Starting phenix.real_space_refine
on Sun Aug 24 03:23:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmn_41395/08_2025/8tmn_41395.cif"
  }
  resolution = 3.3
  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=   0.015 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic.
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
     Mg      3      5.21       5
     S      58      5.16       5
     C   10437      2.51       5
     N    2613      2.21       5
     O    2948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16059
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 983
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
    Chain: "A"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2805
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2925
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 2790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2790
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 13, 'TRANS': 319}
    Chain: "D"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2890
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 15, 'TRANS': 331}
    Chain: "E"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2860
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 15, 'TRANS': 327}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.30, per 1000 atoms: 0.27
  Number of scatterers: 16059
  At special positions: 0
  Unit cell: (125.434, 139.253, 138.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     Mg      3     11.99
     O    2948      8.00
     N    2613      7.00
     C   10437      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 795.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3726

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      52.8% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'H' and resid 65 through 68
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.806A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
      Proline residue:  A  52  - end of helix
      removed outlier: 3.907A  pdb=" N   ASP A  55 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 3.571A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 6.329A  pdb=" N   ARG A 165 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 201
      removed outlier: 3.696A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      Proline residue:  A 227  - end of helix
      removed outlier: 3.969A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 282
      removed outlier: 3.517A  pdb=" N   PHE A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   SER A 282 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 312
      Proline residue:  A 303  - end of helix
    Processing helix  chain 'A' and resid 326 through 349
      removed outlier: 3.559A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 51
      removed outlier: 3.864A  pdb=" N   VAL B  50 " --> pdb=" O   ASP B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 55
      removed outlier: 3.946A  pdb=" N   ASP B  55 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 52 through 55'
    Processing helix  chain 'B' and resid 69 through 81
      removed outlier: 3.655A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 147 through 157
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 165 through 200
      removed outlier: 3.563A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 238
      Proline residue:  B 227  - end of helix
      removed outlier: 3.654A  pdb=" N   TYR B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 311
      removed outlier: 3.871A  pdb=" N   VAL B 290 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 325 through 348
    Processing helix  chain 'C' and resid 70 through 81
    Processing helix  chain 'C' and resid 83 through 92
    Processing helix  chain 'C' and resid 147 through 156
      removed outlier: 3.812A  pdb=" N   ARG C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE C 154 " --> pdb=" O   VAL C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 202
      removed outlier: 3.674A  pdb=" N   LEU C 170 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 236
      removed outlier: 3.588A  pdb=" N   VAL C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
    Processing helix  chain 'C' and resid 246 through 312
      removed outlier: 4.421A  pdb=" N   TYR C 250 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE C 261 " --> pdb=" O   HIS C 257 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA C 262 " --> pdb=" O   THR C 258 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   THR C 264 " --> pdb=" O   GLN C 260 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLU C 266 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR C 267 " --> pdb=" O   ASP C 263 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU C 280 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER C 281 " --> pdb=" O   ASP C 277 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 325 through 347
      removed outlier: 3.973A  pdb=" N   VAL C 329 " --> pdb=" O   TRP C 325 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   MET C 341 " --> pdb=" O   ILE C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 348 through 350
      No H-bonds generated for 'chain 'C' and resid 348 through 350'
    Processing helix  chain 'D' and resid 47 through 51
    Processing helix  chain 'D' and resid 70 through 81
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 147 through 157
      removed outlier: 3.646A  pdb=" N   ARG D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.631A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 238
      removed outlier: 3.702A  pdb=" N   VAL D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN D 209 " --> pdb=" O   LYS D 205 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   TRP D 226 " --> pdb=" O   ARG D 222 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
      removed outlier: 3.815A  pdb=" N   SER D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU D 235 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 311
      removed outlier: 3.790A  pdb=" N   PHE D 251 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG D 252 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP D 253 " --> pdb=" O   PRO D 249 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL D 254 " --> pdb=" O   TYR D 250 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ASP D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   THR D 264 " --> pdb=" O   GLN D 260 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP D 270 " --> pdb=" O   GLU D 266 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU D 275 " --> pdb=" O   ILE D 271 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE D 297 " --> pdb=" O   VAL D 293 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA D 298 " --> pdb=" O   LEU D 294 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 326 through 349
      removed outlier: 3.835A  pdb=" N   VAL D 330 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 56
      removed outlier: 3.547A  pdb=" N   ASP E  55 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 81
      removed outlier: 3.713A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 165 through 202
      removed outlier: 3.660A  pdb=" N   LEU E 169 " --> pdb=" O   ARG E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 237
      Proline residue:  E 227  - end of helix
      removed outlier: 3.643A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 244 through 246
      No H-bonds generated for 'chain 'E' and resid 244 through 246'
    Processing helix  chain 'E' and resid 247 through 312
      removed outlier: 3.782A  pdb=" N   ASP E 253 " --> pdb=" O   PRO E 249 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL E 254 " --> pdb=" O   TYR E 250 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA E 298 " --> pdb=" O   LEU E 294 " (cutoff:3.500A)
      Proline residue:  E 303  - end of helix
    Processing helix  chain 'E' and resid 325 through 348
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.401A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.401A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA5, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.713A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA H  52 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15
      removed outlier: 6.533A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44
      removed outlier: 3.513A  pdb=" N   LYS A  98 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44
    Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 101
      removed outlier: 3.683A  pdb=" N   SER C 128 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44
      removed outlier: 3.867A  pdb=" N   PHE D  42 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL D  31 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR D  44 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ILE D  29 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL D 136 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 32
      removed outlier: 3.808A  pdb=" N   GLU E 121 " --> pdb=" O   ASP E 116 " (cutoff:3.500A)

    996 hydrogen bonds defined for protein.
