Starting phenix.real_space_refine
on Tue Mar  3 23:46:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2026/6lml_0918.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      59      5.16       5
     C    6036      2.51       5
     N    1625      2.21       5
     O    1718      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9438
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1735
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "B"
      Number of atoms: 2322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2322
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 300}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 241
          Classifications: {'peptide': 33}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1742
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 245
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "R"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3153
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 15, 'TRANS': 379}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 43
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU A 234 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 234 " occ=0.00
    residue:
      pdb=" N   ALA A 235 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 235 " occ=0.00
    residue:
      pdb=" N   GLU A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 236 " occ=0.00
    residue:
      pdb=" N   ASP A 237 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ASP A 237 " occ=0.00
    residue:
      pdb=" N   GLU A 238 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 238 " occ=0.00
    residue:
      pdb=" N   GLU A 239 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 239 " occ=0.00
    residue:
      pdb=" N   MET A 240 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  MET A 240 " occ=0.00
  Time building chain proxies: 2.11, per 1000 atoms: 0.22
  Number of scatterers: 9438
  At special positions: 0
  Unit cell: (153.34, 112.34, 109.06, 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      59     16.00
     O    1718      8.00
     N    1625      7.00
     C    6036      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  43 " - pdb=" SG  CYS R  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 344.9 milliseconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 19 sheets defined
      32.3% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 30
      removed outlier: 4.255A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 4.130A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.517A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.572A  pdb=" N   MET A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.699A  pdb=" N   PHE A 259 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 256 through 260'
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 4.738A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   CYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 348
      removed outlier: 3.533A  pdb=" N   THR A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 44
      removed outlier: 3.726A  pdb=" N   ALA C  34 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.630A  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 'D' and resid 28 through 32
      removed outlier: 3.640A  pdb=" N   SER D  31 " --> pdb=" O   ALA D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.596A  pdb=" N   LYS D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'E' and resid 2 through 27
      removed outlier: 4.430A  pdb=" N   SER E   8 " --> pdb=" O   GLY E   4 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS E  12 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER E  16 " --> pdb=" O   LYS E  12 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG E  18 " --> pdb=" O   LEU E  14 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL E  23 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 41
      removed outlier: 3.511A  pdb=" N   GLU R  34 " --> pdb=" O   ASP R  30 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 46
    Processing helix  chain 'R' and resid 118 through 122
      removed outlier: 3.632A  pdb=" N   GLN R 122 " --> pdb=" O   SER R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 166
      removed outlier: 3.521A  pdb=" N   ILE R 128 " --> pdb=" O   ASP R 124 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL R 143 " --> pdb=" O   SER R 139 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   THR R 146 " --> pdb=" O   GLN R 142 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL R 147 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU R 158 " --> pdb=" O   GLY R 154 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE R 162 " --> pdb=" O   LEU R 158 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU R 163 " --> pdb=" O   ALA R 159 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU R 166 " --> pdb=" O   ILE R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 182
    Processing helix  chain 'R' and resid 184 through 197
      removed outlier: 3.921A  pdb=" N   SER R 190 " --> pdb=" O   LEU R 186 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ILE R 194 " --> pdb=" O   SER R 190 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 216
      removed outlier: 3.594A  pdb=" N   THR R 214 " --> pdb=" O   LEU R 210 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU R 216 " --> pdb=" O   VAL R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 222 through 235
