Starting phenix.real_space_refine
on Tue Jul 29 19:12:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2025/8k21_36824.cif"
  }
  resolution = 3.8
  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=   0.002
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 468 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
     P      41      5.49       5
     S      63      5.16       5
     C    7148      2.51       5
     N    1947      2.21       5
     O    2190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11389
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "U"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 439
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "V"
      Number of atoms: 419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 419
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "A"
      Number of atoms: 583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 583
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 2327
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 295, 2317
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
      Conformer: "B"
        Number of residues, atoms: 295, 2322
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 2358
    Chain: "E"
      Number of atoms: 2353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2353
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
    Chain: "a"
      Number of atoms: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 571
          Classifications: {'peptide': 75}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "d"
      Number of atoms: 2360
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 295, 2350
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 295, 2350
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 2388
    Chain: "e"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2337
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 10.08, per 1000 atoms: 0.89
  Number of scatterers: 11389
  At special positions: 0
  Unit cell: (107.8, 119.9, 129.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P      41     15.00
     O    2190      8.00
     N    1947      7.00
     C    7148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.89
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2486

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 8 sheets defined
      53.7% alpha, 9.7% beta
      15 base pairs and 38 stacking pairs defined.
    Time for finding SS restraints: 4.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 4.148A  pdb=" N   LYS A  16 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL A  17 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 51
    Processing helix  chain 'D' and resid 58 through 63
    Processing helix  chain 'D' and resid 100 through 110
      removed outlier: 4.200A  pdb=" N   ARG D 106 " --> pdb=" O   GLN D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 122
    Processing helix  chain 'D' and resid 123 through 132
    Processing helix  chain 'D' and resid 142 through 159
      removed outlier: 3.656A  pdb=" N   GLN D 158 " --> pdb=" O   LYS D 154 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA D 159 " --> pdb=" O   GLY D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 184
    Processing helix  chain 'D' and resid 196 through 221
    Processing helix  chain 'D' and resid 238 through 243
    Processing helix  chain 'D' and resid 243 through 248
      removed outlier: 3.968A  pdb=" N   THR D 248 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 261
    Processing helix  chain 'D' and resid 264 through 279
      removed outlier: 3.556A  pdb=" N   VAL D 273 " --> pdb=" O   LYS D 269 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   PHE D 276 " --> pdb=" O   CYS D 272 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASN D 279 " --> pdb=" O   TYR D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 294
      removed outlier: 3.928A  pdb=" N   LEU D 285 " --> pdb=" O   ILE D 281 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 66
    Processing helix  chain 'E' and resid 98 through 109
    Processing helix  chain 'E' and resid 110 through 123
    Processing helix  chain 'E' and resid 123 through 132
      removed outlier: 4.457A  pdb=" N   ASP E 127 " --> pdb=" O   LYS E 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 142 through 156
      removed outlier: 3.622A  pdb=" N   SER E 146 " --> pdb=" O   ASN E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 184
      removed outlier: 3.704A  pdb=" N   LYS E 178 " --> pdb=" O   LYS E 174 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR E 184 " --> pdb=" O   TYR E 180 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 219
      removed outlier: 3.602A  pdb=" N   ILE E 212 " --> pdb=" O   TYR E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 236 through 248
      removed outlier: 3.648A  pdb=" N   PHE E 240 " --> pdb=" O   GLY E 236 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE E 245 " --> pdb=" O   ASP E 241 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   ILE E 246 " --> pdb=" O   VAL E 242 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   THR E 248 " --> pdb=" O   ASP E 244 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
    Processing helix  chain 'E' and resid 264 through 279
      removed outlier: 3.797A  pdb=" N   ASN E 279 " --> pdb=" O   TYR E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 280 through 294
    Processing helix  chain 'a' and resid 10 through 22
      removed outlier: 4.447A  pdb=" N   LYS a  16 " --> pdb=" O   PRO a  12 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 40 through 51
    Processing helix  chain 'd' and resid 6 through 10
    Processing helix  chain 'd' and resid 58 through 68
    Processing helix  chain 'd' and resid 100 through 110
      removed outlier: 4.280A  pdb=" N   ARG d 106 " --> pdb=" O   GLN d 102 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASP d 110 " --> pdb=" O   ARG d 106 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 110 through 132
      removed outlier: 4.538A  pdb=" N   ARG d 125 " --> pdb=" O   ILE d 121 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   VAL d 126 " --> pdb=" O   LEU d 122 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER d 130 " --> pdb=" O   VAL d 126 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 143 through 158
    Processing helix  chain 'd' and resid 161 through 184
    Processing helix  chain 'd' and resid 196 through 221
