Starting phenix.real_space_refine
on Mon Apr 28 12:24:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/04_2025/8kh4_37236.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.118
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    4814      2.51       5
     N    1286      2.21       5
     O    1370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7521
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2048
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2048
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 255}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1809
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 57
    Chain: "C"
      Number of atoms: 2435
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 336, 2425
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 113
      Conformer: "B"
        Number of residues, atoms: 336, 2425
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 113
          bond proxies already assigned to first conformer: 2458
    Chain: "E"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 936
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 265
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.13, per 1000 atoms: 0.82
  Number of scatterers: 7521
  At special positions: 0
  Unit cell: (72.36, 95.04, 126.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1370      8.00
     N    1286      7.00
     C    4814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 178 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      43.4% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 55
      removed outlier: 3.838A  pdb=" N   ILE A  39 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ILE A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS A  55 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 59
    Processing helix  chain 'A' and resid 60 through 80
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 96 through 131
      removed outlier: 3.655A  pdb=" N   GLY A 119 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
    Processing helix  chain 'A' and resid 140 through 160
      removed outlier: 3.593A  pdb=" N   TRP A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 185 through 197
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.815A  pdb=" N   PHE A 201 " --> pdb=" O   ALA A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 297
      removed outlier: 3.683A  pdb=" N   PHE A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 302 through 327
      removed outlier: 4.122A  pdb=" N   ALA A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      Proline residue:  A 321  - end of helix
      removed outlier: 3.550A  pdb=" N   TRP A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
    Processing helix  chain 'B' and resid 13 through 39
      removed outlier: 3.691A  pdb=" N   ALA B  39 " --> pdb=" O   GLN B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
      removed outlier: 3.658A  pdb=" N   MET B  60 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.039A  pdb=" N   TYR B 311 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 318
    Processing helix  chain 'B' and resid 331 through 352
      removed outlier: 3.683A  pdb=" N   ILE B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   SER B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 391
    Processing helix  chain 'C' and resid 6 through 26
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.739A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.563A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 24
    Processing helix  chain 'D' and resid 29 through 45
    Processing helix  chain 'D' and resid 46 through 48
      No H-bonds generated for 'chain 'D' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172
      removed outlier: 3.657A  pdb=" N   VAL A 179 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP A 172 " --> pdb=" O   MET A 177 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   MET A 177 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 214
      removed outlier: 9.660A  pdb=" N   ALA B 243 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   VAL B 247 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU B  46 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   ASP B 249 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   PHE B 290 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   PHE B 246 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ASN B 292 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL B 248 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52
