Starting phenix.real_space_refine
on Sat Jun 14 23:15:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmn_41395/06_2025/8tmn_41395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmn_41395/06_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_41395/06_2025/8tmn_41395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmn_41395/06_2025/8tmn_41395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmn_41395/06_2025/8tmn_41395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmn_41395/06_2025/8tmn_41395.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.015 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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.07, per 1000 atoms: 0.63
  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: 3.74
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  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: 1.48
  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: 4.84

  Time building geometry restraints manager: 4.49 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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     36.250
  Find NCS groups from input model:        0.770
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.310
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (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
 TRP   0.016   0.001   TRP D 350 
 HIS   0.004   0.001   HIS C 212 
 PHE   0.023   0.001   PHE E  27 
 TYR   0.030   0.001   TYR H 103 
 ARG   0.007   0.001   ARG D  96 

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

*********************** 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  : 1.676 
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: 0.2731
  time to fit residues: 185.6781
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  : 1.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 161 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0770
   chunk 149 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 111 optimal weight:    4.9990
   chunk 173 optimal weight:    1.9990
   overall best weight:    1.1342

-------------------------------------------------------------------------------
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  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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.160138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.124658 restraints weight = 28394.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 3.04
r_work: 0.3280 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  16425  Z= 0.247
  Angle     :  0.697  10.730  22275  Z= 0.362
  Chirality :  0.046   0.222   2532
  Planarity :  0.006   0.057   2785
  Dihedral  :  4.844  23.256   2155
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.89 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.28 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.19), residues: 1930
  helix:  1.41 (0.16), residues: 965
  sheet:  0.50 (0.27), residues: 364
  loop : -1.59 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 226 
 HIS   0.005   0.001   HIS D  68 
 PHE   0.024   0.002   PHE A  79 
 TYR   0.026   0.002   TYR H 106 
 ARG   0.005   0.001   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05782 (  980)
  hydrogen bonds       : angle       5.01275 ( 2847)
  SS BOND              : bond        0.03565 (    2)
  SS BOND              : angle       3.72162 (    4)
  covalent geometry    : bond        0.00581 (16423)
  covalent geometry    : angle       0.69556 (22271)

*********************** 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
  449 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 412
  time to evaluate  : 1.888 
Fit side-chains
   revert: symmetry clash
REVERT: H    4 GLU cc_start: 0.6862 (tp30) cc_final: 0.6600 (tp30)
REVERT: H  123 THR cc_start: 0.8838 (p) cc_final: 0.8618 (p)
REVERT: A   63 ASN cc_start: 0.8453 (t0) cc_final: 0.8243 (t0)
REVERT: A   73 VAL cc_start: 0.8163 (p) cc_final: 0.7961 (t)
REVERT: A   89 ASP cc_start: 0.7351 (m-30) cc_final: 0.6869 (m-30)
REVERT: A  104 ASN cc_start: 0.7899 (m110) cc_final: 0.7651 (m110)
REVERT: A  191 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: A  197 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6321 (tm-30)
REVERT: A  259 ILE cc_start: 0.8740 (mp) cc_final: 0.8214 (mp)
REVERT: A  263 ASP cc_start: 0.7843 (m-30) cc_final: 0.7503 (m-30)
REVERT: A  277 ASP cc_start: 0.7627 (t0) cc_final: 0.6826 (t0)
REVERT: B   85 LEU cc_start: 0.8839 (tp) cc_final: 0.8111 (tt)
REVERT: B   89 ASP cc_start: 0.7835 (m-30) cc_final: 0.7461 (m-30)
REVERT: B  212 HIS cc_start: 0.7367 (m-70) cc_final: 0.6887 (m-70)
REVERT: C  200 LEU cc_start: 0.7365 (mt) cc_final: 0.6961 (mt)
REVERT: C  233 SER cc_start: 0.8256 (m) cc_final: 0.8025 (p)
REVERT: C  257 HIS cc_start: 0.8721 (m170) cc_final: 0.7952 (m90)
REVERT: C  291 MET cc_start: 0.8217 (mmt) cc_final: 0.7713 (mmm)
REVERT: D   63 ASN cc_start: 0.7662 (p0) cc_final: 0.7112 (p0)
REVERT: D   90 ILE cc_start: 0.8755 (pt) cc_final: 0.8256 (mt)
REVERT: D  197 GLU cc_start: 0.8490 (pp20) cc_final: 0.8204 (pp20)
REVERT: D  246 GLU cc_start: 0.8637 (pt0) cc_final: 0.8408 (pp20)
REVERT: E   27 PHE cc_start: 0.6833 (t80) cc_final: 0.6624 (t80)
REVERT: E   85 LEU cc_start: 0.7892 (mm) cc_final: 0.7173 (mm)
REVERT: E   89 ASP cc_start: 0.7309 (m-30) cc_final: 0.6708 (m-30)
REVERT: E  252 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7632 (ttp80)
REVERT: E  256 ASP cc_start: 0.7876 (m-30) cc_final: 0.7648 (m-30)
REVERT: E  318 MET cc_start: 0.3116 (mmp) cc_final: 0.2694 (mmp)
  outliers start: 37
  outliers final: 30
  residues processed: 430
  average time/residue: 0.2761
  time to fit residues: 176.7792
Evaluate side-chains
  425 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 395
  time to evaluate  : 2.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain A residue   78 GLU
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   93 VAL
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  124 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  265 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  185 LEU
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  313 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 180 optimal weight:    0.1980
   chunk 157 optimal weight:    0.7980
   chunk 185 optimal weight:    1.9990
   chunk 155 optimal weight:    5.9990
   chunk 119 optimal weight:    0.0870
   chunk 85 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0570
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.2476