    2847 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 1.84 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: 5048
        1.34 -     1.46: 3075
        1.46 -     1.58: 8193
        1.58 -     1.69: 0
        1.69 -     1.81: 107
  Bond restraints: 16423
  Sorted by residual:
  bond pdb=" C   LEU E  51 "
       pdb=" N   PRO E  52 "
    ideal  model  delta    sigma   weight residual
    1.337  1.357 -0.020 9.80e-03 1.04e+04 4.15e+00
  bond pdb=" CA  ARG D 202 "
       pdb=" CB  ARG D 202 "
    ideal  model  delta    sigma   weight residual
    1.526  1.538 -0.012 9.30e-03 1.16e+04 1.71e+00
  bond pdb=" CB  VAL B 254 "
       pdb=" CG2 VAL B 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.51e+00
  bond pdb=" C   LEU B  51 "
       pdb=" N   PRO B  52 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.06e+00
  bond pdb=" C   ASP D 148 "
       pdb=" N   PRO D 149 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.28e-02 6.10e+03 1.03e+00
  ... (remaining 16418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 21926
        2.13 -     4.25: 291
        4.25 -     6.38: 50
        6.38 -     8.50: 3
        8.50 -    10.63: 1
  Bond angle restraints: 22271
  Sorted by residual:
  angle pdb=" C   VAL C  50 "
        pdb=" N   LEU C  51 "
        pdb=" CA  LEU C  51 "
      ideal   model   delta    sigma   weight residual
     121.80  132.43  -10.63 2.44e+00 1.68e-01 1.90e+01
  angle pdb=" C   GLY D 326 "
        pdb=" N   TYR D 327 "
        pdb=" CA  TYR D 327 "
      ideal   model   delta    sigma   weight residual
     121.80  129.86   -8.06 2.44e+00 1.68e-01 1.09e+01
  angle pdb=" C   LEU E 235 "
        pdb=" N   TYR E 236 "
        pdb=" CA  TYR E 236 "
      ideal   model   delta    sigma   weight residual
     122.36  116.87    5.49 1.72e+00 3.38e-01 1.02e+01
  angle pdb=" N   GLY C 326 "
        pdb=" CA  GLY C 326 "
        pdb=" C   GLY C 326 "
      ideal   model   delta    sigma   weight residual
     113.86  118.34   -4.48 1.50e+00 4.44e-01 8.93e+00
  angle pdb=" N   GLU A  78 "
        pdb=" CA  GLU A  78 "
        pdb=" CB  GLU A  78 "
      ideal   model   delta    sigma   weight residual
     110.16  114.35   -4.19 1.48e+00 4.57e-01 8.03e+00
  ... (remaining 22266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 8761
       17.92 -    35.84: 900
       35.84 -    53.75: 167
       53.75 -    71.67: 18
       71.67 -    89.59: 22
  Dihedral angle restraints: 9868
    sinusoidal: 4103
      harmonic: 5765
  Sorted by residual:
  dihedral pdb=" CA  HIS D  68 "
           pdb=" C   HIS D  68 "
           pdb=" N   ARG D  69 "
           pdb=" CA  ARG D  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  LEU B 321 "
           pdb=" C   LEU B 321 "
           pdb=" N   ARG B 322 "
           pdb=" CA  ARG B 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.22  -20.78     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  PHE C 315 "
           pdb=" C   PHE C 315 "
           pdb=" N   GLU C 316 "
           pdb=" CA  GLU C 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 9865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 2024
       0.053 -    0.106: 434
       0.106 -    0.159: 70
       0.159 -    0.213: 2
       0.213 -    0.266: 2
  Chirality restraints: 2532
  Sorted by residual:
  chirality pdb=" CA  ASP D 148 "
            pdb=" N   ASP D 148 "
            pdb=" C   ASP D 148 "
            pdb=" CB  ASP D 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  ILE D 130 "
            pdb=" CA  ILE D 130 "
            pdb=" CG1 ILE D 130 "
            pdb=" CG2 ILE D 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  PRO D 227 "
            pdb=" N   PRO D 227 "
            pdb=" C   PRO D 227 "
            pdb=" CB  PRO D 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 2529 not shown)

  Planarity restraints: 2785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 202 "    0.058 5.00e-02 4.00e+02   8.85e-02 1.25e+01
        pdb=" N   PRO B 203 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO B 203 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 203 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP D 226 "   -0.048 5.00e-02 4.00e+02   7.16e-02 8.21e+00
        pdb=" N   PRO D 227 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO D 227 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 227 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 148 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.36e+00
        pdb=" N   PRO D 149 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO D 149 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 149 "    0.036 5.00e-02 4.00e+02
  ... (remaining 2782 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 171
        2.64 -     3.21: 15635
        3.21 -     3.77: 25119
        3.77 -     4.34: 33822
        4.34 -     4.90: 54889
  Nonbonded interactions: 129636
  Sorted by model distance:
  nonbonded pdb=" O   LYS C 111 "
            pdb=" OH  TYR C 181 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" O   VAL C 208 "
            pdb=" OG1 THR C 211 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   TYR A 255 "
            pdb=" OG1 THR A 258 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   TYR D 255 "
            pdb=" OG1 THR D 258 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OD1 ASN C  33 "
            pdb=" OG1 THR C  58 "
     model   vdw
     2.233 3.040
  ... (remaining 129631 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 19 through 351)
  selection = (chain 'B' and resid 19 through 351)
  selection = chain 'C'
  selection = (chain 'D' and resid 19 through 351)
  selection = (chain 'E' and resid 19 through 351)
}

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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.970
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16425  Z= 0.147
  Angle     :  0.625  10.629  22275  Z= 0.336
  Chirality :  0.044   0.266   2532
  Planarity :  0.006   0.088   2785
  Dihedral  : 14.945  89.588   6136
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.33 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.01 (0.19), residues: 1930
  helix:  0.82 (0.17), residues: 952
  sheet:  0.57 (0.27), residues: 382
  loop : -1.66 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  96 
 TYR   0.030   0.001   TYR H 103 
 PHE   0.023   0.001   PHE E  27 
 TRP   0.016   0.001   TRP D 350 
 HIS   0.004   0.001   HIS C 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (16423)
  covalent geometry    : angle       0.62518 (22271)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       1.12728 (    4)
  hydrogen bonds       : bond        0.14164 (  980)
  hydrogen bonds       : angle       6.78540 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 461
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  102 SER cc_start: 0.8125 (p) cc_final: 0.7839 (p)