    Processing helix  chain 'd' and resid 238 through 243
    Processing helix  chain 'd' and resid 244 through 249
      removed outlier: 3.760A  pdb=" N   SER d 249 " --> pdb=" O   ILE d 245 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 250 through 261
      removed outlier: 3.636A  pdb=" N   LEU d 254 " --> pdb=" O   ILE d 250 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 264 through 279
    Processing helix  chain 'd' and resid 280 through 294
      removed outlier: 3.568A  pdb=" N   LYS d 290 " --> pdb=" O   ILE d 286 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ARG d 291 " --> pdb=" O   ASN d 287 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU d 292 " --> pdb=" O   ASN d 288 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 58 through 68
      removed outlier: 3.672A  pdb=" N   MET e  63 " --> pdb=" O   GLU e  59 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA e  66 " --> pdb=" O   SER e  62 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASN e  67 " --> pdb=" O   MET e  63 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY e  68 " --> pdb=" O   LEU e  64 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 98 through 110
      removed outlier: 3.541A  pdb=" N   ASN e 103 " --> pdb=" O   LYS e  99 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP e 104 " --> pdb=" O   TYR e 100 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP e 110 " --> pdb=" O   ARG e 106 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 110 through 132
      removed outlier: 4.057A  pdb=" N   VAL e 126 " --> pdb=" O   LEU e 122 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 142 through 157
      removed outlier: 3.932A  pdb=" N   ILE e 148 " --> pdb=" O   ARG e 144 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 161 through 184
    Processing helix  chain 'e' and resid 196 through 221
      removed outlier: 3.682A  pdb=" N   TYR e 208 " --> pdb=" O   LEU e 204 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA e 213 " --> pdb=" O   ALA e 209 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 236 through 244
      removed outlier: 4.171A  pdb=" N   PHE e 240 " --> pdb=" O   GLY e 236 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 250 through 261
    Processing helix  chain 'e' and resid 264 through 279
    Processing helix  chain 'e' and resid 280 through 294
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA2, first strand: chain 'D' and resid 14 through 16
      removed outlier: 6.868A  pdb=" N   TYR D  14 " --> pdb=" O   GLY D  49 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA E  83 " --> pdb=" O   TRP E  73 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE E  48 " --> pdb=" O   PHE E  72 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   THR E  74 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU E  50 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ASN E  12 " --> pdb=" O   PHE E  47 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY E  49 " --> pdb=" O   ASN E  12 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   TYR E  14 " --> pdb=" O   GLY E  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 37 through 40
      removed outlier: 4.574A  pdb=" N   VAL D  28 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER D  55 " --> pdb=" O   CYS D  19 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL D  23 " --> pdb=" O   THR D  57 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE D  56 " --> pdb=" O   ILE E  56 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   VAL E  21 " --> pdb=" O   THR E  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 24
      removed outlier: 3.585A  pdb=" N   GLN E  27 " --> pdb=" O   LYS E  24 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'a' and resid 32 through 36
      removed outlier: 3.720A  pdb=" N   ARG a   4 " --> pdb=" O   ASN a  61 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   VAL a  58 " --> pdb=" O   ALA a  69 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA a  69 " --> pdb=" O   VAL a  58 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   CYS a  60 " --> pdb=" O   LEU a  67 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'd' and resid 21 through 24
      removed outlier: 3.503A  pdb=" N   GLN d  27 " --> pdb=" O   LYS d  24 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'd' and resid 47 through 50
      removed outlier: 3.673A  pdb=" N   PHE d  72 " --> pdb=" O   ILE d  48 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA e  83 " --> pdb=" O   TRP e  73 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE e  48 " --> pdb=" O   PHE e  72 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   THR e  74 " --> pdb=" O   ILE e  48 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   LEU e  50 " --> pdb=" O   THR e  74 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   TYR e  14 " --> pdb=" O   GLY e  49 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET e  13 " --> pdb=" O   ILE e   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'd' and resid 55 through 57
      removed outlier: 3.605A  pdb=" N   SER e  55 " --> pdb=" O   CYS e  19 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR e  57 " --> pdb=" O   VAL e  21 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   VAL e  23 " --> pdb=" O   THR e  57 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   HIS e  30 " --> pdb=" O   TYR e  38 " (cutoff:3.500A)

    544 hydrogen bonds defined for protein.
    1604 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      36 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      38 stacking parallelities
  Total time for adding SS restraints: 3.60

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1804
        1.31 -     1.44: 3432
        1.44 -     1.56: 6286
        1.56 -     1.69: 87
        1.69 -     1.82: 102
  Bond restraints: 11711
  Sorted by residual:
  bond pdb=" N   PHE d 226 "
       pdb=" CA  PHE d 226 "
    ideal  model  delta    sigma   weight residual
    1.464  1.378  0.085 1.09e-02 8.42e+03 6.10e+01
  bond pdb=" CA  ASN d 224 "
       pdb=" C   ASN d 224 "
    ideal  model  delta    sigma   weight residual
    1.522  1.421  0.101 1.32e-02 5.74e+03 5.86e+01
  bond pdb=" CA  ALA d 219 "
       pdb=" C   ALA d 219 "
    ideal  model  delta    sigma   weight residual
    1.522  1.420  0.102 1.40e-02 5.10e+03 5.32e+01
  bond pdb=" CA  ALA D 118 "
       pdb=" C   ALA D 118 "
