Starting phenix.real_space_refine
on Wed Mar  4 00:12:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eoj_28377/03_2026/8eoj_28377.cif"
  }
  resolution = 3.07
  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=   0.016
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      35      5.16       5
     C    5936      2.51       5
     N    1574      2.21       5
     O    1782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 9327
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3326
          Classifications: {'peptide': 438}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 18, 'TRANS': 419}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 129
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 83
    Chain: "B"
      Number of atoms: 6001
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 781, 5996
          Classifications: {'peptide': 781}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 19, 'TRANS': 761}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'PHE:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 104
      Conformer: "B"
        Number of residues, atoms: 781, 5996
          Classifications: {'peptide': 781}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 19, 'TRANS': 761}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'PHE:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 104
          bond proxies already assigned to first conformer: 6064
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE B 824 " occ=0.60
      ... (8 atoms not shown)
      pdb=" CB BPHE B 824 " occ=0.40
  Time building chain proxies: 2.93, per 1000 atoms: 0.31
  Number of scatterers: 9327
  At special positions: 0
  Unit cell: (89.64, 100.44, 158.76, 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      35     16.00
     O    1782      8.00
     N    1574      7.00
     C    5936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 174 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 298 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 440 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 827 " - pdb=" SG  CYS B 878 " 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: 0.62
  Conformation dependent library (CDL) restraints added in 672.8 milliseconds
  

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2290

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 10 sheets defined
      37.7% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 41
    Processing helix  chain 'A' and resid 53 through 73
      Proline residue:  A  61  - end of helix
    Processing helix  chain 'A' and resid 87 through 95
      removed outlier: 3.944A  pdb=" N   ALA A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 134
      removed outlier: 3.957A  pdb=" N   LYS A 130 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LYS A 131 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 134 " --> pdb=" O   LYS A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 179
      removed outlier: 3.913A  pdb=" N   ILE A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.773A  pdb=" N   PHE A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 234
      removed outlier: 3.510A  pdb=" N   LEU A 234 " --> pdb=" O   LYS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 251
      removed outlier: 3.548A  pdb=" N   GLY A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 282
      removed outlier: 3.600A  pdb=" N   SER A 281 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'A' and resid 298 through 305
      removed outlier: 3.570A  pdb=" N   PHE A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 349
      removed outlier: 4.167A  pdb=" N   CYS A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   HIS A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 414
      Proline residue:  A 405  - end of helix
    Processing helix  chain 'A' and resid 464 through 472
      removed outlier: 3.646A  pdb=" N   SER A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 112
    Processing helix  chain 'B' and resid 112 through 121
      removed outlier: 3.673A  pdb=" N   LEU B 116 " --> pdb=" O   GLY B 112 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLU B 117 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
      removed outlier: 3.533A  pdb=" N   LYS B 149 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 154 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 157
      No H-bonds generated for 'chain 'B' and resid 155 through 157'
    Processing helix  chain 'B' and resid 273 through 281
      removed outlier: 4.209A  pdb=" N   ILE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LYS B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 313
      removed outlier: 3.501A  pdb=" N   THR B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LYS B 313 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 320
