
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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: -0.79 (0.26), residues: 1077
  helix:  0.52 (0.19), residues: 717
  sheet: -2.81 (0.51), residues: 91
  loop : -2.36 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 326 
 TYR   0.020   0.001   TYR E 277 
 PHE   0.027   0.002   PHE D  19 
 TRP   0.094   0.003   TRP D 158 
 HIS   0.004   0.001   HIS E 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8918)
  covalent geometry    : angle       0.71401 (12045)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       1.42888 (    4)
  hydrogen bonds       : bond        0.04452 (  566)
  hydrogen bonds       : angle       5.17439 ( 1689)
  metal coordination   : bond        0.00099 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 0.353 
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: A  101 PHE cc_start: 0.7690 (m-80) cc_final: 0.7403 (m-80)
REVERT: A  103 MET cc_start: 0.9006 (tmm) cc_final: 0.8423 (tmm)
REVERT: A  105 ILE cc_start: 0.9159 (mm) cc_final: 0.8928 (tp)
REVERT: A  189 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7477 (mmm160)
REVERT: A  326 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7498 (mmm-85)
REVERT: B   92 THR cc_start: 0.8492 (p) cc_final: 0.8272 (p)
REVERT: B  152 MET cc_start: 0.9068 (mmm) cc_final: 0.8738 (mmm)
REVERT: B  153 ARG cc_start: 0.8872 (ttm170) cc_final: 0.8608 (ptp-170)
REVERT: B  241 GLN cc_start: 0.8090 (pt0) cc_final: 0.7509 (pp30)
REVERT: B  293 GLU cc_start: 0.8382 (pp20) cc_final: 0.7835 (tm-30)
REVERT: C   49 MET cc_start: 0.9418 (ttt) cc_final: 0.9148 (ttm)
REVERT: C   58 GLN cc_start: 0.8683 (pp30) cc_final: 0.8046 (tm-30)
REVERT: C   82 MET cc_start: 0.8895 (mpp) cc_final: 0.8575 (mpp)
REVERT: D   17 PHE cc_start: 0.8778 (m-10) cc_final: 0.8551 (m-80)
REVERT: D   49 MET cc_start: 0.8835 (mmm) cc_final: 0.8198 (mmm)
REVERT: D   55 ASP cc_start: 0.8583 (t70) cc_final: 0.8150 (t70)
REVERT: D   59 GLU cc_start: 0.8853 (pt0) cc_final: 0.8309 (pt0)
REVERT: D   76 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8637 (mm-30)
REVERT: E  255 GLU cc_start: 0.8564 (pm20) cc_final: 0.8301 (pm20)
REVERT: E  277 TYR cc_start: 0.8552 (m-80) cc_final: 0.8130 (m-80)
REVERT: F  221 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8180 (tp-100)
REVERT: F  225 MET cc_start: 0.8937 (mmt) cc_final: 0.8205 (mmm)
REVERT: F  261 MET cc_start: 0.8570 (tpp) cc_final: 0.8065 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 314
  average time/residue: 0.0928
  time to fit residues: 40.3970
Evaluate side-chains
  251 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 84 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.117053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.084643 restraints weight = 27810.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.087102 restraints weight = 16505.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.088716 restraints weight = 11843.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.089676 restraints weight = 9642.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.090207 restraints weight = 8539.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8922  Z= 0.171
  Angle     :  0.753  11.134  12049  Z= 0.385
  Chirality :  0.046   0.316   1386
  Planarity :  0.005   0.068   1497
  Dihedral  :  4.900  19.336   1162
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.76 (0.26), residues: 1077
  helix:  0.52 (0.19), residues: 712
  sheet: -2.65 (0.52), residues: 91
  loop : -2.29 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 326 
 TYR   0.015   0.002   TYR A 148 
