Starting phenix.real_space_refine
on Sat Apr  6 09:52:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_35762_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_35762.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_35762.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_35762_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/04_2024/8iw4_35762_neut_updated.pdb"
  }
  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
    Residue "A ASP  215": "OD1" <-> "OD2"
    Residue "A ARG  389": "NH1" <-> "NH2"
    Residue "B ASP   38": "OD1" <-> "OD2"
    Residue "B ASP  163": "OD1" <-> "OD2"
    Residue "B ASP  195": "OD1" <-> "OD2"
    Residue "B TYR  289": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  290": "OD1" <-> "OD2"
    Residue "R GLU   95": "OE1" <-> "OE2"
    Residue "R TYR   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  174": "OE1" <-> "OE2"
    Residue "R GLU  179": "OE1" <-> "OE2"
    Residue "R ASP  277": "OD1" <-> "OD2"
    Residue "R TYR  302": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.50, per 1000 atoms: 0.57
  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  - 3.50
        Amino acid           : False - 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: 3.07
  Conformation dependent library (CDL) restraints added in 1.4 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...
  running ksdssp...
    Secondary structure from input PDB file:
      19 helices and 12 sheets defined
      29.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 39
      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)
      removed outlier: 4.357A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 270 through 277
    Processing helix  chain 'A' and resid 336 through 351
      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)
    Processing helix  chain 'A' and resid 371 through 390
      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 30 through 43
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'R' and resid 34 through 56
      removed outlier: 3.679A  pdb=" N   LEU R  39 " --> pdb=" O   TYR R  36 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   GLY R  40 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU R  41 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   GLY R  49 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU R  52 " --> pdb=" O   GLY R  49 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE R  54 " --> pdb=" O   LEU R  51 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE R  55 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 84
      removed outlier: 3.527A  pdb=" N   VAL R  81 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 95
    Processing helix  chain 'R' and resid 104 through 135
      removed outlier: 4.179A  pdb=" N   HIS R 108 " --> pdb=" O   CYS R 105 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR R 109 " --> pdb=" O   LYS R 106 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ASP R 112 " --> pdb=" O   THR R 109 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   THR R 113 " --> pdb=" O   CYS R 110 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   CYS R 116 " --> pdb=" O   THR R 113 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR R 135 " --> pdb=" O   ILE R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 143
      No H-bonds generated for 'chain 'R' and resid 140 through 143'
    Processing helix  chain 'R' and resid 146 through 168
      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 196 through 231
      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 282
      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)
    Processing helix  chain 'R' and resid 290 through 311
      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 316 through 326
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing sheet with id=  A, first strand: chain 'A' and resid 286 through 291
      removed outlier: 4.205A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 91 through 94
      removed outlier: 3.802A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
    Processing sheet with id=  C, 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: 5.720A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, 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=  E, 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=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.720A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 276 through 278
      removed outlier: 4.013A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing sheet with id=  H, 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=  I, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.540A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL S  12 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=  L, first strand: chain 'S' and resid 174 through 180
      removed outlier: 3.501A  pdb=" N   TYR S 175 " --> pdb=" O   MET S 230 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    801 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 3.34 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:
       99.54 -   106.44: 189
      106.44 -   113.33: 4282
      113.33 -   120.22: 2811
      120.22 -   127.11: 3615
      127.11 -   134.00: 86
  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: 7284
        3.25 -     3.80: 11617
        3.80 -     4.35: 15326
        4.35 -     4.90: 26190
  Nonbonded interactions: 60612
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.143 2.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.180 2.440
  nonbonded pdb=" OD2 ASP A 215 "
            pdb=" NH1 ARG A 373 "
     model   vdw
     2.224 2.520
  nonbonded pdb=" ND2 ASN B 119 "
            pdb=" O   GLY B 144 "
     model   vdw
     2.234 2.520
  nonbonded pdb=" O   SER S 105 "
            pdb=" NH2 ARG S 191 "
     model   vdw
     2.258 2.520
  ... (remaining 60607 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.240
  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:          1.720
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     25.180
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.210
-------------------------------------------------------------------------------
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= 0.228
  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 fitting.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.851 
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: 0.2324
  time to fit residues: 37.9031
Evaluate side-chains
  96 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 142 HIS
B 230 ASN
S 232 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8081  Z= 0.329
  Angle     :  0.622   7.078  10983  Z= 0.326
  Chirality :  0.046   0.178   1253
  Planarity :  0.005   0.033   1381
  Dihedral  :  5.526  46.925   1136
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.74 %
    Favored  : 83.61 %
  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: -0.83 (0.27), residues: 1013
  helix:  0.41 (0.31), residues: 297
  sheet: -0.21 (0.32), residues: 275
  loop : -1.39 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 317 
 HIS   0.007   0.001   HIS A 362 
 PHE   0.020   0.002   PHE R 117 
 TYR   0.034   0.002   TYR S 235 
 ARG   0.004   0.000   ARG B 314 

