Starting phenix.real_space_refine
on Wed Mar 12 10:10:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iw4_35762/03_2025/8iw4_35762_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iw4_35762/03_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_35762/03_2025/8iw4_35762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iw4_35762/03_2025/8iw4_35762.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iw4_35762/03_2025/8iw4_35762_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iw4_35762/03_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-5624/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: 2.11
  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: 0.94
  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: 2.23

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.20 -     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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.860
-------------------------------------------------------------------------------
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  : 0.844 
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: 0.2338
  time to fit residues: 38.0247
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  : 0.892 
-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.162052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.137394 restraints weight = 8796.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.28
r_work: 0.3435 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
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  : 1.313 
Fit side-chains
REVERT: B  312 ASP cc_start: 0.7059 (t70) cc_final: 0.6806 (t0)
REVERT: R   52 LEU cc_start: 0.8040 (mt) cc_final: 0.7681 (mt)
REVERT: R  277 ASP cc_start: 0.7649 (t0) cc_final: 0.7191 (t0)
REVERT: S  113 GLN cc_start: 0.7065 (mm110) cc_final: 0.6102 (pt0)
  outliers start: 17
  outliers final: 12
  residues processed: 115
  average time/residue: 0.2815
  time to fit residues: 43.7479
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  : 0.894 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 28 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.170507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.158370 restraints weight = 8898.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 0.54
r_work: 0.3524 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8081  Z= 0.184
  Angle     :  0.512   5.488  10983  Z= 0.268
  Chirality :  0.042   0.151   1253
  Planarity :  0.004   0.049   1381
  Dihedral  :  4.856  56.372   1130
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.13 %
    Favored  : 82.85 %
  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: -0.26 (0.27), residues: 1013
  helix:  1.20 (0.32), residues: 308
  sheet:  0.11 (0.33), residues: 265
  loop : -1.34 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.012   0.001   PHE R 117 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.002   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
  126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.922 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7187 (p0) cc_final: 0.6825 (p0)
REVERT: R  165 PHE cc_start: 0.6866 (t80) cc_final: 0.5316 (m-80)
REVERT: S  113 GLN cc_start: 0.7018 (mm110) cc_final: 0.6505 (pt0)
REVERT: S  230 MET cc_start: 0.7980 (tpt) cc_final: 0.7485 (tpt)
  outliers start: 16
  outliers final: 10
  residues processed: 119
  average time/residue: 0.2410
  time to fit residues: 39.1434
Evaluate side-chains
  111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
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 B residue  269 ILE
Chi-restraints excluded: chain R residue   83 VAL
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:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 98 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.160502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.135721 restraints weight = 8828.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.24
r_work: 0.3310 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1893

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= 0.165
  Angle     :  0.489   5.533  10983  Z= 0.256
  Chirality :  0.041   0.148   1253
  Planarity :  0.003   0.041   1381
  Dihedral  :  4.777  55.107   1130
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.65 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.21 (0.27), residues: 1013
  helix:  1.32 (0.32), residues: 308
  sheet: -0.03 (0.31), residues: 284
  loop : -1.30 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE R 117 
 TYR   0.023   0.001   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
  131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 2.944 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.7191 (p0) cc_final: 0.6799 (p0)
REVERT: S  113 GLN cc_start: 0.6989 (mm110) cc_final: 0.6145 (mm110)
REVERT: S  230 MET cc_start: 0.8084 (tpt) cc_final: 0.7399 (tpt)
  outliers start: 22
  outliers final: 18
  residues processed: 122
  average time/residue: 0.2609
  time to fit residues: 44.1442
Evaluate side-chains
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
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   93 ILE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0020
   chunk 65 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0040
   chunk 14 optimal weight:    0.0980
   overall best weight:    1.2204

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.160500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 119)---------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.138897 restraints weight = 8778.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 0.94
r_work: 0.3349 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8081  Z= 0.163
  Angle     :  0.484   5.538  10983  Z= 0.254
  Chirality :  0.041   0.151   1253
  Planarity :  0.003   0.036   1381
  Dihedral  :  4.728  53.423   1130
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.40 %
    Favored  : 79.32 %
  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: -0.16 (0.27), residues: 1013
  helix:  1.45 (0.32), residues: 308
  sheet:  0.02 (0.32), residues: 275
  loop : -1.35 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   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   0.002   0.000   ARG A  38 

