Starting phenix.real_space_refine
on Wed Feb 12 10:01:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iw4_35762/02_2025/8iw4_35762_neut.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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      49      5.16       5
     C    5077      2.51       5
     N    1338      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7900
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1408
          Classifications: {'peptide': 179}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 177}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2230
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 5, 'TRANS': 296}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 69
    Chain: "C"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 239
          Classifications: {'peptide': 35}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 30}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 2226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2226
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 12, 'TRANS': 283}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 65
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SPD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.08, per 1000 atoms: 0.64
  Number of scatterers: 7900
  At special positions: 0
  Unit cell: (91.086, 113.411, 113.411, 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      49     16.00
     O    1436      8.00
     N    1338      7.00
     C    5077      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1946

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 13 sheets defined
      32.5% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
      removed outlier: 3.546A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 52
      removed outlier: 4.309A  pdb=" N   GLY A  52 " --> pdb=" O   ASP A  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 49 through 52'
    Processing helix  chain 'A' and resid 57 through 61
    Processing helix  chain 'A' and resid 269 through 278
    Processing helix  chain 'A' and resid 336 through 352
      removed outlier: 3.826A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.681A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.966A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'R' and resid 35 through 57
      removed outlier: 4.975A  pdb=" N   LEU R  41 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLY R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ASN R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL R  53 " --> pdb=" O   GLY R  49 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE R  55 " --> pdb=" O   LEU R  51 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA R  56 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 85
      removed outlier: 4.114A  pdb=" N   VAL R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R  81 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 96
    Processing helix  chain 'R' and resid 104 through 136
      removed outlier: 3.657A  pdb=" N   THR R 109 " --> pdb=" O   CYS R 105 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   CYS R 110 " --> pdb=" O   LYS R 106 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASP R 112 " --> pdb=" O   HIS R 108 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   THR R 113 " --> pdb=" O   THR R 109 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER R 114 " --> pdb=" O   CYS R 110 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE R 117 " --> pdb=" O   THR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
      removed outlier: 3.735A  pdb=" N   LYS R 143 " --> pdb=" O   THR R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 169
      removed outlier: 3.776A  pdb=" N   PHE R 158 " --> pdb=" O   ALA R 154 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER R 164 " --> pdb=" O   SER R 160 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER R 166 " --> pdb=" O   THR R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 232
      removed outlier: 4.340A  pdb=" N   LEU R 200 " --> pdb=" O   GLN R 196 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LEU R 201 " --> pdb=" O   ASN R 197 " (cutoff:3.500A)
      Proline residue:  R 209  - end of helix
      removed outlier: 3.991A  pdb=" N   VAL R 212 " --> pdb=" O   LEU R 208 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   MET R 213 " --> pdb=" O   PRO R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 246 through 283
      removed outlier: 4.395A  pdb=" N   LYS R 251 " --> pdb=" O   GLU R 247 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG R 252 " --> pdb=" O   ARG R 248 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR R 259 " --> pdb=" O   LYS R 255 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LEU R 260 " --> pdb=" O   ALA R 256 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA R 263 " --> pdb=" O   THR R 259 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 3.772A  pdb=" N   ALA R 282 " --> pdb=" O   ALA R 278 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR R 283 " --> pdb=" O   VAL R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 312
      removed outlier: 3.610A  pdb=" N   TYR R 293 " --> pdb=" O   PRO R 289 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ILE R 295 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL R 300 " --> pdb=" O   LEU R 296 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN R 303 " --> pdb=" O   CYS R 299 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   SER R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ALA R 305 " --> pdb=" O   TYR R 301 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 315 through 327