*********************** 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
  133 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7166 (ttmm)
REVERT: R  165 PHE cc_start: 0.5421 (t80) cc_final: 0.3301 (m-10)
REVERT: R  179 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6057 (pm20)
REVERT: R  311 TYR cc_start: 0.7178 (m-80) cc_final: 0.6951 (m-80)
REVERT: S  113 GLN cc_start: 0.7029 (mm110) cc_final: 0.6407 (pt0)
REVERT: S  230 MET cc_start: 0.7935 (tpt) cc_final: 0.7408 (tpt)
  outliers start: 29
  outliers final: 21
  residues processed: 123
  average time/residue: 0.2107
  time to fit residues: 35.1893
Evaluate side-chains
  115 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain R residue   58 LEU
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  161 VAL
Chi-restraints excluded: chain R residue  179 GLU
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  329 LYS
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.0170
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0770
   overall best weight:    0.7978

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8081  Z= 0.131
  Angle     :  0.481   5.908  10983  Z= 0.250
  Chirality :  0.041   0.158   1253
  Planarity :  0.004   0.044   1381
  Dihedral  :  4.849  52.298   1130
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.15 %
    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: -0.60 (0.27), residues: 1013
  helix:  0.61 (0.32), residues: 304
  sheet: -0.06 (0.32), residues: 270
  loop : -1.30 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  98 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.021   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
  120 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.973 
Fit side-chains
REVERT: B  186 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6102 (p0)
REVERT: R   52 LEU cc_start: 0.7061 (mt) cc_final: 0.6620 (mt)
REVERT: R  213 MET cc_start: 0.5530 (ttm) cc_final: 0.5328 (ttt)
REVERT: R  311 TYR cc_start: 0.6935 (m-80) cc_final: 0.6694 (m-10)
REVERT: S  113 GLN cc_start: 0.6669 (mm110) cc_final: 0.5831 (pt0)
REVERT: S  160 ARG cc_start: 0.7029 (ttp80) cc_final: 0.6702 (ttp80)
REVERT: S  230 MET cc_start: 0.7870 (tpt) cc_final: 0.7225 (tpt)
  outliers start: 18
  outliers final: 8
  residues processed: 110
  average time/residue: 0.2152
  time to fit residues: 31.7413
Evaluate side-chains
  102 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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  168 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0970
   chunk 62 optimal weight:    0.0470
   chunk 93 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9680

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8081  Z= 0.142
  Angle     :  0.472   5.495  10983  Z= 0.245
  Chirality :  0.041   0.154   1253
  Planarity :  0.003   0.037   1381
  Dihedral  :  4.679  55.354   1130
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.41 %
    Favored  : 79.07 %
  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: -0.49 (0.27), residues: 1013
  helix:  0.69 (0.32), residues: 307
  sheet:  0.05 (0.32), residues: 261
  loop : -1.25 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B 251 

*********************** 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
  117 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8513 (ppp) cc_final: 0.8262 (ppp)
REVERT: B  186 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6127 (p0)
REVERT: R   52 LEU cc_start: 0.7000 (mt) cc_final: 0.6556 (mt)
REVERT: R  311 TYR cc_start: 0.7041 (m-80) cc_final: 0.6736 (m-80)
REVERT: S  113 GLN cc_start: 0.6807 (mm110) cc_final: 0.6014 (mm110)
REVERT: S  160 ARG cc_start: 0.7029 (ttp80) cc_final: 0.6695 (ttp80)
REVERT: S  230 MET cc_start: 0.7848 (tpt) cc_final: 0.7289 (tpt)
  outliers start: 20
  outliers final: 15
  residues processed: 109
  average time/residue: 0.2168
  time to fit residues: 31.8908
Evaluate side-chains
  109 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:   30.0000
   chunk 88 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8144