REVERT: A   89 ASP cc_start: 0.7034 (m-30) cc_final: 0.6626 (m-30)
REVERT: A  104 ASN cc_start: 0.7371 (m110) cc_final: 0.7153 (m110)
REVERT: A  178 VAL cc_start: 0.7021 (t) cc_final: 0.5712 (p)
REVERT: A  191 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6664 (mm-30)
REVERT: A  320 GLU cc_start: 0.5501 (pm20) cc_final: 0.4883 (tm-30)
REVERT: B   85 LEU cc_start: 0.8611 (tp) cc_final: 0.8001 (tt)
REVERT: B   89 ASP cc_start: 0.6900 (m-30) cc_final: 0.6565 (m-30)
REVERT: B  318 MET cc_start: 0.3435 (mmt) cc_final: 0.2749 (mmt)
REVERT: C  257 HIS cc_start: 0.8567 (m170) cc_final: 0.7882 (m90)
REVERT: C  304 LEU cc_start: 0.8165 (mm) cc_final: 0.7858 (mm)
REVERT: D   90 ILE cc_start: 0.8706 (pt) cc_final: 0.7995 (mt)
REVERT: D  197 GLU cc_start: 0.8065 (pp20) cc_final: 0.7844 (pp20)
REVERT: D  295 THR cc_start: 0.7565 (m) cc_final: 0.7319 (m)
REVERT: E   85 LEU cc_start: 0.7379 (mm) cc_final: 0.6804 (mm)
REVERT: E   89 ASP cc_start: 0.6993 (m-30) cc_final: 0.6373 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 461
  average time/residue: 0.1345
  time to fit residues: 92.0315
Evaluate side-chains
  395 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 395
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0870
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
L 101 GLN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 ASN
D  74 GLN
** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 209 GLN
E 212 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.163912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.122846 restraints weight = 28597.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.51
r_work: 0.3347 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16425  Z= 0.182
  Angle     :  0.660  10.693  22275  Z= 0.342
  Chirality :  0.045   0.220   2532
  Planarity :  0.005   0.056   2785
  Dihedral  :  4.709  22.797   2155
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.52 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.50 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.61 (0.19), residues: 1930
  helix:  1.52 (0.16), residues: 966
  sheet:  0.49 (0.27), residues: 364
  loop : -1.51 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 202 
 TYR   0.024   0.002   TYR D  19 
 PHE   0.025   0.002   PHE A  79 
 TRP   0.018   0.001   TRP D 226 
 HIS   0.005   0.001   HIS E 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (16423)
  covalent geometry    : angle       0.65911 (22271)
  SS BOND              : bond        0.01233 (    2)
  SS BOND              : angle       3.23470 (    4)
  hydrogen bonds       : bond        0.05553 (  980)
  hydrogen bonds       : angle       4.91168 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 416
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: H  102 SER cc_start: 0.8477 (p) cc_final: 0.8249 (p)
REVERT: A   40 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7358 (ptm-80)
REVERT: A   63 ASN cc_start: 0.8321 (t0) cc_final: 0.7974 (t0)
REVERT: A   89 ASP cc_start: 0.7216 (m-30) cc_final: 0.6678 (m-30)
REVERT: A  104 ASN cc_start: 0.7818 (m110) cc_final: 0.7561 (m110)
REVERT: A  191 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7330 (mm-30)
REVERT: A  197 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6186 (tm-30)
REVERT: A  259 ILE cc_start: 0.8613 (mp) cc_final: 0.8399 (mp)
REVERT: A  277 ASP cc_start: 0.7438 (t0) cc_final: 0.6647 (t0)
REVERT: B   85 LEU cc_start: 0.8734 (tp) cc_final: 0.7989 (tt)
REVERT: B   89 ASP cc_start: 0.7728 (m-30) cc_final: 0.7316 (m-30)
REVERT: B  212 HIS cc_start: 0.7303 (m-70) cc_final: 0.6823 (m-70)
REVERT: C  200 LEU cc_start: 0.7367 (mt) cc_final: 0.6954 (mt)
REVERT: C  233 SER cc_start: 0.8287 (m) cc_final: 0.8058 (p)
REVERT: C  257 HIS cc_start: 0.8704 (m170) cc_final: 0.7920 (m90)
REVERT: C  291 MET cc_start: 0.8186 (mmt) cc_final: 0.7244 (mmm)
REVERT: C  341 MET cc_start: 0.7729 (mpp) cc_final: 0.7318 (mpp)
REVERT: D   63 ASN cc_start: 0.7653 (p0) cc_final: 0.7089 (p0)
REVERT: D   90 ILE cc_start: 0.8700 (pt) cc_final: 0.8426 (mt)
REVERT: D  197 GLU cc_start: 0.8471 (pp20) cc_final: 0.8176 (pp20)
REVERT: D  246 GLU cc_start: 0.8600 (pt0) cc_final: 0.8366 (pp20)
REVERT: D  291 MET cc_start: 0.7975 (mmm) cc_final: 0.7768 (tpt)
REVERT: E   39 PHE cc_start: 0.7284 (p90) cc_final: 0.7015 (p90)
REVERT: E   85 LEU cc_start: 0.7907 (mm) cc_final: 0.7160 (mm)
REVERT: E   89 ASP cc_start: 0.7205 (m-30) cc_final: 0.6579 (m-30)
REVERT: E  252 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7489 (ttp80)
REVERT: E  256 ASP cc_start: 0.7726 (m-30) cc_final: 0.7463 (m-30)
REVERT: E  318 MET cc_start: 0.3098 (mmp) cc_final: 0.2687 (mmp)
  outliers start: 31
  outliers final: 22
  residues processed: 429
  average time/residue: 0.1345
  time to fit residues: 86.1799
Evaluate side-chains
  418 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 396
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  302 MET
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  143 ILE
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  283 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 188 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 186 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0570
   chunk 135 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 168 optimal weight:    2.9990
   overall best weight:    0.9500

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.161962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.121489 restraints weight = 28738.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.83
r_work: 0.3299 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  16425  Z= 0.215
  Angle     :  0.652  10.672  22275  Z= 0.339
  Chirality :  0.045   0.187   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.734  23.912   2155
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.42 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.88 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.71 (0.19), residues: 1930
  helix:  1.69 (0.16), residues: 966
  sheet:  0.46 (0.27), residues: 365
  loop : -1.56 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  40 
 TYR   0.025   0.002   TYR H 106 
 PHE   0.020   0.002   PHE E  27 
 TRP   0.018   0.001   TRP D  61 
 HIS   0.016   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (16423)
  covalent geometry    : angle       0.65087 (22271)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       2.76366 (    4)
  hydrogen bonds       : bond        0.05395 (  980)
  hydrogen bonds       : angle       4.73591 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  460 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 405
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8834 (p) cc_final: 0.8615 (p)
REVERT: A   89 ASP cc_start: 0.7370 (m-30) cc_final: 0.6893 (m-30)