      removed outlier: 3.625A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL C 327 " --> pdb=" O   TRP C 339 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.692A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 4.555A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.579A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 7.112A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.737A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP C 254 " --> pdb=" O   GLN C 259 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.747A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.833A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 125 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1208
        1.29 -     1.42: 2106
        1.42 -     1.56: 4303
        1.56 -     1.69: 3
        1.69 -     1.83: 73
  Bond restraints: 7693
  Sorted by residual:
  bond pdb=" CA  PHE A 201 "
       pdb=" C   PHE A 201 "
    ideal  model  delta    sigma   weight residual
    1.524  1.415  0.109 1.29e-02 6.01e+03 7.08e+01
  bond pdb=" CA  SER A  62 "
       pdb=" C   SER A  62 "
    ideal  model  delta    sigma   weight residual
    1.524  1.426  0.098 1.26e-02 6.30e+03 6.04e+01
  bond pdb=" CA  VAL A 179 "
       pdb=" C   VAL A 179 "
    ideal  model  delta    sigma   weight residual
    1.523  1.427  0.096 1.27e-02 6.20e+03 5.74e+01
  bond pdb=" C   PHE A 201 "
       pdb=" O   PHE A 201 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.080 1.19e-02 7.06e+03 4.57e+01
  bond pdb=" N   VAL A 179 "
       pdb=" CA  VAL A 179 "
    ideal  model  delta    sigma   weight residual
    1.459  1.377  0.082 1.25e-02 6.40e+03 4.26e+01
  ... (remaining 7688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 10227
        2.70 -     5.40: 217
        5.40 -     8.10: 39
        8.10 -    10.79: 14
       10.79 -    13.49: 6
  Bond angle restraints: 10503
  Sorted by residual:
  angle pdb=" N   ARG A 213 "
        pdb=" CA  ARG A 213 "
        pdb=" C   ARG A 213 "
      ideal   model   delta    sigma   weight residual
     111.07  100.56   10.51 1.07e+00 8.73e-01 9.65e+01
  angle pdb=" N   ILE A 211 "
        pdb=" CA  ILE A 211 "
        pdb=" C   ILE A 211 "
      ideal   model   delta    sigma   weight residual
     110.62  102.37    8.25 1.02e+00 9.61e-01 6.55e+01
  angle pdb=" N   ALA D  34 "
        pdb=" CA  ALA D  34 "
        pdb=" C   ALA D  34 "
      ideal   model   delta    sigma   weight residual
     111.28  102.51    8.77 1.09e+00 8.42e-01 6.47e+01
  angle pdb=" N   TYR D  40 "
        pdb=" CA  TYR D  40 "
        pdb=" C   TYR D  40 "
      ideal   model   delta    sigma   weight residual
     111.28  102.91    8.37 1.09e+00 8.42e-01 5.90e+01
  angle pdb=" C   PHE A 199 "
        pdb=" N   PRO A 200 "
        pdb=" CA  PRO A 200 "
      ideal   model   delta    sigma   weight residual
     119.05  110.58    8.47 1.11e+00 8.12e-01 5.82e+01
  ... (remaining 10498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.19: 4320
       24.19 -    48.38: 190
       48.38 -    72.57: 13
       72.57 -    96.76: 10
       96.76 -   120.95: 1
  Dihedral angle restraints: 4534
    sinusoidal: 1614
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" CB  CYS E  99 "
           pdb=" SG  CYS E  99 "
           pdb=" SG  CYS E 107 "
           pdb=" CB  CYS E 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.52  -83.48     1      1.00e+01 1.00e-02 8.51e+01
  dihedral pdb=" C   ASN A  63 "
           pdb=" N   ASN A  63 "
           pdb=" CA  ASN A  63 "
           pdb=" CB  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.96   16.36     0      2.50e+00 1.60e-01 4.28e+01
  dihedral pdb=" N   ASN A  63 "
           pdb=" C   ASN A  63 "
           pdb=" CA  ASN A  63 "
           pdb=" CB  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.06  -16.26     0      2.50e+00 1.60e-01 4.23e+01
  ... (remaining 4531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.163: 1181
       0.163 -    0.327: 29
       0.327 -    0.490: 7
       0.490 -    0.653: 4
       0.653 -    0.817: 2
  Chirality restraints: 1223
  Sorted by residual:
  chirality pdb=" CA  ASN A  63 "
            pdb=" N   ASN A  63 "
            pdb=" C   ASN A  63 "
            pdb=" CB  ASN A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.67e+01
  chirality pdb=" CA  ALA A 219 "
            pdb=" N   ALA A 219 "
            pdb=" C   ALA A 219 "
            pdb=" CB  ALA A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.77    0.72 2.00e-01 2.50e+01 1.28e+01
  chirality pdb=" CA  PHE A 174 "
            pdb=" N   PHE A 174 "
            pdb=" C   PHE A 174 "
            pdb=" CB  PHE A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.06e+01
  ... (remaining 1220 not shown)