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8081  Z= 0.127
  Angle     :  0.451   5.523  10983  Z= 0.233
  Chirality :  0.040   0.150   1253
  Planarity :  0.003   0.033   1381
  Dihedral  :  4.586  58.759   1130
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.66 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.27), residues: 1013
  helix:  0.77 (0.32), residues: 307
  sheet:  0.22 (0.32), residues: 259
  loop : -1.28 (0.29), residues: 447

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   0.008   0.001   PHE A 212 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B 251 

*********************** 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
  117 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.859 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8484 (ppp) cc_final: 0.8240 (ppp)
REVERT: B  186 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6088 (p0)
REVERT: R   52 LEU cc_start: 0.6896 (mt) cc_final: 0.6513 (mt)
REVERT: R  179 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.6035 (pm20)
REVERT: R  311 TYR cc_start: 0.7004 (m-80) cc_final: 0.6664 (m-80)
REVERT: S  113 GLN cc_start: 0.6839 (mm110) cc_final: 0.6009 (mm110)
REVERT: S  160 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6665 (ttp80)
REVERT: S  230 MET cc_start: 0.7866 (tpt) cc_final: 0.7314 (tpt)
  outliers start: 22
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2140
  time to fit residues: 32.1773
Evaluate side-chains
  107 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  179 GLU
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0570
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0570
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.3620

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8081  Z= 0.168
  Angle     :  0.476   6.254  10983  Z= 0.247
  Chirality :  0.041   0.154   1253
  Planarity :  0.003   0.034   1381
  Dihedral  :  4.710  57.533   1130
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.80 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.27), residues: 1013
  helix:  0.95 (0.32), residues: 294
  sheet:  0.13 (0.32), residues: 261
  loop : -1.31 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 108 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.001   0.000   ARG B 314 

*********************** 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
  122 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.903 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.7147 (p0) cc_final: 0.6792 (p0)
REVERT: B  186 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6053 (p0)
REVERT: R   52 LEU cc_start: 0.6761 (mt) cc_final: 0.6324 (mt)
REVERT: R  179 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5985 (pm20)
REVERT: R  311 TYR cc_start: 0.7248 (m-80) cc_final: 0.6871 (m-80)
REVERT: S  113 GLN cc_start: 0.6881 (mm110) cc_final: 0.5925 (mm110)
REVERT: S  160 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6625 (ttp80)
REVERT: S  230 MET cc_start: 0.7876 (tpt) cc_final: 0.7380 (tpt)
  outliers start: 25
  outliers final: 17
  residues processed: 114
  average time/residue: 0.2142
  time to fit residues: 32.9950
Evaluate side-chains
  115 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  179 GLU
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    0.2980
   chunk 98 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0970
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8081  Z= 0.118
  Angle     :  0.445   6.238  10983  Z= 0.230
  Chirality :  0.041   0.215   1253
  Planarity :  0.003   0.032   1381
  Dihedral  :  4.548  59.601   1130
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.18 %
    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: -0.25 (0.27), residues: 1013
  helix:  1.11 (0.32), residues: 294
  sheet:  0.28 (0.32), residues: 259
  loop : -1.28 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.016   0.001   TYR S 235 
 ARG   0.005   0.000   ARG B 129 

*********************** 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
  127 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.841 
Fit side-chains
REVERT: B  186 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6069 (p0)
REVERT: R   52 LEU cc_start: 0.6710 (mt) cc_final: 0.6331 (mt)
REVERT: R  311 TYR cc_start: 0.7061 (m-80) cc_final: 0.6665 (m-80)
REVERT: S  113 GLN cc_start: 0.6753 (mm110) cc_final: 0.5778 (mm110)
REVERT: S  138 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7482 (mt)
REVERT: S  160 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6609 (ttp80)
REVERT: S  230 MET cc_start: 0.7798 (tpt) cc_final: 0.7261 (tpt)
REVERT: S  234 GLU cc_start: 0.6959 (tt0) cc_final: 0.6691 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 117
  average time/residue: 0.2096
  time to fit residues: 33.2763
Evaluate side-chains
  118 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  138 ILE
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:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 94 optimal weight:    9.9990
   chunk 85 optimal weight:    0.6980
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8081  Z= 0.132
  Angle     :  0.455   6.470  10983  Z= 0.234
  Chirality :  0.041   0.215   1253
  Planarity :  0.003   0.032   1381
  Dihedral  :  4.561  59.731   1130
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.43 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.27), residues: 1013
  helix:  1.15 (0.32), residues: 294
  sheet:  0.27 (0.32), residues: 260
  loop : -1.24 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.017   0.001   TYR S 235 
 ARG   0.005   0.000   ARG B 129 