      removed outlier: 3.924A  pdb=" N   LEU B 320 " --> pdb=" O   PRO B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 338
      removed outlier: 3.507A  pdb=" N   VAL B 326 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ASN B 328 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE B 329 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE B 332 " --> pdb=" O   ASN B 328 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE B 333 " --> pdb=" O   PHE B 329 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 348
      removed outlier: 3.668A  pdb=" N   ILE B 347 " --> pdb=" O   GLU B 343 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B 348 " --> pdb=" O   ILE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 365
      removed outlier: 3.575A  pdb=" N   LEU B 359 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
    Processing helix  chain 'B' and resid 386 through 399
      removed outlier: 3.815A  pdb=" N   GLN B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 421 through 441
    Processing helix  chain 'B' and resid 447 through 463
      removed outlier: 3.522A  pdb=" N   GLU B 452 " --> pdb=" O   LYS B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 481
    Processing helix  chain 'B' and resid 482 through 484
      No H-bonds generated for 'chain 'B' and resid 482 through 484'
    Processing helix  chain 'B' and resid 485 through 494
    Processing helix  chain 'B' and resid 497 through 511
      removed outlier: 3.549A  pdb=" N   TYR B 511 " --> pdb=" O   ALA B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 529
      removed outlier: 3.611A  pdb=" N   ARG B 526 " --> pdb=" O   LYS B 522 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE B 527 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 550
    Processing helix  chain 'B' and resid 553 through 564
    Processing helix  chain 'B' and resid 568 through 585
      removed outlier: 3.763A  pdb=" N   TYR B 574 " --> pdb=" O   GLU B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 598
    Processing helix  chain 'B' and resid 604 through 609
      removed outlier: 3.592A  pdb=" N   PHE B 608 " --> pdb=" O   ASN B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 871 through 879
      removed outlier: 4.119A  pdb=" N   MET B 877 " --> pdb=" O   GLU B 873 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.996A  pdb=" N   GLU A  21 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A  29 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ASP A  83 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU A  45 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU A  47 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LEU A  44 " --> pdb=" O   PHE A 105 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE A 105 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
      removed outlier: 8.252A  pdb=" N   THR A 187 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLY A 159 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A 206 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ILE A 158 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL A 204 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   PHE A 160 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY A 202 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239
      removed outlier: 5.777A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ILE A 257 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 318 " --> pdb=" O   HIS A 256 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ARG A 316 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU A 317 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR A 319 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371
      removed outlier: 6.883A  pdb=" N   LYS A 370 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   ASP A 426 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   PHE A 389 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   MET A 425 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLU A 391 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 238
      removed outlier: 3.893A  pdb=" N   ILE B 250 " --> pdb=" O   HIS B 236 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 238 " --> pdb=" O   GLY B 248 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY B 248 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LYS B  35 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B  42 " --> pdb=" O   TYR B  57 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   TYR B  57 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ARG B  58 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   VAL B  89 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   SER B  60 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL B  87 " --> pdb=" O   SER B  60 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 125 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B 124 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   PHE B 135 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   HIS B 126 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE B 135 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER B 137 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 166