  Planarity restraints: 1324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.066 5.00e-02 4.00e+02   9.76e-02 1.53e+01
        pdb=" N   PRO C 236 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 213 "   -0.018 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   ARG A 213 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ARG A 213 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   VAL A 214 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  57 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.07e+00
        pdb=" C   TYR A  57 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   TYR A  57 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A  58 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1321 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 128
        2.62 -     3.19: 6873
        3.19 -     3.76: 12272
        3.76 -     4.33: 16918
        4.33 -     4.90: 28357
  Nonbonded interactions: 64548
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A  61 "
            pdb=" CB  ALA A 144 "
     model   vdw
     2.049 3.880
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" N   VAL A 179 "
            pdb=" O   VAL A 179 "
     model   vdw
     2.218 2.496
  nonbonded pdb=" NH1 ARG B 228 "
            pdb=" OD1 ASP C 186 "
     model   vdw
     2.219 3.120
  ... (remaining 64543 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.130
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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   0.109   7696  Z= 0.635
  Angle     :  1.017  13.493  10509  Z= 0.633
  Chirality :  0.081   0.817   1223
  Planarity :  0.007   0.098   1324
  Dihedral  : 14.018 120.945   2639
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.48 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.95 %
  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:  0.62 (0.27), residues: 988
  helix:  1.63 (0.26), residues: 402
  sheet:  0.16 (0.35), residues: 204
  loop : -0.73 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  99 
 HIS   0.007   0.002   HIS D  44 
 PHE   0.028   0.002   PHE A  65 
 TYR   0.025   0.002   TYR C  85 
 ARG   0.008   0.001   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12467 (  420)
  hydrogen bonds       : angle       6.80101 ( 1212)
  SS BOND              : bond        0.00782 (    3)
  SS BOND              : angle       3.09228 (    6)
  covalent geometry    : bond        0.00893 ( 7693)
  covalent geometry    : angle       1.01418 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 167
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.6682 (m-10)
REVERT: B   34 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7618 (tttt)
REVERT: B  280 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7821 (ttt90)
REVERT: B  317 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7476 (ptp90)
REVERT: C  101 MET cc_start: 0.8895 (mtp) cc_final: 0.8644 (mtp)
REVERT: C  290 ASP cc_start: 0.6802 (m-30) cc_final: 0.6572 (m-30)
REVERT: E   60 TYR cc_start: 0.7386 (m-80) cc_final: 0.7036 (m-80)
REVERT: E   80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7066 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1910
  time to fit residues: 43.7567
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN
E  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.192886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157792 restraints weight = 16004.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 3.53
r_work: 0.3702 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7696  Z= 0.183
  Angle     :  0.647  10.846  10509  Z= 0.340
  Chirality :  0.046   0.303   1223
  Planarity :  0.005   0.076   1324
  Dihedral  :  5.920  56.992   1149
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.36 %
    Favored  : 88.56 %
  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:  0.76 (0.27), residues: 988
  helix:  1.93 (0.27), residues: 384
  sheet:  0.05 (0.33), residues: 222
  loop : -0.65 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  99 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.018   0.002   PHE B 212 
 TYR   0.032   0.002   TYR C  85 
 ARG   0.005   0.001   ARG C 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  420)
  hydrogen bonds       : angle       5.38077 ( 1212)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       1.90972 (    6)
  covalent geometry    : bond        0.00417 ( 7693)
  covalent geometry    : angle       0.64587 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.6250 (ppp)
REVERT: A  327 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.6979 (m-10)
REVERT: B  266 LEU cc_start: 0.8544 (tp) cc_final: 0.8198 (tp)