      removed outlier: 3.824A  pdb=" N   ALA R 228 " --> pdb=" O   CYS R 224 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL R 229 " --> pdb=" O   ARG R 225 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 240 through 253
      removed outlier: 3.523A  pdb=" N   VAL R 244 " --> pdb=" O   CYS R 240 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU R 249 " --> pdb=" O   GLU R 245 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN R 251 " --> pdb=" O   LEU R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 272
      removed outlier: 3.641A  pdb=" N   TYR R 267 " --> pdb=" O   PHE R 263 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY R 269 " --> pdb=" O   SER R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 274 through 277
    Processing helix  chain 'R' and resid 278 through 288
      removed outlier: 3.595A  pdb=" N   LEU R 288 " --> pdb=" O   VAL R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 305
    Processing helix  chain 'R' and resid 308 through 330
      removed outlier: 3.715A  pdb=" N   ILE R 315 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASN R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE R 320 " --> pdb=" O   LEU R 316 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE R 325 " --> pdb=" O   ILE R 321 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLN R 327 " --> pdb=" O   VAL R 323 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU R 329 " --> pdb=" O   ILE R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 331 through 333
      No H-bonds generated for 'chain 'R' and resid 331 through 333'
    Processing helix  chain 'R' and resid 334 through 338
      removed outlier: 3.776A  pdb=" N   GLN R 337 " --> pdb=" O   ARG R 334 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   MET R 338 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 334 through 338'
    Processing helix  chain 'R' and resid 340 through 344
      removed outlier: 3.545A  pdb=" N   TYR R 343 " --> pdb=" O   HIS R 340 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS R 344 " --> pdb=" O   THR R 341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 340 through 344'
    Processing helix  chain 'R' and resid 345 through 350
    Processing helix  chain 'R' and resid 375 through 403
      removed outlier: 3.874A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU R 382 " --> pdb=" O   ARG R 378 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE R 383 " --> pdb=" O   SER R 379 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU R 386 " --> pdb=" O   LEU R 382 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL R 396 " --> pdb=" O   GLN R 392 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR R 400 " --> pdb=" O   VAL R 396 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   CYS R 401 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU R 403 " --> pdb=" O   LEU R 399 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 418
      removed outlier: 3.586A  pdb=" N   ARG R 413 " --> pdb=" O   SER R 409 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.207A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.592A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 322 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.905A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113
      removed outlier: 6.023A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170
      removed outlier: 3.894A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.453A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.560A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.523A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 329
      removed outlier: 3.689A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7
      removed outlier: 4.006A  pdb=" N   GLN D   3 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER D  25 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.503A  pdb=" N   THR D 115 " --> pdb=" O   TYR D  94 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60
      removed outlier: 4.165A  pdb=" N   TYR D  50 " --> pdb=" O   TYR D  59 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39
    Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148
      removed outlier: 6.510A  pdb=" N   VAL D 147 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 155 through 159
      removed outlier: 3.666A  pdb=" N   SER D 206 " --> pdb=" O   THR D 213 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 177 through 179
    Processing sheet with id=AB9, first strand: chain 'D' and resid 189 through 190
    Processing sheet with id=AC1, first strand: chain 'R' and resid 79 through 80
      removed outlier: 4.097A  pdb=" N   ILE R  79 " --> pdb=" O   VAL R  96 " (cutoff:3.500A)

    269 hydrogen bonds defined for protein.
    762 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: 1.22

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3020
        1.34 -     1.46: 2422
        1.46 -     1.58: 4144
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9666
  Sorted by residual:
  bond pdb=" C   ILE R 355 "
       pdb=" N   PRO R 356 "
    ideal  model  delta    sigma   weight residual
    1.334  1.402 -0.068 2.34e-02 1.83e+03 8.47e+00
  bond pdb=" C   TRP B  99 "
       pdb=" N   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.334  1.307  0.027 1.29e-02 6.01e+03 4.49e+00
