Starting phenix.real_space_refine
on Wed Mar 12 07:36:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh4_37236/03_2025/8kh4_37236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/03_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_37236/03_2025/8kh4_37236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/03_2025/8kh4_37236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/03_2025/8kh4_37236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/03_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-5624/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: 5.88, per 1000 atoms: 0.78
  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: 1.73
  Conformation dependent library (CDL) restraints added in 1.7 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: 0.86
  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: 2.35

  Time building geometry restraints manager: 2.09 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.760
  Find NCS groups from input model:        0.090
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
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   7693  Z= 0.581
  Angle     :  1.014  13.493  10503  Z= 0.632
  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 

*********************** 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  : 0.844 
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: 0.1943
  time to fit residues: 44.2731
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  : 0.773 
-------------------------------------------------------------------------------
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:    0.9980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.4294 r_free = 0.4294 target = 0.192474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157699 restraints weight = 15980.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 3.46
r_work: 0.3701 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    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 = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7693  Z= 0.279
  Angle     :  0.649  10.841  10503  Z= 0.341
  Chirality :  0.046   0.199   1223
  Planarity :  0.006   0.077   1324
  Dihedral  :  5.911  57.344   1149
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.77 %
    Favored  : 88.29 %
  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:  0.72 (0.27), residues: 988
  helix:  1.91 (0.26), residues: 384
  sheet:  0.05 (0.34), residues: 217
  loop : -0.69 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  99 
 HIS   0.005   0.002   HIS C 225 
 PHE   0.018   0.002   PHE B 212 
 TYR   0.033   0.002   TYR C  85 
 ARG   0.005   0.001   ARG C 304 

*********************** 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
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.6282 (ppp)
REVERT: A  327 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7067 (m-10)
REVERT: B  266 LEU cc_start: 0.8571 (tp) cc_final: 0.8236 (tp)
REVERT: B  274 LYS cc_start: 0.7912 (tttp) cc_final: 0.7635 (ttmt)
REVERT: B  280 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7957 (ttt90)
REVERT: C  111 TYR cc_start: 0.8488 (m-80) cc_final: 0.8161 (m-80)
REVERT: E   80 TYR cc_start: 0.7766 (m-80) cc_final: 0.7199 (m-80)
REVERT: E   93 VAL cc_start: 0.7443 (t) cc_final: 0.7187 (t)
REVERT: E  115 TYR cc_start: 0.8096 (t80) cc_final: 0.7882 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 158
  average time/residue: 0.1976
  time to fit residues: 42.0955
Evaluate side-chains
  148 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 79 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0070
   overall best weight:    0.8000

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.194764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.162424 restraints weight = 14798.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 3.02
r_work: 0.3740 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3875 r_free = 0.3875    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3875 r_free = 0.3875    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7693  Z= 0.192
  Angle     :  0.578  10.628  10503  Z= 0.302
  Chirality :  0.043   0.170   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.467  55.453   1149
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.52 %
    Favored  : 85.46 %
  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:  2.10 (0.27), residues: 394
  sheet:  0.06 (0.32), residues: 222
  loop : -0.68 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.019   0.001   PHE B 222 
 TYR   0.025   0.002   TYR C  85 
 ARG   0.003   0.000   ARG C 314 