*********************** 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
  130 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7121 (p0) cc_final: 0.6729 (p0)
REVERT: B  234 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.6418 (m-80)
REVERT: B  243 THR cc_start: 0.8309 (p) cc_final: 0.7996 (p)
REVERT: R  186 CYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6470 (t)
REVERT: S  113 GLN cc_start: 0.7022 (mm110) cc_final: 0.6128 (mm110)
REVERT: S  230 MET cc_start: 0.8007 (tpt) cc_final: 0.7430 (tpt)
  outliers start: 26
  outliers final: 17
  residues processed: 119
  average time/residue: 0.2105
  time to fit residues: 33.6808
Evaluate side-chains
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
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   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 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
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:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.159359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.137957 restraints weight = 8805.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 0.93
r_work: 0.3335 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8081  Z= 0.187
  Angle     :  0.495   5.591  10983  Z= 0.260
  Chirality :  0.042   0.149   1253
  Planarity :  0.003   0.034   1381
  Dihedral  :  4.829  53.251   1130
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.79 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.27), residues: 1013
  helix:  1.45 (0.32), residues: 308
  sheet: -0.01 (0.32), residues: 275
  loop : -1.36 (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   0.012   0.001   PHE R 117 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.002   0.000   ARG A  38 

*********************** 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
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.827 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7073 (p0) cc_final: 0.6690 (p0)
REVERT: B  234 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6541 (m-80)
REVERT: R  186 CYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6466 (t)
REVERT: S  113 GLN cc_start: 0.7010 (mm110) cc_final: 0.6058 (mm110)
REVERT: S  230 MET cc_start: 0.8042 (tpt) cc_final: 0.7514 (tpt)
  outliers start: 24
  outliers final: 20
  residues processed: 114
  average time/residue: 0.2231
  time to fit residues: 34.1112
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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 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 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  140 MET
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    0.0020
   chunk 96 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.3592

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.159818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 143)---------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.136284 restraints weight = 8852.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.12
r_work: 0.3283 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8081  Z= 0.172
  Angle     :  0.486   5.552  10983  Z= 0.255
  Chirality :  0.042   0.148   1253
  Planarity :  0.003   0.033   1381
  Dihedral  :  4.809  52.967   1130
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.29 %
    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: -0.14 (0.27), residues: 1013
  helix:  1.52 (0.32), residues: 308
  sheet:  0.02 (0.32), residues: 274
  loop : -1.37 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.001   0.000   ARG A  38 

*********************** 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: 27
    poor density    : 105
  time to evaluate  : 0.790 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7072 (p0) cc_final: 0.6673 (p0)
REVERT: B  234 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.6580 (m-80)
REVERT: R  186 CYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6526 (t)
REVERT: R  230 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6417 (mttt)
REVERT: S  113 GLN cc_start: 0.7078 (mm110) cc_final: 0.6041 (mm110)
REVERT: S  230 MET cc_start: 0.8072 (tpt) cc_final: 0.7514 (tpt)
  outliers start: 27
  outliers final: 20
  residues processed: 120
  average time/residue: 0.2104
  time to fit residues: 33.9080
Evaluate side-chains
  123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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 B residue   59 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
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 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  230 LYS
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  140 MET
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:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.161449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.140232 restraints weight = 8879.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 0.97
r_work: 0.3341 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8081  Z= 0.155
  Angle     :  0.475   5.547  10983  Z= 0.249
  Chirality :  0.041   0.144   1253
  Planarity :  0.003   0.033   1381
  Dihedral  :  4.776  53.022   1130
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.04 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.27), residues: 1013
  helix:  1.60 (0.32), residues: 308
  sheet:  0.04 (0.32), residues: 274
  loop : -1.34 (0.30), residues: 431

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   0.011   0.001   PHE B 241 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.003   0.000   ARG A  38 

