Starting phenix.real_space_refine
on Fri Aug 22 19:59:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh4_37236/08_2025/8kh4_37236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/08_2025/8kh4_37236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/08_2025/8kh4_37236.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kh4_37236/08_2025/8kh4_37236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/08_2025/8kh4_37236.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 2, 'GLU:plan': 3, '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, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 5, '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: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3}
          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: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3}
          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, 'ARG:plan': 1, 'GLU:plan': 3, '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: 2.58, per 1000 atoms: 0.34
  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: 0.65
  Conformation dependent library (CDL) restraints added in 497.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 1.27

  Time building geometry restraints manager: 0.87 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:             0.360
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.360
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.109   7696  Z= 0.635
  Angle     :  1.017  13.493  10509  Z= 0.633
  Chirality :  0.081   0.817   1223
  Planarity :  0.007   0.098   1324
  Dihedral  : 14.018 120.945   2639
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.48 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.95 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG E  72 
 TYR   0.025   0.002   TYR C  85 
 PHE   0.028   0.002   PHE A  65 
 TRP   0.026   0.002   TRP C  99 
 HIS   0.007   0.002   HIS D  44 

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

*********************** 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  : 0.288 
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: 0.0830
  time to fit residues: 19.3056
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  : 0.195 
-------------------------------------------------------------------------------
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 49 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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  74 ASN
E  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.192152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.156983 restraints weight = 17731.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 3.50
r_work: 0.3717 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3857 r_free = 0.3857    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3856 r_free = 0.3856    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7696  Z= 0.158
  Angle     :  0.629  10.589  10509  Z= 0.330
  Chirality :  0.045   0.251   1223
  Planarity :  0.005   0.076   1324
  Dihedral  :  5.810  57.029   1149
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.09 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.27), residues: 988
  helix:  1.97 (0.26), residues: 388
  sheet:  0.09 (0.33), residues: 222
  loop : -0.63 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.028   0.002   TYR C  85 
 PHE   0.017   0.002   PHE B 212 
 TRP   0.022   0.002   TRP C  99 
 HIS   0.005   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7693)
  covalent geometry    : angle       0.62714 (10503)
  SS BOND              : bond        0.00153 (    3)
  SS BOND              : angle       1.88210 (    6)
  hydrogen bonds       : bond        0.04355 (  420)
  hydrogen bonds       : angle       5.34758 ( 1212)

*********************** 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
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.6284 (ppp)
REVERT: A  280 MET cc_start: 0.7643 (mtp) cc_final: 0.7436 (mtm)
REVERT: A  327 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7040 (m-10)
REVERT: B  266 LEU cc_start: 0.8560 (tp) cc_final: 0.8211 (tp)
REVERT: B  274 LYS cc_start: 0.7864 (tttp) cc_final: 0.7582 (ttmt)
REVERT: B  280 ARG cc_start: 0.8274 (tpt90) cc_final: 0.7952 (ttt90)
REVERT: E   80 TYR cc_start: 0.7725 (m-80) cc_final: 0.7167 (m-80)
REVERT: E  115 TYR cc_start: 0.8120 (t80) cc_final: 0.7896 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 159
  average time/residue: 0.0844
  time to fit residues: 18.0273
Evaluate side-chains
  152 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 146
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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   23 ASN
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 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0970
   chunk 5 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
B 294 GLN
** 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 = 0.4321 r_free = 0.4321 target = 0.195622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.159669 restraints weight = 18489.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 3.63
r_work: 0.3708 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3845 r_free = 0.3845    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3845 r_free = 0.3845    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7696  Z= 0.134
  Angle     :  0.582  10.852  10509  Z= 0.304
  Chirality :  0.043   0.162   1223
  Planarity :  0.005   0.070   1324
  Dihedral  :  5.497  56.038   1149
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.79 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.27), residues: 988
  helix:  2.08 (0.26), residues: 394
  sheet:  0.06 (0.32), residues: 224
  loop : -0.63 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 304 
 TYR   0.023   0.002   TYR C  85 
 PHE   0.016   0.001   PHE B 212 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7693)
  covalent geometry    : angle       0.58091 (10503)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       1.50540 (    6)
  hydrogen bonds       : bond        0.03881 (  420)
  hydrogen bonds       : angle       5.08147 ( 1212)

