Starting phenix.real_space_refine
on Wed Feb 12 07:37:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh4_37236/02_2025/8kh4_37236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/02_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_37236/02_2025/8kh4_37236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/02_2025/8kh4_37236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/02_2025/8kh4_37236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/02_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-5592/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: 4.96, per 1000 atoms: 0.66
  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: 2.16
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.84
  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: 2.26

  Time building geometry restraints manager: 2.45 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:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.750
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.650
-------------------------------------------------------------------------------
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  : 0.867 
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: 0.2044
  time to fit residues: 46.8953
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  : 0.752 
-------------------------------------------------------------------------------
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 = 0.157708 restraints weight = 15980.463|
|-----------------------------------------------------------------------------|
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: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3837
-------------------------------------------------------------------------------
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  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.6283 (ppp)
REVERT: A  327 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.7067 (m-10)
REVERT: B  266 LEU cc_start: 0.8572 (tp) cc_final: 0.8238 (tp)
REVERT: B  274 LYS cc_start: 0.7914 (tttp) cc_final: 0.7638 (ttmt)
REVERT: B  280 ARG cc_start: 0.8249 (tpt90) cc_final: 0.7955 (ttt90)
REVERT: C  111 TYR cc_start: 0.8488 (m-80) cc_final: 0.8162 (m-80)
REVERT: E   80 TYR cc_start: 0.7769 (m-80) cc_final: 0.7205 (m-80)
REVERT: E   93 VAL cc_start: 0.7446 (t) cc_final: 0.7191 (t)
REVERT: E  115 TYR cc_start: 0.8097 (t80) cc_final: 0.7882 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 158
  average time/residue: 0.2042
  time to fit residues: 43.4436
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  : 0.828 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.193584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.161098 restraints weight = 14726.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 3.01
r_work: 0.3729 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7693  Z= 0.205
  Angle     :  0.591  11.040  10503  Z= 0.308
  Chirality :  0.043   0.161   1223
  Planarity :  0.005   0.070   1324
  Dihedral  :  5.575  55.947   1149
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.65 %
    Favored  : 85.60 %
  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:  0.85 (0.27), residues: 988
  helix:  2.05 (0.26), residues: 394
  sheet:  0.01 (0.33), residues: 224
  loop : -0.68 (0.31), residues: 370