  bond pdb=" N   THR R 257 "
       pdb=" CA  THR R 257 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.025 1.54e-02 4.22e+03 2.74e+00
  bond pdb=" CB  ASN R 238 "
       pdb=" CG  ASN R 238 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.42e+00
  bond pdb=" CA  ASN R 238 "
       pdb=" CB  ASN R 238 "
    ideal  model  delta    sigma   weight residual
    1.534  1.512  0.022 1.45e-02 4.76e+03 2.23e+00
  ... (remaining 9661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 12851
        2.73 -     5.46: 243
        5.46 -     8.18: 27
        8.18 -    10.91: 4
       10.91 -    13.64: 3
  Bond angle restraints: 13128
  Sorted by residual:
  angle pdb=" N   VAL R 191 "
        pdb=" CA  VAL R 191 "
        pdb=" C   VAL R 191 "
      ideal   model   delta    sigma   weight residual
     112.96  106.65    6.31 1.00e+00 1.00e+00 3.98e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     122.46  129.03   -6.57 1.41e+00 5.03e-01 2.17e+01
  angle pdb=" C   VAL R 368 "
        pdb=" N   THR R 369 "
        pdb=" CA  THR R 369 "
      ideal   model   delta    sigma   weight residual
     121.54  130.16   -8.62 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" N   VAL R 236 "
        pdb=" CA  VAL R 236 "
        pdb=" C   VAL R 236 "
      ideal   model   delta    sigma   weight residual
     113.53  109.12    4.41 9.80e-01 1.04e+00 2.02e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  ... (remaining 13123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 4893
       17.10 -    34.21: 597
       34.21 -    51.31: 126
       51.31 -    68.41: 13
       68.41 -    85.52: 7
  Dihedral angle restraints: 5636
    sinusoidal: 2115
      harmonic: 3521
  Sorted by residual:
  dihedral pdb=" CA  PRO R 356 "
           pdb=" C   PRO R 356 "
           pdb=" N   LEU R 357 "
           pdb=" CA  LEU R 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.63   39.37     0      5.00e+00 4.00e-02 6.20e+01
  dihedral pdb=" CA  VAL R 292 "
           pdb=" C   VAL R 292 "
           pdb=" N   GLN R 293 "
           pdb=" CA  GLN R 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.91  -35.09     0      5.00e+00 4.00e-02 4.93e+01
  dihedral pdb=" CA  GLY B  77 "
           pdb=" C   GLY B  77 "
           pdb=" N   LYS B  78 "
           pdb=" CA  LYS B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.84  -28.16     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 5633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1128
       0.062 -    0.123: 290
       0.123 -    0.185: 40
       0.185 -    0.246: 6
       0.246 -    0.307: 3
  Chirality restraints: 1467
  Sorted by residual:
  chirality pdb=" CB  VAL R  91 "
            pdb=" CA  VAL R  91 "
            pdb=" CG1 VAL R  91 "
            pdb=" CG2 VAL R  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE D 100 "
            pdb=" CA  ILE D 100 "
            pdb=" CG1 ILE D 100 "
            pdb=" CG2 ILE D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 1464 not shown)

  Planarity restraints: 1661
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.031 2.00e-02 2.50e+03   2.23e-02 9.97e+00
        pdb=" CG  TYR B  59 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 355 "    0.042 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO R 356 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO R 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 356 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 184 "   -0.040 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO D 185 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO D 185 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 185 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1658 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2621
        2.79 -     3.32: 8200
        3.32 -     3.84: 15594
        3.84 -     4.37: 17849
        4.37 -     4.90: 30125
  Nonbonded interactions: 74389
  Sorted by model distance:
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   SER R 183 "
            pdb=" OG  SER R 183 "
     model   vdw
     2.296 3.040
  ... (remaining 74384 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.990
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.170
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.006   0.070   9671  Z= 0.281
  Angle     :  0.960  13.638  13138  Z= 0.539
  Chirality :  0.055   0.307   1467
  Planarity :  0.006   0.065   1661
  Dihedral  : 15.401  85.516   3355
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 14.69 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.53 (0.18), residues: 1203
  helix: -4.57 (0.11), residues: 373
  sheet: -3.27 (0.28), residues: 247
  loop : -3.13 (0.22), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  68 
 TYR   0.054   0.002   TYR B  59 
 PHE   0.026   0.002   PHE R 264 
 TRP   0.019   0.002   TRP A 258 
 HIS   0.010   0.002   HIS R 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 9666)
  covalent geometry    : angle       0.95939 (13128)
  SS BOND              : bond        0.00319 (    5)
  SS BOND              : angle       1.45826 (   10)
  hydrogen bonds       : bond        0.31521 (  269)
  hydrogen bonds       : angle      11.62955 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7249 (tmtt)
REVERT: A  287 TYR cc_start: 0.7042 (m-10) cc_final: 0.6792 (m-10)
REVERT: B  129 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.7193 (mtp180)
