Starting phenix.real_space_refine
on Sun Jun 15 18:36:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmb_41383/06_2025/8tmb_41383.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
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 1821 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      6      5.21       5
     S      59      5.16       5
     C   10556      2.51       5
     N    2639      2.21       5
     O    2969      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16229
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2830
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 14, 'TRANS': 324}
    Chain: "B"
      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: "C"
      Number of atoms: 2917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2917
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 15, 'TRANS': 334}
    Chain: "D"
      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: "E"
      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: "H"
      Number of atoms: 998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 998
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 4, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 823
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    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: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      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: 10.46, per 1000 atoms: 0.64
  Number of scatterers: 16229
  At special positions: 0
  Unit cell: (113.3, 139.05, 167.89, 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      59     16.00
     Mg      6     11.99
     O    2969      8.00
     N    2639      7.00
     C   10556      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 4.33
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3758

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 12 sheets defined
      51.1% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 54
    Processing helix  chain 'A' and resid 69 through 81
      removed outlier: 3.563A  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 156
    Processing helix  chain 'A' and resid 160 through 163
      removed outlier: 3.684A  pdb=" N   LYS A 163 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 160 through 163'
    Processing helix  chain 'A' and resid 164 through 199
      removed outlier: 3.805A  pdb=" N   TYR A 168 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      removed outlier: 4.067A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLN A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
      removed outlier: 3.774A  pdb=" N   GLU A 230 " --> pdb=" O   TRP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 247 through 302
      removed outlier: 3.671A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASP A 277 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 325 through 347
    Processing helix  chain 'B' and resid 46 through 54
      removed outlier: 4.206A  pdb=" N   LEU B  51 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      Proline residue:  B  52  - end of helix
    Processing helix  chain 'B' and resid 69 through 80
      removed outlier: 4.090A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
      removed outlier: 3.508A  pdb=" N   LEU B  87 " --> pdb=" O   HIS B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 165 through 202
    Processing helix  chain 'B' and resid 205 through 238
      removed outlier: 3.897A  pdb=" N   GLN B 209 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
      removed outlier: 3.611A  pdb=" N   ASP B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 311
      removed outlier: 4.148A  pdb=" N   ASP B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASN B 288 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.975A  pdb=" N   LYS B 348 " --> pdb=" O   TYR B 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 50
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 4.363A  pdb=" N   ASP C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 81
      removed outlier: 3.764A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 92
      removed outlier: 3.627A  pdb=" N   LEU C  87 " --> pdb=" O   HIS C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 153
    Processing helix  chain 'C' and resid 165 through 201
    Processing helix  chain 'C' and resid 206 through 238
      removed outlier: 3.912A  pdb=" N   THR C 224 " --> pdb=" O   GLU C 220 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
      removed outlier: 4.144A  pdb=" N   TYR C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASP C 238 " --> pdb=" O   SER C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 298
      removed outlier: 3.832A  pdb=" N   ASP C 277 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 312
      removed outlier: 3.687A  pdb=" N   ILE C 307 " --> pdb=" O   PRO C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 345
      removed outlier: 3.958A  pdb=" N   VAL C 330 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   VAL C 333 " --> pdb=" O   VAL C 329 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 56
      removed outlier: 3.530A  pdb=" N   SER D  49 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL D  50 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU D  51 " --> pdb=" O   GLU D  48 " (cutoff:3.500A)
      Proline residue:  D  52  - end of helix
      removed outlier: 3.604A  pdb=" N   ASP D  55 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 81
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 147 through 156
    Processing helix  chain 'D' and resid 160 through 164
      removed outlier: 3.555A  pdb=" N   LYS D 164 " --> pdb=" O   ILE D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 201
      removed outlier: 3.528A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLU D 201 " --> pdb=" O   GLU D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 238
      removed outlier: 4.052A  pdb=" N   ARG D 210 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
      removed outlier: 4.250A  pdb=" N   ASP D 238 " --> pdb=" O   SER D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 311
      removed outlier: 3.546A  pdb=" N   PHE D 251 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      removed outlier: 4.074A  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 327 through 349
      removed outlier: 4.496A  pdb=" N   VAL D 333 " --> pdb=" O   VAL D 329 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   MET D 334 " --> pdb=" O   VAL D 330 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS D 348 " --> pdb=" O   TYR D 344 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 47 through 54
      Proline residue:  E  52  - end of helix
    Processing helix  chain 'E' and resid 69 through 80
      removed outlier: 3.613A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 91
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 165 through 202
    Processing helix  chain 'E' and resid 205 through 237
      removed outlier: 4.152A  pdb=" N   GLN E 209 " --> pdb=" O   LYS E 205 " (cutoff:3.500A)
      Proline residue:  E 227  - end of helix
      removed outlier: 3.947A  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 298
    Processing helix  chain 'E' and resid 301 through 312
    Processing helix  chain 'E' and resid 330 through 348
    Processing helix  chain 'H' and resid 65 through 68
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41
    Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44
      removed outlier: 3.786A  pdb=" N   GLU B  28 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 42
      removed outlier: 4.058A  pdb=" N   GLU C 121 " --> pdb=" O   ASP C 116 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ASP C 116 " --> pdb=" O   GLU C 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41
      removed outlier: 7.110A  pdb=" N   THR D  60 " --> pdb=" O   VAL D 136 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   MET D 138 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE D  62 " --> pdb=" O   MET D 138 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   GLN D 140 " --> pdb=" O   ILE D  62 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ILE D  64 " --> pdb=" O   GLN D 140 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 44
      removed outlier: 6.800A  pdb=" N   THR E  60 " --> pdb=" O   VAL E 136 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   MET E 138 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE E  62 " --> pdb=" O   MET E 138 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   GLN E 140 " --> pdb=" O   ILE E  62 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ILE E  64 " --> pdb=" O   GLN E 140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.619A  pdb=" N   SER H  24 " --> pdb=" O   SER H  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 13 through 14
      removed outlier: 6.426A  pdb=" N   GLY H  13 " --> pdb=" O   THR H 130 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 14
      removed outlier: 6.426A  pdb=" N   GLY H  13 " --> pdb=" O   THR H 130 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TYR H 122 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   PHE H 103 " --> pdb=" O   MET H 120 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   MET H 120 " --> pdb=" O   PHE H 103 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 106 through 107
      removed outlier: 3.709A  pdb=" N   TYR H 114 " --> pdb=" O   LYS H 107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8
      removed outlier: 3.781A  pdb=" N   THR L  73 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.579A  pdb=" N   LEU L  12 " --> pdb=" O   LYS L 104 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA L  14 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.522A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    949 hydrogen bonds defined for protein.