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
L 101 GLN
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
D  74 GLN
** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 209 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.163949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122967 restraints weight = 28518.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.48
r_work: 0.3366 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16425  Z= 0.137
  Angle     :  0.622  10.604  22275  Z= 0.322
  Chirality :  0.044   0.189   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.633  21.860   2155
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.16 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.65 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.19), residues: 1930
  helix:  1.85 (0.16), residues: 965
  sheet:  0.42 (0.28), residues: 363
  loop : -1.47 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  61 
 HIS   0.017   0.001   HIS D  68 
 PHE   0.014   0.001   PHE E 301 
 TYR   0.024   0.001   TYR A  19 
 ARG   0.005   0.000   ARG B 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05077 (  980)
  hydrogen bonds       : angle       4.61434 ( 2847)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       2.26497 (    4)
  covalent geometry    : bond        0.00286 (16423)
  covalent geometry    : angle       0.62145 (22271)

*********************** 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
  455 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 415
  time to evaluate  : 1.913 
Fit side-chains
   revert: symmetry clash
REVERT: H  103 TYR cc_start: 0.8703 (p90) cc_final: 0.8367 (p90)
REVERT: H  123 THR cc_start: 0.8809 (p) cc_final: 0.8579 (p)
REVERT: A   40 ARG cc_start: 0.7593 (ptm-80) cc_final: 0.7390 (ptm-80)
REVERT: A   89 ASP cc_start: 0.7238 (m-30) cc_final: 0.6731 (m-30)
REVERT: A  104 ASN cc_start: 0.7870 (m110) cc_final: 0.7625 (m110)
REVERT: A  173 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: A  197 GLU cc_start: 0.6434 (tm-30) cc_final: 0.6151 (tm-30)
REVERT: A  199 VAL cc_start: 0.7872 (t) cc_final: 0.7672 (t)
REVERT: A  259 ILE cc_start: 0.8604 (mt) cc_final: 0.7901 (mp)
REVERT: A  263 ASP cc_start: 0.7693 (m-30) cc_final: 0.7283 (m-30)
REVERT: A  277 ASP cc_start: 0.7502 (t0) cc_final: 0.6782 (t0)
REVERT: B   85 LEU cc_start: 0.8718 (tp) cc_final: 0.8030 (tt)
REVERT: B   89 ASP cc_start: 0.7712 (m-30) cc_final: 0.7310 (m-30)
REVERT: B  212 HIS cc_start: 0.7296 (m-70) cc_final: 0.6866 (m-70)
REVERT: C  132 THR cc_start: 0.5364 (OUTLIER) cc_final: 0.4973 (p)
REVERT: C  233 SER cc_start: 0.8039 (m) cc_final: 0.7818 (p)
REVERT: C  257 HIS cc_start: 0.8701 (m170) cc_final: 0.7999 (m90)
REVERT: C  291 MET cc_start: 0.8181 (mmt) cc_final: 0.7790 (mmm)
REVERT: C  304 LEU cc_start: 0.8121 (mp) cc_final: 0.7901 (mp)
REVERT: C  341 MET cc_start: 0.7708 (mpp) cc_final: 0.7420 (mtm)
REVERT: D   61 TRP cc_start: 0.7452 (t60) cc_final: 0.7053 (t-100)
REVERT: D   63 ASN cc_start: 0.7460 (p0) cc_final: 0.6551 (p0)
REVERT: D   90 ILE cc_start: 0.8704 (pt) cc_final: 0.8418 (mt)
REVERT: D  197 GLU cc_start: 0.8404 (pp20) cc_final: 0.8092 (pp20)
REVERT: D  295 THR cc_start: 0.7980 (m) cc_final: 0.7712 (m)
REVERT: E   39 PHE cc_start: 0.7316 (p90) cc_final: 0.7081 (p90)
REVERT: E   85 LEU cc_start: 0.7748 (mm) cc_final: 0.7194 (mm)
REVERT: E   89 ASP cc_start: 0.7216 (m-30) cc_final: 0.6598 (m-30)
REVERT: E  165 ARG cc_start: 0.8075 (mmp80) cc_final: 0.7823 (mmp80)
REVERT: E  204 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.4995 (pm20)
REVERT: E  318 MET cc_start: 0.3485 (mmp) cc_final: 0.3063 (mmp)
  outliers start: 40
  outliers final: 24
  residues processed: 433
  average time/residue: 0.2772
  time to fit residues: 177.9813
Evaluate side-chains
  420 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 393
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   82 GLU
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  276 LEU
Chi-restraints excluded: chain A residue  289 GLU
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  193 ASP
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain C residue  132 THR
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 174 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 167 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 168 optimal weight:    0.7980
   chunk 162 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 148 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
** 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  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 126 GLN ** 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 = 0.4111 r_free = 0.4111 target = 0.162508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121162 restraints weight = 28481.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.47
r_work: 0.3329 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1880