REVERT: B  291 ASP cc_start: 0.7748 (t0) cc_final: 0.7494 (t0)
REVERT: D   13 GLN cc_start: 0.7547 (pp30) cc_final: 0.7347 (pp30)
REVERT: D   18 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7237 (tpp80)
REVERT: D   19 LYS cc_start: 0.8430 (tmmt) cc_final: 0.8045 (tttt)
REVERT: D  109 ASP cc_start: 0.7976 (t0) cc_final: 0.7755 (t0)
REVERT: D  139 VAL cc_start: 0.8383 (t) cc_final: 0.8061 (p)
REVERT: D  188 LEU cc_start: 0.8942 (mp) cc_final: 0.8741 (mp)
REVERT: E   21 ASP cc_start: 0.8373 (m-30) cc_final: 0.8151 (t0)
REVERT: E   24 GLN cc_start: 0.8333 (tp40) cc_final: 0.7791 (tm-30)
REVERT: R   39 TYR cc_start: 0.8538 (t80) cc_final: 0.8074 (t80)
REVERT: R  231 MET cc_start: 0.7937 (tmm) cc_final: 0.7692 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 212
  average time/residue: 0.1110
  time to fit residues: 31.2837
Evaluate side-chains
  151 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain B residue  295 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.1980
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 333 GLN
B  62 HIS
B 142 HIS
D  77 ASN
D  82 GLN
** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   1 HIS
** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 GLN
R 250 HIS
R 408 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.117058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.087726 restraints weight = 20228.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.090267 restraints weight = 12265.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.091951 restraints weight = 8989.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093054 restraints weight = 7410.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.093495 restraints weight = 6585.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9671  Z= 0.127
  Angle     :  0.622   8.712  13138  Z= 0.328
  Chirality :  0.042   0.169   1467
  Planarity :  0.005   0.057   1661
  Dihedral  :  6.072  35.931   1321
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.22 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.20), residues: 1203
  helix: -3.21 (0.19), residues: 368
  sheet: -2.73 (0.29), residues: 251
  loop : -2.70 (0.23), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  87 
 TYR   0.017   0.001   TYR R 145 
 PHE   0.016   0.001   PHE A 191 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9666)
  covalent geometry    : angle       0.62205 (13128)
  SS BOND              : bond        0.00115 (    5)
  SS BOND              : angle       0.88904 (   10)
  hydrogen bonds       : bond        0.04855 (  269)
  hydrogen bonds       : angle       6.00270 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7173 (tmtt)
REVERT: A  333 GLN cc_start: 0.8671 (tp40) cc_final: 0.8033 (tm-30)
REVERT: B  129 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7452 (mtp180)
REVERT: B  175 GLN cc_start: 0.8139 (pt0) cc_final: 0.7872 (pt0)
REVERT: B  278 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7089 (m-10)
REVERT: B  294 CYS cc_start: 0.8807 (m) cc_final: 0.8422 (m)
REVERT: B  295 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7563 (p0)
REVERT: D   14 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.7215 (Cg_exo)
REVERT: D   83 MET cc_start: 0.6097 (ptp) cc_final: 0.5857 (ptp)
REVERT: D  188 LEU cc_start: 0.9008 (mp) cc_final: 0.8671 (mp)
REVERT: D  235 TYR cc_start: 0.7535 (m-80) cc_final: 0.7288 (m-80)
REVERT: E   21 ASP cc_start: 0.8526 (m-30) cc_final: 0.8245 (t0)
REVERT: E   24 GLN cc_start: 0.8254 (tp40) cc_final: 0.7615 (tm-30)
REVERT: R   39 TYR cc_start: 0.8270 (t80) cc_final: 0.7896 (t80)
REVERT: R  131 GLN cc_start: 0.8276 (tt0) cc_final: 0.7493 (tm-30)
REVERT: R  140 SER cc_start: 0.8914 (m) cc_final: 0.8679 (p)
REVERT: R  231 MET cc_start: 0.7681 (tmm) cc_final: 0.7366 (tmm)
  outliers start: 31
  outliers final: 14
  residues processed: 202
  average time/residue: 0.0992
  time to fit residues: 27.3849
Evaluate side-chains
  161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 94 optimal weight:    0.2980
   chunk 93 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 98 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   1 HIS
** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.115642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.087672 restraints weight = 20256.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089865 restraints weight = 13005.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.090850 restraints weight = 9104.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.090894 restraints weight = 7941.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.091043 restraints weight = 7687.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9671  Z= 0.133
  Angle     :  0.599   8.110  13138  Z= 0.317
  Chirality :  0.042   0.147   1467
  Planarity :  0.004   0.051   1661
  Dihedral  :  5.760  36.786   1321
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.86 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.73 (0.22), residues: 1203
  helix: -2.34 (0.23), residues: 367
  sheet: -2.49 (0.30), residues: 251
  loop : -2.49 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  87 
 TYR   0.020   0.001   TYR R 145 
 PHE   0.024   0.001   PHE R 384 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9666)
  covalent geometry    : angle       0.59855 (13128)
  SS BOND              : bond        0.00100 (    5)