REVERT: A  104 ASN cc_start: 0.7910 (m110) cc_final: 0.7641 (m110)
REVERT: A  191 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7377 (mm-30)
REVERT: A  259 ILE cc_start: 0.8736 (mt) cc_final: 0.8110 (mp)
REVERT: A  263 ASP cc_start: 0.7791 (m-30) cc_final: 0.7400 (m-30)
REVERT: A  277 ASP cc_start: 0.7547 (t0) cc_final: 0.6792 (t0)
REVERT: A  320 GLU cc_start: 0.5734 (pm20) cc_final: 0.4950 (tm-30)
REVERT: B   85 LEU cc_start: 0.8820 (tp) cc_final: 0.8101 (tt)
REVERT: B   89 ASP cc_start: 0.7810 (m-30) cc_final: 0.7414 (m-30)
REVERT: B  212 HIS cc_start: 0.7378 (m-70) cc_final: 0.6927 (m-70)
REVERT: C  132 THR cc_start: 0.5384 (OUTLIER) cc_final: 0.5037 (p)
REVERT: C  232 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7336 (tt)
REVERT: C  257 HIS cc_start: 0.8693 (m170) cc_final: 0.7910 (m90)
REVERT: C  291 MET cc_start: 0.8222 (mmt) cc_final: 0.7831 (mmm)
REVERT: C  341 MET cc_start: 0.7810 (mpp) cc_final: 0.7566 (mtm)
REVERT: D   61 TRP cc_start: 0.7393 (t60) cc_final: 0.7009 (t-100)
REVERT: D   63 ASN cc_start: 0.7376 (p0) cc_final: 0.6444 (p0)
REVERT: D   90 ILE cc_start: 0.8734 (pt) cc_final: 0.8475 (mt)
REVERT: D  197 GLU cc_start: 0.8422 (pp20) cc_final: 0.8136 (pp20)
REVERT: D  246 GLU cc_start: 0.8644 (pt0) cc_final: 0.8407 (pp20)
REVERT: E   39 PHE cc_start: 0.7370 (p90) cc_final: 0.7125 (p90)
REVERT: E   85 LEU cc_start: 0.7752 (mm) cc_final: 0.7253 (mm)
REVERT: E   89 ASP cc_start: 0.7329 (m-30) cc_final: 0.6717 (m-30)
REVERT: E  165 ARG cc_start: 0.8114 (mmp80) cc_final: 0.7856 (mmp80)
REVERT: E  204 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5117 (pm20)
REVERT: E  252 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7603 (ttp80)
REVERT: E  256 ASP cc_start: 0.7725 (m-30) cc_final: 0.7492 (m-30)
REVERT: E  318 MET cc_start: 0.3462 (mmp) cc_final: 0.3022 (mmp)
  outliers start: 55
  outliers final: 38
  residues processed: 430
  average time/residue: 0.1239
  time to fit residues: 79.4134
Evaluate side-chains
  428 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 387
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain D residue  120 HIS
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 173 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    0.2980
   chunk 104 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 133 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  74 GLN
D 126 GLN
E 209 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.163393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.127405 restraints weight = 28626.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.87
r_work: 0.3321 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16425  Z= 0.161
  Angle     :  0.620  10.598  22275  Z= 0.323
  Chirality :  0.044   0.181   2532
  Planarity :  0.005   0.051   2785
  Dihedral  :  4.662  22.070   2155
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.87 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.83 (0.19), residues: 1930
  helix:  1.83 (0.17), residues: 966
  sheet:  0.29 (0.27), residues: 367
  loop : -1.44 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  40 
 TYR   0.027   0.001   TYR A  19 
 PHE   0.022   0.002   PHE B 306 
 TRP   0.012   0.001   TRP H  50 
 HIS   0.012   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (16423)
  covalent geometry    : angle       0.61899 (22271)
  SS BOND              : bond        0.00031 (    2)
  SS BOND              : angle       2.29753 (    4)
  hydrogen bonds       : bond        0.05038 (  980)
  hydrogen bonds       : angle       4.56176 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 392
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8840 (p) cc_final: 0.8615 (p)
REVERT: A   89 ASP cc_start: 0.7353 (m-30) cc_final: 0.6849 (m-30)
REVERT: A  104 ASN cc_start: 0.7822 (m110) cc_final: 0.7551 (m110)
REVERT: A  173 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8084 (mt)
REVERT: A  191 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A  259 ILE cc_start: 0.8684 (mt) cc_final: 0.7961 (mp)
REVERT: A  263 ASP cc_start: 0.7767 (m-30) cc_final: 0.7378 (m-30)
REVERT: A  277 ASP cc_start: 0.7588 (t0) cc_final: 0.6913 (t0)
REVERT: B   85 LEU cc_start: 0.8790 (tp) cc_final: 0.8114 (tt)
REVERT: B   89 ASP cc_start: 0.7807 (m-30) cc_final: 0.7414 (m-30)
REVERT: B  212 HIS cc_start: 0.7351 (m-70) cc_final: 0.6944 (m-70)
REVERT: C  232 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7252 (tt)
REVERT: C  257 HIS cc_start: 0.8708 (m170) cc_final: 0.7998 (m90)
REVERT: C  341 MET cc_start: 0.7829 (mpp) cc_final: 0.7627 (mtm)
REVERT: D   32 MET cc_start: 0.7451 (ptp) cc_final: 0.7222 (mtm)
REVERT: D   90 ILE cc_start: 0.8775 (pt) cc_final: 0.8486 (mt)
REVERT: D  197 GLU cc_start: 0.8408 (pp20) cc_final: 0.8117 (pp20)
REVERT: D  246 GLU cc_start: 0.8598 (pt0) cc_final: 0.8394 (pp20)
REVERT: E   39 PHE cc_start: 0.7351 (p90) cc_final: 0.7113 (p90)
REVERT: E   85 LEU cc_start: 0.7684 (mm) cc_final: 0.7184 (mm)
REVERT: E   89 ASP cc_start: 0.7368 (m-30) cc_final: 0.6791 (m-30)
REVERT: E  165 ARG cc_start: 0.8122 (mmp80) cc_final: 0.7819 (mmp80)
REVERT: E  204 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5009 (pm20)
REVERT: E  291 MET cc_start: 0.8137 (mmt) cc_final: 0.7924 (mmt)
REVERT: E  318 MET cc_start: 0.3555 (mmp) cc_final: 0.3206 (mmp)
  outliers start: 65
  outliers final: 41
  residues processed: 427
  average time/residue: 0.1152
  time to fit residues: 73.8998
Evaluate side-chains
  427 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 383
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain D residue  120 HIS
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  283 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 156 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 145 optimal weight:    0.6980
   chunk 188 optimal weight:    5.9990
   chunk 165 optimal weight:    0.0980
   chunk 180 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.162971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.127338 restraints weight = 28596.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.84
r_work: 0.3310 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3301
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3301
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16425  Z= 0.169
  Angle     :  0.617  10.609  22275  Z= 0.323
  Chirality :  0.044   0.176   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.656  22.662   2155
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.52 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 18.25 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.85 (0.19), residues: 1930
  helix:  1.84 (0.17), residues: 965
  sheet:  0.38 (0.27), residues: 362
  loop : -1.47 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 237 
 TYR   0.021   0.001   TYR H 106 
 PHE   0.020   0.001   PHE E  27 