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   0.017   0.001   PHE B 212 
 TYR   0.027   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
  168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6543 (ppp)
REVERT: A  327 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.6975 (m-10)
REVERT: B   27 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8075 (tp30)
REVERT: B  266 LEU cc_start: 0.8576 (tp) cc_final: 0.8256 (tp)
REVERT: B  274 LYS cc_start: 0.7826 (tttp) cc_final: 0.7592 (ttmt)
REVERT: B  280 ARG cc_start: 0.8286 (tpt90) cc_final: 0.7885 (ttt90)
REVERT: E   50 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8187 (p0)
REVERT: E   80 TYR cc_start: 0.7728 (m-80) cc_final: 0.7208 (m-80)
REVERT: E   94 TYR cc_start: 0.7257 (m-80) cc_final: 0.6336 (m-80)
REVERT: E  115 TYR cc_start: 0.8112 (t80) cc_final: 0.7910 (t80)
REVERT: D   38 MET cc_start: 0.6743 (mtm) cc_final: 0.6459 (mtp)
  outliers start: 13
  outliers final: 7
  residues processed: 161
  average time/residue: 0.1963
  time to fit residues: 42.7393
Evaluate side-chains
  151 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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   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:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 92 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4261 r_free = 0.4261 target = 0.189177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151154 restraints weight = 11363.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.64
r_work: 0.3691 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3830 r_free = 0.3830    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3830 r_free = 0.3830    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7693  Z= 0.292
  Angle     :  0.631  11.651  10503  Z= 0.328
  Chirality :  0.045   0.161   1223
  Planarity :  0.005   0.070   1324
  Dihedral  :  5.730  55.783   1149
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.27 %
    Favored  : 83.18 %
  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:  0.71 (0.27), residues: 988
  helix:  2.06 (0.27), residues: 385
  sheet: -0.16 (0.33), residues: 220
  loop : -0.77 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 169 
 HIS   0.008   0.002   HIS B 220 
 PHE   0.019   0.002   PHE B 222 
 TYR   0.032   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
  172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8693 (m) cc_final: 0.8326 (p)
REVERT: A  327 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.6727 (m-10)
REVERT: B  266 LEU cc_start: 0.8689 (tp) cc_final: 0.8428 (tp)
REVERT: B  274 LYS cc_start: 0.7887 (tttp) cc_final: 0.7634 (ttmt)
REVERT: B  280 ARG cc_start: 0.8267 (tpt90) cc_final: 0.7840 (ttt90)
REVERT: B  319 THR cc_start: 0.8058 (p) cc_final: 0.7851 (t)
REVERT: C  263 THR cc_start: 0.8249 (m) cc_final: 0.7994 (p)
REVERT: E    3 GLN cc_start: 0.6240 (mp10) cc_final: 0.5760 (mp10)
REVERT: E   50 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8193 (p0)
REVERT: E   80 TYR cc_start: 0.7733 (m-80) cc_final: 0.7210 (m-80)
REVERT: D   38 MET cc_start: 0.6835 (mtm) cc_final: 0.6541 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 165
  average time/residue: 0.1869
  time to fit residues: 41.9967
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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   43 ILE
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  338 ILE
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:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0770
   chunk 58 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** 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 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.193141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.155702 restraints weight = 14417.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 3.54
r_work: 0.3715 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7693  Z= 0.187
  Angle     :  0.576  11.838  10503  Z= 0.300
  Chirality :  0.043   0.182   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.474  54.960   1149
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.61 %
    Favored  : 82.23 %
  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:  0.99 (0.27), residues: 988
  helix:  2.37 (0.27), residues: 384
  sheet: -0.07 (0.33), residues: 230
  loop : -0.65 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 212 
 TYR   0.025   0.002   TYR C  85 
 ARG   0.002   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
  174 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8598 (m) cc_final: 0.8249 (p)
REVERT: A  140 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.6230 (t)
REVERT: A  327 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.6939 (m-10)
REVERT: B  266 LEU cc_start: 0.8616 (tp) cc_final: 0.8338 (tp)
REVERT: B  274 LYS cc_start: 0.7892 (tttp) cc_final: 0.7668 (ttmt)
REVERT: B  280 ARG cc_start: 0.8329 (tpt90) cc_final: 0.7846 (ttt90)
REVERT: B  319 THR cc_start: 0.8052 (p) cc_final: 0.7833 (t)
REVERT: C  263 THR cc_start: 0.8053 (m) cc_final: 0.7801 (p)
REVERT: E    3 GLN cc_start: 0.6132 (mp10) cc_final: 0.5343 (mp10)
REVERT: E   50 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8168 (p0)
REVERT: E   80 TYR cc_start: 0.7749 (m-80) cc_final: 0.7253 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 168
  average time/residue: 0.1884
  time to fit residues: 43.1160
Evaluate side-chains
  158 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  184 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0050
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0570
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.4312