    2727 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: 4.92

  Time building geometry restraints manager: 5.10 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: 5076
        1.34 -     1.46: 3235
        1.46 -     1.58: 8178
        1.58 -     1.70: 0
        1.70 -     1.82: 109
  Bond restraints: 16598
  Sorted by residual:
  bond pdb=" CA  ARG D 202 "
       pdb=" CB  ARG D 202 "
    ideal  model  delta    sigma   weight residual
    1.525  1.539 -0.015 8.30e-03 1.45e+04 3.09e+00
  bond pdb=" C   TYR E 327 "
       pdb=" N   PRO E 328 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.32e+00
  bond pdb=" CB  PRO L  45 "
       pdb=" CG  PRO L  45 "
    ideal  model  delta    sigma   weight residual
    1.492  1.559 -0.067 5.00e-02 4.00e+02 1.78e+00
  bond pdb=" CA  TYR D 327 "
       pdb=" C   TYR D 327 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 6.50e-03 2.37e+04 1.78e+00
  bond pdb=" C   ASP A 148 "
       pdb=" N   PRO A 149 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.30e-02 5.92e+03 1.55e+00
  ... (remaining 16593 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 22212
        2.71 -     5.41: 266
        5.41 -     8.12: 25
        8.12 -    10.82: 1
       10.82 -    13.53: 1
  Bond angle restraints: 22505
  Sorted by residual:
  angle pdb=" C   LEU C 321 "
        pdb=" CA  LEU C 321 "
        pdb=" CB  LEU C 321 "
      ideal   model   delta    sigma   weight residual
     117.23  111.19    6.04 1.36e+00 5.41e-01 1.97e+01
  angle pdb=" C   LEU D 235 "
        pdb=" N   TYR D 236 "
        pdb=" CA  TYR D 236 "
      ideal   model   delta    sigma   weight residual
     122.09  114.78    7.31 1.79e+00 3.12e-01 1.67e+01
  angle pdb=" N   VAL D 290 "
        pdb=" CA  VAL D 290 "
        pdb=" C   VAL D 290 "
      ideal   model   delta    sigma   weight residual
     110.42  106.58    3.84 9.60e-01 1.09e+00 1.60e+01
  angle pdb=" N   VAL A  93 "
        pdb=" CA  VAL A  93 "
        pdb=" C   VAL A  93 "
      ideal   model   delta    sigma   weight residual
     112.17  108.40    3.77 9.50e-01 1.11e+00 1.57e+01
  angle pdb=" C   LEU B 235 "
        pdb=" N   TYR B 236 "
        pdb=" CA  TYR B 236 "
      ideal   model   delta    sigma   weight residual
     122.53  114.94    7.59 1.92e+00 2.71e-01 1.56e+01
  ... (remaining 22500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 8887
       17.94 -    35.87: 888
       35.87 -    53.81: 164
       53.81 -    71.74: 27
       71.74 -    89.68: 17
  Dihedral angle restraints: 9983
    sinusoidal: 4164
      harmonic: 5819
  Sorted by residual:
  dihedral pdb=" CB  CYS H  25 "
           pdb=" SG  CYS H  25 "
           pdb=" SG  CYS H  99 "
           pdb=" CB  CYS H  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.00   54.00     1      1.00e+01 1.00e-02 3.96e+01
  dihedral pdb=" CA  ILE A 307 "
           pdb=" C   ILE A 307 "
           pdb=" N   ALA A 308 "
           pdb=" CA  ALA A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.88   22.12     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  PHE B 315 "
           pdb=" C   PHE B 315 "
           pdb=" N   GLU B 316 "
           pdb=" CA  GLU B 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.03  -20.97     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 9980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1902
       0.048 -    0.096: 527
       0.096 -    0.145: 112
       0.145 -    0.193: 9
       0.193 -    0.241: 1
  Chirality restraints: 2551
  Sorted by residual:
  chirality pdb=" CA  PRO L  45 "
            pdb=" N   PRO L  45 "
            pdb=" C   PRO L  45 "
            pdb=" CB  PRO L  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CG  LEU A 304 "
            pdb=" CB  LEU A 304 "
            pdb=" CD1 LEU A 304 "
            pdb=" CD2 LEU A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CB  ILE D 296 "
            pdb=" CA  ILE D 296 "
            pdb=" CG1 ILE D 296 "
            pdb=" CG2 ILE D 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 2548 not shown)

  Planarity restraints: 2816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  44 "    0.074 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO L  45 "   -0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO L  45 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO L  45 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 306 "   -0.028 2.00e-02 2.50e+03   2.28e-02 9.10e+00
        pdb=" CG  PHE E 306 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 306 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 306 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 306 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 306 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 306 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   8 "   -0.038 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO L   9 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO L   9 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L   9 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2813 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 201
        2.66 -     3.22: 16161
        3.22 -     3.78: 25581
        3.78 -     4.34: 34069
        4.34 -     4.90: 55918
  Nonbonded interactions: 131930
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 186 "
            pdb=" OG  SER E   7 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O   THR C 295 "
            pdb=" OG1 THR C 299 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OE2 GLU E  30 "
            pdb=" NZ  LYS E  43 "
     model   vdw
     2.164 3.120
  nonbonded pdb=" ND2 ASN B 314 "
            pdb=" OD1 ASN C 314 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OG  SER A  35 "
            pdb=" O   GLU A  38 "
     model   vdw
     2.216 3.040
  ... (remaining 131925 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 17 through 351)
  selection = (chain 'B' and resid 17 through 351)
  selection = (chain 'C' and resid 17 through 351)
  selection = (chain 'D' and resid 17 through 351)
  selection = (chain 'E' and resid 17 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.130
  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:          0.680
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     38.590
  Find NCS groups from input model:        0.790
  Set up NCS constraints:                  0.070
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
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      :  0.004   0.067  16600  Z= 0.166
  Angle     :  0.706  13.530  22509  Z= 0.378
  Chirality :  0.045   0.241   2551
  Planarity :  0.006   0.112   2816
  Dihedral  : 14.696  89.679   6219
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.39 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.38 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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: -0.35 (0.19), residues: 1947
  helix:  1.22 (0.17), residues: 929
  sheet: -0.66 (0.28), residues: 345
  loop : -2.09 (0.23), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 350 
 HIS   0.004   0.001   HIS C 212 
 PHE   0.052   0.002   PHE E 306 
 TYR   0.023   0.001   TYR A 236 
 ARG   0.015   0.001   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13366 (  945)
  hydrogen bonds       : angle       6.33738 ( 2727)
  SS BOND              : bond        0.00541 (    2)
  SS BOND              : angle       1.23855 (    4)
  covalent geometry    : bond        0.00372 (16598)
  covalent geometry    : angle       0.70552 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 432
  time to evaluate  : 1.681 
Fit side-chains