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.535A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.523A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.856A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.275A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.074A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153
      removed outlier: 6.602A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.009A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP B 211 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.395A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.379A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.814A  pdb=" N   VAL S  12 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.814A  pdb=" N   VAL S  12 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG S  98 " --> pdb=" O   PHE S 110 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.545A  pdb=" N   TYR S 190 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR S 175 " --> pdb=" O   MET S 230 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    960 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1372
        1.33 -     1.45: 2261
        1.45 -     1.57: 4380
        1.57 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 8081
  Sorted by residual:
  bond pdb=" CA  ASN A 271 "
       pdb=" C   ASN A 271 "
    ideal  model  delta    sigma   weight residual
    1.522  1.445  0.077 1.36e-02 5.41e+03 3.24e+01
  bond pdb=" C   TYR A 360 "
       pdb=" O   TYR A 360 "
    ideal  model  delta    sigma   weight residual
    1.249  1.222  0.027 8.50e-03 1.38e+04 9.82e+00
  bond pdb=" C   VAL R  94 "
       pdb=" O   VAL R  94 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.034 1.23e-02 6.61e+03 7.83e+00
  bond pdb=" N   GLN A 267 "
       pdb=" CA  GLN A 267 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.28e-02 6.10e+03 4.92e+00
  bond pdb=" CA  VAL R  94 "
       pdb=" CB  VAL R  94 "
    ideal  model  delta    sigma   weight residual
    1.540  1.510  0.030 1.37e-02 5.33e+03 4.72e+00
  ... (remaining 8076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 10762
        2.56 -     5.12: 184
        5.12 -     7.68: 29
        7.68 -    10.25: 6
       10.25 -    12.81: 2
  Bond angle restraints: 10983
  Sorted by residual:
  angle pdb=" N   HIS A 357 "
        pdb=" CA  HIS A 357 "
        pdb=" C   HIS A 357 "
      ideal   model   delta    sigma   weight residual
     111.14  123.05  -11.91 1.08e+00 8.57e-01 1.22e+02
  angle pdb=" N   TYR A 358 "
        pdb=" CA  TYR A 358 "
        pdb=" C   TYR A 358 "
      ideal   model   delta    sigma   weight residual
     111.30  124.11  -12.81 1.36e+00 5.41e-01 8.87e+01
  angle pdb=" N   ASN R 303 "
        pdb=" CA  ASN R 303 "
        pdb=" C   ASN R 303 "
      ideal   model   delta    sigma   weight residual
     112.38  103.43    8.95 1.22e+00 6.72e-01 5.38e+01
  angle pdb=" N   CYS A 359 "
        pdb=" CA  CYS A 359 "
        pdb=" C   CYS A 359 "
      ideal   model   delta    sigma   weight residual
     110.24  119.64   -9.40 1.30e+00 5.92e-01 5.23e+01
  angle pdb=" N   ALA A 269 "
        pdb=" CA  ALA A 269 "
        pdb=" C   ALA A 269 "
      ideal   model   delta    sigma   weight residual
     113.41  104.60    8.81 1.22e+00 6.72e-01 5.22e+01
  ... (remaining 10978 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 4141
       17.16 -    34.31: 421
       34.31 -    51.47: 101
       51.47 -    68.62: 14
       68.62 -    85.78: 6
  Dihedral angle restraints: 4683
    sinusoidal: 1663
      harmonic: 3020
  Sorted by residual:
  dihedral pdb=" C   VAL R 279 "
           pdb=" N   VAL R 279 "
           pdb=" CA  VAL R 279 "
           pdb=" CB  VAL R 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.52   15.52     0      2.50e+00 1.60e-01 3.85e+01
  dihedral pdb=" N   GLN A 267 "
           pdb=" C   GLN A 267 "
           pdb=" CA  GLN A 267 "
           pdb=" CB  GLN A 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.97  -11.17     0      2.50e+00 1.60e-01 2.00e+01
  dihedral pdb=" C   GLN A 267 "
           pdb=" N   GLN A 267 "
           pdb=" CA  GLN A 267 "
           pdb=" CB  GLN A 267 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.05   10.45     0      2.50e+00 1.60e-01 1.75e+01
  ... (remaining 4680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 1154
       0.102 -    0.205: 75
       0.205 -    0.307: 16
       0.307 -    0.410: 6
       0.410 -    0.512: 2
  Chirality restraints: 1253
  Sorted by residual:
  chirality pdb=" CA  TYR A 358 "
            pdb=" N   TYR A 358 "
            pdb=" C   TYR A 358 "
            pdb=" CB  TYR A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.55e+00
  chirality pdb=" CA  VAL R 279 "
            pdb=" N   VAL R 279 "
            pdb=" C   VAL R 279 "
            pdb=" CB  VAL R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.99    0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CA  LYS A 216 "
            pdb=" N   LYS A 216 "
            pdb=" C   LYS A 216 "
            pdb=" CB  LYS A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  ... (remaining 1250 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 301 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.25e+00
        pdb=" C   TYR R 301 "    0.053 2.00e-02 2.50e+03
        pdb=" O   TYR R 301 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR R 302 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 351 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   ALA A 351 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ALA A 351 "    0.014 2.00e-02 2.50e+03