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

Flipped N/Q/H residues before XYZ refinement:
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
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 = 0.4328 r_free = 0.4328 target = 0.196287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.161367 restraints weight = 18103.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 3.58
r_work: 0.3739 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3876 r_free = 0.3876    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 = 0.3876 r_free = 0.3876    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7693  Z= 0.161
  Angle     :  0.548  11.707  10503  Z= 0.286
  Chirality :  0.042   0.166   1223
  Planarity :  0.005   0.067   1324
  Dihedral  :  5.172  54.394   1149
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.02 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.27), residues: 988
  helix:  2.56 (0.27), residues: 381
  sheet:  0.18 (0.33), residues: 222
  loop : -0.65 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 212 
 TYR   0.017   0.001   TYR C  85 
 ARG   0.003   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
  173 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5813 (t-100) cc_final: 0.5147 (t-100)
REVERT: A  327 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.6936 (m-10)
REVERT: A  338 MET cc_start: 0.7956 (mtp) cc_final: 0.7596 (mtp)
REVERT: B  266 LEU cc_start: 0.8506 (tp) cc_final: 0.8175 (tp)
REVERT: B  274 LYS cc_start: 0.7855 (tttp) cc_final: 0.7628 (ttmt)
REVERT: B  319 THR cc_start: 0.8012 (p) cc_final: 0.7800 (t)
REVERT: C  263 THR cc_start: 0.8012 (m) cc_final: 0.7702 (p)
REVERT: E    3 GLN cc_start: 0.6190 (mp10) cc_final: 0.5332 (mp10)
REVERT: E   50 ASP cc_start: 0.8751 (p0) cc_final: 0.8157 (p0)
REVERT: E   80 TYR cc_start: 0.7721 (m-80) cc_final: 0.7262 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 164
  average time/residue: 0.1789
  time to fit residues: 39.9731
Evaluate side-chains
  157 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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 B residue  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain E residue   60 TYR
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:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.9364

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

Flipped N/Q/H residues before XYZ refinement:
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  84 ASN
E 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.193903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.159503 restraints weight = 16726.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 3.38
r_work: 0.3717 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7693  Z= 0.204
  Angle     :  0.575  11.945  10503  Z= 0.299
  Chirality :  0.043   0.168   1223
  Planarity :  0.005   0.067   1324
  Dihedral  :  5.172  54.512   1149
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.90 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 988
  helix:  2.50 (0.27), residues: 381
  sheet:  0.02 (0.32), residues: 235
  loop : -0.58 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 212 
 TYR   0.017   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 

*********************** 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
  171 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5867 (t-100) cc_final: 0.5174 (t-100)
REVERT: A  327 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.6936 (m-10)
REVERT: A  338 MET cc_start: 0.8117 (mtp) cc_final: 0.7814 (mtp)
REVERT: B  266 LEU cc_start: 0.8525 (tp) cc_final: 0.8225 (tp)
REVERT: B  274 LYS cc_start: 0.7866 (tttp) cc_final: 0.7646 (ttmt)
REVERT: B  319 THR cc_start: 0.8072 (p) cc_final: 0.7859 (t)
REVERT: C   75 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7072 (mm-40)
REVERT: E   50 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8127 (p0)
REVERT: E   80 TYR cc_start: 0.7797 (m-80) cc_final: 0.7329 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1850
  time to fit residues: 41.6737
Evaluate side-chains
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
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  184 THR
Chi-restraints excluded: chain C residue  296 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 95 optimal weight:   20.0000
   overall best weight:    1.1384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.192234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.157977 restraints weight = 18874.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 3.85
r_work: 0.3672 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7693  Z= 0.223
  Angle     :  0.584  12.182  10503  Z= 0.304
  Chirality :  0.043   0.168   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.216  54.323   1149
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.90 %
    Favored  : 79.54 %
  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:  1.10 (0.27), residues: 988
  helix:  2.48 (0.27), residues: 381
  sheet: -0.07 (0.32), residues: 235
  loop : -0.56 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 311 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 222 
 TYR   0.020   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
  166 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5840 (t-100) cc_final: 0.5121 (t-100)
REVERT: A  134 VAL cc_start: 0.8630 (m) cc_final: 0.8267 (p)
REVERT: A  327 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.6884 (m-10)
REVERT: A  338 MET cc_start: 0.8157 (mtp) cc_final: 0.7885 (mtp)
REVERT: B  274 LYS cc_start: 0.7922 (tttp) cc_final: 0.7701 (ttmt)
REVERT: B  319 THR cc_start: 0.8067 (p) cc_final: 0.7866 (t)
REVERT: E    3 GLN cc_start: 0.6192 (mp10) cc_final: 0.5507 (mp10)
REVERT: E   50 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8093 (p0)
REVERT: E   80 TYR cc_start: 0.7796 (m-80) cc_final: 0.7333 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 158
  average time/residue: 0.1877
  time to fit residues: 40.6226
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 93 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4287 r_free = 0.4287 target = 0.191833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.158908 restraints weight = 21138.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 4.75
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    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 = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7693  Z= 0.229
  Angle     :  0.592  12.375  10503  Z= 0.308
  Chirality :  0.043   0.168   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.249  54.087   1149
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.03 %
    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:  1.05 (0.27), residues: 988
  helix:  2.44 (0.27), residues: 381
  sheet: -0.11 (0.32), residues: 235
  loop : -0.58 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.015   0.001   PHE B 222 
 TYR   0.020   0.002   TYR C  85 
 ARG   0.006   0.000   ARG B  38 