REVERT: A  100 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8428 (mt-10)
REVERT: A  174 ILE cc_start: 0.8583 (mm) cc_final: 0.8382 (mm)
REVERT: A  186 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5783 (mm-30)
REVERT: A  286 LYS cc_start: 0.7954 (tptt) cc_final: 0.7091 (tmtt)
REVERT: A  317 TYR cc_start: 0.5759 (t80) cc_final: 0.5398 (t80)
REVERT: A  334 MET cc_start: 0.5044 (mmp) cc_final: 0.4813 (tpp)
REVERT: B   96 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7468 (ttm170)
REVERT: B  155 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7027 (tpp80)
REVERT: B  186 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6891 (tm-30)
REVERT: B  197 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6552 (mm-30)
REVERT: B  313 MET cc_start: 0.5462 (mtp) cc_final: 0.5132 (mtp)
REVERT: B  318 MET cc_start: 0.0792 (tpt) cc_final: -0.0651 (tpt)
REVERT: C   22 LYS cc_start: 0.7524 (pttm) cc_final: 0.7301 (pttm)
REVERT: C   35 SER cc_start: 0.8753 (t) cc_final: 0.8422 (t)
REVERT: D   23 TYR cc_start: 0.7675 (m-10) cc_final: 0.7364 (m-80)
REVERT: D  163 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7887 (mtmt)
REVERT: D  318 MET cc_start: 0.5639 (ttp) cc_final: 0.4553 (ttt)
REVERT: E  104 ASN cc_start: 0.8103 (t0) cc_final: 0.7716 (t0)
REVERT: E  174 ILE cc_start: 0.8047 (mm) cc_final: 0.7841 (mm)
REVERT: H   46 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6019 (mmmm)
REVERT: H   66 SER cc_start: 0.7174 (p) cc_final: 0.6410 (m)
REVERT: H   83 TYR cc_start: 0.6849 (m-10) cc_final: 0.6378 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 433
  average time/residue: 0.2878
  time to fit residues: 182.4799
Evaluate side-chains
  372 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 371
  time to evaluate  : 1.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 162 optimal weight:    1.9990
   chunk 146 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 98 optimal weight:    0.3980
   chunk 78 optimal weight:    1.9990
   chunk 151 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 112 optimal weight:    0.6980
   chunk 175 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 126 GLN
A 288 ASN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 ASN
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 GLN
D 288 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.177209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.152465 restraints weight = 21907.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.156925 restraints weight = 11210.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.159968 restraints weight = 7045.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16600  Z= 0.186
  Angle     :  0.653   9.547  22509  Z= 0.340
  Chirality :  0.045   0.244   2551
  Planarity :  0.005   0.114   2816
  Dihedral  :  4.768  31.775   2181
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.75 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.03 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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: -0.07 (0.19), residues: 1947
  helix:  1.58 (0.17), residues: 940
  sheet: -0.70 (0.28), residues: 339
  loop : -2.09 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 350 
 HIS   0.005   0.001   HIS C  83 
 PHE   0.039   0.002   PHE C 301 
 TYR   0.023   0.002   TYR E 236 
 ARG   0.005   0.001   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04617 (  945)
  hydrogen bonds       : angle       4.98850 ( 2727)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       2.09982 (    4)
  covalent geometry    : bond        0.00434 (16598)
  covalent geometry    : angle       0.65268 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 403
  time to evaluate  : 1.784 
Fit side-chains
REVERT: A  174 ILE cc_start: 0.8496 (mm) cc_final: 0.8280 (mm)
REVERT: A  186 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5805 (mm-30)
REVERT: A  237 ARG cc_start: 0.6337 (mmm-85) cc_final: 0.5943 (mtm-85)
REVERT: A  286 LYS cc_start: 0.7866 (tptt) cc_final: 0.6938 (tmtt)
REVERT: B   96 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7489 (ttp-170)
REVERT: B  100 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7247 (mt-10)
REVERT: B  155 ARG cc_start: 0.7407 (mmm160) cc_final: 0.6951 (tpp80)
REVERT: B  186 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6923 (tm-30)
REVERT: B  187 LYS cc_start: 0.7631 (tttt) cc_final: 0.7243 (tttt)
REVERT: B  197 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6526 (mm-30)
REVERT: B  313 MET cc_start: 0.6032 (mtp) cc_final: 0.5451 (mtp)
REVERT: B  318 MET cc_start: 0.0810 (tpt) cc_final: -0.0818 (tpt)
REVERT: C   75 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7667 (tpp-160)
REVERT: C  291 MET cc_start: 0.7625 (tpp) cc_final: 0.7181 (tpp)
REVERT: C  327 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.5069 (t80)
REVERT: D  163 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7838 (mtmm)
REVERT: D  294 LEU cc_start: 0.8907 (tp) cc_final: 0.8699 (tp)
REVERT: D  318 MET cc_start: 0.5703 (ttp) cc_final: 0.4588 (ttt)
REVERT: E  104 ASN cc_start: 0.8200 (t0) cc_final: 0.7864 (t0)
REVERT: E  125 GLU cc_start: 0.7723 (tt0) cc_final: 0.7502 (tt0)
REVERT: E  162 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6633 (tpt90)
REVERT: E  174 ILE cc_start: 0.7971 (mm) cc_final: 0.7722 (mm)
REVERT: H   46 LYS cc_start: 0.6814 (mmmt) cc_final: 0.6417 (mmmm)
REVERT: H   66 SER cc_start: 0.7243 (p) cc_final: 0.6548 (m)
  outliers start: 37
  outliers final: 30
  residues processed: 416
  average time/residue: 0.3007
  time to fit residues: 188.2796
Evaluate side-chains
  415 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 384
  time to evaluate  : 1.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  306 PHE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  134 ASN
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain L residue   21 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 192 optimal weight:    0.7980
   chunk 127 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 123 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 171 optimal weight:    0.0040
   chunk 70 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 180 optimal weight:    0.7980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 ASN
B 314 ASN
C 134 ASN
D  95 GLN
D 288 ASN
L   7 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.176254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.152171 restraints weight = 21723.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.156355 restraints weight = 11577.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.159175 restraints weight = 7451.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  16600  Z= 0.165
  Angle     :  0.628   8.870  22509  Z= 0.325
  Chirality :  0.044   0.243   2551
  Planarity :  0.005   0.114   2816
  Dihedral  :  4.687  32.279   2181
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.75 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.91 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.02 (0.19), residues: 1947
  helix:  1.67 (0.17), residues: 939
  sheet: -0.66 (0.28), residues: 348
  loop : -2.08 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.025   0.002   PHE E 306 
 TYR   0.018   0.001   TYR E 236 
 ARG   0.010   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04343 (  945)
  hydrogen bonds       : angle       4.83275 ( 2727)
  SS BOND              : bond        0.00564 (    2)
  SS BOND              : angle       1.68154 (    4)
  covalent geometry    : bond        0.00387 (16598)
  covalent geometry    : angle       0.62759 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 402