REVERT: B  274 LYS cc_start: 0.7896 (tttp) cc_final: 0.7618 (ttmt)
REVERT: B  280 ARG cc_start: 0.8269 (tpt90) cc_final: 0.7971 (ttt90)
REVERT: E   80 TYR cc_start: 0.7768 (m-80) cc_final: 0.7196 (m-80)
REVERT: E   93 VAL cc_start: 0.7453 (t) cc_final: 0.7178 (t)
REVERT: E  115 TYR cc_start: 0.8111 (t80) cc_final: 0.7887 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 160
  average time/residue: 0.2060
  time to fit residues: 43.8441
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0370
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0040
   chunk 10 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0270
   overall best weight:    0.3528

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.197925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.161744 restraints weight = 14776.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 3.37
r_work: 0.3769 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7696  Z= 0.117
  Angle     :  0.567  10.572  10509  Z= 0.296
  Chirality :  0.043   0.169   1223
  Planarity :  0.005   0.070   1324
  Dihedral  :  5.355  55.703   1149
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.79 %
    Favored  : 86.00 %
  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:  0.96 (0.27), residues: 988
  helix:  2.17 (0.27), residues: 394
  sheet:  0.09 (0.33), residues: 219
  loop : -0.65 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.004   0.001   HIS C 225 
 PHE   0.016   0.001   PHE B 212 
 TYR   0.019   0.002   TYR C  85 
 ARG   0.003   0.000   ARG C 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  420)
  hydrogen bonds       : angle       5.01970 ( 1212)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       1.41594 (    6)
  covalent geometry    : bond        0.00251 ( 7693)
  covalent geometry    : angle       0.56604 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.6582 (ppp)
REVERT: A  327 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7102 (m-10)
REVERT: B  266 LEU cc_start: 0.8522 (tp) cc_final: 0.8204 (tp)
REVERT: B  274 LYS cc_start: 0.7810 (tttp) cc_final: 0.7590 (ttmt)
REVERT: B  280 ARG cc_start: 0.8293 (tpt90) cc_final: 0.7960 (ttt90)
REVERT: B  319 THR cc_start: 0.8128 (p) cc_final: 0.7922 (t)
REVERT: E   50 ASP cc_start: 0.8694 (p0) cc_final: 0.8222 (p0)
REVERT: E   80 TYR cc_start: 0.7707 (m-80) cc_final: 0.7242 (m-80)
REVERT: D   38 MET cc_start: 0.6816 (mtm) cc_final: 0.6551 (mtp)
  outliers start: 9
  outliers final: 3
  residues processed: 158
  average time/residue: 0.1985
  time to fit residues: 42.4054
Evaluate side-chains
  145 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN
E  77 ASN
E 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.193933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156362 restraints weight = 11396.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 2.68
r_work: 0.3751 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3885 r_free = 0.3885    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3885 r_free = 0.3885    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7696  Z= 0.147
  Angle     :  0.586  11.340  10509  Z= 0.305
  Chirality :  0.044   0.177   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.353  56.060   1149
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.46 %
    Favored  : 84.39 %
  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:  0.95 (0.27), residues: 988
  helix:  2.21 (0.27), residues: 391
  sheet: -0.05 (0.32), residues: 226
  loop : -0.61 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.016   0.002   PHE B 212 
 TYR   0.027   0.002   TYR C  85 
 ARG   0.004   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  420)
  hydrogen bonds       : angle       4.92502 ( 1212)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       1.28129 (    6)
  covalent geometry    : bond        0.00333 ( 7693)
  covalent geometry    : angle       0.58578 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5770 (t-100) cc_final: 0.5117 (t-100)
REVERT: A  177 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.6718 (ppp)
REVERT: A  327 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.6920 (m-10)
REVERT: B  266 LEU cc_start: 0.8625 (tp) cc_final: 0.8344 (tp)
REVERT: B  274 LYS cc_start: 0.7841 (tttp) cc_final: 0.7597 (ttmt)
REVERT: B  280 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7837 (ttt90)
REVERT: B  319 THR cc_start: 0.8062 (p) cc_final: 0.7859 (t)
REVERT: E   50 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8119 (p0)
REVERT: E   80 TYR cc_start: 0.7715 (m-80) cc_final: 0.7239 (m-80)
REVERT: D   38 MET cc_start: 0.6775 (mtm) cc_final: 0.6479 (mtp)
  outliers start: 16