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= 0.188
  Angle     :  0.630  10.620  22275  Z= 0.329
  Chirality :  0.044   0.174   2532
  Planarity :  0.005   0.048   2785
  Dihedral  :  4.685  21.852   2155
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.58 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.92 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.19), residues: 1930
  helix:  1.82 (0.16), residues: 965
  sheet:  0.47 (0.27), residues: 365
  loop : -1.50 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  50 
 HIS   0.013   0.001   HIS D  68 
 PHE   0.020   0.002   PHE E  27 
 TYR   0.024   0.002   TYR H 106 
 ARG   0.006   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05131 (  980)
  hydrogen bonds       : angle       4.57898 ( 2847)
  SS BOND              : bond        0.00016 (    2)
  SS BOND              : angle       2.04580 (    4)
  covalent geometry    : bond        0.00440 (16423)
  covalent geometry    : angle       0.62955 (22271)

*********************** 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: 57
    poor density    : 400
  time to evaluate  : 1.731 
Fit side-chains
REVERT: H  123 THR cc_start: 0.8822 (p) cc_final: 0.8588 (p)
REVERT: A   40 ARG cc_start: 0.7616 (ptm-80) cc_final: 0.7360 (ttp-110)
REVERT: A   89 ASP cc_start: 0.7310 (m-30) cc_final: 0.6781 (m-30)
REVERT: A  104 ASN cc_start: 0.7812 (m110) cc_final: 0.7545 (m110)
REVERT: A  197 GLU cc_start: 0.6430 (tm-30) cc_final: 0.6124 (tm-30)
REVERT: A  199 VAL cc_start: 0.7893 (t) cc_final: 0.7682 (t)
REVERT: A  259 ILE cc_start: 0.8621 (mt) cc_final: 0.8242 (mp)
REVERT: A  277 ASP cc_start: 0.7608 (t0) cc_final: 0.6900 (t0)
REVERT: B   85 LEU cc_start: 0.8749 (tp) cc_final: 0.8041 (tt)
REVERT: B   89 ASP cc_start: 0.7779 (m-30) cc_final: 0.7359 (m-30)
REVERT: B  212 HIS cc_start: 0.7378 (m-70) cc_final: 0.6948 (m-70)
REVERT: B  341 MET cc_start: 0.6134 (tmm) cc_final: 0.5656 (ptt)
REVERT: C   43 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7577 (mtmt)
REVERT: C  250 TYR cc_start: 0.8279 (m-80) cc_final: 0.7978 (m-80)
REVERT: C  257 HIS cc_start: 0.8700 (m170) cc_final: 0.7976 (m90)
REVERT: C  291 MET cc_start: 0.8204 (mmt) cc_final: 0.7808 (mmm)
REVERT: C  341 MET cc_start: 0.7772 (mpp) cc_final: 0.7488 (mtm)
REVERT: D   32 MET cc_start: 0.7452 (ptp) cc_final: 0.7198 (mtm)
REVERT: D   90 ILE cc_start: 0.8763 (pt) cc_final: 0.8509 (mt)
REVERT: D  197 GLU cc_start: 0.8427 (pp20) cc_final: 0.8132 (pp20)
REVERT: D  297 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7567 (tt)
REVERT: E   39 PHE cc_start: 0.7343 (p90) cc_final: 0.7070 (p90)
REVERT: E   85 LEU cc_start: 0.7741 (mm) cc_final: 0.7280 (mm)
REVERT: E   89 ASP cc_start: 0.7057 (m-30) cc_final: 0.6440 (m-30)
REVERT: E  158 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7879 (mtt180)
REVERT: E  204 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5023 (pm20)
REVERT: E  318 MET cc_start: 0.3487 (mmp) cc_final: 0.3200 (mmp)
  outliers start: 57
  outliers final: 43
  residues processed: 432
  average time/residue: 0.2959
  time to fit residues: 189.3816
Evaluate side-chains
  432 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 387
  time to evaluate  : 1.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   73 THR
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 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  247 THR
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  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 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  278 VAL
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  297 ILE
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  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  284 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 133 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0970
   chunk 158 optimal weight:    0.1980
   chunk 107 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 110 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
L  28 GLN
** 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**
C 285 ASN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 126 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.163612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.127781 restraints weight = 28761.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.70
r_work: 0.3356 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  16425  Z= 0.189
  Angle     :  0.631  10.618  22275  Z= 0.331
  Chirality :  0.044   0.192   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.698  22.543   2155
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.42 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.19), residues: 1930
  helix:  1.80 (0.17), residues: 965
  sheet:  0.46 (0.27), residues: 369
  loop : -1.50 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D  61 
 HIS   0.010   0.001   HIS D  68 
 PHE   0.020   0.001   PHE E  27 
 TYR   0.024   0.002   TYR H 106 
 ARG   0.005   0.000   ARG E  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05087 (  980)
  hydrogen bonds       : angle       4.54465 ( 2847)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       2.54155 (    4)
  covalent geometry    : bond        0.00443 (16423)
  covalent geometry    : angle       0.63029 (22271)