*********************** 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
  166 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6524 (ppp)
REVERT: A  280 MET cc_start: 0.7636 (mtp) cc_final: 0.7392 (mtm)
REVERT: A  327 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.6985 (m-10)
REVERT: B   23 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7854 (t0)
REVERT: B   27 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7971 (tp30)
REVERT: B  266 LEU cc_start: 0.8586 (tp) cc_final: 0.8251 (tp)
REVERT: B  274 LYS cc_start: 0.7845 (tttp) cc_final: 0.7583 (ttmt)
REVERT: B  280 ARG cc_start: 0.8317 (tpt90) cc_final: 0.7983 (ttt90)
REVERT: E   50 ASP cc_start: 0.8744 (p0) cc_final: 0.8280 (p0)
REVERT: E   80 TYR cc_start: 0.7748 (m-80) cc_final: 0.7227 (m-80)
REVERT: E   94 TYR cc_start: 0.7317 (m-80) cc_final: 0.6450 (m-80)
REVERT: E  115 TYR cc_start: 0.8107 (t80) cc_final: 0.7875 (t80)
REVERT: D   38 MET cc_start: 0.6675 (mtm) cc_final: 0.6411 (mtp)
  outliers start: 8
  outliers final: 3
  residues processed: 163
  average time/residue: 0.0896
  time to fit residues: 19.7540
Evaluate side-chains
  151 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 53 optimal weight:    0.3980
   chunk 96 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 74 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** 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 = 0.4325 r_free = 0.4325 target = 0.196087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.160606 restraints weight = 19133.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 3.88
r_work: 0.3720 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
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 = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7696  Z= 0.121
  Angle     :  0.564  11.083  10509  Z= 0.293
  Chirality :  0.042   0.163   1223
  Planarity :  0.005   0.067   1324
  Dihedral  :  5.314  56.096   1149
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.73 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.27), residues: 988
  helix:  2.22 (0.26), residues: 393
  sheet:  0.10 (0.32), residues: 224
  loop : -0.64 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 304 
 TYR   0.025   0.002   TYR C  85 
 PHE   0.015   0.001   PHE B 212 
 TRP   0.012   0.001   TRP C 169 
 HIS   0.004   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7693)
  covalent geometry    : angle       0.56306 (10503)
  SS BOND              : bond        0.00093 (    3)
  SS BOND              : angle       1.25969 (    6)
  hydrogen bonds       : bond        0.03699 (  420)
  hydrogen bonds       : angle       4.92373 ( 1212)