        pdb=" N   SER A 352 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 147 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   SER R 147 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   SER R 147 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL R 148 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 195
        2.69 -     3.25: 7248
        3.25 -     3.80: 11631
        3.80 -     4.35: 15289
        4.35 -     4.90: 26177
  Nonbonded interactions: 60540
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OD2 ASP A 215 "
            pdb=" NH1 ARG A 373 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" ND2 ASN B 119 "
            pdb=" O   GLY B 144 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   SER S 105 "
            pdb=" NH2 ARG S 191 "
     model   vdw
     2.258 3.120
  ... (remaining 60535 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=1.00 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:             0.620
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.700
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
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      :  0.003   0.077   8081  Z= 0.223
  Angle     :  0.813  12.808  10983  Z= 0.544
  Chirality :  0.063   0.512   1253
  Planarity :  0.004   0.033   1381
  Dihedral  : 14.913  85.776   2728
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  8.07 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.27), residues: 1013
  helix:  0.78 (0.33), residues: 288
  sheet: -0.04 (0.32), residues: 265
  loop : -1.41 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 317 
 HIS   0.002   0.001   HIS S 232 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.003   0.000   ARG A  38 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.815 
Fit side-chains
REVERT: R   94 VAL cc_start: 0.7301 (t) cc_final: 0.6964 (p)
REVERT: R   98 TRP cc_start: 0.5655 (t-100) cc_final: 0.4917 (t-100)
REVERT: R  128 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6256 (mt)
REVERT: R  264 MET cc_start: 0.5059 (mmp) cc_final: 0.4741 (mmt)
REVERT: S    6 GLU cc_start: 0.4100 (mm-30) cc_final: 0.3409 (mm-30)
REVERT: S  160 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6732 (ttp80)
  outliers start: 11
  outliers final: 4
  residues processed: 124
  average time/residue: 0.2298
  time to fit residues: 37.3622
Evaluate side-chains
  96 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain R residue  128 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0030
   overall best weight:    1.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 218 ASN
A 236 GLN
B 119 ASN
B 142 HIS
B 225 HIS
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 232 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.160237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 121)---------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.137006 restraints weight = 8800.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.08
r_work: 0.3329 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8081  Z= 0.198
  Angle     :  0.536   5.849  10983  Z= 0.283
  Chirality :  0.043   0.148   1253
  Planarity :  0.004   0.032   1381
  Dihedral  :  5.032  52.557   1136
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.61 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 1013
  helix:  1.10 (0.32), residues: 306
  sheet:  0.08 (0.32), residues: 271
  loop : -1.32 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 317 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.014   0.001   PHE R 117 
 TYR   0.025   0.002   TYR S 235 
 ARG   0.003   0.000   ARG B 251 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.831 
Fit side-chains
REVERT: B  312 ASP cc_start: 0.7055 (t70) cc_final: 0.6766 (t0)
REVERT: R   52 LEU cc_start: 0.8034 (mt) cc_final: 0.7681 (mt)
REVERT: R  277 ASP cc_start: 0.7693 (t0) cc_final: 0.7235 (t0)
REVERT: S  113 GLN cc_start: 0.7063 (mm110) cc_final: 0.6152 (pt0)
  outliers start: 17
  outliers final: 12
  residues processed: 115
  average time/residue: 0.2196
  time to fit residues: 33.8561
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain S residue   81 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0060
   chunk 5 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B  88 ASN
C  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.162044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.140309 restraints weight = 8909.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 0.96
r_work: 0.3301 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8081  Z= 0.152
  Angle     :  0.489   5.488  10983  Z= 0.256
  Chirality :  0.041   0.146   1253
  Planarity :  0.003   0.049   1381
  Dihedral  :  4.723  54.203   1130
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.63 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.28), residues: 1013
  helix:  1.29 (0.32), residues: 308
  sheet:  0.13 (0.33), residues: 267
  loop : -1.31 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.003   0.000   ARG B 251 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.803 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8661 (ppp) cc_final: 0.8432 (ppp)
REVERT: B  163 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7520 (p0)
REVERT: R  165 PHE cc_start: 0.6807 (t80) cc_final: 0.4972 (m-80)
REVERT: R  277 ASP cc_start: 0.7619 (t0) cc_final: 0.7277 (t0)
REVERT: S  113 GLN cc_start: 0.7034 (mm110) cc_final: 0.6215 (pt0)