*********************** 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
  460 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 394
  time to evaluate  : 1.864 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8851 (p) cc_final: 0.8626 (p)
REVERT: A   40 ARG cc_start: 0.7562 (ptm-80) cc_final: 0.7361 (ttp-110)
REVERT: A   89 ASP cc_start: 0.7341 (m-30) cc_final: 0.6866 (m-30)
REVERT: A  104 ASN cc_start: 0.7805 (m110) cc_final: 0.7580 (m110)
REVERT: A  173 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8062 (mt)
REVERT: A  197 GLU cc_start: 0.6486 (tm-30) cc_final: 0.6169 (tm-30)
REVERT: A  199 VAL cc_start: 0.8037 (t) cc_final: 0.7834 (t)
REVERT: A  259 ILE cc_start: 0.8695 (mt) cc_final: 0.8269 (mp)
REVERT: A  277 ASP cc_start: 0.7648 (t0) cc_final: 0.6997 (t0)
REVERT: B   85 LEU cc_start: 0.8846 (tp) cc_final: 0.8123 (tt)
REVERT: B   89 ASP cc_start: 0.7752 (m-30) cc_final: 0.7361 (m-30)
REVERT: B  212 HIS cc_start: 0.7394 (m-70) cc_final: 0.6915 (m-70)
REVERT: B  341 MET cc_start: 0.6123 (tmm) cc_final: 0.5790 (ptt)
REVERT: C   43 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7677 (mtmt)
REVERT: C  209 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: C  213 GLN cc_start: 0.8104 (pt0) cc_final: 0.7894 (pt0)
REVERT: C  257 HIS cc_start: 0.8701 (m170) cc_final: 0.8003 (m90)
REVERT: C  278 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8390 (m)
REVERT: D   32 MET cc_start: 0.7255 (ptp) cc_final: 0.7010 (mtm)
REVERT: D   90 ILE cc_start: 0.8808 (pt) cc_final: 0.8550 (mt)
REVERT: D  143 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7794 (mt)
REVERT: D  197 GLU cc_start: 0.8347 (pp20) cc_final: 0.8054 (pp20)
REVERT: D  297 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7698 (tt)
REVERT: E   39 PHE cc_start: 0.7371 (p90) cc_final: 0.7096 (p90)
REVERT: E   85 LEU cc_start: 0.7653 (mm) cc_final: 0.7151 (mm)
REVERT: E   89 ASP cc_start: 0.7096 (m-30) cc_final: 0.6495 (m-30)
REVERT: E  132 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6937 (t)
REVERT: E  158 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7910 (mtt180)
REVERT: E  204 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.4993 (pm20)
REVERT: E  318 MET cc_start: 0.3700 (mmp) cc_final: 0.3428 (mmp)
  outliers start: 66
  outliers final: 43
  residues processed: 435
  average time/residue: 0.2814
  time to fit residues: 181.2457
Evaluate side-chains
  429 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 380
  time to evaluate  : 1.776 
-------------------------------------------------------------------------------
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 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 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  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 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  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  120 HIS
Chi-restraints excluded: chain D residue  143 ILE
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  297 ILE
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  122 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  185 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  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 105 optimal weight:    7.9990
   chunk 115 optimal weight:    0.5980
   chunk 129 optimal weight:    0.6980
   chunk 128 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 174 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 145 optimal weight:    0.6980
   chunk 112 optimal weight:    8.9990
   chunk 106 optimal weight:    0.8980
   chunk 166 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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
C 126 GLN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 126 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.163336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127644 restraints weight = 28516.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.75
r_work: 0.3348 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16425  Z= 0.178
  Angle     :  0.630  10.587  22275  Z= 0.328
  Chirality :  0.044   0.175   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.681  21.290   2155
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.47 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.69 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.20), residues: 1930
  helix:  1.80 (0.17), residues: 965
  sheet:  0.44 (0.27), residues: 371
  loop : -1.48 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  50 
 HIS   0.006   0.001   HIS C 212 
 PHE   0.020   0.001   PHE E  27 
 TYR   0.026   0.002   TYR A  19 
 ARG   0.006   0.000   ARG E  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  980)
  hydrogen bonds       : angle       4.53581 ( 2847)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       2.36211 (    4)
  covalent geometry    : bond        0.00416 (16423)
  covalent geometry    : angle       0.62913 (22271)