    ideal  model  delta    sigma   weight residual
    1.524  1.430  0.094 1.29e-02 6.01e+03 5.29e+01
  bond pdb=" CA  VAL d 239 "
       pdb=" C   VAL d 239 "
    ideal  model  delta    sigma   weight residual
    1.524  1.437  0.087 1.22e-02 6.72e+03 5.07e+01
  ... (remaining 11706 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 15336
        2.83 -     5.66: 525
        5.66 -     8.49: 114
        8.49 -    11.32: 19
       11.32 -    14.15: 6
  Bond angle restraints: 16000
  Sorted by residual:
  angle pdb=" N   ALA D 118 "
        pdb=" CA  ALA D 118 "
        pdb=" C   ALA D 118 "
      ideal   model   delta    sigma   weight residual
     111.36   99.78   11.58 1.09e+00 8.42e-01 1.13e+02
  angle pdb=" N   ASN d 224 "
        pdb=" CA  ASN d 224 "
        pdb=" C   ASN d 224 "
      ideal   model   delta    sigma   weight residual
     113.50  101.30   12.20 1.23e+00 6.61e-01 9.83e+01
  angle pdb=" N   LEU d 238 "
        pdb=" CA  LEU d 238 "
        pdb=" C   LEU d 238 "
      ideal   model   delta    sigma   weight residual
     113.23  102.53   10.70 1.24e+00 6.50e-01 7.45e+01
  angle pdb=" N   VAL D 273 "
        pdb=" CA  VAL D 273 "
        pdb=" C   VAL D 273 "
      ideal   model   delta    sigma   weight residual
     111.90  105.24    6.66 8.10e-01 1.52e+00 6.76e+01
  angle pdb=" N   HIS E 257 "
        pdb=" CA  HIS E 257 "
        pdb=" C   HIS E 257 "
      ideal   model   delta    sigma   weight residual
     112.23  102.12   10.11 1.26e+00 6.30e-01 6.44e+01
  ... (remaining 15995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5283
       17.94 -    35.89: 985
       35.89 -    53.83: 454
       53.83 -    71.77: 107
       71.77 -    89.71: 24
  Dihedral angle restraints: 6853
    sinusoidal: 2972
      harmonic: 3881
  Sorted by residual:
  dihedral pdb=" CA  THR e  45 "
           pdb=" C   THR e  45 "
           pdb=" N   VAL e  46 "
           pdb=" CA  VAL e  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.28   26.72     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  SER d 175 "
           pdb=" C   SER d 175 "
           pdb=" N   LEU d 176 "
           pdb=" CA  LEU d 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  PHE E 188 "
           pdb=" C   PHE E 188 "
           pdb=" N   LYS E 189 "
           pdb=" CA  LYS E 189 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.20   24.80     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 6850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1498
       0.097 -    0.194: 228
       0.194 -    0.291: 42
       0.291 -    0.388: 12
       0.388 -    0.485: 2
  Chirality restraints: 1782
  Sorted by residual:
  chirality pdb=" CB  ILE D 245 "
            pdb=" CA  ILE D 245 "
            pdb=" CG1 ILE D 245 "
            pdb=" CG2 ILE D 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.16    0.48 2.00e-01 2.50e+01 5.88e+00
  chirality pdb=" CB  VAL e 105 "
            pdb=" CA  VAL e 105 "
            pdb=" CG1 VAL e 105 "
            pdb=" CG2 VAL e 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.68e+00
  chirality pdb=" CA  ILE d 251 "
            pdb=" N   ILE d 251 "
            pdb=" C   ILE d 251 "
            pdb=" CB  ILE d 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.05    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 1779 not shown)

  Planarity restraints: 1878
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 255 "   -0.025 2.00e-02 2.50e+03   5.14e-02 2.64e+01
        pdb=" C   ALA E 255 "    0.089 2.00e-02 2.50e+03
        pdb=" O   ALA E 255 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   PHE E 256 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA d 209 "   -0.023 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   ALA d 209 "    0.081 2.00e-02 2.50e+03
        pdb=" O   ALA d 209 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   TYR d 210 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 268 "    0.024 2.00e-02 2.50e+03   2.77e-02 1.35e+01
        pdb=" CG  PHE E 268 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 268 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 268 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 268 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 268 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 268 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1875 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2126
        2.77 -     3.30: 10428
        3.30 -     3.83: 21040
        3.83 -     4.37: 24563
        4.37 -     4.90: 39521
  Nonbonded interactions: 97678
  Sorted by model distance:
  nonbonded pdb=" O   THR d 171 "
            pdb=" OG  SER d 175 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ASP e 153 "
            pdb=" OG1 THR e 157 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD1 ASP d 127 "
            pdb=" OH  TYR d 284 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ASP d 153 "
            pdb=" OG1 THR d 157 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   SER D 225 "
            pdb=" OG  SER D 225 "
     model   vdw
     2.264 3.040
  ... (remaining 97673 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 1 through 9 or (resid 10 through 11 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 12 through 14 or (resid 15 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 16 through 75))
  selection = chain 'a'
}
ncs_group {
  reference = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 76 through 141 or (resid 142 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 143 through 149 or \ 
 resid 151 through 234 or (resid 235 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 236 through 286 or resid 288 through 295))
  selection = (chain 'E' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ 
h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ 
h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 120 through 141 or (resid 142 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 143 through 149 or resid 151 through 2 \ 
34 or (resid 235 and (name N or name CA or name C or name O or name CB )) or res \ 
id 236 through 286 or resid 288 through 295))
  selection = (chain 'd' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ 
h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ 
h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 120 through 149 or resid 151 through 234 or (resid 235 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 236 through 2 \ 