      removed outlier: 9.491A  pdb=" N   ASN B 173 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   ASP B 192 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LYS B 175 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 185 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 617 through 623
      removed outlier: 6.238A  pdb=" N   THR B 618 " --> pdb=" O   LEU B 633 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   LEU B 633 " --> pdb=" O   THR B 618 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   TYR B 620 " --> pdb=" O   TYR B 631 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TYR B 631 " --> pdb=" O   TYR B 620 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU B 622 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ARG B 644 " --> pdb=" O   ALA B 668 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   GLN B 652 " --> pdb=" O   HIS B 660 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   HIS B 660 " --> pdb=" O   GLN B 652 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE B 654 " --> pdb=" O   GLY B 658 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   GLY B 658 " --> pdb=" O   ILE B 654 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ALA B 690 " --> pdb=" O   PHE B 706 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 728 through 737
      removed outlier: 6.562A  pdb=" N   GLY B 755 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ASP B 736 " --> pdb=" O   VAL B 753 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 753 " --> pdb=" O   ASP B 736 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 728 through 737
      removed outlier: 6.562A  pdb=" N   GLY B 755 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ASP B 736 " --> pdb=" O   VAL B 753 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 753 " --> pdb=" O   ASP B 736 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS B 748 " --> pdb=" O   ASP B 793 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN B 754 " --> pdb=" O   THR B 787 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ALA B 758 " --> pdb=" O   THR B 783 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   THR B 783 " --> pdb=" O   ALA B 758 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASP B 760 " --> pdb=" O   ARG B 781 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ARG B 781 " --> pdb=" O   ASP B 760 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER B 804 " --> pdb=" O   PHE B 840 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE B 840 " --> pdb=" O   SER B 804 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU B 808 " --> pdb=" O   PRO B 836 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 835 " --> pdb=" O   LEU B 863 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER B 855 " --> pdb=" O   LYS B 843 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 763 through 764
      removed outlier: 3.879A  pdb=" N   ALA B 764 " --> pdb=" O   ARG B 777 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   MET B 830 " --> pdb=" O   PHE B 868 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1167 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: 1.71

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3037
        1.34 -     1.46: 1959
        1.46 -     1.58: 4424
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 9474
  Sorted by residual:
  bond pdb=" CA  LYS B 299 "
       pdb=" C   LYS B 299 "
    ideal  model  delta    sigma   weight residual
    1.529  1.513  0.017 9.30e-03 1.16e+04 3.19e+00
  bond pdb=" C   LEU B 870 "
       pdb=" O   LEU B 870 "
    ideal  model  delta    sigma   weight residual
    1.243  1.230  0.013 9.50e-03 1.11e+04 1.98e+00
  bond pdb=" N   PRO A 441 "
       pdb=" CA  PRO A 441 "
    ideal  model  delta    sigma   weight residual
    1.469  1.478 -0.010 7.40e-03 1.83e+04 1.66e+00
  bond pdb=" C   LEU B 356 "
       pdb=" N   PRO B 357 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.63e+00
  bond pdb=" C   ILE B 486 "
       pdb=" N   PRO B 487 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.016 1.28e-02 6.10e+03 1.47e+00
  ... (remaining 9469 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 12571
        1.75 -     3.49: 166
        3.49 -     5.24: 27
        5.24 -     6.98: 15
        6.98 -     8.73: 1
  Bond angle restraints: 12780
  Sorted by residual:
  angle pdb=" C   LEU B 870 "
        pdb=" CA  LEU B 870 "
        pdb=" CB  LEU B 870 "
      ideal   model   delta    sigma   weight residual
     117.23  110.90    6.33 1.36e+00 5.41e-01 2.17e+01
  angle pdb=" N   THR A 110 "
        pdb=" CA  THR A 110 "
        pdb=" C   THR A 110 "