REVERT: S  230 MET cc_start: 0.8004 (tpt) cc_final: 0.7311 (tpt)
  outliers start: 13
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2202
  time to fit residues: 34.9005
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  329 LYS
Chi-restraints excluded: chain S residue   81 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0770
   overall best weight:    2.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.153706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.128280 restraints weight = 8938.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.44
r_work: 0.3269 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8081  Z= 0.246
  Angle     :  0.543   5.901  10983  Z= 0.286
  Chirality :  0.043   0.153   1253
  Planarity :  0.004   0.042   1381
  Dihedral  :  5.015  55.734   1130
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.27), residues: 1013
  helix:  1.14 (0.32), residues: 309
  sheet:  0.05 (0.32), residues: 275
  loop : -1.41 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.017   0.002   PHE R 117 
 TYR   0.029   0.002   TYR S 235 
 ARG   0.002   0.000   ARG A  38 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: R  277 ASP cc_start: 0.7733 (t70) cc_final: 0.7375 (t0)
REVERT: S  230 MET cc_start: 0.8127 (tpt) cc_final: 0.7505 (tpt)
  outliers start: 21
  outliers final: 19
  residues processed: 111
  average time/residue: 0.2141
  time to fit residues: 32.0399
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  329 LYS
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 65 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0970
   chunk 14 optimal weight:    6.9990
   overall best weight:    2.3582

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

Flipped N/Q/H residues before XYZ refinement:
C  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.155752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130856 restraints weight = 8869.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.22
r_work: 0.3275 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8081  Z= 0.253
  Angle     :  0.549   6.073  10983  Z= 0.289
  Chirality :  0.043   0.158   1253
  Planarity :  0.004   0.039   1381
  Dihedral  :  5.125  55.138   1130
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 18.16 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.27), residues: 1013
  helix:  1.08 (0.31), residues: 309
  sheet: -0.14 (0.31), residues: 282
  loop : -1.44 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.016   0.002   PHE R 117 
 TYR   0.029   0.002   TYR S 235 
 ARG   0.003   0.000   ARG S  98 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7193 (ttmm)
REVERT: B   66 ASP cc_start: 0.7420 (p0) cc_final: 0.7056 (p0)
REVERT: R  277 ASP cc_start: 0.7685 (t70) cc_final: 0.7369 (t0)
REVERT: S  113 GLN cc_start: 0.7056 (mm110) cc_final: 0.6430 (mm110)
REVERT: S  230 MET cc_start: 0.8144 (tpt) cc_final: 0.7543 (tpt)
  outliers start: 28
  outliers final: 23
  residues processed: 119
  average time/residue: 0.2165
  time to fit residues: 34.7132
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  329 LYS
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0050
   chunk 99 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.156339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131914 restraints weight = 8843.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.17
r_work: 0.3294 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8081  Z= 0.160
  Angle     :  0.487   5.578  10983  Z= 0.256
  Chirality :  0.041   0.152   1253
  Planarity :  0.003   0.036   1381
  Dihedral  :  4.915  54.117   1130
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.55 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 1013
  helix:  1.32 (0.32), residues: 308
  sheet: -0.06 (0.32), residues: 275
  loop : -1.44 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.010   0.001   HIS C  44 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.002   0.000   ARG S  98 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.7213 (p0) cc_final: 0.6751 (p0)
REVERT: R  277 ASP cc_start: 0.7678 (t70) cc_final: 0.7436 (t0)
REVERT: S  113 GLN cc_start: 0.7095 (mm110) cc_final: 0.6413 (mm110)
REVERT: S  230 MET cc_start: 0.8092 (tpt) cc_final: 0.7489 (tpt)
  outliers start: 25
  outliers final: 18
  residues processed: 118
  average time/residue: 0.2187
  time to fit residues: 34.5957
Evaluate side-chains
  116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 88 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0770
   chunk 31 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.5740

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.154785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 146)---------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.131222 restraints weight = 8889.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.05
r_work: 0.3268 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8081  Z= 0.193
  Angle     :  0.505   5.552  10983  Z= 0.266
  Chirality :  0.042   0.151   1253
  Planarity :  0.003   0.036   1381
  Dihedral  :  4.966  57.169   1130
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.04 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 1013
  helix:  1.33 (0.31), residues: 308
  sheet: -0.10 (0.32), residues: 275
  loop : -1.42 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.002   0.000   ARG S 191 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.7166 (p0) cc_final: 0.6693 (p0)
REVERT: R  232 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7239 (mm-30)
REVERT: R  277 ASP cc_start: 0.7775 (t70) cc_final: 0.7495 (t0)