  outliers final: 8
  residues processed: 154
  average time/residue: 0.1954
  time to fit residues: 41.0493
Evaluate side-chains
  153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   95 TYR
Chi-restraints excluded: chain E residue  114 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.192162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.154776 restraints weight = 14048.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 3.29
r_work: 0.3707 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7696  Z= 0.159
  Angle     :  0.592  11.748  10509  Z= 0.308
  Chirality :  0.044   0.169   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.410  55.866   1149
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.27 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.97 (0.27), residues: 988
  helix:  2.35 (0.27), residues: 384
  sheet: -0.13 (0.33), residues: 226
  loop : -0.63 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 220 
 PHE   0.017   0.002   PHE B 222 
 TYR   0.026   0.002   TYR C  85 
 ARG   0.003   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  420)
  hydrogen bonds       : angle       4.91710 ( 1212)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       1.30308 (    6)
  covalent geometry    : bond        0.00362 ( 7693)
  covalent geometry    : angle       0.59106 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8629 (m) cc_final: 0.8263 (p)
REVERT: A  140 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6265 (t)
REVERT: A  327 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.6829 (m-10)
REVERT: B  266 LEU cc_start: 0.8659 (tp) cc_final: 0.8383 (tp)
REVERT: B  274 LYS cc_start: 0.7916 (tttp) cc_final: 0.7681 (ttmt)
REVERT: B  280 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7861 (ttt90)
REVERT: C  263 THR cc_start: 0.8058 (m) cc_final: 0.7752 (p)
REVERT: E   50 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8132 (p0)
REVERT: E   80 TYR cc_start: 0.7737 (m-80) cc_final: 0.7258 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1937
  time to fit residues: 42.9336
Evaluate side-chains
  155 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   95 TYR
Chi-restraints excluded: chain E residue  114 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  77 ASN
E 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.192933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.158858 restraints weight = 18152.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.64
r_work: 0.3683 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7696  Z= 0.151
  Angle     :  0.589  11.785  10509  Z= 0.307
  Chirality :  0.043   0.175   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.354  55.122   1149
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.75 %
    Favored  : 81.56 %
  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:  1.02 (0.27), residues: 988
  helix:  2.45 (0.27), residues: 381
  sheet: -0.12 (0.33), residues: 232
  loop : -0.64 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 212 
 TYR   0.023   0.002   TYR C  85 
 ARG   0.004   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  420)
  hydrogen bonds       : angle       4.89921 ( 1212)
  SS BOND              : bond        0.00095 (    3)
  SS BOND              : angle       1.23019 (    6)
  covalent geometry    : bond        0.00348 ( 7693)
  covalent geometry    : angle       0.58852 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8620 (m) cc_final: 0.8250 (p)
REVERT: A  327 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.6909 (m-10)
REVERT: A  338 MET cc_start: 0.8007 (mtp) cc_final: 0.7674 (mtp)
REVERT: B  266 LEU cc_start: 0.8627 (tp) cc_final: 0.8339 (tp)
REVERT: B  274 LYS cc_start: 0.7879 (tttp) cc_final: 0.7644 (ttmt)
REVERT: B  280 ARG cc_start: 0.8327 (tpt90) cc_final: 0.7862 (ttt90)
REVERT: C  263 THR cc_start: 0.8118 (m) cc_final: 0.7770 (p)
REVERT: E   50 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8128 (p0)
REVERT: E   80 TYR cc_start: 0.7751 (m-80) cc_final: 0.7262 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 157
  average time/residue: 0.1961
  time to fit residues: 42.0228
Evaluate side-chains
  158 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0070
   chunk 32 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7202

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  84 ASN
E 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.194729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.160350 restraints weight = 15813.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 3.22
r_work: 0.3740 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7696  Z= 0.125