  SS BOND              : angle       0.96272 (   10)
  hydrogen bonds       : bond        0.04084 (  269)
  hydrogen bonds       : angle       5.29615 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8366 (ttm110)
REVERT: A   36 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8649 (pp)
REVERT: A   54 LYS cc_start: 0.7395 (ttmt) cc_final: 0.7125 (tmtt)
REVERT: A  333 GLN cc_start: 0.8499 (tp40) cc_final: 0.7921 (tm-30)
REVERT: B   68 ARG cc_start: 0.8218 (tpt90) cc_final: 0.8011 (mmm160)
REVERT: B  278 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7056 (m-10)
REVERT: B  294 CYS cc_start: 0.8841 (m) cc_final: 0.8399 (m)
REVERT: B  295 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7559 (p0)
REVERT: B  318 LEU cc_start: 0.8008 (mt) cc_final: 0.7779 (mt)
REVERT: D  235 TYR cc_start: 0.7639 (m-80) cc_final: 0.7394 (m-80)
REVERT: E   21 ASP cc_start: 0.8578 (m-30) cc_final: 0.8289 (t0)
REVERT: E   24 GLN cc_start: 0.8156 (tp40) cc_final: 0.7602 (tm-30)
REVERT: R  131 GLN cc_start: 0.8351 (tt0) cc_final: 0.7521 (tm-30)
REVERT: R  140 SER cc_start: 0.8936 (m) cc_final: 0.8633 (p)
REVERT: R  231 MET cc_start: 0.7693 (tmm) cc_final: 0.7418 (tmm)
REVERT: R  382 LEU cc_start: 0.9140 (mt) cc_final: 0.8874 (mt)
  outliers start: 31
  outliers final: 19
  residues processed: 179
  average time/residue: 0.0903
  time to fit residues: 23.0416
Evaluate side-chains
  160 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 109 optimal weight:    0.0770
   chunk 116 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0870
   chunk 97 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.6322

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
R 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.114774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.086792 restraints weight = 20521.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.088515 restraints weight = 13540.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.089833 restraints weight = 9532.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089974 restraints weight = 8296.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.090371 restraints weight = 8140.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9671  Z= 0.136
  Angle     :  0.586   7.672  13138  Z= 0.309
  Chirality :  0.042   0.141   1467
  Planarity :  0.004   0.053   1661
  Dihedral  :  5.656  44.684   1321
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.38 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.22), residues: 1203
  helix: -1.84 (0.25), residues: 364
  sheet: -2.34 (0.30), residues: 250
  loop : -2.35 (0.24), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 308 
 TYR   0.020   0.001   TYR R 145 
 PHE   0.024   0.001   PHE R 365 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9666)
  covalent geometry    : angle       0.58569 (13128)
  SS BOND              : bond        0.00378 (    5)
  SS BOND              : angle       0.84897 (   10)
  hydrogen bonds       : bond        0.03761 (  269)
  hydrogen bonds       : angle       4.99136 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8342 (ttm110)
REVERT: A   36 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8721 (pp)
REVERT: A   54 LYS cc_start: 0.7452 (ttmt) cc_final: 0.7174 (tmtt)
REVERT: A  333 GLN cc_start: 0.8492 (tp40) cc_final: 0.7930 (tm-30)
REVERT: B  278 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7079 (m-10)
REVERT: B  292 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7895 (m-80)
REVERT: B  294 CYS cc_start: 0.8841 (m) cc_final: 0.8346 (m)
REVERT: B  295 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7581 (p0)
REVERT: B  318 LEU cc_start: 0.8036 (mt) cc_final: 0.7825 (mt)
REVERT: D   20 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7619 (mm)
REVERT: E   21 ASP cc_start: 0.8553 (m-30) cc_final: 0.8246 (t0)
REVERT: E   24 GLN cc_start: 0.8115 (tp40) cc_final: 0.7576 (tm-30)
REVERT: R   29 MET cc_start: 0.8422 (ppp) cc_final: 0.8079 (ppp)
REVERT: R   34 GLU cc_start: 0.8044 (pp20) cc_final: 0.7583 (pp20)
REVERT: R  111 ARG cc_start: 0.8292 (tpt170) cc_final: 0.7510 (mpp80)
REVERT: R  131 GLN cc_start: 0.8420 (tt0) cc_final: 0.7553 (tm-30)
REVERT: R  140 SER cc_start: 0.8913 (m) cc_final: 0.8632 (p)
REVERT: R  231 MET cc_start: 0.7661 (tmm) cc_final: 0.7396 (tmm)
REVERT: R  309 PHE cc_start: 0.8212 (t80) cc_final: 0.8011 (t80)
  outliers start: 38
  outliers final: 25
  residues processed: 182
  average time/residue: 0.0844
  time to fit residues: 21.8384
Evaluate side-chains
  168 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 142 HIS
B 239 ASN
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.115235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.087290 restraints weight = 20416.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.088655 restraints weight = 12178.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.089359 restraints weight = 10213.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089998 restraints weight = 9218.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089998 restraints weight = 8313.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9671  Z= 0.128
  Angle     :  0.582   7.420  13138  Z= 0.304
  Chirality :  0.041   0.142   1467
  Planarity :  0.004   0.053   1661
  Dihedral  :  5.496  43.222   1321
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.80 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.05 (0.23), residues: 1203