*********************** 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
  172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.6647 (ppp)
REVERT: A  327 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7022 (m-10)
REVERT: B  266 LEU cc_start: 0.8562 (tp) cc_final: 0.8247 (tp)
REVERT: B  274 LYS cc_start: 0.7813 (tttp) cc_final: 0.7586 (ttmt)
REVERT: B  280 ARG cc_start: 0.8268 (tpt90) cc_final: 0.7859 (ttt90)
REVERT: E   50 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8072 (p0)
REVERT: E   80 TYR cc_start: 0.7721 (m-80) cc_final: 0.7213 (m-80)
REVERT: E  115 TYR cc_start: 0.8107 (t80) cc_final: 0.7904 (t80)
REVERT: D   38 MET cc_start: 0.6752 (mtm) cc_final: 0.6487 (mtp)
  outliers start: 15
  outliers final: 8
  residues processed: 163
  average time/residue: 0.2020
  time to fit residues: 44.2356
Evaluate side-chains
  151 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  177 MET
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 C residue  317 CYS
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   50 ASP
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:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 92 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 227 GLN ** 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 = 0.4295 r_free = 0.4295 target = 0.192890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.155376 restraints weight = 11429.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 2.67
r_work: 0.3740 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3875 r_free = 0.3875    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 = 0.3875 r_free = 0.3875    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7693  Z= 0.216
  Angle     :  0.581  11.385  10503  Z= 0.302
  Chirality :  0.043   0.162   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.412  55.779   1149
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.59 %
    Favored  : 84.25 %
  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:  0.91 (0.27), residues: 988
  helix:  2.17 (0.27), residues: 392
  sheet: -0.05 (0.32), residues: 226
  loop : -0.65 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.006   0.001   HIS B 220 
 PHE   0.016   0.001   PHE B 212 
 TYR   0.028   0.002   TYR C  85 
 ARG   0.004   0.000   ARG B  38 

*********************** 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
  160 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.6876 (m-10)
REVERT: B  266 LEU cc_start: 0.8628 (tp) cc_final: 0.8345 (tp)
REVERT: B  274 LYS cc_start: 0.7853 (tttp) cc_final: 0.7614 (ttmt)
REVERT: B  280 ARG cc_start: 0.8248 (tpt90) cc_final: 0.7820 (ttt90)
REVERT: B  319 THR cc_start: 0.8066 (p) cc_final: 0.7861 (t)
REVERT: E   50 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8189 (p0)
REVERT: E   80 TYR cc_start: 0.7705 (m-80) cc_final: 0.7220 (m-80)
REVERT: D   38 MET cc_start: 0.6736 (mtm) cc_final: 0.6449 (mtp)
  outliers start: 16
  outliers final: 9
  residues processed: 155
  average time/residue: 0.1996
  time to fit residues: 41.7793
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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  75 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.194122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.156979 restraints weight = 14155.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 3.31
r_work: 0.3734 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    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 = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7693  Z= 0.194
  Angle     :  0.566  11.601  10503  Z= 0.295
  Chirality :  0.043   0.182   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.305  55.322   1149
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.34 %
    Favored  : 82.77 %
  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:  1.15 (0.27), residues: 988
  helix:  2.47 (0.27), residues: 382
  sheet:  0.20 (0.33), residues: 223
  loop : -0.65 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 169 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.016   0.001   PHE B 212 
 TYR   0.023   0.002   TYR C  85 
 ARG   0.003   0.000   ARG B  38 

*********************** 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
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8591 (m) cc_final: 0.8235 (p)
REVERT: A  327 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.6949 (m-10)
REVERT: B  266 LEU cc_start: 0.8626 (tp) cc_final: 0.8343 (tp)
REVERT: B  274 LYS cc_start: 0.7895 (tttp) cc_final: 0.7664 (ttmt)
REVERT: B  319 THR cc_start: 0.8050 (p) cc_final: 0.7845 (t)
REVERT: E   50 ASP cc_start: 0.8724 (p0) cc_final: 0.8166 (p0)
REVERT: E   80 TYR cc_start: 0.7725 (m-80) cc_final: 0.7255 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 164
  average time/residue: 0.1910
  time to fit residues: 42.5795
Evaluate side-chains
  155 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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  284 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   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:    3.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  77 ASN
E  84 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 = 0.4277 r_free = 0.4277 target = 0.190745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.156359 restraints weight = 18134.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.93
r_work: 0.3652 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3795 r_free = 0.3795    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 = 0.3795 r_free = 0.3795    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3795
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7693  Z= 0.262
  Angle     :  0.602  12.014  10503  Z= 0.314
  Chirality :  0.044   0.165   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.434  55.153   1149
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.29 %
    Favored  : 81.29 %
  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:  1.04 (0.27), residues: 988
  helix:  2.41 (0.27), residues: 381
  sheet:  0.02 (0.33), residues: 227
  loop : -0.66 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 169 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.016   0.002   PHE E 108 
 TYR   0.026   0.002   TYR C  85 
 ARG   0.004   0.000   ARG B  38 