 TRP   0.022   0.001   TRP D  61 
 HIS   0.011   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (16423)
  covalent geometry    : angle       0.61639 (22271)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       2.11028 (    4)
  hydrogen bonds       : bond        0.04953 (  980)
  hydrogen bonds       : angle       4.50701 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 398
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8854 (p) cc_final: 0.8627 (p)
REVERT: A   40 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.7133 (ptm-80)
REVERT: A   63 ASN cc_start: 0.8445 (t0) cc_final: 0.8173 (t0)
REVERT: A   89 ASP cc_start: 0.7390 (m-30) cc_final: 0.6875 (m-30)
REVERT: A  104 ASN cc_start: 0.7850 (m110) cc_final: 0.7625 (m110)
REVERT: A  173 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8095 (mt)
REVERT: A  191 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: A  259 ILE cc_start: 0.8667 (mt) cc_final: 0.7925 (mp)
REVERT: A  263 ASP cc_start: 0.7779 (m-30) cc_final: 0.7388 (m-30)
REVERT: A  277 ASP cc_start: 0.7725 (t0) cc_final: 0.7075 (t0)
REVERT: B   85 LEU cc_start: 0.8781 (tp) cc_final: 0.8136 (tt)
REVERT: B   89 ASP cc_start: 0.7840 (m-30) cc_final: 0.7449 (m-30)
REVERT: B  212 HIS cc_start: 0.7373 (m-70) cc_final: 0.6897 (m-70)
REVERT: C  232 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7299 (tt)
REVERT: C  257 HIS cc_start: 0.8702 (m170) cc_final: 0.7996 (m90)
REVERT: C  341 MET cc_start: 0.7899 (mpp) cc_final: 0.7659 (mtm)
REVERT: D   23 TYR cc_start: 0.8125 (m-80) cc_final: 0.7855 (m-10)
REVERT: D   32 MET cc_start: 0.7247 (ptp) cc_final: 0.7017 (mtm)
REVERT: D   90 ILE cc_start: 0.8799 (pt) cc_final: 0.8535 (mt)
REVERT: D  143 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7779 (mt)
REVERT: D  197 GLU cc_start: 0.8455 (pp20) cc_final: 0.8157 (pp20)
REVERT: D  246 GLU cc_start: 0.8569 (pt0) cc_final: 0.8324 (pp20)
REVERT: E   39 PHE cc_start: 0.7389 (p90) cc_final: 0.7141 (p90)
REVERT: E   85 LEU cc_start: 0.7736 (mm) cc_final: 0.7248 (mm)
REVERT: E   89 ASP cc_start: 0.7375 (m-30) cc_final: 0.6784 (m-30)
REVERT: E  204 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5080 (pm20)
REVERT: E  318 MET cc_start: 0.3738 (mmp) cc_final: 0.3430 (mmp)
  outliers start: 68
  outliers final: 54
  residues processed: 434
  average time/residue: 0.1090
  time to fit residues: 70.6777
Evaluate side-chains
  441 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 383
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 184 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 168 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** 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 = 0.4127 r_free = 0.4127 target = 0.163832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.127777 restraints weight = 28596.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.68
r_work: 0.3358 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16425  Z= 0.182
  Angle     :  0.632  10.638  22275  Z= 0.329
  Chirality :  0.044   0.223   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.660  21.232   2155
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 18.86 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.85 (0.19), residues: 1930
  helix:  1.83 (0.17), residues: 965
  sheet:  0.42 (0.27), residues: 371
  loop : -1.49 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 237 
 TYR   0.027   0.002   TYR A  19 
 PHE   0.020   0.001   PHE E  27 
 TRP   0.014   0.001   TRP H  50 
 HIS   0.005   0.001   HIS E 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (16423)
  covalent geometry    : angle       0.63137 (22271)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       2.08361 (    4)
  hydrogen bonds       : bond        0.04967 (  980)
  hydrogen bonds       : angle       4.49230 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 391
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8860 (p) cc_final: 0.8632 (p)
REVERT: A   40 ARG cc_start: 0.7331 (ttt-90) cc_final: 0.7093 (ptm-80)
REVERT: A   89 ASP cc_start: 0.7355 (m-30) cc_final: 0.6888 (m-30)
REVERT: A  104 ASN cc_start: 0.7853 (m110) cc_final: 0.7636 (m110)
REVERT: A  173 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (mt)
REVERT: A  259 ILE cc_start: 0.8676 (mt) cc_final: 0.7908 (mp)
REVERT: A  263 ASP cc_start: 0.7696 (m-30) cc_final: 0.7313 (m-30)
REVERT: A  277 ASP cc_start: 0.7709 (t0) cc_final: 0.7055 (t0)
REVERT: B   85 LEU cc_start: 0.8775 (tp) cc_final: 0.8106 (tt)
REVERT: B   89 ASP cc_start: 0.7735 (m-30) cc_final: 0.7337 (m-30)
REVERT: B  212 HIS cc_start: 0.7390 (m-70) cc_final: 0.6923 (m-70)
REVERT: C  257 HIS cc_start: 0.8718 (m170) cc_final: 0.8028 (m90)
REVERT: C  291 MET cc_start: 0.7848 (mmm) cc_final: 0.7632 (mmm)
REVERT: C  341 MET cc_start: 0.7892 (mpp) cc_final: 0.7678 (mtm)
REVERT: D   32 MET cc_start: 0.7209 (ptp) cc_final: 0.6982 (mtm)
REVERT: D   90 ILE cc_start: 0.8827 (pt) cc_final: 0.8561 (mt)
REVERT: D  143 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (mt)
REVERT: D  197 GLU cc_start: 0.8380 (pp20) cc_final: 0.8071 (pp20)
REVERT: D  246 GLU cc_start: 0.8655 (pt0) cc_final: 0.8398 (pp20)
REVERT: E   39 PHE cc_start: 0.7363 (p90) cc_final: 0.7080 (p90)
REVERT: E   85 LEU cc_start: 0.7691 (mm) cc_final: 0.7164 (mm)
REVERT: E   89 ASP cc_start: 0.7354 (m-30) cc_final: 0.6778 (m-30)
REVERT: E  132 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6881 (t)
REVERT: E  204 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5102 (pm20)
REVERT: E  291 MET cc_start: 0.8159 (mmt) cc_final: 0.7638 (mmt)
REVERT: E  318 MET cc_start: 0.3676 (mmp) cc_final: 0.3449 (mmp)
  outliers start: 80
  outliers final: 64
  residues processed: 438
  average time/residue: 0.1131
  time to fit residues: 74.5915
Evaluate side-chains
  449 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 381
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 GLU
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  120 HIS
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 93 optimal weight:    0.2980
   chunk 176 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 151 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 171 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0970
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 GLN
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 GLN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.163575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.127868 restraints weight = 28438.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.75
r_work: 0.3352 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16425  Z= 0.166
  Angle     :  0.640  10.766  22275  Z= 0.332
  Chirality :  0.044   0.211   2532
  Planarity :  0.005   0.053   2785
  Dihedral  :  4.660  20.870   2155