86 or resid 288 through 295))
  selection = (chain 'e' and (resid 1 through 78 or (resid 79 through 84 and (name N or name C \ 
A or name C or name O or name CB )) or resid 85 through 110 or (resid 111 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 114 through 118  \ 
or (resid 119 and (name N or name CA or name C or name O or name CB )) or resid  \ 
120 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 143 through 149 or resid 151 through 286 or resid 288 through 29 \ 
5))
}

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=0.15 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     35.260
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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      :  0.009   0.102  11711  Z= 0.546
  Angle     :  1.288  14.150  16000  Z= 0.783
  Chirality :  0.079   0.485   1782
  Planarity :  0.008   0.112   1878
  Dihedral  : 22.880  89.714   4367
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.91 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  8.12 %
    Allowed  : 36.28 %
    Favored  : 55.60 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.31 (0.19), residues: 1321
  helix: -1.77 (0.16), residues: 685
  sheet: -1.71 (0.48), residues: 111
  loop : -2.76 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP d 218 
 HIS   0.014   0.002   HIS D  30 
 PHE   0.064   0.004   PHE E 268 
 TYR   0.045   0.004   TYR d 100 
 ARG   0.016   0.001   ARG d 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17037 (  580)
  hydrogen bonds       : angle       7.33930 ( 1676)
  covalent geometry    : bond        0.00899 (11711)
  covalent geometry    : angle       1.28761 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 261
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.7258 (tt0) cc_final: 0.6781 (tt0)
REVERT: E  260 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8292 (m-30)
REVERT: a   48 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8358 (mttp)
REVERT: d  228 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8807 (tp)
REVERT: e   61 MET cc_start: 0.8323 (ttm) cc_final: 0.7781 (ttm)
  outliers start: 91
  outliers final: 15
  residues processed: 322
  average time/residue: 0.3060
  time to fit residues: 130.9532
Evaluate side-chains
  160 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue  123 LYS
Chi-restraints excluded: chain D residue  279 ASN
Chi-restraints excluded: chain E residue  125 ARG
Chi-restraints excluded: chain E residue  134 HIS
Chi-restraints excluded: chain E residue  260 ASP
Chi-restraints excluded: chain E residue  261 GLN
Chi-restraints excluded: chain d residue   61 MET
Chi-restraints excluded: chain d residue  138 VAL
Chi-restraints excluded: chain d residue  194 SER
Chi-restraints excluded: chain d residue  228 LEU
Chi-restraints excluded: chain d residue  233 THR
Chi-restraints excluded: chain d residue  244 ASP
Chi-restraints excluded: chain d residue  248 THR
Chi-restraints excluded: chain e residue   27 GLN
Chi-restraints excluded: chain e residue  242 VAL
Chi-restraints excluded: chain e residue  294 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
D 142 ASN
** D 150 ASN    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 192 HIS
D 279 ASN
E   9 GLN
E  44 ASN
E 132 HIS
E 261 GLN
a  72 ASN
d 199 ASN
e  27 GLN
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.044703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033628 restraints weight = 158870.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.035328 restraints weight = 62201.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.036522 restraints weight = 35800.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11711  Z= 0.191
  Angle     :  0.744  10.112  16000  Z= 0.402
  Chirality :  0.045   0.174   1782
  Planarity :  0.005   0.054   1878
  Dihedral  : 18.945  83.201   1955
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.54 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 33.36 %
    Favored  : 61.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.83 (0.21), residues: 1321
  helix: -0.34 (0.18), residues: 696
  sheet: -1.44 (0.47), residues: 114
  loop : -2.35 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP e 218 
 HIS   0.014   0.002   HIS D 192 
 PHE   0.024   0.002   PHE e 152 
 TYR   0.023   0.002   TYR d 284 
 ARG   0.009   0.001   ARG d  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  580)
  hydrogen bonds       : angle       4.90056 ( 1676)
  covalent geometry    : bond        0.00435 (11711)
  covalent geometry    : angle       0.74436 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 137
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8053 (tt0) cc_final: 0.7556 (tt0)
REVERT: A   40 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8182 (tp-100)
REVERT: D   50 LEU cc_start: 0.9309 (mt) cc_final: 0.9109 (mt)
REVERT: D  101 MET cc_start: 0.8450 (mmt) cc_final: 0.8178 (tpt)
REVERT: D  202 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9289 (tp)
REVERT: E  261 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9113 (mp10)
REVERT: a   20 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7909 (mp0)
REVERT: a   43 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9191 (p)
REVERT: e   30 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.6860 (m170)
REVERT: e   61 MET cc_start: 0.8958 (ttm) cc_final: 0.8673 (ttm)
REVERT: e  124 MET cc_start: 0.9163 (ptp) cc_final: 0.8801 (ptp)
REVERT: e  178 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8397 (pttt)
REVERT: e  222 ILE cc_start: 0.9137 (mm) cc_final: 0.8915 (mm)
  outliers start: 58
  outliers final: 21
  residues processed: 178
  average time/residue: 0.2374
  time to fit residues: 60.0712
Evaluate side-chains
  138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue  180 TYR
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  279 ASN
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  124 MET
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  261 GLN
Chi-restraints excluded: chain E residue  276 PHE
Chi-restraints excluded: chain a residue   43 SER
Chi-restraints excluded: chain a residue   73 VAL
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   87 ILE
Chi-restraints excluded: chain d residue  153 ASP
Chi-restraints excluded: chain d residue  233 THR
Chi-restraints excluded: chain d residue  244 ASP
Chi-restraints excluded: chain d residue  248 THR
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue   20 LYS