 PHE   0.031   0.002   PHE D  19 
 TRP   0.098   0.003   TRP D 158 
 HIS   0.007   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8918)
  covalent geometry    : angle       0.75246 (12045)
  SS BOND              : bond        0.00177 (    2)
  SS BOND              : angle       1.74240 (    4)
  hydrogen bonds       : bond        0.04573 (  566)
  hydrogen bonds       : angle       5.26814 ( 1689)
  metal coordination   : bond        0.00130 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.8509 (tpt90) cc_final: 0.8283 (tpm170)
REVERT: A  326 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7591 (mmm-85)
REVERT: B   92 THR cc_start: 0.8560 (p) cc_final: 0.8334 (p)
REVERT: B  152 MET cc_start: 0.9092 (mmm) cc_final: 0.8761 (mmm)
REVERT: B  153 ARG cc_start: 0.8918 (ttm170) cc_final: 0.8689 (ptp-170)
REVERT: B  241 GLN cc_start: 0.8128 (pt0) cc_final: 0.7565 (pp30)
REVERT: B  293 GLU cc_start: 0.8436 (pp20) cc_final: 0.7923 (tm-30)
REVERT: B  315 ILE cc_start: 0.9028 (mp) cc_final: 0.8771 (mp)
REVERT: C   49 MET cc_start: 0.9480 (ttt) cc_final: 0.9260 (ttm)
REVERT: C   58 GLN cc_start: 0.8718 (pp30) cc_final: 0.8150 (tm-30)
REVERT: C   82 MET cc_start: 0.8947 (mpp) cc_final: 0.8599 (mpp)
REVERT: D   49 MET cc_start: 0.8793 (mmm) cc_final: 0.8137 (mmm)
REVERT: D   55 ASP cc_start: 0.8615 (t70) cc_final: 0.8153 (t70)
REVERT: D   59 GLU cc_start: 0.8849 (pt0) cc_final: 0.8240 (pt0)
REVERT: D   91 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8675 (mtpp)
REVERT: D  163 ASN cc_start: 0.8581 (m110) cc_final: 0.8071 (m110)
REVERT: E  204 ARG cc_start: 0.8409 (ppt170) cc_final: 0.8067 (ppt170)
REVERT: E  255 GLU cc_start: 0.8590 (pm20) cc_final: 0.8339 (pm20)
REVERT: E  273 ASP cc_start: 0.9453 (m-30) cc_final: 0.9208 (m-30)
REVERT: E  277 TYR cc_start: 0.8559 (m-80) cc_final: 0.8108 (m-80)
REVERT: F  221 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8142 (tp-100)
REVERT: F  225 MET cc_start: 0.8956 (mmt) cc_final: 0.8191 (mmm)
REVERT: F  261 MET cc_start: 0.8510 (tpp) cc_final: 0.8064 (ptt)
REVERT: F  286 GLU cc_start: 0.7982 (mp0) cc_final: 0.7754 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.0919
  time to fit residues: 38.0039
Evaluate side-chains
  245 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.116702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084017 restraints weight = 28079.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.086577 restraints weight = 16637.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.088239 restraints weight = 11890.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.089223 restraints weight = 9644.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.089829 restraints weight = 8531.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8922  Z= 0.178
  Angle     :  0.768  10.445  12049  Z= 0.397
  Chirality :  0.047   0.323   1386
  Planarity :  0.005   0.069   1497
  Dihedral  :  4.929  19.449   1162
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.90 (0.26), residues: 1077
  helix:  0.39 (0.19), residues: 714
  sheet: -2.64 (0.51), residues: 91
  loop : -2.33 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 295 
 TYR   0.012   0.002   TYR E 277 
 PHE   0.060   0.002   PHE D  17 
 TRP   0.103   0.003   TRP D 158 
 HIS   0.009   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8918)
  covalent geometry    : angle       0.76804 (12045)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       1.61781 (    4)
  hydrogen bonds       : bond        0.04582 (  566)
  hydrogen bonds       : angle       5.28921 ( 1689)