  time to evaluate  : 1.885 
Fit side-chains
REVERT: A  138 MET cc_start: 0.6605 (mtm) cc_final: 0.6343 (mtm)
REVERT: A  174 ILE cc_start: 0.8412 (mm) cc_final: 0.8179 (mm)
REVERT: A  186 GLU cc_start: 0.6271 (mm-30) cc_final: 0.5635 (mm-30)
REVERT: A  237 ARG cc_start: 0.6303 (mmm-85) cc_final: 0.5963 (mtm-85)
REVERT: A  247 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (m)
REVERT: A  286 LYS cc_start: 0.7932 (tptt) cc_final: 0.7001 (tmtt)
REVERT: A  311 TYR cc_start: 0.7364 (m-80) cc_final: 0.7161 (m-80)
REVERT: A  318 MET cc_start: 0.5082 (mtt) cc_final: 0.4660 (mpp)
REVERT: B   96 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7555 (ttp-170)
REVERT: B  125 GLU cc_start: 0.6741 (tt0) cc_final: 0.6390 (tt0)
REVERT: B  142 LYS cc_start: 0.7410 (mttp) cc_final: 0.7192 (mttp)
REVERT: B  155 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6940 (tpp80)
REVERT: B  186 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6861 (tm-30)
REVERT: B  187 LYS cc_start: 0.7654 (tttt) cc_final: 0.7287 (tttt)
REVERT: B  197 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6478 (mm-30)
REVERT: B  275 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7137 (mm)
REVERT: B  313 MET cc_start: 0.6245 (mtp) cc_final: 0.5853 (mtp)
REVERT: B  318 MET cc_start: 0.0680 (tpt) cc_final: -0.0970 (tpt)
REVERT: C  225 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8569 (tt)
REVERT: C  291 MET cc_start: 0.7881 (tpp) cc_final: 0.7482 (tpp)
REVERT: C  327 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5012 (t80)
REVERT: D   23 TYR cc_start: 0.7953 (m-80) cc_final: 0.7276 (m-80)
REVERT: D   48 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7555 (mm-30)
REVERT: D  163 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7818 (mtmm)
REVERT: D  294 LEU cc_start: 0.8898 (tp) cc_final: 0.8657 (tp)
REVERT: D  318 MET cc_start: 0.5668 (ttp) cc_final: 0.4574 (ttt)
REVERT: E  146 VAL cc_start: 0.8473 (m) cc_final: 0.8072 (p)
REVERT: E  204 GLU cc_start: 0.7276 (tt0) cc_final: 0.6942 (tt0)
REVERT: E  252 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6915 (ttm-80)
REVERT: E  313 MET cc_start: 0.5335 (tpp) cc_final: 0.4814 (tpp)
REVERT: H   46 LYS cc_start: 0.6773 (mmmt) cc_final: 0.6353 (mmmm)
REVERT: H   66 SER cc_start: 0.7236 (p) cc_final: 0.6536 (m)
REVERT: L    2 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7507 (t0)
  outliers start: 46
  outliers final: 31
  residues processed: 417
  average time/residue: 0.2698
  time to fit residues: 169.1294
Evaluate side-chains
  418 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 382
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain B residue   38 GLU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  134 ASN
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   21 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0870
   chunk 51 optimal weight:    0.8980
   chunk 171 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.175178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.150930 restraints weight = 21764.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.155101 restraints weight = 11656.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.157896 restraints weight = 7548.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  16600  Z= 0.169
  Angle     :  0.626   8.885  22509  Z= 0.322
  Chirality :  0.044   0.244   2551
  Planarity :  0.005   0.115   2816
  Dihedral  :  4.652  32.286   2181
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.01 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.72 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.05 (0.19), residues: 1947
  helix:  1.69 (0.17), residues: 939
  sheet: -0.62 (0.28), residues: 348
  loop : -2.08 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.023   0.002   PHE E 306 
 TYR   0.020   0.001   TYR D  23 
 ARG   0.009   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  945)
  hydrogen bonds       : angle       4.73216 ( 2727)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       1.39271 (    4)
  covalent geometry    : bond        0.00399 (16598)
  covalent geometry    : angle       0.62627 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  458 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 397
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7245 (tp30) cc_final: 0.7045 (tp30)
REVERT: A  174 ILE cc_start: 0.8415 (mm) cc_final: 0.8137 (mm)
REVERT: A  186 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5704 (mm-30)
REVERT: A  237 ARG cc_start: 0.6262 (mmm-85) cc_final: 0.5977 (mtm-85)
REVERT: A  247 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7982 (m)
REVERT: A  286 LYS cc_start: 0.7982 (tptt) cc_final: 0.7067 (tmtt)
REVERT: A  311 TYR cc_start: 0.7457 (m-80) cc_final: 0.7215 (m-80)
REVERT: A  317 TYR cc_start: 0.5598 (t80) cc_final: 0.5369 (t80)
REVERT: A  334 MET cc_start: 0.6006 (tpp) cc_final: 0.5763 (mmt)
REVERT: B   96 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7437 (ttm170)
REVERT: B  154 ILE cc_start: 0.8401 (mt) cc_final: 0.8086 (mt)
REVERT: B  155 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6931 (tpp80)
REVERT: B  163 LYS cc_start: 0.7684 (mttm) cc_final: 0.7380 (mttm)
REVERT: B  186 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6800 (tm-30)
REVERT: B  187 LYS cc_start: 0.7667 (tttt) cc_final: 0.7280 (tttt)
REVERT: B  197 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6553 (mm-30)
REVERT: B  275 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7113 (mm)
REVERT: B  313 MET cc_start: 0.6458 (mtp) cc_final: 0.6199 (mtp)
REVERT: B  318 MET cc_start: 0.0350 (tpt) cc_final: -0.1338 (tpt)
REVERT: C   22 LYS cc_start: 0.7744 (pttm) cc_final: 0.7396 (pttp)
REVERT: C   23 TYR cc_start: 0.6799 (m-80) cc_final: 0.6248 (m-10)
REVERT: C  225 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8614 (tt)
REVERT: C  244 GLU cc_start: 0.7654 (mp0) cc_final: 0.7409 (mp0)
REVERT: C  291 MET cc_start: 0.7935 (tpp) cc_final: 0.7572 (tpp)
REVERT: C  327 TYR cc_start: 0.5653 (OUTLIER) cc_final: 0.4976 (t80)
REVERT: D   42 PHE cc_start: 0.7663 (t80) cc_final: 0.7318 (t80)
REVERT: D  163 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7803 (mtmm)
REVERT: D  181 TYR cc_start: 0.8558 (m-80) cc_final: 0.8188 (m-80)
REVERT: D  318 MET cc_start: 0.5687 (ttp) cc_final: 0.4826 (ttt)
REVERT: E   90 ILE cc_start: 0.8154 (mm) cc_final: 0.7901 (mm)
REVERT: E  131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6917 (tt)
REVERT: E  174 ILE cc_start: 0.8017 (mm) cc_final: 0.7714 (mm)
REVERT: E  177 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8556 (mm)
REVERT: E  252 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6829 (ttm-80)
REVERT: E  313 MET cc_start: 0.5380 (tpp) cc_final: 0.4816 (tpp)
REVERT: H   46 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6108 (mmmm)
REVERT: H   66 SER cc_start: 0.7120 (p) cc_final: 0.6405 (m)
REVERT: L    2 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7598 (t0)
  outliers start: 61
  outliers final: 41
  residues processed: 420
  average time/residue: 0.2861
  time to fit residues: 178.7508
Evaluate side-chains
  432 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 384
  time to evaluate  : 1.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  134 ASN
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   21 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0870
   chunk 28 optimal weight:    0.4980
   chunk 103 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 192 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 ASN