Chi-restraints excluded: chain e residue   30 HIS
Chi-restraints excluded: chain e residue   34 ASP
Chi-restraints excluded: chain e residue   57 THR
Chi-restraints excluded: chain e residue  266 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
D 150 ASN    B
D 168 HIS
E   4 GLN
E  25 ASN
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
a  36 HIS
** a  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  61 ASN
a  72 ASN
d 134 HIS
** d 150 ASN    B ** both conformations clash, **PLEASE CHECK MANUALLY**
d 168 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.044508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.034066 restraints weight = 136923.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.035687 restraints weight = 57623.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.036805 restraints weight = 33918.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11711  Z= 0.144
  Angle     :  0.678  12.973  16000  Z= 0.359
  Chirality :  0.043   0.223   1782
  Planarity :  0.004   0.050   1878
  Dihedral  : 18.497  84.397   1925
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.39 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 31.69 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.14 (0.23), residues: 1321
  helix:  0.32 (0.19), residues: 700
  sheet: -1.92 (0.44), residues: 136
  loop : -1.95 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 218 
 HIS   0.007   0.001   HIS d  30 
 PHE   0.023   0.002   PHE E 276 
 TYR   0.016   0.001   TYR d 284 
 ARG   0.007   0.001   ARG d  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 (  580)
  hydrogen bonds       : angle       4.41756 ( 1676)
  covalent geometry    : bond        0.00331 (11711)
  covalent geometry    : angle       0.67796 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.7972 (tt0) cc_final: 0.7693 (tt0)
REVERT: A   40 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8203 (tp-100)
REVERT: A   54 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8056 (tmtt)
REVERT: D  176 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9279 (mm)
REVERT: D  202 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9296 (tp)
REVERT: D  261 GLN cc_start: 0.8677 (mp10) cc_final: 0.8409 (mp10)
REVERT: E   63 MET cc_start: 0.8794 (ptm) cc_final: 0.8407 (ptm)
REVERT: E  124 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (mtt)
REVERT: E  192 HIS cc_start: 0.8510 (p90) cc_final: 0.8159 (p90)
REVERT: E  214 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8666 (ptp-110)
REVERT: E  261 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9022 (mp10)
REVERT: a   43 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9228 (p)
REVERT: a   72 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8721 (t0)
REVERT: e   22 LEU cc_start: 0.9114 (tp) cc_final: 0.8776 (tt)
REVERT: e   61 MET cc_start: 0.8975 (ttm) cc_final: 0.8708 (ttm)
REVERT: e  178 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8275 (pttt)
REVERT: e  285 LEU cc_start: 0.9785 (mp) cc_final: 0.9491 (mt)
  outliers start: 40
  outliers final: 21
  residues processed: 149
  average time/residue: 0.2315
  time to fit residues: 49.9213
Evaluate side-chains
  132 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  180 TYR
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  279 ASN
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue  124 MET
Chi-restraints excluded: chain E residue  126 VAL
Chi-restraints excluded: chain E residue  214 ARG
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  261 GLN
Chi-restraints excluded: chain a residue   43 SER
Chi-restraints excluded: chain a residue   72 ASN
Chi-restraints excluded: chain a residue   73 VAL
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   81 MET
Chi-restraints excluded: chain d residue  233 THR
Chi-restraints excluded: chain d residue  248 THR
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue   20 LYS
Chi-restraints excluded: chain e residue   57 THR
Chi-restraints excluded: chain e residue  180 TYR
Chi-restraints excluded: chain e residue  256 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 26 optimal weight:    0.0050
   chunk 108 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 121 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
D  44 ASN
D 158 GLN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  89 HIS
** d 150 ASN    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.033832 restraints weight = 161263.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.035507 restraints weight = 63670.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.036668 restraints weight = 36528.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11711  Z= 0.131
  Angle     :  0.650  12.989  16000  Z= 0.340
  Chirality :  0.042   0.205   1782
  Planarity :  0.004   0.049   1878
  Dihedral  : 18.350  81.699   1923
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.86 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 30.27 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.79 (0.23), residues: 1321
  helix:  0.70 (0.20), residues: 701
  sheet: -1.70 (0.45), residues: 136
  loop : -1.98 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 218 
 HIS   0.007   0.001   HIS d 168 
 PHE   0.020   0.002   PHE A  68 
 TYR   0.014   0.001   TYR d 284 
 ARG   0.007   0.001   ARG e 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  580)
  hydrogen bonds       : angle       4.18417 ( 1676)
  covalent geometry    : bond        0.00299 (11711)
  covalent geometry    : angle       0.65042 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 110
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.7937 (tt0) cc_final: 0.7487 (tt0)
REVERT: D   44 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8779 (t0)
REVERT: D   50 LEU cc_start: 0.9307 (mt) cc_final: 0.9030 (mt)
REVERT: D   61 MET cc_start: 0.9365 (mmm) cc_final: 0.9160 (mmm)
REVERT: D  202 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9274 (tp)
REVERT: E  109 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8975 (mm)
REVERT: E  192 HIS cc_start: 0.8511 (p90) cc_final: 0.8147 (p90)
REVERT: a   20 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7856 (tt0)
REVERT: a   43 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9261 (p)
REVERT: e   22 LEU cc_start: 0.9057 (tp) cc_final: 0.8707 (tt)
REVERT: e   61 MET cc_start: 0.8947 (ttm) cc_final: 0.8712 (ttm)
REVERT: e  106 ARG cc_start: 0.9295 (mmt90) cc_final: 0.8804 (mmt90)