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.32 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.47 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.83 (0.19), residues: 1930
  helix:  1.83 (0.17), residues: 963
  sheet:  0.35 (0.27), residues: 371
  loop : -1.48 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 237 
 TYR   0.027   0.002   TYR H 103 
 PHE   0.020   0.001   PHE E  27 
 TRP   0.013   0.001   TRP C 226 
 HIS   0.010   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (16423)
  covalent geometry    : angle       0.63993 (22271)
  SS BOND              : bond        0.00040 (    2)
  SS BOND              : angle       1.92893 (    4)
  hydrogen bonds       : bond        0.04866 (  980)
  hydrogen bonds       : angle       4.47551 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  464 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 389
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8866 (p) cc_final: 0.8631 (p)
REVERT: A   63 ASN cc_start: 0.8429 (t0) cc_final: 0.8137 (t0)
REVERT: A   89 ASP cc_start: 0.7282 (m-30) cc_final: 0.6775 (m-30)
REVERT: A  104 ASN cc_start: 0.7863 (m110) cc_final: 0.7656 (m110)
REVERT: A  173 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (mt)
REVERT: A  191 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: A  259 ILE cc_start: 0.8667 (mt) cc_final: 0.7969 (mp)
REVERT: A  263 ASP cc_start: 0.7697 (m-30) cc_final: 0.7320 (m-30)
REVERT: A  277 ASP cc_start: 0.7779 (t0) cc_final: 0.7100 (t0)
REVERT: B   85 LEU cc_start: 0.8779 (tp) cc_final: 0.8102 (tt)
REVERT: B   89 ASP cc_start: 0.7753 (m-30) cc_final: 0.7344 (m-30)
REVERT: B  212 HIS cc_start: 0.7403 (m-70) cc_final: 0.6942 (m-70)
REVERT: C   43 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7547 (mptt)
REVERT: C  209 GLN cc_start: 0.8218 (tm130) cc_final: 0.7884 (tm-30)
REVERT: C  232 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7361 (tt)
REVERT: C  257 HIS cc_start: 0.8667 (m170) cc_final: 0.7987 (m90)
REVERT: C  278 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8363 (m)
REVERT: C  341 MET cc_start: 0.7726 (mpp) cc_final: 0.7510 (mtm)
REVERT: D   90 ILE cc_start: 0.8802 (pt) cc_final: 0.8493 (mt)
REVERT: D  143 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7851 (mt)
REVERT: D  197 GLU cc_start: 0.8379 (pp20) cc_final: 0.8067 (pp20)
REVERT: D  246 GLU cc_start: 0.8687 (pt0) cc_final: 0.8430 (pp20)
REVERT: D  257 HIS cc_start: 0.7419 (m90) cc_final: 0.7065 (m90)
REVERT: E   39 PHE cc_start: 0.7392 (p90) cc_final: 0.7083 (p90)
REVERT: E   85 LEU cc_start: 0.7686 (mm) cc_final: 0.7143 (mm)
REVERT: E   89 ASP cc_start: 0.7355 (m-30) cc_final: 0.6779 (m-30)
REVERT: E  132 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6889 (t)
REVERT: E  158 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7832 (mtt180)
REVERT: E  204 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5186 (pm20)
  outliers start: 75
  outliers final: 61
  residues processed: 429
  average time/residue: 0.1129
  time to fit residues: 72.6339
Evaluate side-chains
  447 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 380
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 187 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0770
   chunk 167 optimal weight:    0.9980
   chunk 95 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 168 optimal weight:    0.9980
   chunk 122 optimal weight:    0.7980
   chunk 130 optimal weight:    0.0870
   chunk 2 optimal weight:    0.7980
   chunk 178 optimal weight:    0.9980
   overall best weight:    0.5516

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 GLN
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.164819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129401 restraints weight = 28550.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.82
r_work: 0.3352 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16425  Z= 0.161
  Angle     :  0.646  10.586  22275  Z= 0.335
  Chirality :  0.044   0.206   2532
  Planarity :  0.005   0.049   2785
  Dihedral  :  4.645  20.429   2155
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 19.91 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.84 (0.19), residues: 1930
  helix:  1.85 (0.16), residues: 960
  sheet:  0.36 (0.27), residues: 371
  loop : -1.48 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  54 
 TYR   0.028   0.001   TYR A  19 
 PHE   0.019   0.001   PHE E  27 
 TRP   0.013   0.001   TRP C 226 
 HIS   0.007   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (16423)
  covalent geometry    : angle       0.64511 (22271)
  SS BOND              : bond        0.00044 (    2)
  SS BOND              : angle       1.89284 (    4)
  hydrogen bonds       : bond        0.04810 (  980)
  hydrogen bonds       : angle       4.46058 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  464 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 382
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 GLU cc_start: 0.7066 (tp30) cc_final: 0.6799 (tp30)
REVERT: H  123 THR cc_start: 0.8869 (p) cc_final: 0.8628 (p)
REVERT: A   40 ARG cc_start: 0.7530 (ptm-80) cc_final: 0.7105 (ttp-110)
REVERT: A   63 ASN cc_start: 0.8428 (t0) cc_final: 0.8092 (t0)
REVERT: A   89 ASP cc_start: 0.7303 (m-30) cc_final: 0.6846 (m-30)
REVERT: A  104 ASN cc_start: 0.7869 (m110) cc_final: 0.7657 (m110)
REVERT: A  173 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8071 (mt)
REVERT: A  259 ILE cc_start: 0.8619 (mt) cc_final: 0.7879 (mp)
REVERT: A  263 ASP cc_start: 0.7708 (m-30) cc_final: 0.7302 (m-30)
REVERT: A  277 ASP cc_start: 0.7776 (t0) cc_final: 0.7026 (t0)
REVERT: A  320 GLU cc_start: 0.5754 (pm20) cc_final: 0.4789 (tm-30)
REVERT: B   58 THR cc_start: 0.8366 (m) cc_final: 0.8135 (t)
REVERT: B   85 LEU cc_start: 0.8772 (tp) cc_final: 0.8099 (tt)
REVERT: B   89 ASP cc_start: 0.7745 (m-30) cc_final: 0.7339 (m-30)
REVERT: B  212 HIS cc_start: 0.7354 (m-70) cc_final: 0.6875 (m-70)
REVERT: C   41 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6379 (tp30)
REVERT: C   43 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7629 (mptt)
REVERT: C  232 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7483 (tt)
REVERT: C  257 HIS cc_start: 0.8685 (m170) cc_final: 0.7994 (m90)
REVERT: C  291 MET cc_start: 0.7775 (mmm) cc_final: 0.7543 (mmm)
REVERT: C  341 MET cc_start: 0.7848 (mpp) cc_final: 0.7621 (mtm)
REVERT: D   90 ILE cc_start: 0.8785 (pt) cc_final: 0.8493 (mt)
REVERT: D  143 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7807 (mt)
REVERT: D  197 GLU cc_start: 0.8406 (pp20) cc_final: 0.8090 (pp20)
REVERT: D  246 GLU cc_start: 0.8675 (pt0) cc_final: 0.8417 (pp20)
REVERT: E   39 PHE cc_start: 0.7402 (p90) cc_final: 0.7057 (p90)
REVERT: E   85 LEU cc_start: 0.7718 (mm) cc_final: 0.7181 (mm)
REVERT: E   89 ASP cc_start: 0.7348 (m-30) cc_final: 0.6772 (m-30)
REVERT: E  132 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6857 (t)