      ideal   model   delta    sigma   weight residual
     110.80  119.53   -8.73 2.13e+00 2.20e-01 1.68e+01
  angle pdb=" C   ARG A  30 "
        pdb=" N   LYS A  31 "
        pdb=" CA  LYS A  31 "
      ideal   model   delta    sigma   weight residual
     121.54  128.13   -6.59 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" CA  LYS B 299 "
        pdb=" C   LYS B 299 "
        pdb=" N   GLY B 300 "
      ideal   model   delta    sigma   weight residual
     119.52  116.81    2.71 7.90e-01 1.60e+00 1.18e+01
  angle pdb=" C   TYR B 138 "
        pdb=" N   GLN B 139 "
        pdb=" CA  GLN B 139 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  ... (remaining 12775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 5407
       17.39 -    34.79: 273
       34.79 -    52.18: 75
       52.18 -    69.58: 6
       69.58 -    86.97: 2
  Dihedral angle restraints: 5763
    sinusoidal: 2234
      harmonic: 3529
  Sorted by residual:
  dihedral pdb=" CB  CYS B 298 "
           pdb=" SG  CYS B 298 "
           pdb=" SG  CYS B 301 "
           pdb=" CB  CYS B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.60   80.60     1      1.00e+01 1.00e-02 8.03e+01
  dihedral pdb=" CA  ASP A 451 "
           pdb=" C   ASP A 451 "
           pdb=" N   ARG A 452 "
           pdb=" CA  ARG A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.66  -18.34     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  LEU B 741 "
           pdb=" C   LEU B 741 "
           pdb=" N   GLN B 742 "
           pdb=" CA  GLN B 742 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.25   15.75     0      5.00e+00 4.00e-02 9.92e+00
  ... (remaining 5760 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1046
       0.037 -    0.073: 294
       0.073 -    0.110: 102
       0.110 -    0.147: 39
       0.147 -    0.184: 1
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CA  THR A 110 "
            pdb=" N   THR A 110 "
            pdb=" C   THR A 110 "
            pdb=" CB  THR A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.43e-01
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  PHE A 440 "
            pdb=" N   PHE A 440 "
            pdb=" C   PHE A 440 "
            pdb=" CB  PHE A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1629
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  99 "   -0.033 5.00e-02 4.00e+02   4.95e-02 3.91e+00
        pdb=" N   PRO A 100 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 100 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 100 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 567 "    0.028 5.00e-02 4.00e+02   4.24e-02 2.88e+00
        pdb=" N   PRO B 568 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 568 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 568 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 440 "   -0.027 5.00e-02 4.00e+02   4.01e-02 2.58e+00
        pdb=" N   PRO A 441 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 441 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 441 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1626 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 918
        2.75 -     3.29: 8798
        3.29 -     3.83: 15426
        3.83 -     4.36: 17538
        4.36 -     4.90: 30571
  Nonbonded interactions: 73251
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 116 "
            pdb=" O   GLY A 119 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLU B 167 "
            pdb=" OH  TYR B 178 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ILE B 560 "
            pdb=" OG  SER B 563 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ALA A 336 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OD1 ASP A  83 "
            pdb=" OG1 THR A  85 "
     model   vdw
     2.307 3.040
  ... (remaining 73246 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=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6042
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      :  0.002   0.034   9478  Z= 0.128
  Angle     :  0.555   8.731  12788  Z= 0.308
  Chirality :  0.042   0.184   1482
  Planarity :  0.004   0.049   1629
  Dihedral  : 11.261  86.970   3461
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  :  7.92 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.48 (0.22), residues: 1186
  helix: -0.69 (0.22), residues: 411
  sheet: -0.40 (0.33), residues: 274
  loop : -1.44 (0.24), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 132 
 TYR   0.008   0.001   TYR B 620 
 PHE   0.014   0.001   PHE A 209 
 TRP   0.008   0.001   TRP A 396 
 HIS   0.003   0.001   HIS B 529 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9474)
  covalent geometry    : angle       0.55468 (12780)
  SS BOND              : bond        0.00225 (    4)
  SS BOND              : angle       0.56624 (    8)
  hydrogen bonds       : bond        0.24295 (  402)