  Angle     :  0.568  11.726  10509  Z= 0.295
  Chirality :  0.042   0.167   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.166  54.702   1149
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.82 %
    Favored  : 80.75 %
  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:  1.08 (0.27), residues: 988
  helix:  2.54 (0.27), residues: 381
  sheet: -0.12 (0.32), residues: 234
  loop : -0.62 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 212 
 TYR   0.018   0.001   TYR C  85 
 ARG   0.005   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  420)
  hydrogen bonds       : angle       4.80207 ( 1212)
  SS BOND              : bond        0.00077 (    3)
  SS BOND              : angle       1.01266 (    6)
  covalent geometry    : bond        0.00284 ( 7693)
  covalent geometry    : angle       0.56794 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5799 (t-100) cc_final: 0.5142 (t-100)
REVERT: A  134 VAL cc_start: 0.8584 (m) cc_final: 0.8236 (p)
REVERT: A  327 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.6814 (m-10)
REVERT: A  338 MET cc_start: 0.8129 (mtp) cc_final: 0.7809 (mtp)
REVERT: B   38 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7301 (ttp80)
REVERT: B  266 LEU cc_start: 0.8516 (tp) cc_final: 0.8216 (tp)
REVERT: B  274 LYS cc_start: 0.7876 (tttp) cc_final: 0.7660 (ttmt)
REVERT: C  110 ASN cc_start: 0.7410 (m-40) cc_final: 0.7193 (m110)
REVERT: E   50 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8060 (p0)
REVERT: E   80 TYR cc_start: 0.7803 (m-80) cc_final: 0.7315 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 166
  average time/residue: 0.1937
  time to fit residues: 43.7094
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  74 ASN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.190623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.156608 restraints weight = 18410.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 3.80
r_work: 0.3651 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7696  Z= 0.179
  Angle     :  0.618  12.537  10509  Z= 0.323
  Chirality :  0.044   0.167   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.329  54.600   1149
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.09 %
    Favored  : 80.22 %
  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:  0.96 (0.27), residues: 988
  helix:  2.37 (0.27), residues: 383
  sheet: -0.19 (0.33), residues: 232
  loop : -0.62 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 169 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.017   0.002   PHE E 108 
 TYR   0.024   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  420)
  hydrogen bonds       : angle       4.93115 ( 1212)
  SS BOND              : bond        0.00091 (    3)
  SS BOND              : angle       1.30051 (    6)
  covalent geometry    : bond        0.00415 ( 7693)
  covalent geometry    : angle       0.61756 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8678 (m) cc_final: 0.8320 (p)
REVERT: A  327 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.6656 (m-10)
REVERT: A  338 MET cc_start: 0.8198 (mtp) cc_final: 0.7905 (mtp)
REVERT: B   38 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7179 (ttp80)
REVERT: B  274 LYS cc_start: 0.7980 (tttp) cc_final: 0.7724 (ttmt)
REVERT: B  280 ARG cc_start: 0.8361 (tpt90) cc_final: 0.7915 (ttt90)
REVERT: E   50 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8187 (p0)
REVERT: E   80 TYR cc_start: 0.7850 (m-80) cc_final: 0.7314 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1901
  time to fit residues: 41.2285
Evaluate side-chains
  160 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   70 ILE
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 93 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  74 ASN
E 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.177805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.141549 restraints weight = 20611.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 4.67
r_work: 0.3468 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7696  Z= 0.225
  Angle     :  0.672  13.041  10509  Z= 0.351
  Chirality :  0.046   0.166   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.630  54.043   1149
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.09 %
    Favored  : 80.08 %
  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:  0.75 (0.27), residues: 988
  helix:  2.23 (0.27), residues: 377
  sheet: -0.38 (0.32), residues: 230
  loop : -0.66 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 169 
 HIS   0.009   0.002   HIS B 220 
 PHE   0.021   0.002   PHE E 108 
 TYR   0.028   0.002   TYR C  85 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  420)