  helix: -1.47 (0.25), residues: 366
  sheet: -2.17 (0.31), residues: 247
  loop : -2.27 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 308 
 TYR   0.019   0.001   TYR R 145 
 PHE   0.022   0.001   PHE R 365 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9666)
  covalent geometry    : angle       0.58147 (13128)
  SS BOND              : bond        0.00124 (    5)
  SS BOND              : angle       0.98676 (   10)
  hydrogen bonds       : bond        0.03525 (  269)
  hydrogen bonds       : angle       4.85376 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 147
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8318 (ttm110)
REVERT: A   36 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8706 (pp)
REVERT: A  333 GLN cc_start: 0.8434 (tp40) cc_final: 0.8210 (tm-30)
REVERT: B  278 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6930 (m-10)
REVERT: B  294 CYS cc_start: 0.8778 (m) cc_final: 0.8253 (m)
REVERT: B  295 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7626 (p0)
REVERT: B  318 LEU cc_start: 0.8070 (mt) cc_final: 0.7868 (mt)
REVERT: D  235 TYR cc_start: 0.7811 (m-80) cc_final: 0.7602 (m-80)
REVERT: E   21 ASP cc_start: 0.8554 (m-30) cc_final: 0.8231 (t0)
REVERT: E   24 GLN cc_start: 0.8122 (tp40) cc_final: 0.7494 (tm-30)
REVERT: R   34 GLU cc_start: 0.8089 (pp20) cc_final: 0.7638 (pp20)
REVERT: R  111 ARG cc_start: 0.8291 (tpt170) cc_final: 0.7515 (mpp80)
REVERT: R  131 GLN cc_start: 0.8460 (tt0) cc_final: 0.7540 (tm-30)
REVERT: R  140 SER cc_start: 0.8920 (m) cc_final: 0.8669 (p)
REVERT: R  231 MET cc_start: 0.7642 (tmm) cc_final: 0.7381 (tmm)
  outliers start: 41
  outliers final: 28
  residues processed: 181
  average time/residue: 0.0849
  time to fit residues: 22.2711
Evaluate side-chains
  165 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 22 optimal weight:    0.0020
   chunk 106 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 114 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 92 optimal weight:    0.6980
   chunk 85 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
R 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.117668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.090068 restraints weight = 20092.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091408 restraints weight = 12428.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.092308 restraints weight = 10028.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.092843 restraints weight = 9253.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.092799 restraints weight = 8461.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   9671  Z= 0.105
  Angle     :  0.582  10.348  13138  Z= 0.298
  Chirality :  0.041   0.142   1467
  Planarity :  0.003   0.053   1661
  Dihedral  :  5.246  44.190   1321
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.40 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.23), residues: 1203
  helix: -1.09 (0.26), residues: 366
  sheet: -2.13 (0.32), residues: 245
  loop : -2.14 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TYR   0.017   0.001   TYR R 145 
 PHE   0.021   0.001   PHE R 365 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.010   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9666)
  covalent geometry    : angle       0.58170 (13128)
  SS BOND              : bond        0.00068 (    5)
  SS BOND              : angle       0.97519 (   10)
  hydrogen bonds       : bond        0.03216 (  269)
  hydrogen bonds       : angle       4.64435 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8735 (pp)
REVERT: B  278 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6895 (m-10)
REVERT: B  295 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7564 (p0)
REVERT: D  235 TYR cc_start: 0.7827 (m-80) cc_final: 0.7566 (m-80)
REVERT: E   21 ASP cc_start: 0.8498 (m-30) cc_final: 0.8196 (t0)
REVERT: E   24 GLN cc_start: 0.8015 (tp40) cc_final: 0.7555 (tm-30)
REVERT: R   34 GLU cc_start: 0.7942 (pp20) cc_final: 0.7473 (pp20)
REVERT: R  260 GLU cc_start: 0.2901 (tp30) cc_final: 0.2694 (tp30)
  outliers start: 36
  outliers final: 27
  residues processed: 174
  average time/residue: 0.0836
  time to fit residues: 21.0207
Evaluate side-chains
  158 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 104 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 80 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0170
   chunk 6 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7422

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
R 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.115115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.088155 restraints weight = 20302.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.087811 restraints weight = 13270.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.088533 restraints weight = 12870.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.089092 restraints weight = 10728.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.089267 restraints weight = 9594.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9671  Z= 0.140
  Angle     :  0.601   8.393  13138  Z= 0.311
  Chirality :  0.042   0.139   1467
  Planarity :  0.003   0.052   1661
  Dihedral  :  5.248  39.196   1321
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.10 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.23), residues: 1203