  hydrogen bonds       : angle       8.94228 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 238
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.6536 (tt0) cc_final: 0.6153 (tp30)
REVERT: A   92 GLN cc_start: 0.1837 (tt0) cc_final: 0.1136 (pp30)
REVERT: A  154 GLU cc_start: 0.7191 (tp30) cc_final: 0.6891 (tp30)
REVERT: A  216 PHE cc_start: 0.6288 (t80) cc_final: 0.6017 (t80)
REVERT: A  229 ILE cc_start: 0.5436 (OUTLIER) cc_final: 0.5110 (mt)
REVERT: A  316 ARG cc_start: 0.4856 (mmt-90) cc_final: 0.4378 (tpp-160)
REVERT: A  322 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: A  376 ASN cc_start: 0.8043 (m-40) cc_final: 0.7733 (m110)
REVERT: A  412 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5812 (mp0)
REVERT: B  262 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5950 (mt-10)
REVERT: B  277 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5339 (mp)
REVERT: B  343 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7453 (tm-30)
REVERT: B  491 LYS cc_start: 0.8654 (tttm) cc_final: 0.8238 (ttpp)
REVERT: B  551 ASN cc_start: 0.6391 (t0) cc_final: 0.6032 (t0)
REVERT: B  555 MET cc_start: 0.8492 (mmm) cc_final: 0.8118 (mmm)
REVERT: B  777 ARG cc_start: 0.7810 (ptp90) cc_final: 0.6938 (mmt180)
  outliers start: 37
  outliers final: 11
  residues processed: 265
  average time/residue: 0.1082
  time to fit residues: 38.5557
Evaluate side-chains
  179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  797 VAL
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
A 430 ASN
B  93 ASN
B 502 HIS
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.179689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.164474 restraints weight = 26108.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.4548 rms_B_bonded: 3.54
r_work: 0.4450 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4454 r_free = 0.4454    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4454 r_free = 0.4454    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9478  Z= 0.160
  Angle     :  0.671  14.644  12788  Z= 0.335
  Chirality :  0.046   0.253   1482
  Planarity :  0.004   0.040   1629
  Dihedral  :  5.996  54.669   1305
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.11 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.23), residues: 1186
  helix:  0.27 (0.24), residues: 422
  sheet: -0.25 (0.33), residues: 271
  loop : -1.35 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 132 
 TYR   0.014   0.002   TYR A 268 
 PHE   0.013   0.002   PHE B 813 
 TRP   0.019   0.002   TRP A 128 
 HIS   0.007   0.002   HIS B 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9474)
  covalent geometry    : angle       0.66925 (12780)
  SS BOND              : bond        0.00831 (    4)
  SS BOND              : angle       2.00554 (    8)
  hydrogen bonds       : bond        0.04280 (  402)
  hydrogen bonds       : angle       6.12111 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.6584 (ptpp) cc_final: 0.6320 (ptpp)
REVERT: A   92 GLN cc_start: 0.2355 (tt0) cc_final: 0.1188 (pp30)
REVERT: A  181 ASP cc_start: 0.6854 (p0) cc_final: 0.6601 (p0)
REVERT: A  216 PHE cc_start: 0.6531 (t80) cc_final: 0.6270 (t80)
REVERT: A  303 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8386 (mt-10)
REVERT: A  322 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A  376 ASN cc_start: 0.8016 (m-40) cc_final: 0.7690 (m110)
REVERT: A  408 ASP cc_start: 0.1425 (m-30) cc_final: 0.1082 (m-30)
REVERT: B   89 VAL cc_start: 0.4757 (OUTLIER) cc_final: 0.4555 (m)
REVERT: B  170 ILE cc_start: 0.5773 (OUTLIER) cc_final: 0.5528 (tp)
REVERT: B  777 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7091 (mmt180)
REVERT: B  877 MET cc_start: 0.0254 (OUTLIER) cc_final: -0.0069 (tpt)
  outliers start: 34
  outliers final: 15
  residues processed: 201
  average time/residue: 0.0989
  time to fit residues: 27.3598
Evaluate side-chains
  170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  877 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 89 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0970
   chunk 47 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 GLN
A 256 HIS
A 298 ASN
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.179292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.164259 restraints weight = 26115.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4553 rms_B_bonded: 3.52
r_work: 0.4457 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4460 r_free = 0.4460    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4460 r_free = 0.4460    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9478  Z= 0.143
  Angle     :  0.622  12.399  12788  Z= 0.313
  Chirality :  0.044   0.179   1482
  Planarity :  0.004   0.043   1629
  Dihedral  :  5.266  44.942   1293
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.97 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 15.84 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.24), residues: 1186