D  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.175463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.151147 restraints weight = 22122.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.155323 restraints weight = 11778.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.158179 restraints weight = 7625.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  16600  Z= 0.158
  Angle     :  0.623   9.030  22509  Z= 0.321
  Chirality :  0.044   0.267   2551
  Planarity :  0.005   0.116   2816
  Dihedral  :  4.643  32.227   2181
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.65 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.38 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.09 (0.20), residues: 1947
  helix:  1.74 (0.17), residues: 939
  sheet: -0.61 (0.28), residues: 349
  loop : -2.11 (0.23), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 350 
 HIS   0.005   0.001   HIS C  83 
 PHE   0.022   0.002   PHE E 306 
 TYR   0.015   0.001   TYR B 236 
 ARG   0.008   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  945)
  hydrogen bonds       : angle       4.68766 ( 2727)
  SS BOND              : bond        0.00464 (    2)
  SS BOND              : angle       1.34764 (    4)
  covalent geometry    : bond        0.00374 (16598)
  covalent geometry    : angle       0.62313 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  467 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 399
  time to evaluate  : 1.697 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7295 (tp30) cc_final: 0.7080 (tp30)
REVERT: A  174 ILE cc_start: 0.8218 (mm) cc_final: 0.7854 (mm)
REVERT: A  186 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5723 (mm-30)
REVERT: A  237 ARG cc_start: 0.6269 (mmm-85) cc_final: 0.5974 (mtm-85)
REVERT: A  247 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7985 (m)
REVERT: A  286 LYS cc_start: 0.7967 (tptt) cc_final: 0.7020 (tmtt)
REVERT: A  311 TYR cc_start: 0.7509 (m-80) cc_final: 0.7237 (m-80)
REVERT: A  317 TYR cc_start: 0.5587 (t80) cc_final: 0.5288 (t80)
REVERT: B   96 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7428 (ttm170)
REVERT: B  100 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7007 (mt-10)
REVERT: B  155 ARG cc_start: 0.7367 (mmm160) cc_final: 0.6923 (tpp80)
REVERT: B  163 LYS cc_start: 0.7704 (mttm) cc_final: 0.7389 (mttm)
REVERT: B  186 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: B  187 LYS cc_start: 0.7644 (tttt) cc_final: 0.7258 (tttt)
REVERT: B  197 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6463 (mm-30)
REVERT: B  245 LYS cc_start: 0.7189 (mppt) cc_final: 0.6892 (mtmm)
REVERT: B  275 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7100 (mm)
REVERT: B  313 MET cc_start: 0.6476 (mtp) cc_final: 0.6209 (mtp)
REVERT: B  318 MET cc_start: 0.0415 (tpt) cc_final: -0.1265 (tpt)
REVERT: C   23 TYR cc_start: 0.6808 (m-80) cc_final: 0.6216 (m-10)
REVERT: C  134 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7642 (p0)
REVERT: C  225 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8573 (tt)
REVERT: C  232 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8052 (mm)
REVERT: C  244 GLU cc_start: 0.7616 (mp0) cc_final: 0.7369 (mp0)
REVERT: C  302 MET cc_start: 0.7280 (mmp) cc_final: 0.7020 (mmt)
REVERT: C  318 MET cc_start: 0.3708 (mmm) cc_final: 0.3355 (mmm)
REVERT: C  327 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.4906 (t80)
REVERT: D  121 GLU cc_start: 0.7006 (pm20) cc_final: 0.6529 (pm20)
REVERT: D  163 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7792 (mtmm)
REVERT: D  181 TYR cc_start: 0.8604 (m-80) cc_final: 0.8238 (m-80)
REVERT: D  184 LEU cc_start: 0.8720 (tt) cc_final: 0.8509 (tt)
REVERT: D  318 MET cc_start: 0.5686 (ttp) cc_final: 0.5183 (ttt)
REVERT: E   51 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6865 (mm)
REVERT: E  174 ILE cc_start: 0.8016 (mm) cc_final: 0.7753 (mm)
REVERT: E  177 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8603 (mm)
REVERT: E  252 ARG cc_start: 0.7437 (mtp85) cc_final: 0.6794 (ttm-80)
REVERT: H   46 LYS cc_start: 0.6561 (mmmt) cc_final: 0.6119 (mmmm)
REVERT: H   66 SER cc_start: 0.7136 (p) cc_final: 0.6414 (m)
REVERT: H  114 TYR cc_start: 0.8794 (t80) cc_final: 0.8458 (t80)
REVERT: H  117 TYR cc_start: 0.8919 (m-80) cc_final: 0.8519 (m-80)
REVERT: L    2 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7690 (t0)
  outliers start: 68
  outliers final: 47
  residues processed: 431
  average time/residue: 0.2665
  time to fit residues: 172.5185
Evaluate side-chains
  441 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 385
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   38 GLU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  134 ASN
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  124 SER
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 171 optimal weight:    0.0870
   chunk 189 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
B 285 ASN
E 212 HIS
L   7 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.174588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.150004 restraints weight = 21832.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.154203 restraints weight = 11740.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.157021 restraints weight = 7637.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
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   0.060  16600  Z= 0.174
  Angle     :  0.633   8.540  22509  Z= 0.326
  Chirality :  0.045   0.247   2551
  Planarity :  0.005   0.117   2816
  Dihedral  :  4.661  33.091   2181
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.47 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 18.98 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.05 (0.19), residues: 1947
  helix:  1.73 (0.17), residues: 939
  sheet: -0.59 (0.28), residues: 344
  loop : -2.17 (0.23), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.021   0.002   PHE C 301 
 TYR   0.016   0.001   TYR B 327 
 ARG   0.008   0.000   ARG E 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04198 (  945)
  hydrogen bonds       : angle       4.68279 ( 2727)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       2.68743 (    4)
  covalent geometry    : bond        0.00414 (16598)
  covalent geometry    : angle       0.63168 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 382
  time to evaluate  : 2.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7253 (tp30) cc_final: 0.7036 (tp30)
REVERT: A  174 ILE cc_start: 0.8274 (mm) cc_final: 0.7926 (mm)
REVERT: A  186 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5711 (mm-30)
REVERT: A  237 ARG cc_start: 0.6280 (mmm-85) cc_final: 0.6011 (mtm-85)
REVERT: A  247 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8060 (m)
REVERT: A  286 LYS cc_start: 0.7991 (tptt) cc_final: 0.7079 (tmtt)
REVERT: A  311 TYR cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80)
REVERT: A  317 TYR cc_start: 0.5544 (t80) cc_final: 0.5189 (t80)
REVERT: B   40 ARG cc_start: 0.6019 (ptp90) cc_final: 0.5767 (ptt-90)
REVERT: B   96 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7379 (ttm170)
REVERT: B  155 ARG cc_start: 0.7371 (mmm160) cc_final: 0.6937 (tpp80)
REVERT: B  163 LYS cc_start: 0.7732 (mttm) cc_final: 0.7446 (mttm)
REVERT: B  186 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7125 (tm-30)
REVERT: B  197 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6496 (mm-30)
REVERT: B  245 LYS cc_start: 0.7198 (mppt) cc_final: 0.6902 (mtmm)
REVERT: B  275 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7124 (mm)
REVERT: B  313 MET cc_start: 0.6343 (mtp) cc_final: 0.6113 (mtp)
REVERT: B  318 MET cc_start: 0.0488 (tpt) cc_final: -0.1228 (tpt)
REVERT: C   23 TYR cc_start: 0.6801 (m-80) cc_final: 0.6516 (m-10)