*********************** 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
  168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8662 (m) cc_final: 0.8295 (p)
REVERT: A  327 TRP cc_start: 0.7882 (OUTLIER) cc_final: 0.6852 (m-10)
REVERT: A  338 MET cc_start: 0.8165 (mtp) cc_final: 0.7873 (mtp)
REVERT: B  274 LYS cc_start: 0.7933 (tttp) cc_final: 0.7693 (ttmt)
REVERT: B  280 ARG cc_start: 0.8340 (tpt90) cc_final: 0.7883 (ttt90)
REVERT: B  319 THR cc_start: 0.8049 (p) cc_final: 0.7835 (t)
REVERT: E   50 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8141 (p0)
REVERT: E   80 TYR cc_start: 0.7774 (m-80) cc_final: 0.7279 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 162
  average time/residue: 0.1890
  time to fit residues: 41.7838
Evaluate side-chains
  159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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  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   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:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 227 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.192206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.157421 restraints weight = 16893.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 3.34
r_work: 0.3687 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3828 r_free = 0.3828    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3828 r_free = 0.3828    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7693  Z= 0.215
  Angle     :  0.586  11.975  10503  Z= 0.305
  Chirality :  0.043   0.169   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.310  54.616   1149
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.09 %
    Favored  : 80.48 %
  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:  1.07 (0.27), residues: 988
  helix:  2.45 (0.27), residues: 382
  sheet: -0.02 (0.32), residues: 227
  loop : -0.61 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  99 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 212 
 TYR   0.022   0.002   TYR C  85 
 ARG   0.002   0.000   ARG B  38 

*********************** 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
  173 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8645 (m) cc_final: 0.8292 (p)
REVERT: A  327 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.6941 (m-10)
REVERT: A  338 MET cc_start: 0.8160 (mtp) cc_final: 0.7865 (mtp)
REVERT: B  266 LEU cc_start: 0.8541 (tp) cc_final: 0.8131 (tp)
REVERT: B  274 LYS cc_start: 0.7913 (tttp) cc_final: 0.7694 (ttmt)
REVERT: B  319 THR cc_start: 0.8034 (p) cc_final: 0.7831 (t)
REVERT: C   75 GLN cc_start: 0.7653 (mt0) cc_final: 0.7167 (mm-40)
REVERT: C  340 ASN cc_start: 0.8439 (t0) cc_final: 0.8209 (t0)
REVERT: E   50 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8070 (p0)
REVERT: E   80 TYR cc_start: 0.7782 (m-80) cc_final: 0.7264 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 164
  average time/residue: 0.1833
  time to fit residues: 41.1299
Evaluate side-chains
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
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  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  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  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   95 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.5782

-------------------------------------------------------------------------------
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 227 GLN ** 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 = 0.4270 r_free = 0.4270 target = 0.189958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.156208 restraints weight = 19238.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 4.13
r_work: 0.3619 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3763 r_free = 0.3763    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3763 r_free = 0.3763    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7693  Z= 0.270
  Angle     :  0.614  12.367  10503  Z= 0.321
  Chirality :  0.044   0.168   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.412  54.613   1149
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.90 %
    Favored  : 79.81 %
  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:  2.39 (0.27), residues: 381
  sheet: -0.06 (0.33), residues: 222
  loop : -0.70 (0.31), residues: 385

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   0.027   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 

*********************** 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
  165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8680 (m) cc_final: 0.8318 (p)
REVERT: A  194 ILE cc_start: 0.8280 (mm) cc_final: 0.7951 (mt)
REVERT: A  327 TRP cc_start: 0.7919 (OUTLIER) cc_final: 0.6785 (m-10)
REVERT: A  338 MET cc_start: 0.8255 (mtp) cc_final: 0.7958 (mtp)
REVERT: B  266 LEU cc_start: 0.8642 (tp) cc_final: 0.8292 (tp)
REVERT: B  274 LYS cc_start: 0.8009 (tttp) cc_final: 0.7768 (ttmt)
REVERT: B  319 THR cc_start: 0.8028 (p) cc_final: 0.7804 (t)
REVERT: E   50 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8137 (p0)
REVERT: E   80 TYR cc_start: 0.7761 (m-80) cc_final: 0.7232 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 160
  average time/residue: 0.1903
  time to fit residues: 42.0626
Evaluate side-chains
  159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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 A residue  330 THR
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  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain E residue   50 ASP
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:    0.1980
   chunk 80 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0370
   chunk 73 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.0262