REVERT: e  178 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8312 (pttt)
  outliers start: 39
  outliers final: 18
  residues processed: 141
  average time/residue: 0.2437
  time to fit residues: 49.9453
Evaluate side-chains
  114 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 1.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   44 ASN
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  279 ASN
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  261 GLN
Chi-restraints excluded: chain a residue   43 SER
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue  233 THR
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue   57 THR
Chi-restraints excluded: chain e residue  180 TYR
Chi-restraints excluded: chain e residue  256 PHE
Chi-restraints excluded: chain e residue  266 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 107 optimal weight:    0.0170
   chunk 85 optimal weight:    0.0980
   chunk 113 optimal weight:    9.9990
   chunk 111 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 129 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 83 optimal weight:    0.0060
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
D  44 ASN
E  25 ASN
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  58 ASN
E 230 HIS
d  36 ASN
d 150 ASN    B
** e  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.045056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.034740 restraints weight = 115141.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.036313 restraints weight = 50879.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.037378 restraints weight = 30578.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11711  Z= 0.123
  Angle     :  0.641  13.114  16000  Z= 0.333
  Chirality :  0.042   0.186   1782
  Planarity :  0.004   0.050   1878
  Dihedral  : 18.122  77.995   1922
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.16 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.39 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.50 (0.23), residues: 1321
  helix:  0.92 (0.20), residues: 700
  sheet: -1.59 (0.49), residues: 124
  loop : -1.80 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 218 
 HIS   0.006   0.001   HIS d 168 
 PHE   0.017   0.002   PHE A  68 
 TYR   0.013   0.001   TYR e 100 
 ARG   0.006   0.001   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03236 (  580)
  hydrogen bonds       : angle       4.01607 ( 1676)
  covalent geometry    : bond        0.00275 (11711)
  covalent geometry    : angle       0.64134 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 114
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8026 (tt0) cc_final: 0.7553 (tp30)
REVERT: A   59 VAL cc_start: 0.9275 (t) cc_final: 0.9028 (p)
REVERT: D   50 LEU cc_start: 0.9350 (mt) cc_final: 0.8975 (mt)
REVERT: D  202 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9285 (tp)
REVERT: D  261 GLN cc_start: 0.8720 (mp10) cc_final: 0.8505 (mp10)
REVERT: D  267 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8670 (mt-10)
REVERT: E   63 MET cc_start: 0.8863 (ptm) cc_final: 0.8540 (ppp)
REVERT: E  192 HIS cc_start: 0.8595 (p90) cc_final: 0.8247 (p90)
REVERT: E  214 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8672 (ptp-110)
REVERT: E  261 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9253 (mm-40)
REVERT: d   61 MET cc_start: 0.9335 (tpp) cc_final: 0.9108 (tpt)
REVERT: d   63 MET cc_start: 0.8961 (mmm) cc_final: 0.8563 (mtp)
REVERT: e    6 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7886 (mm)
REVERT: e   22 LEU cc_start: 0.9089 (tp) cc_final: 0.8776 (mp)
REVERT: e   61 MET cc_start: 0.8999 (ttm) cc_final: 0.8733 (ttm)
REVERT: e  101 MET cc_start: 0.9027 (tpt) cc_final: 0.8820 (tpt)
REVERT: e  178 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8292 (pttt)
REVERT: e  263 MET cc_start: 0.9010 (ttm) cc_final: 0.8774 (ttm)
  outliers start: 37
  outliers final: 12
  residues processed: 143
  average time/residue: 0.2332
  time to fit residues: 49.0342
Evaluate side-chains
  121 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  267 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  214 ARG
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain E residue  261 GLN
Chi-restraints excluded: chain a residue   73 VAL
Chi-restraints excluded: chain d residue   81 MET
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue  180 TYR
Chi-restraints excluded: chain e residue  192 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 129 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0060
   chunk 44 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
D 287 ASN    B
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.044835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.034172 restraints weight = 142112.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.035815 restraints weight = 57529.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.036941 restraints weight = 33400.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11711  Z= 0.129
  Angle     :  0.649  19.499  16000  Z= 0.335
  Chirality :  0.042   0.199   1782
  Planarity :  0.004   0.048   1878
  Dihedral  : 18.065  75.717   1919
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 30.63 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.41 (0.23), residues: 1321
  helix:  1.02 (0.20), residues: 699
  sheet: -1.44 (0.50), residues: 124
  loop : -1.84 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 218 
 HIS   0.006   0.001   HIS d 168 
 PHE   0.017   0.002   PHE A  68 
 TYR   0.011   0.001   TYR e 198 
 ARG   0.007   0.001   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03155 (  580)
  hydrogen bonds       : angle       3.94006 ( 1676)
  covalent geometry    : bond        0.00295 (11711)
  covalent geometry    : angle       0.64915 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8091 (tt0) cc_final: 0.7535 (tp30)
REVERT: A   59 VAL cc_start: 0.9275 (t) cc_final: 0.9014 (p)
REVERT: D   50 LEU cc_start: 0.9389 (mt) cc_final: 0.9009 (mt)
REVERT: D  202 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9285 (tp)
REVERT: D  261 GLN cc_start: 0.8717 (mp10) cc_final: 0.8511 (mp10)
REVERT: D  267 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8579 (mt-10)
REVERT: E   61 MET cc_start: 0.9310 (mmm) cc_final: 0.8892 (tpp)
REVERT: E   63 MET cc_start: 0.8895 (ptm) cc_final: 0.8529 (tmm)
REVERT: d   61 MET cc_start: 0.9347 (tpp) cc_final: 0.9137 (tpt)
REVERT: d   63 MET cc_start: 0.8936 (mmm) cc_final: 0.8581 (mtp)