*********************** 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
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5628 (t-100) cc_final: 0.5000 (t-100)
REVERT: A  134 VAL cc_start: 0.8510 (m) cc_final: 0.8243 (p)
REVERT: A  327 TRP cc_start: 0.7615 (OUTLIER) cc_final: 0.6654 (m-10)
REVERT: A  338 MET cc_start: 0.8238 (mtp) cc_final: 0.7977 (mtp)
REVERT: B   38 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6686 (ttp80)
REVERT: B  266 LEU cc_start: 0.8485 (tp) cc_final: 0.7975 (tp)
REVERT: B  319 THR cc_start: 0.8075 (p) cc_final: 0.7871 (t)
REVERT: E    3 GLN cc_start: 0.6262 (mp10) cc_final: 0.5510 (mp10)
REVERT: E   50 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8024 (p0)
REVERT: E   80 TYR cc_start: 0.7533 (m-80) cc_final: 0.7152 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 154
  average time/residue: 0.1872
  time to fit residues: 39.3984
Evaluate side-chains
  158 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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  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  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:    9.9990
   chunk 86 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 95 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.8384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.193828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.160145 restraints weight = 19070.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 4.44
r_work: 0.3660 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3802 r_free = 0.3802    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3802 r_free = 0.3802    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7693  Z= 0.197
  Angle     :  0.574  12.219  10503  Z= 0.299
  Chirality :  0.042   0.170   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.166  53.635   1149
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.44 %
    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:  1.10 (0.27), residues: 988
  helix:  2.49 (0.27), residues: 381
  sheet: -0.09 (0.32), residues: 235
  loop : -0.54 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 311 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 222 
 TYR   0.016   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
  155 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5838 (t-100) cc_final: 0.5131 (t-100)
REVERT: A  134 VAL cc_start: 0.8607 (m) cc_final: 0.8238 (p)
REVERT: A  327 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.6708 (m-10)
REVERT: A  338 MET cc_start: 0.8234 (mtp) cc_final: 0.7953 (mtp)
REVERT: B  266 LEU cc_start: 0.8557 (tp) cc_final: 0.8139 (tp)
REVERT: B  319 THR cc_start: 0.8024 (p) cc_final: 0.7795 (t)
REVERT: E    3 GLN cc_start: 0.6283 (mp10) cc_final: 0.5545 (mp10)
REVERT: E   50 ASP cc_start: 0.8735 (p0) cc_final: 0.8120 (p0)
REVERT: E   80 TYR cc_start: 0.7841 (m-80) cc_final: 0.7364 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 149
  average time/residue: 0.1801
  time to fit residues: 37.1269
Evaluate side-chains
  153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  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  184 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
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:    0.0270
   chunk 85 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.8640

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.193790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.159047 restraints weight = 15374.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 3.37
r_work: 0.3712 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3848 r_free = 0.3848    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3848 r_free = 0.3848    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7693  Z= 0.199
  Angle     :  0.575  12.206  10503  Z= 0.300
  Chirality :  0.043   0.176   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.141  53.583   1149
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.71 %
    Favored  : 79.54 %
  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:  1.10 (0.27), residues: 988
  helix:  2.50 (0.27), residues: 380
  sheet: -0.11 (0.32), residues: 235
  loop : -0.54 (0.32), residues: 373

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   0.016   0.002   TYR C  85 
 ARG   0.005   0.000   ARG E  72 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3951.76 seconds
wall clock time: 70 minutes 51.53 seconds (4251.53 seconds total)