*********************** 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
  456 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 387
  time to evaluate  : 1.720 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8851 (p) cc_final: 0.8614 (p)
REVERT: A   89 ASP cc_start: 0.7295 (m-30) cc_final: 0.6830 (m-30)
REVERT: A  104 ASN cc_start: 0.7877 (m110) cc_final: 0.7663 (m110)
REVERT: A  173 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8049 (mt)
REVERT: A  197 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6163 (tm-30)
REVERT: A  199 VAL cc_start: 0.7995 (t) cc_final: 0.7776 (t)
REVERT: A  259 ILE cc_start: 0.8658 (mt) cc_final: 0.8233 (mp)
REVERT: A  277 ASP cc_start: 0.7760 (t0) cc_final: 0.7072 (t0)
REVERT: B    4 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7337 (ptmt)
REVERT: B   85 LEU cc_start: 0.8888 (tp) cc_final: 0.8126 (tt)
REVERT: B   89 ASP cc_start: 0.7762 (m-30) cc_final: 0.7358 (m-30)
REVERT: B  212 HIS cc_start: 0.7384 (m-70) cc_final: 0.6908 (m-70)
REVERT: C  209 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: C  213 GLN cc_start: 0.8062 (pt0) cc_final: 0.7645 (pt0)
REVERT: C  257 HIS cc_start: 0.8717 (m170) cc_final: 0.8018 (m90)
REVERT: C  278 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8388 (m)
REVERT: C  291 MET cc_start: 0.7859 (mmm) cc_final: 0.7600 (mmm)
REVERT: C  341 MET cc_start: 0.7431 (mtm) cc_final: 0.6695 (mpp)
REVERT: D   32 MET cc_start: 0.7283 (ptp) cc_final: 0.7052 (mtm)
REVERT: D   90 ILE cc_start: 0.8857 (pt) cc_final: 0.8600 (mt)
REVERT: D  143 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7835 (mt)
REVERT: D  197 GLU cc_start: 0.8381 (pp20) cc_final: 0.8084 (pp20)
REVERT: D  297 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7706 (tt)
REVERT: E   39 PHE cc_start: 0.7379 (p90) cc_final: 0.7070 (p90)
REVERT: E   85 LEU cc_start: 0.7656 (mm) cc_final: 0.7160 (mm)
REVERT: E   89 ASP cc_start: 0.7355 (m-30) cc_final: 0.6781 (m-30)
REVERT: E  132 THR cc_start: 0.7142 (OUTLIER) cc_final: 0.6911 (t)
REVERT: E  204 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5039 (pm20)
  outliers start: 69
  outliers final: 54
  residues processed: 426
  average time/residue: 0.2714
  time to fit residues: 171.7975
Evaluate side-chains
  441 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 381
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
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  117 ASP
Chi-restraints excluded: chain A residue   57 SER
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 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  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  341 MET
Chi-restraints excluded: chain C residue   35 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  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  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  283 VAL
Chi-restraints excluded: chain D residue  297 ILE
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  122 LEU
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  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  276 LEU
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 60 optimal weight:    0.0070
   chunk 93 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0050
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4612

-------------------------------------------------------------------------------
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**
A  74 GLN
B  74 GLN
C 126 GLN
C 288 ASN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.164698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.129041 restraints weight = 28588.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.64
r_work: 0.3369 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16425  Z= 0.150
  Angle     :  0.627  10.584  22275  Z= 0.324
  Chirality :  0.044   0.176   2532
  Planarity :  0.005   0.054   2785
  Dihedral  :  4.623  20.792   2155
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.58 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.46 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.20), residues: 1930
  helix:  1.90 (0.17), residues: 964
  sheet:  0.37 (0.27), residues: 363
  loop : -1.42 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 226 
 HIS   0.010   0.001   HIS D  68 
 PHE   0.020   0.001   PHE E  27 
 TYR   0.019   0.001   TYR H 106 
 ARG   0.006   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04790 (  980)
  hydrogen bonds       : angle       4.46145 ( 2847)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       2.08651 (    4)
  covalent geometry    : bond        0.00340 (16423)
  covalent geometry    : angle       0.62644 (22271)

*********************** 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
  453 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 392
  time to evaluate  : 2.684 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8857 (p) cc_final: 0.8620 (p)
REVERT: A   40 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.7068 (ptm-80)
REVERT: A   63 ASN cc_start: 0.8454 (t0) cc_final: 0.8163 (t0)
REVERT: A   89 ASP cc_start: 0.7270 (m-30) cc_final: 0.6757 (m-30)
REVERT: A  104 ASN cc_start: 0.7833 (m110) cc_final: 0.7626 (m110)
REVERT: A  173 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (mt)
REVERT: A  197 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6169 (tm-30)
REVERT: A  199 VAL cc_start: 0.8061 (t) cc_final: 0.7822 (t)
REVERT: A  259 ILE cc_start: 0.8669 (mt) cc_final: 0.8309 (mp)
REVERT: A  277 ASP cc_start: 0.7725 (t0) cc_final: 0.7058 (t0)
REVERT: B    4 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7417 (ptmt)
REVERT: B   85 LEU cc_start: 0.8902 (tp) cc_final: 0.8158 (tt)
REVERT: B   89 ASP cc_start: 0.7737 (m-30) cc_final: 0.7343 (m-30)
REVERT: B  212 HIS cc_start: 0.7328 (m-70) cc_final: 0.6858 (m-70)
REVERT: C   43 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7616 (mptt)
REVERT: C  209 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7689 (tm-30)
REVERT: C  213 GLN cc_start: 0.8004 (pt0) cc_final: 0.7513 (pt0)
REVERT: C  257 HIS cc_start: 0.8731 (m170) cc_final: 0.8034 (m90)
REVERT: C  278 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8327 (m)
REVERT: C  291 MET cc_start: 0.7897 (mmm) cc_final: 0.7616 (mmm)
REVERT: D   90 ILE cc_start: 0.8778 (pt) cc_final: 0.8458 (mt)
REVERT: D  143 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7812 (mt)
REVERT: D  197 GLU cc_start: 0.8355 (pp20) cc_final: 0.8040 (pp20)
REVERT: E   39 PHE cc_start: 0.7362 (p90) cc_final: 0.7083 (p90)
REVERT: E   89 ASP cc_start: 0.7339 (m-30) cc_final: 0.6764 (m-30)
REVERT: E  132 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6849 (t)
REVERT: E  204 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5339 (pt0)
REVERT: E  318 MET cc_start: 0.3006 (mmp) cc_final: 0.2726 (mmp)
  outliers start: 61
  outliers final: 48
  residues processed: 429
  average time/residue: 0.3527
  time to fit residues: 227.9929
Evaluate side-chains
  426 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 373
  time to evaluate  : 2.003 
-------------------------------------------------------------------------------
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 A residue   57 SER
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  276 LEU
Chi-restraints excluded: chain A residue  289 GLU
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  272 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  128 SER
Chi-restraints excluded: chain C residue  150 VAL
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  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  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  122 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  199 VAL
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  276 LEU
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 69 optimal weight:    0.0980
   chunk 155 optimal weight:    0.8980
   chunk 124 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 142 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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**
** 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**
C 126 GLN
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.163950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.128080 restraints weight = 28513.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.60
r_work: 0.3359 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2332