*********************** 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
  168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5894 (t-100) cc_final: 0.5232 (t-100)
REVERT: A  177 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6749 (ppp)
REVERT: A  280 MET cc_start: 0.7677 (mtp) cc_final: 0.7430 (mtm)
REVERT: A  327 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.6983 (m-10)
REVERT: B  266 LEU cc_start: 0.8606 (tp) cc_final: 0.8292 (tp)
REVERT: B  274 LYS cc_start: 0.7841 (tttp) cc_final: 0.7614 (ttmt)
REVERT: B  280 ARG cc_start: 0.8316 (tpt90) cc_final: 0.7906 (ttt90)
REVERT: B  319 THR cc_start: 0.7927 (p) cc_final: 0.7687 (t)
REVERT: E   50 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8122 (p0)
REVERT: E   80 TYR cc_start: 0.7723 (m-80) cc_final: 0.7238 (m-80)
REVERT: E  115 TYR cc_start: 0.8156 (t80) cc_final: 0.7936 (t80)
REVERT: D   38 MET cc_start: 0.6664 (mtm) cc_final: 0.6402 (mtp)
  outliers start: 17
  outliers final: 7
  residues processed: 161
  average time/residue: 0.0725
  time to fit residues: 16.0309
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  : 0.273 
-------------------------------------------------------------------------------
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  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 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 = 0.4316 r_free = 0.4316 target = 0.194999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.162520 restraints weight = 22050.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 5.33
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7696  Z= 0.135
  Angle     :  0.569  11.450  10509  Z= 0.296
  Chirality :  0.043   0.179   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.246  56.137   1149
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.13 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.27), residues: 988
  helix:  2.45 (0.27), residues: 381
  sheet: -0.04 (0.33), residues: 221
  loop : -0.62 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 314 
 TYR   0.023   0.002   TYR C  85 
 PHE   0.016   0.001   PHE B 222 
 TRP   0.013   0.001   TRP C 211 
 HIS   0.004   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7693)
  covalent geometry    : angle       0.56820 (10503)
  SS BOND              : bond        0.00068 (    3)
  SS BOND              : angle       1.19037 (    6)
  hydrogen bonds       : bond        0.03660 (  420)
  hydrogen bonds       : angle       4.84459 ( 1212)

*********************** 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
  167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5703 (t-100) cc_final: 0.5127 (t-100)
REVERT: A  280 MET cc_start: 0.7278 (mtp) cc_final: 0.7058 (mtm)
REVERT: A  327 TRP cc_start: 0.7571 (OUTLIER) cc_final: 0.6754 (m-10)
REVERT: B  266 LEU cc_start: 0.8637 (tp) cc_final: 0.8302 (tp)
REVERT: E   50 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8011 (p0)
REVERT: E   80 TYR cc_start: 0.7519 (m-80) cc_final: 0.7065 (m-80)
REVERT: D   38 MET cc_start: 0.6585 (mtm) cc_final: 0.6286 (mtp)
  outliers start: 17
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0855
  time to fit residues: 18.4553
Evaluate side-chains
  151 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain 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 42 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 69 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN
E  77 ASN
E  84 ASN
E 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.191031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.155819 restraints weight = 17038.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 3.42
r_work: 0.3684 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    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 = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7696  Z= 0.176
  Angle     :  0.612  12.060  10509  Z= 0.318
  Chirality :  0.044   0.163   1223
  Planarity :  0.005   0.069   1324
  Dihedral  :  5.454  55.748   1149
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.34 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.27), residues: 988
  helix:  2.32 (0.26), residues: 381
  sheet: -0.13 (0.32), residues: 232
  loop : -0.62 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  38 
 TYR   0.025   0.002   TYR C  85 
 PHE   0.018   0.002   PHE B 222 
 TRP   0.015   0.002   TRP C 169 
 HIS   0.007   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7693)
  covalent geometry    : angle       0.61111 (10503)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       1.31232 (    6)
  hydrogen bonds       : bond        0.03873 (  420)
  hydrogen bonds       : angle       4.95408 ( 1212)

*********************** 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
  165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8665 (m) cc_final: 0.8295 (p)
REVERT: A  140 THR cc_start: 0.6482 (OUTLIER) cc_final: 0.6240 (t)
REVERT: A  327 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.6732 (m-10)
REVERT: A  338 MET cc_start: 0.7983 (mtp) cc_final: 0.7634 (mtp)
REVERT: B  280 ARG cc_start: 0.8355 (tpt90) cc_final: 0.7899 (ttt90)
REVERT: C   43 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6649 (mm)
REVERT: E   50 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8157 (p0)
REVERT: E   80 TYR cc_start: 0.7729 (m-80) cc_final: 0.7177 (m-80)
  outliers start: 22
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0798
  time to fit residues: 17.3953
Evaluate side-chains
  153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 90 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  74 ASN
E 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.193020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.159759 restraints weight = 20268.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 4.63
r_work: 0.3643 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7696  Z= 0.146
  Angle     :  0.599  12.106  10509  Z= 0.311
  Chirality :  0.043   0.167   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.340  55.150   1149
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.09 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.27), residues: 988
  helix:  2.37 (0.26), residues: 382
  sheet:  0.03 (0.33), residues: 222
  loop : -0.59 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.021   0.002   TYR C  85 
 PHE   0.016   0.001   PHE B 222 
 TRP   0.011   0.001   TRP C 169 
 HIS   0.004   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7693)
  covalent geometry    : angle       0.59895 (10503)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       1.17809 (    6)
  hydrogen bonds       : bond        0.03698 (  420)
  hydrogen bonds       : angle       4.88900 ( 1212)