  hydrogen bonds       : angle       5.10707 ( 1212)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       1.51996 (    6)
  covalent geometry    : bond        0.00521 ( 7693)
  covalent geometry    : angle       0.67075 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8510 (m) cc_final: 0.8091 (p)
REVERT: A  175 LYS cc_start: 0.7044 (mttp) cc_final: 0.6806 (mttp)
REVERT: A  194 ILE cc_start: 0.8215 (mm) cc_final: 0.7857 (mt)
REVERT: A  327 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.6756 (m-10)
REVERT: B  266 LEU cc_start: 0.8445 (tp) cc_final: 0.7993 (tp)
REVERT: B  274 LYS cc_start: 0.7727 (tttp) cc_final: 0.7433 (ttmt)
REVERT: B  280 ARG cc_start: 0.8267 (tpt90) cc_final: 0.7808 (ttt90)
REVERT: E   50 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8014 (p0)
REVERT: E   80 TYR cc_start: 0.7621 (m-80) cc_final: 0.7002 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 164
  average time/residue: 0.1877
  time to fit residues: 41.8017
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   70 ILE
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:   30.0000
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0770
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  74 ASN
E  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.182042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.140196 restraints weight = 18832.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 3.78
r_work: 0.3547 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7696  Z= 0.144
  Angle     :  0.612  12.554  10509  Z= 0.319
  Chirality :  0.044   0.198   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.328  53.252   1149
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.17 %
    Favored  : 79.68 %
  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:  0.92 (0.27), residues: 988
  helix:  2.38 (0.27), residues: 377
  sheet: -0.36 (0.32), residues: 235
  loop : -0.52 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 311 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 222 
 TYR   0.019   0.002   TYR C  85 
 ARG   0.006   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  420)
  hydrogen bonds       : angle       4.95448 ( 1212)
  SS BOND              : bond        0.00097 (    3)
  SS BOND              : angle       1.17756 (    6)
  covalent geometry    : bond        0.00333 ( 7693)
  covalent geometry    : angle       0.61177 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8403 (m) cc_final: 0.7990 (p)
REVERT: A  194 ILE cc_start: 0.8228 (mm) cc_final: 0.7863 (mt)
REVERT: A  327 TRP cc_start: 0.7964 (OUTLIER) cc_final: 0.6780 (m-10)
REVERT: B  266 LEU cc_start: 0.8420 (tp) cc_final: 0.8040 (tp)
REVERT: B  274 LYS cc_start: 0.7615 (tttp) cc_final: 0.7349 (ttmt)
REVERT: B  280 ARG cc_start: 0.8183 (tpt90) cc_final: 0.7668 (ttt90)
REVERT: E   50 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7944 (p0)
REVERT: E   80 TYR cc_start: 0.7567 (m-80) cc_final: 0.6967 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 155
  average time/residue: 0.1752
  time to fit residues: 37.3744
Evaluate side-chains
  157 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 85 optimal weight:    0.0070
   chunk 63 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.181739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.140864 restraints weight = 15441.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 3.40
r_work: 0.3564 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3565 r_free = 0.3565    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3565 r_free = 0.3565    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7696  Z= 0.155
  Angle     :  0.628  12.745  10509  Z= 0.325
  Chirality :  0.044   0.191   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.274  53.549   1149
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.11 %
    Favored  : 78.87 %
  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:  0.90 (0.27), residues: 988
  helix:  2.36 (0.27), residues: 377
  sheet: -0.29 (0.32), residues: 230
  loop : -0.60 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 211 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.014   0.002   PHE B 222 
 TYR   0.020   0.002   TYR C  85 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  420)
  hydrogen bonds       : angle       4.91863 ( 1212)
  SS BOND              : bond        0.00081 (    3)
  SS BOND              : angle       1.21844 (    6)
  covalent geometry    : bond        0.00361 ( 7693)
  covalent geometry    : angle       0.62800 (10503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4396.08 seconds
wall clock time: 76 minutes 2.27 seconds (4562.27 seconds total)