  metal coordination   : bond        0.00092 (    2)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.364 
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: A  103 MET cc_start: 0.8862 (tmm) cc_final: 0.8521 (tmm)
REVERT: A  148 TYR cc_start: 0.8806 (t80) cc_final: 0.8584 (t80)
REVERT: A  185 ARG cc_start: 0.8484 (tpt90) cc_final: 0.8273 (tpm170)
REVERT: A  299 GLN cc_start: 0.8639 (mt0) cc_final: 0.8412 (mt0)
REVERT: A  326 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7514 (mmm-85)
REVERT: B  152 MET cc_start: 0.9101 (mmm) cc_final: 0.8770 (mmm)
REVERT: B  153 ARG cc_start: 0.8903 (ttm170) cc_final: 0.8703 (ptp-170)
REVERT: B  226 LEU cc_start: 0.9165 (mm) cc_final: 0.8770 (tt)
REVERT: B  241 GLN cc_start: 0.8170 (pt0) cc_final: 0.7590 (pp30)
REVERT: B  293 GLU cc_start: 0.8481 (pp20) cc_final: 0.8136 (tm-30)
REVERT: C   58 GLN cc_start: 0.8715 (pp30) cc_final: 0.8147 (tm-30)
REVERT: C   82 MET cc_start: 0.9031 (mpp) cc_final: 0.8624 (mpp)
REVERT: D   17 PHE cc_start: 0.8713 (m-80) cc_final: 0.8344 (m-80)
REVERT: D   49 MET cc_start: 0.8784 (mmm) cc_final: 0.8136 (mmm)
REVERT: D   55 ASP cc_start: 0.8644 (t70) cc_final: 0.8194 (t70)
REVERT: D   59 GLU cc_start: 0.8886 (pt0) cc_final: 0.8318 (pt0)
REVERT: D   91 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8777 (mtpp)
REVERT: D  163 ASN cc_start: 0.8618 (m110) cc_final: 0.8076 (m110)
REVERT: E  255 GLU cc_start: 0.8592 (pm20) cc_final: 0.8336 (pm20)
REVERT: E  273 ASP cc_start: 0.9456 (m-30) cc_final: 0.9236 (m-30)
REVERT: E  277 TYR cc_start: 0.8597 (m-80) cc_final: 0.8224 (m-80)
REVERT: F  221 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8113 (tp-100)
REVERT: F  225 MET cc_start: 0.8949 (mmt) cc_final: 0.8141 (mmm)
REVERT: F  261 MET cc_start: 0.8496 (tpp) cc_final: 0.8033 (ptt)
REVERT: F  286 GLU cc_start: 0.7973 (mp0) cc_final: 0.7771 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.0955
  time to fit residues: 39.3959
Evaluate side-chains
  251 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 105 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 52 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.116322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.083101 restraints weight = 28572.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.085590 restraints weight = 17200.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087189 restraints weight = 12465.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.088086 restraints weight = 10226.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.088744 restraints weight = 9113.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8922  Z= 0.196
  Angle     :  0.788  10.495  12049  Z= 0.407
  Chirality :  0.046   0.315   1386
  Planarity :  0.005   0.065   1497
  Dihedral  :  4.970  20.337   1162
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -1.03 (0.26), residues: 1077
  helix:  0.30 (0.19), residues: 720
  sheet: -2.74 (0.50), residues: 91
  loop : -2.46 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 326 
 TYR   0.028   0.002   TYR E 264 
 PHE   0.056   0.002   PHE D  17 
 TRP   0.104   0.003   TRP D 158 
 HIS   0.009   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8918)
  covalent geometry    : angle       0.78758 (12045)
  SS BOND              : bond        0.00095 (    2)
  SS BOND              : angle       1.59724 (    4)
  hydrogen bonds       : bond        0.04681 (  566)
  hydrogen bonds       : angle       5.33296 ( 1689)
  metal coordination   : bond        0.00162 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1821.27 seconds
wall clock time: 32 minutes 6.00 seconds (1926.00 seconds total)