REVERT: S  113 GLN cc_start: 0.7135 (mm110) cc_final: 0.6451 (mm110)
REVERT: S  230 MET cc_start: 0.8131 (tpt) cc_final: 0.7614 (tpt)
  outliers start: 31
  outliers final: 22
  residues processed: 121
  average time/residue: 0.2142
  time to fit residues: 35.0135
Evaluate side-chains
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.165611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.153475 restraints weight = 8893.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 0.56
r_work: 0.3400 rms_B_bonded: 1.04 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8081  Z= 0.222
  Angle     :  0.527   5.885  10983  Z= 0.277
  Chirality :  0.043   0.157   1253
  Planarity :  0.003   0.036   1381
  Dihedral  :  5.066  57.743   1130
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.67 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.27), residues: 1013
  helix:  1.29 (0.31), residues: 309
  sheet: -0.13 (0.32), residues: 273
  loop : -1.43 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.002   0.000   ARG S 191 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7157 (ttmm)
REVERT: R  232 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7081 (mm-30)
REVERT: R  277 ASP cc_start: 0.7692 (t70) cc_final: 0.7384 (t0)
REVERT: R  286 PHE cc_start: 0.7679 (m-80) cc_final: 0.7460 (m-80)
REVERT: S  113 GLN cc_start: 0.7036 (mm110) cc_final: 0.6276 (mm110)
REVERT: S  230 MET cc_start: 0.8028 (tpt) cc_final: 0.7511 (tpt)
REVERT: S  234 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7142 (mt-10)
  outliers start: 29
  outliers final: 24
  residues processed: 119
  average time/residue: 0.2266
  time to fit residues: 36.4520
Evaluate side-chains
  122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.159349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.134131 restraints weight = 9001.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.24
r_work: 0.3304 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8081  Z= 0.178
  Angle     :  0.497   5.564  10983  Z= 0.261
  Chirality :  0.042   0.150   1253
  Planarity :  0.003   0.034   1381
  Dihedral  :  4.935  56.572   1130
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.05 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.27), residues: 1013
  helix:  1.41 (0.32), residues: 308
  sheet: -0.10 (0.32), residues: 275
  loop : -1.42 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.001   0.000   ARG S 160 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: R  277 ASP cc_start: 0.7672 (t70) cc_final: 0.7409 (t0)
REVERT: R  286 PHE cc_start: 0.7676 (m-80) cc_final: 0.7467 (m-80)
REVERT: S  113 GLN cc_start: 0.7030 (mm110) cc_final: 0.6201 (mm110)
REVERT: S  230 MET cc_start: 0.8084 (tpt) cc_final: 0.7490 (tpt)
  outliers start: 25
  outliers final: 22
  residues processed: 116
  average time/residue: 0.2134
  time to fit residues: 33.5862
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 91 optimal weight:    8.9990
   chunk 12 optimal weight:    0.1980
   chunk 28 optimal weight:    0.7980
   chunk 86 optimal weight:    8.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.160280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 107)---------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.138060 restraints weight = 8844.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 0.98
r_work: 0.3325 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8081  Z= 0.162
  Angle     :  0.482   5.571  10983  Z= 0.253
  Chirality :  0.041   0.145   1253
  Planarity :  0.003   0.033   1381
  Dihedral  :  4.801  54.504   1130
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.05 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.27), residues: 1013
  helix:  1.59 (0.32), residues: 305
  sheet: -0.03 (0.32), residues: 269
  loop : -1.36 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 362 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.002   0.000   ARG S 191 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.908 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6361 (m-80)
REVERT: R  186 CYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6617 (t)
REVERT: R  277 ASP cc_start: 0.7741 (t70) cc_final: 0.7444 (t0)
REVERT: S  113 GLN cc_start: 0.7058 (mm110) cc_final: 0.6120 (mm110)
REVERT: S  230 MET cc_start: 0.8045 (tpt) cc_final: 0.7442 (tpt)
REVERT: S  235 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.5534 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 112
  average time/residue: 0.2163
  time to fit residues: 32.6371
Evaluate side-chains
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain R residue  110 CYS
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.161263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 113)---------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.140164 restraints weight = 8907.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 0.92
r_work: 0.3351 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8081  Z= 0.139
  Angle     :  0.466   5.579  10983  Z= 0.244
  Chirality :  0.041   0.143   1253
  Planarity :  0.003   0.032   1381
  Dihedral  :  4.690  52.754   1130
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.43 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.27), residues: 1013
  helix:  1.72 (0.32), residues: 305
  sheet:  0.10 (0.32), residues: 267
  loop : -1.31 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.001   0.000   ARG S 191 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4041.26 seconds
wall clock time: 72 minutes 32.08 seconds (4352.08 seconds total)