  helix:  0.50 (0.24), residues: 423
  sheet: -0.24 (0.32), residues: 271
  loop : -1.27 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 425 
 TYR   0.014   0.002   TYR A 196 
 PHE   0.020   0.002   PHE A 282 
 TRP   0.024   0.002   TRP A 128 
 HIS   0.005   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9474)
  covalent geometry    : angle       0.62185 (12780)
  SS BOND              : bond        0.00355 (    4)
  SS BOND              : angle       1.29058 (    8)
  hydrogen bonds       : bond        0.03787 (  402)
  hydrogen bonds       : angle       5.73051 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 165
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLN cc_start: 0.2584 (tt0) cc_final: 0.1734 (pp30)
REVERT: A   97 ARG cc_start: 0.6039 (mmt180) cc_final: 0.5802 (mmt180)
REVERT: A  216 PHE cc_start: 0.6353 (t80) cc_final: 0.6069 (t80)
REVERT: A  299 GLN cc_start: 0.6666 (tp-100) cc_final: 0.6270 (tp-100)
REVERT: A  322 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: A  376 ASN cc_start: 0.8043 (m-40) cc_final: 0.7812 (m110)
REVERT: B   89 VAL cc_start: 0.4831 (OUTLIER) cc_final: 0.4379 (t)
REVERT: B  268 MET cc_start: 0.4979 (mtt) cc_final: 0.4699 (ptp)
REVERT: B  277 ILE cc_start: 0.5729 (OUTLIER) cc_final: 0.5371 (mp)
REVERT: B  741 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5388 (tt)
REVERT: B  777 ARG cc_start: 0.7200 (ptp90) cc_final: 0.6931 (mmt180)
  outliers start: 40
  outliers final: 24
  residues processed: 192
  average time/residue: 0.1064
  time to fit residues: 27.7057
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  603 HIS
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 118 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 101 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 256 HIS
A 298 ASN
B 358 GLN
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.180290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.165227 restraints weight = 26008.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.4566 rms_B_bonded: 3.53
r_work: 0.4467 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4471 r_free = 0.4471    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4471 r_free = 0.4471    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9478  Z= 0.128
  Angle     :  0.600  12.103  12788  Z= 0.302
  Chirality :  0.044   0.160   1482
  Planarity :  0.004   0.046   1629
  Dihedral  :  5.167  43.709   1293
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.43 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.56 (0.24), residues: 1186
  helix:  0.71 (0.25), residues: 422
  sheet: -0.30 (0.32), residues: 271
  loop : -1.32 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  46 
 TYR   0.014   0.002   TYR A 196 
 PHE   0.026   0.002   PHE A 446 
 TRP   0.029   0.002   TRP A 128 
 HIS   0.004   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9474)
  covalent geometry    : angle       0.59954 (12780)
  SS BOND              : bond        0.00355 (    4)
  SS BOND              : angle       0.82731 (    8)
  hydrogen bonds       : bond        0.03415 (  402)
  hydrogen bonds       : angle       5.50239 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 159
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ARG cc_start: 0.6053 (mmt180) cc_final: 0.5811 (mmt180)
REVERT: A  216 PHE cc_start: 0.6473 (t80) cc_final: 0.6159 (t80)
REVERT: A  299 GLN cc_start: 0.6630 (tp-100) cc_final: 0.6316 (tp-100)
REVERT: A  322 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7007 (tm-30)
REVERT: A  408 ASP cc_start: 0.1290 (m-30) cc_final: 0.0094 (t70)
REVERT: A  412 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.4303 (mp0)
REVERT: B   89 VAL cc_start: 0.4469 (OUTLIER) cc_final: 0.4110 (t)
REVERT: B  268 MET cc_start: 0.5007 (mtt) cc_final: 0.4299 (ptp)
REVERT: B  741 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5397 (tt)
REVERT: B  777 ARG cc_start: 0.7248 (ptp90) cc_final: 0.6930 (mpt180)
  outliers start: 39
  outliers final: 26
  residues processed: 188
  average time/residue: 0.1122
  time to fit residues: 28.3428
Evaluate side-chains
  173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  827 CYS
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 47 optimal weight:    0.3980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 376 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 GLN
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.178990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.163835 restraints weight = 25892.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.4544 rms_B_bonded: 3.55
r_work: 0.4444 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9478  Z= 0.151
  Angle     :  0.619  11.735  12788  Z= 0.312
  Chirality :  0.044   0.176   1482
  Planarity :  0.004   0.049   1629
  Dihedral  :  5.310  43.834   1293
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 16.95 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.24), residues: 1186