*********************** 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
  133 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.809 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7071 (p0) cc_final: 0.6681 (p0)
REVERT: B  234 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.6593 (m-80)
REVERT: R  186 CYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6513 (t)
REVERT: R  230 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6365 (mttt)
REVERT: S  113 GLN cc_start: 0.7013 (mm110) cc_final: 0.5928 (mm110)
REVERT: S  140 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6914 (mtp)
REVERT: S  230 MET cc_start: 0.8003 (tpt) cc_final: 0.7432 (tpt)
REVERT: S  234 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7415 (mt-10)
  outliers start: 30
  outliers final: 18
  residues processed: 122
  average time/residue: 0.2123
  time to fit residues: 34.5105
Evaluate side-chains
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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 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  230 LYS
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  140 MET
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:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 83 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.162109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 128)---------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.138994 restraints weight = 8961.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.08
r_work: 0.3315 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8081  Z= 0.141
  Angle     :  0.474   5.924  10983  Z= 0.246
  Chirality :  0.041   0.141   1253
  Planarity :  0.003   0.032   1381
  Dihedral  :  4.719  55.773   1130
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  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:  0.06 (0.28), residues: 1013
  helix:  1.73 (0.32), residues: 308
  sheet:  0.18 (0.32), residues: 267
  loop : -1.31 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.002   0.000   ARG A  38 

*********************** 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
  127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.831 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.6975 (p0) cc_final: 0.6607 (p0)
REVERT: B  234 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6530 (m-80)
REVERT: R  186 CYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6549 (t)
REVERT: R  230 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6216 (mttt)
REVERT: R  286 PHE cc_start: 0.7733 (m-80) cc_final: 0.7514 (m-80)
REVERT: S   93 MET cc_start: 0.7553 (ttp) cc_final: 0.7241 (ttm)
REVERT: S  113 GLN cc_start: 0.6935 (mm110) cc_final: 0.5815 (mm110)
REVERT: S  140 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6878 (mtp)
REVERT: S  230 MET cc_start: 0.7915 (tpt) cc_final: 0.7300 (tpt)
REVERT: S  234 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7252 (mt-10)
  outliers start: 24
  outliers final: 18
  residues processed: 118
  average time/residue: 0.3197
  time to fit residues: 50.4602
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
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  110 CYS
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  230 LYS
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   81 LEU
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0050
   chunk 12 optimal weight:    0.0870
   chunk 28 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.0178

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.161341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 124)---------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.138996 restraints weight = 8835.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 0.99
r_work: 0.3283 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8081  Z= 0.150
  Angle     :  0.473   5.546  10983  Z= 0.246
  Chirality :  0.041   0.141   1253
  Planarity :  0.003   0.033   1381
  Dihedral  :  4.741  57.627   1130
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.30 %
    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:  0.07 (0.27), residues: 1013
  helix:  1.74 (0.32), residues: 308
  sheet:  0.19 (0.32), residues: 267
  loop : -1.29 (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 A 362 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.003   0.000   ARG A  38 

********************** 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
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.816 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.6843 (p0) cc_final: 0.6480 (p0)
REVERT: B  234 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6643 (m-80)
REVERT: R  186 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6649 (t)
REVERT: S  113 GLN cc_start: 0.6946 (mm110) cc_final: 0.5778 (mm110)
REVERT: S  140 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6906 (mtp)
REVERT: S  230 MET cc_start: 0.7939 (tpt) cc_final: 0.7369 (tpt)
REVERT: S  234 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7415 (mt-10)
  outliers start: 24
  outliers final: 18
  residues processed: 116
  average time/residue: 0.2193
  time to fit residues: 33.8231
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  : 0.815 
-------------------------------------------------------------------------------
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  110 CYS
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   81 LEU
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.163185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 113)---------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.141103 restraints weight = 8894.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 0.98
r_work: 0.3357 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2422

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= 0.132
  Angle     :  0.463   5.555  10983  Z= 0.240
  Chirality :  0.041   0.138   1253
  Planarity :  0.003   0.038   1381
  Dihedral  :  4.676  59.674   1130
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.68 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.28), residues: 1013
  helix:  1.95 (0.32), residues: 305
  sheet:  0.23 (0.32), residues: 267
  loop : -1.20 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.017   0.001   TYR S 235 
 ARG   0.003   0.000   ARG A  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4665.38 seconds
wall clock time: 84 minutes 0.20 seconds (5040.20 seconds total)