REVERT: E  158 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7961 (mtt180)
REVERT: E  165 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7794 (mmp80)
REVERT: E  204 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5158 (pm20)
REVERT: E  318 MET cc_start: 0.3238 (mmp) cc_final: 0.2951 (mmp)
  outliers start: 82
  outliers final: 66
  residues processed: 432
  average time/residue: 0.1057
  time to fit residues: 68.0613
Evaluate side-chains
  445 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 373
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 GLU
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 183 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0770
   chunk 36 optimal weight:    0.5980
   chunk 105 optimal weight:    8.9990
   chunk 78 optimal weight:    0.8980
   chunk 187 optimal weight:    0.6980
   chunk 160 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 GLN
B  74 GLN
C 126 GLN
** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.165361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.129946 restraints weight = 28511.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.67
r_work: 0.3355 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16425  Z= 0.167
  Angle     :  0.658  10.585  22275  Z= 0.343
  Chirality :  0.045   0.226   2532
  Planarity :  0.005   0.055   2785
  Dihedral  :  4.664  20.385   2155
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.42 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.19 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.81 (0.19), residues: 1930
  helix:  1.81 (0.16), residues: 961
  sheet:  0.35 (0.27), residues: 371
  loop : -1.46 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  54 
 TYR   0.022   0.001   TYR C 156 
 PHE   0.019   0.001   PHE E  27 
 TRP   0.015   0.001   TRP C 226 
 HIS   0.008   0.001   HIS C 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16423)
  covalent geometry    : angle       0.65709 (22271)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       1.91371 (    4)
  hydrogen bonds       : bond        0.04800 (  980)
  hydrogen bonds       : angle       4.49317 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 382
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 GLU cc_start: 0.7067 (tp30) cc_final: 0.6859 (tm-30)
REVERT: H  123 THR cc_start: 0.8879 (p) cc_final: 0.8641 (p)
REVERT: A   40 ARG cc_start: 0.7529 (ptm-80) cc_final: 0.7109 (ttp-110)
REVERT: A   63 ASN cc_start: 0.8417 (t0) cc_final: 0.8159 (t0)
REVERT: A   74 GLN cc_start: 0.6785 (tp40) cc_final: 0.6530 (tp-100)
REVERT: A   89 ASP cc_start: 0.7264 (m-30) cc_final: 0.6761 (m-30)
REVERT: A  104 ASN cc_start: 0.7865 (m110) cc_final: 0.7657 (m110)
REVERT: A  173 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (mt)
REVERT: A  259 ILE cc_start: 0.8619 (mt) cc_final: 0.7879 (mp)
REVERT: A  263 ASP cc_start: 0.7727 (m-30) cc_final: 0.7322 (m-30)
REVERT: A  277 ASP cc_start: 0.7808 (t0) cc_final: 0.7183 (t0)
REVERT: A  320 GLU cc_start: 0.5754 (pm20) cc_final: 0.4875 (tm-30)
REVERT: B   58 THR cc_start: 0.8371 (m) cc_final: 0.8140 (t)
REVERT: B   85 LEU cc_start: 0.8779 (tp) cc_final: 0.8111 (tt)
REVERT: B   89 ASP cc_start: 0.7733 (m-30) cc_final: 0.7332 (m-30)
REVERT: B  212 HIS cc_start: 0.7360 (m-70) cc_final: 0.7023 (m-70)
REVERT: B  268 PHE cc_start: 0.8491 (m-10) cc_final: 0.8275 (m-10)
REVERT: C   41 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6386 (tp30)
REVERT: C   43 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7625 (mptt)
REVERT: C  126 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7965 (mt0)
REVERT: C  232 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7528 (tt)
REVERT: C  257 HIS cc_start: 0.8669 (m170) cc_final: 0.7936 (m90)
REVERT: C  341 MET cc_start: 0.7709 (mpp) cc_final: 0.7471 (mtm)
REVERT: D   90 ILE cc_start: 0.8798 (pt) cc_final: 0.8496 (mt)
REVERT: D  143 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7812 (mt)
REVERT: D  155 ARG cc_start: 0.8648 (mpp80) cc_final: 0.8370 (mtm-85)
REVERT: D  162 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8022 (mmm160)
REVERT: D  197 GLU cc_start: 0.8386 (pp20) cc_final: 0.8070 (pp20)
REVERT: D  246 GLU cc_start: 0.8673 (pt0) cc_final: 0.8438 (pp20)
REVERT: D  257 HIS cc_start: 0.7466 (m90) cc_final: 0.7138 (m90)
REVERT: E   39 PHE cc_start: 0.7435 (p90) cc_final: 0.7108 (p90)
REVERT: E   85 LEU cc_start: 0.7683 (mm) cc_final: 0.7156 (mm)
REVERT: E   89 ASP cc_start: 0.7341 (m-30) cc_final: 0.6763 (m-30)
REVERT: E  132 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6918 (t)
REVERT: E  158 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7659 (mpt-90)
REVERT: E  204 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5169 (pm20)
REVERT: E  318 MET cc_start: 0.3209 (mmp) cc_final: 0.2943 (mmp)
  outliers start: 80
  outliers final: 64
  residues processed: 431
  average time/residue: 0.1185
  time to fit residues: 76.3533
Evaluate side-chains
  445 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 374
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 GLU
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 30 optimal weight:    0.0000
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 150 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0070
   chunk 121 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 188 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.4602

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 140 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.162736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.126390 restraints weight = 28325.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.60
r_work: 0.3364 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16425  Z= 0.155
  Angle     :  0.663  10.585  22275  Z= 0.343
  Chirality :  0.044   0.214   2532
  Planarity :  0.005   0.057   2785
  Dihedral  :  4.653  20.219   2155
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.37 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.13 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.81 (0.19), residues: 1930
  helix:  1.84 (0.16), residues: 961
  sheet:  0.28 (0.27), residues: 361
  loop : -1.45 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 155 
 TYR   0.029   0.001   TYR A  19 
 PHE   0.029   0.001   PHE A 306 
 TRP   0.015   0.001   TRP C 226 
 HIS   0.008   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (16423)
  covalent geometry    : angle       0.66251 (22271)
  SS BOND              : bond        0.00040 (    2)
  SS BOND              : angle       1.85083 (    4)
  hydrogen bonds       : bond        0.04736 (  980)
  hydrogen bonds       : angle       4.47526 ( 2847)

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

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

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3860 Ramachandran restraints generated.