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= 0.182
  Angle     :  0.664  10.599  22275  Z= 0.342
  Chirality :  0.045   0.217   2532
  Planarity :  0.005   0.050   2785
  Dihedral  :  4.696  20.814   2155
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.47 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.35 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.20), residues: 1930
  helix:  1.84 (0.17), residues: 962
  sheet:  0.36 (0.27), residues: 371
  loop : -1.55 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  50 
 HIS   0.007   0.001   HIS D  68 
 PHE   0.019   0.001   PHE E  27 
 TYR   0.028   0.002   TYR A  19 
 ARG   0.007   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04896 (  980)
  hydrogen bonds       : angle       4.51115 ( 2847)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       2.27473 (    4)
  covalent geometry    : bond        0.00427 (16423)
  covalent geometry    : angle       0.66367 (22271)

*********************** 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
  449 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 381
  time to evaluate  : 1.847 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8864 (p) cc_final: 0.8628 (p)
REVERT: A   40 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7083 (ptm-80)
REVERT: A   63 ASN cc_start: 0.8493 (t0) cc_final: 0.8247 (t0)
REVERT: A   89 ASP cc_start: 0.7270 (m-30) cc_final: 0.6821 (m-30)
REVERT: A  104 ASN cc_start: 0.7857 (m110) cc_final: 0.7649 (m110)
REVERT: A  173 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8052 (mt)
REVERT: A  197 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6253 (tm-30)
REVERT: A  199 VAL cc_start: 0.8041 (t) cc_final: 0.7810 (t)
REVERT: A  259 ILE cc_start: 0.8652 (mt) cc_final: 0.8247 (mp)
REVERT: A  277 ASP cc_start: 0.7787 (t0) cc_final: 0.7137 (t0)
REVERT: A  320 GLU cc_start: 0.5641 (pm20) cc_final: 0.4785 (tm-30)
REVERT: B    4 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7413 (ptmt)
REVERT: B   85 LEU cc_start: 0.8908 (tp) cc_final: 0.8149 (tt)
REVERT: B   89 ASP cc_start: 0.7708 (m-30) cc_final: 0.7310 (m-30)
REVERT: B  209 GLN cc_start: 0.8447 (mm110) cc_final: 0.8183 (mm-40)
REVERT: B  212 HIS cc_start: 0.7350 (m-70) cc_final: 0.6887 (m-70)
REVERT: C  209 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: C  213 GLN cc_start: 0.8103 (pt0) cc_final: 0.7601 (pt0)
REVERT: C  257 HIS cc_start: 0.8655 (m170) cc_final: 0.7986 (m90)
REVERT: C  291 MET cc_start: 0.7886 (mmm) cc_final: 0.7633 (mmm)
REVERT: C  341 MET cc_start: 0.7331 (mtm) cc_final: 0.6513 (mpp)
REVERT: D   90 ILE cc_start: 0.8805 (pt) cc_final: 0.8511 (mt)
REVERT: D  143 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7842 (mt)
REVERT: D  197 GLU cc_start: 0.8367 (pp20) cc_final: 0.8051 (pp20)
REVERT: E   39 PHE cc_start: 0.7405 (p90) cc_final: 0.7072 (p90)
REVERT: E   85 LEU cc_start: 0.7659 (mm) cc_final: 0.7157 (mm)
REVERT: E   89 ASP cc_start: 0.7346 (m-30) cc_final: 0.6778 (m-30)
REVERT: E  158 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7855 (mtt180)
REVERT: E  204 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5334 (pt0)
REVERT: E  291 MET cc_start: 0.8167 (mmt) cc_final: 0.7721 (mmt)
REVERT: E  318 MET cc_start: 0.3151 (mmp) cc_final: 0.2802 (mmp)
  outliers start: 68
  outliers final: 59
  residues processed: 422
  average time/residue: 0.2728
  time to fit residues: 171.0649
Evaluate side-chains
  431 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 369
  time to evaluate  : 1.816 
-------------------------------------------------------------------------------
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   79 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 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 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  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  341 MET
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  150 VAL
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  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  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  131 LEU
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  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 163 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 126 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0970
   chunk 138 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.5336

-------------------------------------------------------------------------------
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**
B  74 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 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 = 0.4110 r_free = 0.4110 target = 0.161389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125955 restraints weight = 28315.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 3.24
r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2390