  helix: -0.92 (0.26), residues: 369
  sheet: -2.02 (0.32), residues: 249
  loop : -2.12 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TYR   0.019   0.001   TYR R 145 
 PHE   0.019   0.001   PHE R 365 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9666)
  covalent geometry    : angle       0.60058 (13128)
  SS BOND              : bond        0.00146 (    5)
  SS BOND              : angle       0.97659 (   10)
  hydrogen bonds       : bond        0.03428 (  269)
  hydrogen bonds       : angle       4.56153 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 135
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8798 (pp)
REVERT: B  278 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6937 (m-10)
REVERT: B  295 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7723 (p0)
REVERT: D  235 TYR cc_start: 0.7909 (m-80) cc_final: 0.7643 (m-80)
REVERT: E   21 ASP cc_start: 0.8492 (m-30) cc_final: 0.8082 (t0)
REVERT: E   24 GLN cc_start: 0.7971 (tp40) cc_final: 0.7589 (tm-30)
REVERT: R   34 GLU cc_start: 0.8011 (pp20) cc_final: 0.7534 (pp20)
REVERT: R  131 GLN cc_start: 0.8464 (tt0) cc_final: 0.7600 (tm-30)
REVERT: R  144 MET cc_start: 0.7972 (tmm) cc_final: 0.7753 (tmm)
REVERT: R  260 GLU cc_start: 0.2851 (tp30) cc_final: 0.2644 (tp30)
  outliers start: 44
  outliers final: 34
  residues processed: 170
  average time/residue: 0.0865
  time to fit residues: 21.1837
Evaluate side-chains
  166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 95 optimal weight:    0.6980
   chunk 59 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 220 GLN
B 295 ASN
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.114271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.086507 restraints weight = 20441.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.086914 restraints weight = 14718.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.087692 restraints weight = 12462.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.088310 restraints weight = 11121.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.088249 restraints weight = 10190.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9671  Z= 0.155
  Angle     :  0.617   8.645  13138  Z= 0.317
  Chirality :  0.042   0.143   1467
  Planarity :  0.004   0.054   1661
  Dihedral  :  5.302  35.341   1321
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 23.20 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.24), residues: 1203
  helix: -0.88 (0.27), residues: 371
  sheet: -1.97 (0.32), residues: 249
  loop : -2.07 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.018   0.001   TYR R 145 
 PHE   0.026   0.001   PHE E  22 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9666)
  covalent geometry    : angle       0.61636 (13128)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       1.08871 (   10)
  hydrogen bonds       : bond        0.03478 (  269)
  hydrogen bonds       : angle       4.59241 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 136
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8876 (pp)
REVERT: B  278 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6933 (m-10)
REVERT: B  286 LEU cc_start: 0.8880 (mm) cc_final: 0.8650 (mp)
REVERT: B  295 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7830 (p0)
REVERT: D  235 TYR cc_start: 0.7864 (m-80) cc_final: 0.7602 (m-80)
REVERT: E   21 ASP cc_start: 0.8460 (m-30) cc_final: 0.8057 (t0)
REVERT: E   24 GLN cc_start: 0.7957 (tp40) cc_final: 0.7629 (tm-30)
REVERT: R   34 GLU cc_start: 0.7967 (pp20) cc_final: 0.7484 (pp20)
REVERT: R  131 GLN cc_start: 0.8409 (tt0) cc_final: 0.7567 (tm-30)
REVERT: R  144 MET cc_start: 0.7936 (tmm) cc_final: 0.7715 (tmm)
REVERT: R  260 GLU cc_start: 0.2961 (tp30) cc_final: 0.2756 (tp30)
REVERT: R  401 CYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (m)
  outliers start: 48
  outliers final: 37
  residues processed: 173
  average time/residue: 0.0797
  time to fit residues: 20.0867
Evaluate side-chains
  170 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  352 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 82 optimal weight:   30.0000
   chunk 106 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 220 GLN
B 266 HIS
B 295 ASN
R 361 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.115993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.089026 restraints weight = 20233.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.089074 restraints weight = 13191.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.089618 restraints weight = 12021.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.090188 restraints weight = 10573.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.090404 restraints weight = 9437.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9671  Z= 0.119
  Angle     :  0.613   9.049  13138  Z= 0.310
  Chirality :  0.042   0.145   1467
  Planarity :  0.003   0.055   1661
  Dihedral  :  5.121  34.979   1321
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.81 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.24), residues: 1203
  helix: -0.68 (0.27), residues: 371
  sheet: -1.90 (0.32), residues: 249
  loop : -1.94 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  32 
 TYR   0.018   0.001   TYR R  39 
 PHE   0.019   0.001   PHE D  68 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9666)
  covalent geometry    : angle       0.61207 (13128)
  SS BOND              : bond        0.00124 (    5)