REVERT: e    6 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7954 (mm)
REVERT: e   22 LEU cc_start: 0.9055 (tp) cc_final: 0.8783 (mp)
REVERT: e   61 MET cc_start: 0.9020 (ttm) cc_final: 0.8751 (ttm)
REVERT: e  101 MET cc_start: 0.9016 (tpt) cc_final: 0.8810 (tpt)
REVERT: e  178 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8242 (pttt)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2257
  time to fit residues: 39.0667
Evaluate side-chains
  117 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  267 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain a residue   73 VAL
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   81 MET
Chi-restraints excluded: chain d residue  101 MET
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue  180 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
D 279 ASN
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.044701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033895 restraints weight = 162065.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.035591 restraints weight = 61578.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.036768 restraints weight = 35026.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11711  Z= 0.130
  Angle     :  0.660  18.843  16000  Z= 0.337
  Chirality :  0.043   0.226   1782
  Planarity :  0.003   0.047   1878
  Dihedral  : 17.976  75.755   1916
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.78 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 30.36 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.32 (0.23), residues: 1321
  helix:  1.08 (0.20), residues: 700
  sheet: -1.31 (0.50), residues: 124
  loop : -1.80 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 218 
 HIS   0.006   0.001   HIS d 168 
 PHE   0.017   0.001   PHE A  68 
 TYR   0.011   0.001   TYR e 198 
 ARG   0.005   0.000   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03118 (  580)
  hydrogen bonds       : angle       3.88178 ( 1676)
  covalent geometry    : bond        0.00300 (11711)
  covalent geometry    : angle       0.65975 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8098 (tt0) cc_final: 0.7506 (tt0)
REVERT: A   40 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8369 (tp-100)
REVERT: A   59 VAL cc_start: 0.9322 (t) cc_final: 0.9053 (p)
REVERT: D   50 LEU cc_start: 0.9355 (mt) cc_final: 0.8956 (mt)
REVERT: D   99 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8789 (pttm)
REVERT: D  202 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9266 (tp)
REVERT: E   63 MET cc_start: 0.8805 (ptm) cc_final: 0.8432 (tmm)
REVERT: a   20 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7818 (tt0)
REVERT: a   34 GLU cc_start: 0.7874 (tt0) cc_final: 0.7527 (tt0)
REVERT: a   75 MET cc_start: 0.7745 (tmm) cc_final: 0.7128 (tmm)
REVERT: d   61 MET cc_start: 0.9369 (tpp) cc_final: 0.9136 (tpt)
REVERT: e   61 MET cc_start: 0.9009 (ttm) cc_final: 0.8745 (ttm)
REVERT: e  178 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8196 (pttt)
  outliers start: 26
  outliers final: 14
  residues processed: 125
  average time/residue: 0.2398
  time to fit residues: 43.6979
Evaluate side-chains
  110 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   81 MET
Chi-restraints excluded: chain d residue  101 MET
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue  180 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.044354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.033548 restraints weight = 167166.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.035226 restraints weight = 63736.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.036391 restraints weight = 36195.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11711  Z= 0.134
  Angle     :  0.672  18.985  16000  Z= 0.342
  Chirality :  0.043   0.212   1782
  Planarity :  0.003   0.046   1878
  Dihedral  : 17.934  76.071   1916
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.33 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 30.63 %
    Favored  : 67.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.31 (0.23), residues: 1321
  helix:  1.05 (0.20), residues: 710
  sheet: -1.18 (0.50), residues: 124
  loop : -1.82 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 218 
 HIS   0.006   0.001   HIS d 168 
 PHE   0.017   0.002   PHE A  68 
 TYR   0.013   0.001   TYR e 198 
 ARG   0.004   0.000   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  580)
  hydrogen bonds       : angle       3.93567 ( 1676)
  covalent geometry    : bond        0.00308 (11711)
  covalent geometry    : angle       0.67199 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8164 (tt0) cc_final: 0.7831 (tt0)
REVERT: A   40 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8374 (tp-100)
REVERT: D   99 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8776 (pttm)
REVERT: D  202 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9261 (tp)
REVERT: D  267 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8372 (mt-10)
REVERT: E   63 MET cc_start: 0.8828 (ptm) cc_final: 0.8448 (tmm)
REVERT: a   34 GLU cc_start: 0.7909 (tt0) cc_final: 0.7561 (tt0)
REVERT: d   61 MET cc_start: 0.9404 (tpp) cc_final: 0.9174 (tpt)
REVERT: e   61 MET cc_start: 0.9015 (ttm) cc_final: 0.8762 (ttm)
REVERT: e  101 MET cc_start: 0.8961 (tpt) cc_final: 0.8650 (tpt)
REVERT: e  178 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8194 (pttt)
  outliers start: 18
  outliers final: 11
  residues processed: 115
  average time/residue: 0.2435
  time to fit residues: 41.5420
Evaluate side-chains
  102 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  267 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain e residue    6 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 25 optimal weight:    0.1980
   chunk 119 optimal weight:    3.9990
   chunk 126 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 115 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.044564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.034038 restraints weight = 143821.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.035669 restraints weight = 58753.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.036783 restraints weight = 34220.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.5205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11711  Z= 0.132
  Angle     :  0.698  19.248  16000  Z= 0.351
  Chirality :  0.043   0.209   1782
  Planarity :  0.004   0.046   1878
  Dihedral  : 17.900  75.855   1916