*********************** 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
  123 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.919 
Fit side-chains
REVERT: B  186 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6067 (p0)
REVERT: R   52 LEU cc_start: 0.6717 (mt) cc_final: 0.6321 (mt)
REVERT: R  311 TYR cc_start: 0.7209 (m-80) cc_final: 0.6790 (m-80)
REVERT: S  113 GLN cc_start: 0.6761 (mm110) cc_final: 0.5731 (mm110)
REVERT: S  138 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7496 (mt)
REVERT: S  160 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6538 (ttp80)
REVERT: S  230 MET cc_start: 0.7797 (tpt) cc_final: 0.7278 (tpt)
REVERT: S  234 GLU cc_start: 0.6999 (tt0) cc_final: 0.6740 (tt0)
  outliers start: 22
  outliers final: 19
  residues processed: 114
  average time/residue: 0.2091
  time to fit residues: 32.4475
Evaluate side-chains
  118 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  138 ILE
Chi-restraints excluded: chain S residue  159 CYS
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8081  Z= 0.227
  Angle     :  0.523   6.836  10983  Z= 0.270
  Chirality :  0.043   0.202   1253
  Planarity :  0.004   0.036   1381
  Dihedral  :  4.898  54.636   1130
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.55 %
    Favored  : 76.17 %
  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: -0.43 (0.27), residues: 1013
  helix:  0.89 (0.32), residues: 294
  sheet: -0.02 (0.32), residues: 268
  loop : -1.21 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 108 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.004   0.000   ARG B 129 

*********************** 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
  124 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7051 (ttmm)
REVERT: B  186 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6027 (p0)
REVERT: R  311 TYR cc_start: 0.7324 (m-80) cc_final: 0.6933 (m-80)
REVERT: S  113 GLN cc_start: 0.6863 (mm110) cc_final: 0.5809 (mm110)
REVERT: S  138 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7650 (mt)
REVERT: S  230 MET cc_start: 0.7883 (tpt) cc_final: 0.7423 (tpt)
  outliers start: 26
  outliers final: 20
  residues processed: 115
  average time/residue: 0.2035
  time to fit residues: 31.7156
Evaluate side-chains
  119 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  138 ILE
Chi-restraints excluded: chain S residue  159 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 80 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8081  Z= 0.189
  Angle     :  0.499   6.577  10983  Z= 0.258
  Chirality :  0.042   0.200   1253
  Planarity :  0.004   0.038   1381
  Dihedral  :  4.881  55.361   1130
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.93 %
    Favored  : 76.04 %
  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: -0.41 (0.27), residues: 1013
  helix:  0.90 (0.32), residues: 294
  sheet:  0.04 (0.32), residues: 262
  loop : -1.22 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 108 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.005   0.000   ARG B 129 

********************** 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
  123 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.813 
Fit side-chains
REVERT: B  186 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6108 (p0)
REVERT: R  286 PHE cc_start: 0.7442 (m-80) cc_final: 0.7234 (m-80)
REVERT: R  311 TYR cc_start: 0.7313 (m-80) cc_final: 0.6935 (m-80)
REVERT: S  113 GLN cc_start: 0.6847 (mm110) cc_final: 0.5720 (mm110)
REVERT: S  138 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7618 (mt)
REVERT: S  230 MET cc_start: 0.7865 (tpt) cc_final: 0.7392 (tpt)
REVERT: S  235 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.5797 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 113
  average time/residue: 0.1931
  time to fit residues: 30.1364
Evaluate side-chains
  119 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  191 GLN
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  138 ILE
Chi-restraints excluded: chain S residue  159 CYS
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 81 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 58 optimal weight:    0.0980
   chunk 92 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.147414 restraints weight = 8809.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 0.73
r_work: 0.3420 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8081  Z= 0.130
  Angle     :  0.460   6.333  10983  Z= 0.237
  Chirality :  0.041   0.190   1253
  Planarity :  0.003   0.039   1381
  Dihedral  :  4.716  57.934   1130
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.56 %
    Favored  : 75.79 %
  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: -0.20 (0.27), residues: 1013
  helix:  1.16 (0.32), residues: 289
  sheet:  0.16 (0.32), residues: 265
  loop : -1.14 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.017   0.001   TYR S 235 
 ARG   0.005   0.000   ARG B 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1923.77 seconds
wall clock time: 35 minutes 55.10 seconds (2155.10 seconds total)