  SS BOND              : angle       1.05779 (   10)
  hydrogen bonds       : bond        0.03266 (  269)
  hydrogen bonds       : angle       4.51409 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 138
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8795 (pp)
REVERT: B  278 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6943 (m-10)
REVERT: B  295 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7666 (p0)
REVERT: D  235 TYR cc_start: 0.7921 (m-80) cc_final: 0.7634 (m-80)
REVERT: E   21 ASP cc_start: 0.8489 (m-30) cc_final: 0.8086 (t0)
REVERT: E   24 GLN cc_start: 0.7922 (tp40) cc_final: 0.7568 (tm-30)
REVERT: R   34 GLU cc_start: 0.8011 (pp20) cc_final: 0.7542 (pp20)
REVERT: R  144 MET cc_start: 0.7938 (tmm) cc_final: 0.7700 (tmm)
REVERT: R  231 MET cc_start: 0.7586 (tmm) cc_final: 0.7385 (tmm)
REVERT: R  260 GLU cc_start: 0.2789 (tp30) cc_final: 0.2516 (tp30)
  outliers start: 40
  outliers final: 32
  residues processed: 167
  average time/residue: 0.0883
  time to fit residues: 21.0969
Evaluate side-chains
  163 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 88 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0050
   chunk 102 optimal weight:    4.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 220 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 339 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.117368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.090404 restraints weight = 20185.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.090351 restraints weight = 13866.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091455 restraints weight = 11827.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091661 restraints weight = 10618.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.091731 restraints weight = 9741.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9671  Z= 0.110
  Angle     :  0.619  11.746  13138  Z= 0.311
  Chirality :  0.041   0.143   1467
  Planarity :  0.003   0.052   1661
  Dihedral  :  4.996  36.082   1321
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 24.42 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.24), residues: 1203
  helix: -0.48 (0.27), residues: 371
  sheet: -1.81 (0.32), residues: 254
  loop : -1.86 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 208 
 TYR   0.021   0.001   TYR R  39 
 PHE   0.026   0.001   PHE E  22 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.013   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9666)
  covalent geometry    : angle       0.61896 (13128)
  SS BOND              : bond        0.00110 (    5)
  SS BOND              : angle       1.03845 (   10)
  hydrogen bonds       : bond        0.03141 (  269)
  hydrogen bonds       : angle       4.41186 (  762)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8800 (pp)
REVERT: A  208 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7525 (mtt90)
REVERT: B   68 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7578 (mmm160)
REVERT: B  156 GLN cc_start: 0.7751 (mp10) cc_final: 0.7452 (mp10)
REVERT: B  295 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7746 (p0)
REVERT: D  235 TYR cc_start: 0.7902 (m-80) cc_final: 0.7644 (m-80)
REVERT: E   21 ASP cc_start: 0.8436 (m-30) cc_final: 0.8079 (t0)
REVERT: E   24 GLN cc_start: 0.7863 (tp40) cc_final: 0.7574 (tm-30)
REVERT: R   34 GLU cc_start: 0.7891 (pp20) cc_final: 0.7426 (pp20)
  outliers start: 34
  outliers final: 32
  residues processed: 154
  average time/residue: 0.0844
  time to fit residues: 18.7501
Evaluate side-chains
  161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:   30.0000
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 116 optimal weight:    0.0980
   chunk 61 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 220 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 GLN
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.115683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.089195 restraints weight = 20269.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.088614 restraints weight = 14519.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.089275 restraints weight = 13225.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.089627 restraints weight = 11894.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.090281 restraints weight = 10706.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9671  Z= 0.142
  Angle     :  0.646  13.025  13138  Z= 0.325
  Chirality :  0.042   0.152   1467
  Planarity :  0.003   0.051   1661
  Dihedral  :  5.049  33.530   1321
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.11 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.24), residues: 1203
  helix: -0.45 (0.27), residues: 374
  sheet: -1.84 (0.32), residues: 254
  loop : -1.87 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 208 
 TYR   0.021   0.001   TYR R  39 
 PHE   0.014   0.001   PHE R 365 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.010   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9666)
  covalent geometry    : angle       0.64546 (13128)
  SS BOND              : bond        0.00141 (    5)
  SS BOND              : angle       1.07431 (   10)
  hydrogen bonds       : bond        0.03325 (  269)
  hydrogen bonds       : angle       4.45513 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1720.53 seconds
wall clock time: 30 minutes 24.74 seconds (1824.74 seconds total)