REVERT: C  190 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7046 (m-30)
REVERT: C  206 GLU cc_start: 0.6826 (pt0) cc_final: 0.6618 (mp0)
REVERT: C  225 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (tt)
REVERT: C  232 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8202 (mm)
REVERT: C  318 MET cc_start: 0.3668 (mmm) cc_final: 0.3307 (mmm)
REVERT: C  327 TYR cc_start: 0.5649 (OUTLIER) cc_final: 0.4899 (t80)
REVERT: D   42 PHE cc_start: 0.7580 (t80) cc_final: 0.7084 (t80)
REVERT: D  121 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6491 (pm20)
REVERT: D  163 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7796 (mtmm)
REVERT: D  318 MET cc_start: 0.5659 (ttp) cc_final: 0.5148 (ttt)
REVERT: E    6 LEU cc_start: 0.7224 (pt) cc_final: 0.6941 (pt)
REVERT: E   51 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (mm)
REVERT: E  174 ILE cc_start: 0.8065 (mm) cc_final: 0.7811 (mm)
REVERT: E  177 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8596 (mm)
REVERT: E  252 ARG cc_start: 0.7507 (mtp85) cc_final: 0.6941 (ttm-80)
REVERT: E  313 MET cc_start: 0.5263 (tpp) cc_final: 0.4780 (tpp)
REVERT: H   46 LYS cc_start: 0.6559 (mmmt) cc_final: 0.6123 (mmmm)
REVERT: H   66 SER cc_start: 0.7221 (p) cc_final: 0.6521 (m)
REVERT: H  117 TYR cc_start: 0.8990 (m-80) cc_final: 0.8564 (m-80)
REVERT: L    2 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7665 (t0)
  outliers start: 75
  outliers final: 56
  residues processed: 412
  average time/residue: 0.3021
  time to fit residues: 186.6869
Evaluate side-chains
  437 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 371
  time to evaluate  : 1.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   55 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  124 SER
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  211 THR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain H residue   49 GLU
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 114 optimal weight:    0.0970
   chunk 148 optimal weight:    3.9990
   chunk 136 optimal weight:    0.0770
   chunk 89 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 133 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0870
   chunk 68 optimal weight:    0.3980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.2514

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

Flipped N/Q/H residues before XYZ refinement:
C 134 ASN
L   7 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.178173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.153207 restraints weight = 21891.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.157481 restraints weight = 11768.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.160375 restraints weight = 7671.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  16600  Z= 0.132
  Angle     :  0.616   9.750  22509  Z= 0.315
  Chirality :  0.044   0.240   2551
  Planarity :  0.005   0.116   2816
  Dihedral  :  4.570  32.275   2181
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.34 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.75 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.19 (0.20), residues: 1947
  helix:  1.87 (0.17), residues: 938
  sheet: -0.57 (0.28), residues: 344
  loop : -2.10 (0.23), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 350 
 HIS   0.005   0.001   HIS C  83 
 PHE   0.025   0.001   PHE E 306 
 TYR   0.022   0.001   TYR C  19 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  945)
  hydrogen bonds       : angle       4.57936 ( 2727)
  SS BOND              : bond        0.00555 (    2)
  SS BOND              : angle       2.20831 (    4)
  covalent geometry    : bond        0.00303 (16598)
  covalent geometry    : angle       0.61562 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 383
  time to evaluate  : 1.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 ILE cc_start: 0.8164 (mm) cc_final: 0.7856 (mm)
REVERT: A  186 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5722 (mm-30)
REVERT: A  237 ARG cc_start: 0.6224 (mmm-85) cc_final: 0.5922 (mtm-85)
REVERT: A  247 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7888 (m)
REVERT: A  286 LYS cc_start: 0.7980 (tptt) cc_final: 0.7045 (tmtt)
REVERT: A  311 TYR cc_start: 0.7345 (m-80) cc_final: 0.6935 (m-80)
REVERT: A  320 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6451 (mm-30)
REVERT: B   40 ARG cc_start: 0.5975 (ptp90) cc_final: 0.5739 (ptt-90)
REVERT: B   96 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7228 (ttm170)
REVERT: B  100 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6890 (mt-10)
REVERT: B  133 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7486 (ttmt)
REVERT: B  155 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6930 (tpp80)
REVERT: B  186 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6690 (tm-30)
REVERT: B  187 LYS cc_start: 0.7435 (tttt) cc_final: 0.7088 (tttt)
REVERT: B  197 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6416 (mm-30)
REVERT: B  275 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7355 (mm)
REVERT: B  313 MET cc_start: 0.6317 (mtp) cc_final: 0.6079 (mtp)
REVERT: B  318 MET cc_start: 0.0526 (tpt) cc_final: -0.1085 (tpt)
REVERT: C  190 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7044 (m-30)
REVERT: C  232 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7834 (mm)
REVERT: C  244 GLU cc_start: 0.7560 (mp0) cc_final: 0.7325 (mp0)
REVERT: C  318 MET cc_start: 0.3775 (mmm) cc_final: 0.3423 (mmm)
REVERT: C  327 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.4853 (t80)
REVERT: D   42 PHE cc_start: 0.7570 (t80) cc_final: 0.7060 (t80)
REVERT: D  121 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6518 (pm20)
REVERT: D  163 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7756 (mtmm)
REVERT: D  181 TYR cc_start: 0.8500 (m-80) cc_final: 0.8039 (m-80)
REVERT: D  318 MET cc_start: 0.5695 (ttp) cc_final: 0.4917 (ttt)
REVERT: E    6 LEU cc_start: 0.7102 (pt) cc_final: 0.6827 (pt)
REVERT: E   51 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6871 (mm)
REVERT: E  174 ILE cc_start: 0.8056 (mm) cc_final: 0.7786 (mm)
REVERT: E  177 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8568 (mm)
REVERT: E  252 ARG cc_start: 0.7276 (mtp85) cc_final: 0.6870 (ttm-80)
REVERT: E  313 MET cc_start: 0.5401 (tpp) cc_final: 0.4877 (tpp)
REVERT: H   46 LYS cc_start: 0.6619 (mmmt) cc_final: 0.6194 (mmmm)
REVERT: H   66 SER cc_start: 0.7012 (p) cc_final: 0.6305 (m)
REVERT: H  117 TYR cc_start: 0.8964 (m-80) cc_final: 0.8560 (m-80)
REVERT: L    2 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7688 (t0)
  outliers start: 73
  outliers final: 51
  residues processed: 422
  average time/residue: 0.2782
  time to fit residues: 178.5378
Evaluate side-chains
  437 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 377
  time to evaluate  : 2.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   38 GLU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  134 ASN
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 162 optimal weight:    0.5980
   chunk 129 optimal weight:    0.5980
   chunk 146 optimal weight:    0.8980
   chunk 148 optimal weight:    1.9990
   chunk 149 optimal weight:    0.5980
   chunk 133 optimal weight:    0.0980
   chunk 73 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0980
   chunk 151 optimal weight:    0.9990
   overall best weight:    0.3980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.177494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.152784 restraints weight = 21602.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.157023 restraints weight = 11680.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.159874 restraints weight = 7619.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  16600  Z= 0.144