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= 0.159
  Angle     :  0.655  10.582  22275  Z= 0.336
  Chirality :  0.044   0.201   2532
  Planarity :  0.005   0.055   2785
  Dihedral  :  4.659  20.536   2155
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.52 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 20.63 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.20), residues: 1930
  helix:  1.92 (0.17), residues: 960
  sheet:  0.35 (0.27), residues: 369
  loop : -1.51 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 226 
 HIS   0.006   0.001   HIS D  68 
 PHE   0.019   0.001   PHE E  27 
 TYR   0.023   0.001   TYR C 156 
 ARG   0.007   0.000   ARG E  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04772 (  980)
  hydrogen bonds       : angle       4.46683 ( 2847)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       2.05562 (    4)
  covalent geometry    : bond        0.00367 (16423)
  covalent geometry    : angle       0.65402 (22271)

*********************** 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
  448 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 378
  time to evaluate  : 1.838 
Fit side-chains
   revert: symmetry clash
REVERT: H  123 THR cc_start: 0.8875 (p) cc_final: 0.8628 (p)
REVERT: A   63 ASN cc_start: 0.8511 (t0) cc_final: 0.8256 (t0)
REVERT: A   89 ASP cc_start: 0.7310 (m-30) cc_final: 0.6802 (m-30)
REVERT: A  104 ASN cc_start: 0.7912 (m110) cc_final: 0.7707 (m110)
REVERT: A  173 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (mt)
REVERT: A  197 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6190 (tm-30)
REVERT: A  199 VAL cc_start: 0.7974 (t) cc_final: 0.7747 (t)
REVERT: A  259 ILE cc_start: 0.8671 (mt) cc_final: 0.8255 (mp)
REVERT: A  277 ASP cc_start: 0.7969 (t0) cc_final: 0.7354 (t0)
REVERT: A  320 GLU cc_start: 0.5690 (pm20) cc_final: 0.4827 (tm-30)
REVERT: B    4 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7487 (ptmt)
REVERT: B   85 LEU cc_start: 0.8915 (tp) cc_final: 0.8194 (tt)
REVERT: B   89 ASP cc_start: 0.7893 (m-30) cc_final: 0.7501 (m-30)
REVERT: B  209 GLN cc_start: 0.8497 (mm110) cc_final: 0.8205 (mm-40)
REVERT: B  212 HIS cc_start: 0.7414 (m-70) cc_final: 0.7006 (m-70)
REVERT: B  268 PHE cc_start: 0.8497 (m-10) cc_final: 0.8296 (m-10)
REVERT: C  209 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7573 (tm-30)
REVERT: C  213 GLN cc_start: 0.8079 (pt0) cc_final: 0.7574 (pt0)
REVERT: C  250 TYR cc_start: 0.8419 (m-80) cc_final: 0.8177 (m-80)
REVERT: C  257 HIS cc_start: 0.8686 (m170) cc_final: 0.8020 (m90)
REVERT: D   19 TYR cc_start: 0.5496 (p90) cc_final: 0.4823 (p90)
REVERT: D   90 ILE cc_start: 0.8817 (pt) cc_final: 0.8507 (mt)
REVERT: D  122 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7330 (mm)
REVERT: D  143 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: D  155 ARG cc_start: 0.8686 (mpp80) cc_final: 0.8399 (mtm-85)
REVERT: D  197 GLU cc_start: 0.8436 (pp20) cc_final: 0.8121 (pp20)
REVERT: D  257 HIS cc_start: 0.7579 (m90) cc_final: 0.7309 (m-70)
REVERT: E   39 PHE cc_start: 0.7464 (p90) cc_final: 0.7132 (p90)
REVERT: E   85 LEU cc_start: 0.7695 (mm) cc_final: 0.7195 (mm)
REVERT: E   89 ASP cc_start: 0.7462 (m-30) cc_final: 0.6898 (m-30)
REVERT: E  158 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7927 (mtt-85)
REVERT: E  165 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7838 (mmp80)
REVERT: E  204 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5436 (pt0)
REVERT: E  252 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7550 (mtp85)
REVERT: E  318 MET cc_start: 0.3314 (mmp) cc_final: 0.3085 (mmp)
  outliers start: 70
  outliers final: 57
  residues processed: 425
  average time/residue: 0.2927
  time to fit residues: 185.8041
Evaluate side-chains
  427 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 366
  time to evaluate  : 1.933 
-------------------------------------------------------------------------------
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   79 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 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 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  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  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  122 LEU
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  185 LEU
Chi-restraints excluded: chain E residue  199 VAL
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  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 85 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 147 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 182 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
B  74 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4130 r_free = 0.4130 target = 0.162384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.126532 restraints weight = 28625.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.73
r_work: 0.3354 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16425  Z= 0.176
  Angle     :  0.683  11.553  22275  Z= 0.349
  Chirality :  0.045   0.193   2532
  Planarity :  0.005   0.058   2785
  Dihedral  :  4.694  20.683   2155
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.52 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.18 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.19), residues: 1930
  helix:  1.84 (0.16), residues: 959
  sheet:  0.27 (0.27), residues: 372
  loop : -1.56 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 226 
 HIS   0.008   0.001   HIS D  68 
 PHE   0.020   0.001   PHE E  27 
 TYR   0.028   0.002   TYR A  19 
 ARG   0.007   0.000   ARG B  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  980)
  hydrogen bonds       : angle       4.51823 ( 2847)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       2.18612 (    4)
  covalent geometry    : bond        0.00415 (16423)
  covalent geometry    : angle       0.68258 (22271)