-------------------------------------------------------------------------------
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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.191867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.158408 restraints weight = 21416.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 5.06
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7693  Z= 0.216
  Angle     :  0.588  12.304  10503  Z= 0.308
  Chirality :  0.043   0.170   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.256  54.039   1149
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.90 %
    Favored  : 79.41 %
  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:  1.05 (0.27), residues: 988
  helix:  2.43 (0.27), residues: 382
  sheet: -0.02 (0.33), residues: 215
  loop : -0.62 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 311 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 212 
 TYR   0.023   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 

*********************** 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
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8548 (m) cc_final: 0.8291 (p)
REVERT: A  327 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.6632 (m-10)
REVERT: A  338 MET cc_start: 0.8387 (mtp) cc_final: 0.8148 (mtp)
REVERT: B  266 LEU cc_start: 0.8670 (tp) cc_final: 0.8267 (tp)
REVERT: B  319 THR cc_start: 0.8079 (p) cc_final: 0.7862 (t)
REVERT: E   50 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7979 (p0)
REVERT: E   80 TYR cc_start: 0.7470 (m-80) cc_final: 0.7043 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 160
  average time/residue: 0.1775
  time to fit residues: 39.1212
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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 C residue   85 TYR
Chi-restraints excluded: chain C residue  100 VAL
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   60 TYR
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:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   chunk 39 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8540

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.192913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.159355 restraints weight = 19136.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 4.27
r_work: 0.3656 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    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 = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7693  Z= 0.204
  Angle     :  0.588  12.234  10503  Z= 0.307
  Chirality :  0.043   0.170   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.168  53.876   1149
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.17 %
    Favored  : 79.41 %
  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:  1.09 (0.27), residues: 988
  helix:  2.44 (0.27), residues: 382
  sheet: -0.02 (0.33), residues: 217
  loop : -0.56 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 311 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.013   0.001   PHE B 212 
 TYR   0.019   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 

********************** 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
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8607 (m) cc_final: 0.8235 (p)
REVERT: A  327 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.6758 (m-10)
REVERT: A  338 MET cc_start: 0.8340 (mtp) cc_final: 0.8043 (mtp)
REVERT: B  266 LEU cc_start: 0.8656 (tp) cc_final: 0.8288 (tp)
REVERT: B  319 THR cc_start: 0.8018 (p) cc_final: 0.7790 (t)
REVERT: C   59 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7543 (m-80)
REVERT: E   50 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8123 (p0)
REVERT: E   80 TYR cc_start: 0.7831 (m-80) cc_final: 0.7337 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 161
  average time/residue: 0.1884
  time to fit residues: 41.4063
Evaluate side-chains
  169 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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 C residue   59 TYR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  100 VAL
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   60 TYR
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:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.179192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.137929 restraints weight = 15801.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 3.42
r_work: 0.3525 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7693  Z= 0.317
  Angle     :  0.648  12.807  10503  Z= 0.340
  Chirality :  0.045   0.188   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.459  54.139   1149
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.44 %
    Favored  : 79.14 %
  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:  0.87 (0.27), residues: 988
  helix:  2.27 (0.27), residues: 378
  sheet: -0.17 (0.33), residues: 222
  loop : -0.64 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 169 
 HIS   0.008   0.002   HIS B 220 
 PHE   0.019   0.002   PHE E 108 
 TYR   0.026   0.002   TYR C  85 
 ARG   0.007   0.001   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4198.21 seconds
wall clock time: 72 minutes 37.97 seconds (4357.97 seconds total)