  Angle     :  0.626  10.086  22509  Z= 0.320
  Chirality :  0.044   0.241   2551
  Planarity :  0.005   0.117   2816
  Dihedral  :  4.526  32.796   2181
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.75 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 19.91 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.22 (0.20), residues: 1947
  helix:  1.85 (0.17), residues: 939
  sheet: -0.53 (0.28), residues: 347
  loop : -2.05 (0.23), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 350 
 HIS   0.005   0.001   HIS C  83 
 PHE   0.023   0.001   PHE E 306 
 TYR   0.020   0.001   TYR B 327 
 ARG   0.007   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  945)
  hydrogen bonds       : angle       4.55627 ( 2727)
  SS BOND              : bond        0.00501 (    2)
  SS BOND              : angle       2.15856 (    4)
  covalent geometry    : bond        0.00336 (16598)
  covalent geometry    : angle       0.62586 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 385
  time to evaluate  : 1.975 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8585 (Cg_endo)
REVERT: A  174 ILE cc_start: 0.8158 (mm) cc_final: 0.7805 (mm)
REVERT: A  186 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5724 (mm-30)
REVERT: A  237 ARG cc_start: 0.6191 (mmm-85) cc_final: 0.5930 (mtm-85)
REVERT: A  247 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7916 (m)
REVERT: A  286 LYS cc_start: 0.7995 (tptt) cc_final: 0.7088 (tmtt)
REVERT: B   40 ARG cc_start: 0.5961 (ptp90) cc_final: 0.5756 (ptt-90)
REVERT: B   96 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7237 (ttm170)
REVERT: B  100 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6879 (mt-10)
REVERT: B  133 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7486 (ttmt)
REVERT: B  155 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6933 (tpp80)
REVERT: B  186 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6745 (tm-30)
REVERT: B  187 LYS cc_start: 0.7474 (tttt) cc_final: 0.7011 (ttpt)
REVERT: B  197 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6477 (mm-30)
REVERT: B  275 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7384 (mm)
REVERT: B  318 MET cc_start: 0.0402 (tpt) cc_final: -0.1316 (tpt)
REVERT: C   23 TYR cc_start: 0.6655 (m-80) cc_final: 0.6403 (m-10)
REVERT: C  190 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7028 (m-30)
REVERT: C  225 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8527 (tt)
REVERT: C  232 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7872 (mm)
REVERT: C  244 GLU cc_start: 0.7553 (mp0) cc_final: 0.7320 (mp0)
REVERT: C  318 MET cc_start: 0.3483 (mmm) cc_final: 0.3079 (mmm)
REVERT: C  327 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4803 (t80)
REVERT: D   42 PHE cc_start: 0.7633 (t80) cc_final: 0.7117 (t80)
REVERT: D  121 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6604 (pm20)
REVERT: D  163 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7752 (mtmm)
REVERT: D  318 MET cc_start: 0.5713 (ttp) cc_final: 0.5206 (ttt)
REVERT: E    6 LEU cc_start: 0.7008 (pt) cc_final: 0.6748 (pt)
REVERT: E   51 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6861 (mm)
REVERT: E  174 ILE cc_start: 0.8071 (mm) cc_final: 0.7815 (mm)
REVERT: E  177 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8586 (mm)
REVERT: E  252 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6875 (ttm-80)
REVERT: H   46 LYS cc_start: 0.6626 (mmmt) cc_final: 0.6204 (mmmm)
REVERT: H   66 SER cc_start: 0.6995 (p) cc_final: 0.6294 (m)
REVERT: H  117 TYR cc_start: 0.9006 (m-80) cc_final: 0.8622 (m-80)
REVERT: L    2 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7698 (t0)
  outliers start: 72
  outliers final: 56
  residues processed: 423
  average time/residue: 0.3205
  time to fit residues: 204.1290
Evaluate side-chains
  440 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 374
  time to evaluate  : 1.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 142 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 143 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 176 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 177 optimal weight:    0.4980
   chunk 60 optimal weight:    0.7980
   chunk 185 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.174097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.149642 restraints weight = 21760.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.153742 restraints weight = 11780.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.156529 restraints weight = 7709.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16600  Z= 0.183
  Angle     :  0.663  11.602  22509  Z= 0.339
  Chirality :  0.045   0.244   2551
  Planarity :  0.005   0.118   2816
  Dihedral  :  4.612  31.993   2181
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.42 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.52 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.11 (0.19), residues: 1947
  helix:  1.73 (0.17), residues: 940
  sheet: -0.54 (0.29), residues: 338
  loop : -2.06 (0.23), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.021   0.002   PHE E 306 
 TYR   0.018   0.002   TYR A 311 
 ARG   0.007   0.001   ARG E 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04207 (  945)
  hydrogen bonds       : angle       4.62929 ( 2727)
  SS BOND              : bond        0.00453 (    2)
  SS BOND              : angle       2.33721 (    4)
  covalent geometry    : bond        0.00437 (16598)
  covalent geometry    : angle       0.66226 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 394
  time to evaluate  : 3.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6804 (t80) cc_final: 0.6194 (t80)
REVERT: A  174 ILE cc_start: 0.8204 (mm) cc_final: 0.7872 (mm)
REVERT: A  186 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5745 (mm-30)
REVERT: A  237 ARG cc_start: 0.6189 (mmm-85) cc_final: 0.5916 (mtm-85)
REVERT: A  247 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8184 (m)
REVERT: A  286 LYS cc_start: 0.8011 (tptt) cc_final: 0.7112 (tmtt)
REVERT: B   24 ARG cc_start: 0.7942 (mmt90) cc_final: 0.7696 (mmt90)
REVERT: B   96 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7323 (ttm170)
REVERT: B  155 ARG cc_start: 0.7352 (mmm160) cc_final: 0.6951 (tpp80)
REVERT: B  186 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6842 (tm-30)
REVERT: B  187 LYS cc_start: 0.7469 (tttt) cc_final: 0.6987 (ttpt)
REVERT: B  227 PRO cc_start: 0.9053 (Cg_exo) cc_final: 0.8704 (Cg_endo)
REVERT: B  275 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7427 (mm)
REVERT: B  318 MET cc_start: 0.0629 (tpt) cc_final: -0.1072 (tpt)
REVERT: C  124 SER cc_start: 0.8735 (p) cc_final: 0.8499 (p)
REVERT: C  190 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6978 (m-30)
REVERT: C  225 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8613 (tt)
REVERT: C  232 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8235 (mm)
REVERT: C  263 ASP cc_start: 0.7545 (m-30) cc_final: 0.7133 (m-30)
REVERT: C  318 MET cc_start: 0.3696 (mmm) cc_final: 0.3305 (mmm)
REVERT: C  327 TYR cc_start: 0.5629 (OUTLIER) cc_final: 0.4865 (t80)
REVERT: D   42 PHE cc_start: 0.7727 (t80) cc_final: 0.7278 (t80)
REVERT: D  121 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6663 (pm20)
REVERT: D  134 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7233 (t0)
REVERT: D  163 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7767 (mtmm)
REVERT: D  318 MET cc_start: 0.5683 (ttp) cc_final: 0.5208 (ttt)
REVERT: E    6 LEU cc_start: 0.6942 (pt) cc_final: 0.6664 (pt)
REVERT: E   51 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6908 (mm)