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.56 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 31.16 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.24), residues: 1321
  helix:  1.08 (0.20), residues: 711
  sheet: -0.94 (0.51), residues: 120
  loop : -1.78 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 218 
 HIS   0.005   0.001   HIS d 168 
 PHE   0.017   0.001   PHE A  68 
 TYR   0.012   0.001   TYR e 198 
 ARG   0.005   0.001   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03186 (  580)
  hydrogen bonds       : angle       3.94662 ( 1676)
  covalent geometry    : bond        0.00306 (11711)
  covalent geometry    : angle       0.69824 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8232 (tt0) cc_final: 0.7880 (tt0)
REVERT: A   40 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8366 (tp-100)
REVERT: D   99 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8748 (pttm)
REVERT: D  202 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9261 (tp)
REVERT: d   63 MET cc_start: 0.8858 (mmm) cc_final: 0.8536 (mtp)
REVERT: d  263 MET cc_start: 0.9124 (mtp) cc_final: 0.8913 (ptp)
REVERT: e   13 MET cc_start: 0.8767 (tpp) cc_final: 0.8155 (tpp)
REVERT: e   61 MET cc_start: 0.9000 (ttm) cc_final: 0.8748 (ttm)
REVERT: e  101 MET cc_start: 0.8986 (tpt) cc_final: 0.8704 (tpt)
REVERT: e  178 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8138 (pttt)
REVERT: e  254 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9283 (mt)
  outliers start: 17
  outliers final: 13
  residues processed: 110
  average time/residue: 0.2156
  time to fit residues: 36.0111
Evaluate side-chains
  108 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  293 CYS
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue  180 TYR
Chi-restraints excluded: chain e residue  254 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 115 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0470
   chunk 86 optimal weight:    0.3980
   chunk 56 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 49 optimal weight:    0.3980
   chunk 101 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.045180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.034582 restraints weight = 144803.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.036222 restraints weight = 58186.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.037355 restraints weight = 33831.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11711  Z= 0.130
  Angle     :  0.704  19.500  16000  Z= 0.353
  Chirality :  0.043   0.198   1782
  Planarity :  0.004   0.047   1878
  Dihedral  : 17.862  75.413   1916
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.48 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 31.24 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.21 (0.23), residues: 1321
  helix:  1.08 (0.20), residues: 706
  sheet: -1.01 (0.48), residues: 136
  loop : -1.71 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 218 
 HIS   0.009   0.001   HIS e 168 
 PHE   0.019   0.002   PHE e 172 
 TYR   0.012   0.001   TYR e 198 
 ARG   0.005   0.001   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  580)
  hydrogen bonds       : angle       3.93928 ( 1676)
  covalent geometry    : bond        0.00300 (11711)
  covalent geometry    : angle       0.70418 (16000)

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

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

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2642 Ramachandran restraints generated.
    1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLU cc_start: 0.8208 (tt0) cc_final: 0.7861 (tt0)
REVERT: A   40 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8360 (tp-100)
REVERT: A   59 VAL cc_start: 0.9330 (t) cc_final: 0.9063 (p)
REVERT: D   61 MET cc_start: 0.9506 (mmm) cc_final: 0.9135 (tpp)
REVERT: D   99 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8682 (pttm)
REVERT: D  202 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9255 (tp)
REVERT: E   63 MET cc_start: 0.8787 (ptm) cc_final: 0.8506 (ppp)
REVERT: a   20 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7879 (tt0)
REVERT: a   34 GLU cc_start: 0.7906 (tt0) cc_final: 0.7569 (tt0)
REVERT: e   61 MET cc_start: 0.9028 (ttm) cc_final: 0.8799 (ttm)
REVERT: e  101 MET cc_start: 0.8979 (tpt) cc_final: 0.8687 (tpt)
REVERT: e  178 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8102 (pttt)
REVERT: e  254 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9278 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.2080
  time to fit residues: 35.0494
Evaluate side-chains
  108 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 PHE
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   39 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain D residue   99 LYS
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  293 CYS
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain e residue    6 LEU
Chi-restraints excluded: chain e residue  180 TYR
Chi-restraints excluded: chain e residue  254 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 120 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.042979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.032385 restraints weight = 169166.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.033995 restraints weight = 64106.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.035131 restraints weight = 36567.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11711  Z= 0.183
  Angle     :  0.724  19.286  16000  Z= 0.367
  Chirality :  0.043   0.190   1782
  Planarity :  0.004   0.043   1878
  Dihedral  : 17.976  79.094   1916
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.71 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 31.33 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.24), residues: 1321
  helix:  1.12 (0.20), residues: 709
  sheet: -1.00 (0.49), residues: 130
  loop : -1.72 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 218 
 HIS   0.009   0.001   HIS e 168 
 PHE   0.019   0.002   PHE A  68 
 TYR   0.018   0.002   TYR D 100 
 ARG   0.005   0.001   ARG e 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  580)
  hydrogen bonds       : angle       4.03850 ( 1676)
  covalent geometry    : bond        0.00415 (11711)
  covalent geometry    : angle       0.72406 (16000)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3819.81 seconds
wall clock time: 67 minutes 11.91 seconds (4031.91 seconds total)