*********************** 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
  172 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8645 (m) cc_final: 0.8282 (p)
REVERT: A  140 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6372 (t)
REVERT: A  327 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.6899 (m-10)
REVERT: A  338 MET cc_start: 0.8178 (mtp) cc_final: 0.7878 (mtp)
REVERT: B   23 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (t0)
REVERT: B  266 LEU cc_start: 0.8625 (tp) cc_final: 0.8220 (tp)
REVERT: E   50 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8128 (p0)
REVERT: E   80 TYR cc_start: 0.7807 (m-80) cc_final: 0.7265 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 166
  average time/residue: 0.0746
  time to fit residues: 17.0252
Evaluate side-chains
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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   23 ASN
Chi-restraints excluded: chain B residue  253 TYR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
E  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 = 0.4270 r_free = 0.4270 target = 0.190389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.152301 restraints weight = 11953.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.75
r_work: 0.3700 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7696  Z= 0.179
  Angle     :  0.620  12.549  10509  Z= 0.323
  Chirality :  0.044   0.166   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.435  55.022   1149
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.36 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 988
  helix:  2.21 (0.26), residues: 384
  sheet: -0.04 (0.33), residues: 217
  loop : -0.64 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.022   0.002   TYR C  85 
 PHE   0.016   0.002   PHE E 108 
 TRP   0.014   0.002   TRP C 169 
 HIS   0.007   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7693)
  covalent geometry    : angle       0.61903 (10503)
  SS BOND              : bond        0.00121 (    3)
  SS BOND              : angle       1.28663 (    6)
  hydrogen bonds       : bond        0.03832 (  420)
  hydrogen bonds       : angle       4.94689 ( 1212)

*********************** 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
  160 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8663 (m) cc_final: 0.8305 (p)
REVERT: A  140 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.6297 (t)
REVERT: A  327 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.6762 (m-10)
REVERT: A  338 MET cc_start: 0.8171 (mtp) cc_final: 0.7882 (mtp)
REVERT: B  266 LEU cc_start: 0.8551 (tp) cc_final: 0.8224 (tp)
REVERT: B  280 ARG cc_start: 0.8277 (tpt90) cc_final: 0.7820 (ttt90)
REVERT: E   50 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8103 (p0)
REVERT: E   80 TYR cc_start: 0.7720 (m-80) cc_final: 0.7212 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 154
  average time/residue: 0.0765
  time to fit residues: 16.0378
Evaluate side-chains
  161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 94 optimal weight:   30.0000
   chunk 83 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  74 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 = 0.4314 r_free = 0.4314 target = 0.195223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.161443 restraints weight = 18060.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 3.89
r_work: 0.3695 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7696  Z= 0.125
  Angle     :  0.573  12.118  10509  Z= 0.299
  Chirality :  0.043   0.169   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.129  54.019   1149
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.27), residues: 988
  helix:  2.45 (0.26), residues: 381
  sheet:  0.00 (0.33), residues: 222
  loop : -0.54 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.015   0.001   TYR C  85 
 PHE   0.013   0.001   PHE B 212 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7693)
  covalent geometry    : angle       0.57246 (10503)
  SS BOND              : bond        0.00090 (    3)
  SS BOND              : angle       1.02407 (    6)
  hydrogen bonds       : bond        0.03500 (  420)
  hydrogen bonds       : angle       4.79674 ( 1212)