REVERT: E   90 ILE cc_start: 0.8231 (mm) cc_final: 0.7991 (mm)
REVERT: E  174 ILE cc_start: 0.8167 (mm) cc_final: 0.7928 (mm)
REVERT: E  177 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8586 (mm)
REVERT: E  204 GLU cc_start: 0.7303 (tt0) cc_final: 0.6997 (tt0)
REVERT: E  252 ARG cc_start: 0.7348 (mtp85) cc_final: 0.6957 (ttm-80)
REVERT: H   46 LYS cc_start: 0.6536 (mmmt) cc_final: 0.6115 (mmmm)
REVERT: H   66 SER cc_start: 0.7147 (p) cc_final: 0.6460 (m)
REVERT: H  117 TYR cc_start: 0.9056 (m-80) cc_final: 0.8579 (m-80)
REVERT: L    2 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7701 (t0)
REVERT: L   51 SER cc_start: 0.8534 (m) cc_final: 0.8306 (m)
  outliers start: 72
  outliers final: 56
  residues processed: 432
  average time/residue: 0.4225
  time to fit residues: 284.5843
Evaluate side-chains
  453 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 386
  time to evaluate  : 2.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 176 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 137 optimal weight:    0.1980
   chunk 144 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.5538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.175333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.150242 restraints weight = 22045.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.154515 restraints weight = 11901.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.157382 restraints weight = 7783.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16600  Z= 0.165
  Angle     :  0.668  13.455  22509  Z= 0.339
  Chirality :  0.046   0.252   2551
  Planarity :  0.005   0.118   2816
  Dihedral  :  4.645  33.436   2181
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.21 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 21.06 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.10 (0.19), residues: 1947
  helix:  1.76 (0.17), residues: 938
  sheet: -0.57 (0.28), residues: 343
  loop : -2.13 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.021   0.002   PHE E 306 
 TYR   0.023   0.001   TYR D  19 
 ARG   0.007   0.000   ARG E 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 (  945)
  hydrogen bonds       : angle       4.63784 ( 2727)
  SS BOND              : bond        0.00534 (    2)
  SS BOND              : angle       2.45271 (    4)
  covalent geometry    : bond        0.00391 (16598)
  covalent geometry    : angle       0.66770 (22505)

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

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

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3894 Ramachandran restraints generated.
    1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 388
  time to evaluate  : 2.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8228 (ptm-80)
REVERT: A   97 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8624 (Cg_endo)
REVERT: A  174 ILE cc_start: 0.8187 (mm) cc_final: 0.7865 (mm)
REVERT: A  186 GLU cc_start: 0.6120 (mm-30) cc_final: 0.5699 (mm-30)
REVERT: A  237 ARG cc_start: 0.6173 (mmm-85) cc_final: 0.5858 (mtm-85)
REVERT: A  247 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8159 (m)
REVERT: A  286 LYS cc_start: 0.8000 (tptt) cc_final: 0.7089 (tmtt)
REVERT: B   96 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7302 (ttm170)
REVERT: B  155 ARG cc_start: 0.7342 (mmm160) cc_final: 0.6936 (tpp80)
REVERT: B  186 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: B  187 LYS cc_start: 0.7447 (tttt) cc_final: 0.6991 (ttpt)
REVERT: B  227 PRO cc_start: 0.9020 (Cg_exo) cc_final: 0.8696 (Cg_endo)
REVERT: B  275 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7413 (mm)
REVERT: B  318 MET cc_start: 0.0610 (tpt) cc_final: -0.1082 (tpt)
REVERT: C  124 SER cc_start: 0.8710 (p) cc_final: 0.8509 (p)
REVERT: C  190 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6979 (m-30)
REVERT: C  225 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (tt)
REVERT: C  232 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8182 (mm)
REVERT: C  263 ASP cc_start: 0.7507 (m-30) cc_final: 0.7125 (m-30)
REVERT: C  318 MET cc_start: 0.3631 (mmm) cc_final: 0.3286 (mmm)
REVERT: C  327 TYR cc_start: 0.5591 (OUTLIER) cc_final: 0.4794 (t80)
REVERT: D   42 PHE cc_start: 0.7686 (t80) cc_final: 0.7312 (t80)
REVERT: D  121 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6667 (pm20)
REVERT: D  154 ILE cc_start: 0.9072 (mm) cc_final: 0.8749 (mm)
REVERT: D  163 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7749 (mtmm)
REVERT: D  318 MET cc_start: 0.5659 (ttp) cc_final: 0.5154 (ttt)
REVERT: E    6 LEU cc_start: 0.6872 (pt) cc_final: 0.6605 (pt)
REVERT: E   51 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6927 (mm)
REVERT: E   90 ILE cc_start: 0.8186 (mm) cc_final: 0.7948 (mm)
REVERT: E  177 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8609 (mm)
REVERT: E  204 GLU cc_start: 0.7275 (tt0) cc_final: 0.6967 (tt0)
REVERT: E  252 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6884 (ttm-80)
REVERT: H   15 VAL cc_start: 0.8277 (p) cc_final: 0.8077 (m)
REVERT: H   66 SER cc_start: 0.7186 (p) cc_final: 0.6493 (m)
REVERT: H  117 TYR cc_start: 0.9037 (m-80) cc_final: 0.8665 (m-80)
REVERT: L    2 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7771 (t0)
  outliers start: 68
  outliers final: 55
  residues processed: 420
  average time/residue: 0.3700
  time to fit residues: 233.2176
Evaluate side-chains
  450 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 385
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain C residue   36 ILE
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  327 TYR
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 LEU
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  225 ILE
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  283 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue    2 ASP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 132 optimal weight:    0.8980
   chunk 186 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 169 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   chunk 81 optimal weight:    1.9990
   chunk 147 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.174994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.149910 restraints weight = 21840.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.154184 restraints weight = 11827.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.157056 restraints weight = 7728.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  16600  Z= 0.165
  Angle     :  0.663  13.581  22509  Z= 0.336
  Chirality :  0.045   0.252   2551
  Planarity :  0.005   0.118   2816
  Dihedral  :  4.657  32.500   2181
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.52 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 20.84 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.22 %
    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:  0.13 (0.19), residues: 1947
  helix:  1.77 (0.17), residues: 938
  sheet: -0.51 (0.29), residues: 332
  loop : -2.07 (0.23), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 350 
 HIS   0.006   0.001   HIS C  83 
 PHE   0.024   0.002   PHE E 306 
 TYR   0.026   0.001   TYR B  23 
 ARG   0.009   0.001   ARG E 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  945)
  hydrogen bonds       : angle       4.62510 ( 2727)
  SS BOND              : bond        0.00473 (    2)
  SS BOND              : angle       2.39644 (    4)
  covalent geometry    : bond        0.00393 (16598)
  covalent geometry    : angle       0.66276 (22505)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7354.09 seconds
wall clock time: 131 minutes 9.81 seconds (7869.81 seconds total)