    1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 385
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8879 (p) cc_final: 0.8638 (p)
REVERT: A   40 ARG cc_start: 0.7503 (ptm-80) cc_final: 0.7063 (ttp-110)
REVERT: A   63 ASN cc_start: 0.8467 (t0) cc_final: 0.8192 (t0)
REVERT: A   74 GLN cc_start: 0.6974 (tp40) cc_final: 0.6299 (tp-100)
REVERT: A   78 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6900 (mp0)
REVERT: A   89 ASP cc_start: 0.7227 (m-30) cc_final: 0.6731 (m-30)
REVERT: A  104 ASN cc_start: 0.7813 (m110) cc_final: 0.7601 (m110)
REVERT: A  173 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8047 (mt)
REVERT: A  259 ILE cc_start: 0.8608 (mt) cc_final: 0.7878 (mp)
REVERT: A  263 ASP cc_start: 0.7724 (m-30) cc_final: 0.7320 (m-30)
REVERT: A  277 ASP cc_start: 0.7815 (t0) cc_final: 0.7187 (t0)
REVERT: A  320 GLU cc_start: 0.5716 (pm20) cc_final: 0.4890 (tm-30)
REVERT: B   58 THR cc_start: 0.8333 (m) cc_final: 0.8092 (t)
REVERT: B   85 LEU cc_start: 0.8775 (tp) cc_final: 0.8100 (tt)
REVERT: B   89 ASP cc_start: 0.7722 (m-30) cc_final: 0.7320 (m-30)
REVERT: B  212 HIS cc_start: 0.7367 (m-70) cc_final: 0.7025 (m-70)
REVERT: C   41 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6331 (tp30)
REVERT: C   43 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7640 (mptt)
REVERT: C  232 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7548 (tt)
REVERT: C  257 HIS cc_start: 0.8662 (m170) cc_final: 0.7940 (m90)
REVERT: C  341 MET cc_start: 0.7834 (mpp) cc_final: 0.7616 (mtm)
REVERT: D   90 ILE cc_start: 0.8802 (pt) cc_final: 0.8510 (mt)
REVERT: D  155 ARG cc_start: 0.8653 (mpp80) cc_final: 0.8390 (mtm-85)
REVERT: D  197 GLU cc_start: 0.8387 (pp20) cc_final: 0.8075 (pp20)
REVERT: D  257 HIS cc_start: 0.7402 (m90) cc_final: 0.7063 (m90)
REVERT: E   39 PHE cc_start: 0.7448 (p90) cc_final: 0.7129 (p90)
REVERT: E   85 LEU cc_start: 0.7643 (mm) cc_final: 0.7095 (mm)
REVERT: E   89 ASP cc_start: 0.7348 (m-30) cc_final: 0.6782 (m-30)
REVERT: E  132 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6852 (t)
REVERT: E  158 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7706 (mtt180)
REVERT: E  165 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7818 (mmp80)
REVERT: E  204 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5140 (pm20)
REVERT: E  252 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7393 (mtp85)
REVERT: E  291 MET cc_start: 0.8249 (mmm) cc_final: 0.7851 (mmt)
REVERT: E  318 MET cc_start: 0.3307 (mmp) cc_final: 0.3052 (mmp)
  outliers start: 63
  outliers final: 54
  residues processed: 423
  average time/residue: 0.1262
  time to fit residues: 79.8029
Evaluate side-chains
  438 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 378
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   42 PHE
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  273 SER
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  289 GLU
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain E residue   26 ASP
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  204 GLU
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  270 ASP
Chi-restraints excluded: chain E residue  276 LEU
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  284 SER
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 140 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 159 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 163 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 180 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.162612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127526 restraints weight = 28488.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.99
r_work: 0.3314 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  16425  Z= 0.239
  Angle     :  0.718  10.693  22275  Z= 0.372
  Chirality :  0.046   0.209   2532
  Planarity :  0.005   0.057   2785
  Dihedral  :  4.825  21.154   2155
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.73 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.46 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    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 aren not related in a simple way.
  whole:  0.56 (0.19), residues: 1930
  helix:  1.62 (0.16), residues: 960
  sheet:  0.21 (0.27), residues: 371
  loop : -1.62 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  54 
 TYR   0.030   0.002   TYR H 106 
 PHE   0.026   0.002   PHE A 306 
 TRP   0.015   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 (16423)
  covalent geometry    : angle       0.71754 (22271)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       2.35657 (    4)
  hydrogen bonds       : bond        0.05144 (  980)
  hydrogen bonds       : angle       4.65661 ( 2847)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4223.79 seconds
wall clock time: 73 minutes 12.84 seconds (4392.84 seconds total)