*********************** 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
  175 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 VAL cc_start: 0.8551 (m) cc_final: 0.8196 (p)
REVERT: A  327 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6824 (m-10)
REVERT: A  338 MET cc_start: 0.8256 (mtp) cc_final: 0.7968 (mtp)
REVERT: B  266 LEU cc_start: 0.8606 (tp) cc_final: 0.8254 (tp)
REVERT: C  110 ASN cc_start: 0.7447 (m-40) cc_final: 0.7184 (m110)
REVERT: E   50 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8120 (p0)
REVERT: E   80 TYR cc_start: 0.7782 (m-80) cc_final: 0.7336 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 167
  average time/residue: 0.0823
  time to fit residues: 19.0795
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  : 0.237 
-------------------------------------------------------------------------------
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   85 TYR
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:    0.0770
   chunk 83 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0370
   chunk 87 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4416

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.197012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.163172 restraints weight = 16451.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 3.46
r_work: 0.3750 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7696  Z= 0.118
  Angle     :  0.574  12.065  10509  Z= 0.300
  Chirality :  0.042   0.171   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.012  54.008   1149
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.30 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.27), residues: 988
  helix:  2.47 (0.26), residues: 386
  sheet:  0.10 (0.33), residues: 227
  loop : -0.48 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  72 
 TYR   0.012   0.001   TYR E 115 
 PHE   0.013   0.001   PHE B 212 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7693)
  covalent geometry    : angle       0.57408 (10503)
  SS BOND              : bond        0.00104 (    3)
  SS BOND              : angle       0.91070 (    6)
  hydrogen bonds       : bond        0.03485 (  420)
  hydrogen bonds       : angle       4.76300 ( 1212)

********************** 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
  167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TRP cc_start: 0.5883 (t-100) cc_final: 0.5237 (t-100)
REVERT: A  205 LEU cc_start: 0.7874 (tp) cc_final: 0.7457 (tp)
REVERT: A  327 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.6785 (m-10)
REVERT: A  338 MET cc_start: 0.8190 (mtp) cc_final: 0.7879 (mtp)
REVERT: B   23 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7414 (t0)
REVERT: B   38 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7162 (ttp80)
REVERT: B  266 LEU cc_start: 0.8546 (tp) cc_final: 0.8191 (tp)
REVERT: C  110 ASN cc_start: 0.7378 (m-40) cc_final: 0.7154 (m110)
REVERT: E   50 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8105 (p0)
REVERT: E   80 TYR cc_start: 0.7785 (m-80) cc_final: 0.7358 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 159
  average time/residue: 0.0765
  time to fit residues: 16.9137
Evaluate side-chains
  160 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  311 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 78 optimal weight:    6.9990
   chunk 42 optimal weight:    0.5980
   chunk 73 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 93 optimal weight:   30.0000
   chunk 61 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.195652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.160455 restraints weight = 14475.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 3.26
r_work: 0.3734 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    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 = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7696  Z= 0.137
  Angle     :  0.593  12.252  10509  Z= 0.309
  Chirality :  0.043   0.180   1223
  Planarity :  0.005   0.068   1324
  Dihedral  :  5.021  54.022   1149
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.30 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.27), residues: 988
  helix:  2.41 (0.26), residues: 384
  sheet:  0.02 (0.32), residues: 229
  loop : -0.43 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  72 
 TYR   0.015   0.002   TYR E 115 
 PHE   0.013   0.001   PHE B 212 
 TRP   0.011   0.001   TRP A 311 
 HIS   0.004   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7693)
  covalent geometry    : angle       0.59304 (10503)
  SS BOND              : bond        0.00053 (    3)
  SS BOND              : angle       1.00009 (    6)
  hydrogen bonds       : bond        0.03561 (  420)
  hydrogen bonds       : angle       4.77203 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1964.69 seconds
wall clock time: 34 minutes 27.28 seconds (2067.28 seconds total)