********************** 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
  440 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 379
  time to evaluate  : 1.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.8459 (t0) cc_final: 0.8194 (t0)
REVERT: A   89 ASP cc_start: 0.7233 (m-30) cc_final: 0.6725 (m-30)
REVERT: A  104 ASN cc_start: 0.7859 (m110) cc_final: 0.7641 (m110)
REVERT: A  173 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8043 (mt)
REVERT: A  197 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6127 (tm-30)
REVERT: A  199 VAL cc_start: 0.7994 (t) cc_final: 0.7748 (t)
REVERT: A  259 ILE cc_start: 0.8656 (mt) cc_final: 0.8230 (mp)
REVERT: A  277 ASP cc_start: 0.7891 (t0) cc_final: 0.7249 (t0)
REVERT: A  320 GLU cc_start: 0.5677 (pm20) cc_final: 0.4856 (tm-30)
REVERT: B    4 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7387 (ptmt)
REVERT: B   58 THR cc_start: 0.8332 (m) cc_final: 0.8103 (t)
REVERT: B   85 LEU cc_start: 0.8898 (tp) cc_final: 0.8144 (tt)
REVERT: B   89 ASP cc_start: 0.7750 (m-30) cc_final: 0.7342 (m-30)
REVERT: B  209 GLN cc_start: 0.8496 (mm110) cc_final: 0.8199 (mm-40)
REVERT: B  212 HIS cc_start: 0.7408 (m-70) cc_final: 0.6988 (m-70)
REVERT: C  209 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: C  213 GLN cc_start: 0.8043 (pt0) cc_final: 0.7556 (pt0)
REVERT: C  250 TYR cc_start: 0.8472 (m-80) cc_final: 0.8238 (m-80)
REVERT: C  257 HIS cc_start: 0.8690 (m170) cc_final: 0.8031 (m90)
REVERT: C  291 MET cc_start: 0.7710 (mmm) cc_final: 0.7451 (mmm)
REVERT: D   90 ILE cc_start: 0.8831 (pt) cc_final: 0.8561 (mt)
REVERT: D  122 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6981 (mm)
REVERT: D  143 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7842 (mt)
REVERT: D  155 ARG cc_start: 0.8684 (mpp80) cc_final: 0.8407 (mtm-85)
REVERT: D  197 GLU cc_start: 0.8399 (pp20) cc_final: 0.8083 (pp20)
REVERT: D  217 ASN cc_start: 0.8501 (t0) cc_final: 0.7730 (t0)
REVERT: D  257 HIS cc_start: 0.7508 (m90) cc_final: 0.7234 (m-70)
REVERT: E   39 PHE cc_start: 0.7454 (p90) cc_final: 0.7122 (p90)
REVERT: E   85 LEU cc_start: 0.7700 (mm) cc_final: 0.7171 (mm)
REVERT: E   89 ASP cc_start: 0.7379 (m-30) cc_final: 0.6809 (m-30)
REVERT: E  158 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7864 (mtt-85)
REVERT: E  165 ARG cc_start: 0.8029 (mmp80) cc_final: 0.7753 (mmp80)
REVERT: E  204 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5079 (pm20)
REVERT: E  252 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7440 (mtp85)
REVERT: E  318 MET cc_start: 0.3241 (mmp) cc_final: 0.3039 (mmp)
  outliers start: 61
  outliers final: 55
  residues processed: 414
  average time/residue: 0.3118
  time to fit residues: 190.6392
Evaluate side-chains
  428 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 369
  time to evaluate  : 1.971 
-------------------------------------------------------------------------------
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   79 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 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   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  341 MET
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue  150 VAL
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  122 LEU
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   60 THR
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  133 LYS
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  221 LEU
Chi-restraints excluded: chain E residue  225 ILE
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 127 optimal weight:    0.9980
   chunk 141 optimal weight:    0.4980
   chunk 181 optimal weight:    0.9990
   chunk 156 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 177 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 165 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 142 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
B  74 GLN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.161916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126423 restraints weight = 28370.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.82
r_work: 0.3340 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16425  Z= 0.191
  Angle     :  0.686  10.903  22275  Z= 0.351
  Chirality :  0.045   0.199   2532
  Planarity :  0.005   0.058   2785
  Dihedral  :  4.751  20.930   2155
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.58 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.18 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.19), residues: 1930
  helix:  1.80 (0.16), residues: 958
  sheet:  0.22 (0.27), residues: 371
  loop : -1.59 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 226 
 HIS   0.006   0.001   HIS D  68 
 PHE   0.021   0.002   PHE E  27 
 TYR   0.025   0.002   TYR H 106 
 ARG   0.010   0.001   ARG C 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04928 (  980)
  hydrogen bonds       : angle       4.55066 ( 2847)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       2.28971 (    4)
  covalent geometry    : bond        0.00453 (16423)
  covalent geometry    : angle       0.68581 (22271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9662.31 seconds
wall clock time: 170 minutes 33.52 seconds (10233.52 seconds total)