  helix:  0.60 (0.25), residues: 424
  sheet: -0.26 (0.32), residues: 272
  loop : -1.46 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 425 
 TYR   0.015   0.002   TYR A 414 
 PHE   0.019   0.002   PHE A 282 
 TRP   0.009   0.002   TRP A 396 
 HIS   0.006   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9474)
  covalent geometry    : angle       0.61909 (12780)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       0.89587 (    8)
  hydrogen bonds       : bond        0.03429 (  402)
  hydrogen bonds       : angle       5.41143 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.7027 (ptpp) cc_final: 0.6693 (ptpp)
REVERT: A   97 ARG cc_start: 0.6087 (mmt180) cc_final: 0.5841 (mmt180)
REVERT: A  216 PHE cc_start: 0.6516 (t80) cc_final: 0.6175 (t80)
REVERT: A  322 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7032 (tm-30)
REVERT: A  376 ASN cc_start: 0.8197 (m-40) cc_final: 0.7758 (m-40)
REVERT: A  412 GLU cc_start: 0.4867 (OUTLIER) cc_final: 0.4610 (mp0)
REVERT: B   89 VAL cc_start: 0.4454 (OUTLIER) cc_final: 0.4196 (t)
REVERT: B  268 MET cc_start: 0.5027 (mtt) cc_final: 0.4301 (ptp)
REVERT: B  277 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5501 (mp)
REVERT: B  741 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5713 (tt)
REVERT: B  777 ARG cc_start: 0.7287 (ptp90) cc_final: 0.6989 (mmt180)
  outliers start: 39
  outliers final: 28
  residues processed: 176
  average time/residue: 0.0983
  time to fit residues: 23.8697
Evaluate side-chains
  171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  603 HIS
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  757 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  827 CYS
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0970
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.180116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.164878 restraints weight = 25875.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.4562 rms_B_bonded: 3.61
r_work: 0.4462 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4465 r_free = 0.4465    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4465 r_free = 0.4465    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9478  Z= 0.120
  Angle     :  0.616  19.036  12788  Z= 0.303
  Chirality :  0.044   0.154   1482
  Planarity :  0.004   0.043   1629
  Dihedral  :  5.131  43.528   1293
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.17 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.24), residues: 1186
  helix:  0.82 (0.25), residues: 433
  sheet: -0.26 (0.32), residues: 277
  loop : -1.53 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 392 
 TYR   0.022   0.002   TYR A 268 
 PHE   0.017   0.001   PHE A 282 
 TRP   0.010   0.001   TRP A 396 
 HIS   0.004   0.001   HIS B 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9474)
  covalent geometry    : angle       0.61573 (12780)
  SS BOND              : bond        0.00232 (    4)
  SS BOND              : angle       0.57460 (    8)
  hydrogen bonds       : bond        0.03186 (  402)
  hydrogen bonds       : angle       5.21316 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ARG cc_start: 0.5958 (mmt180) cc_final: 0.5168 (mmt180)
REVERT: A  216 PHE cc_start: 0.6642 (t80) cc_final: 0.6312 (t80)
REVERT: A  299 GLN cc_start: 0.6754 (tp-100) cc_final: 0.6200 (mt0)
REVERT: A  412 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4608 (mp0)
REVERT: B   89 VAL cc_start: 0.4695 (OUTLIER) cc_final: 0.4219 (t)
REVERT: B  268 MET cc_start: 0.4952 (mtt) cc_final: 0.4435 (ptp)
REVERT: B  277 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5402 (mp)
REVERT: B  741 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5547 (tt)
REVERT: B  777 ARG cc_start: 0.7413 (ptp90) cc_final: 0.7016 (mpt180)
REVERT: B  825 LEU cc_start: 0.8266 (pp) cc_final: 0.8044 (mp)
  outliers start: 38
  outliers final: 25
  residues processed: 170
  average time/residue: 0.0960
  time to fit residues: 22.7799
Evaluate side-chains
  171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 117 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 102 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.178688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.163618 restraints weight = 25927.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4557 rms_B_bonded: 3.55
r_work: 0.4457 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4460 r_free = 0.4460    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4460 r_free = 0.4460    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9478  Z= 0.125
  Angle     :  0.612  15.912  12788  Z= 0.302
  Chirality :  0.044   0.147   1482
  Planarity :  0.004   0.039   1629
  Dihedral  :  5.118  42.907   1293
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.77 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.24), residues: 1186
  helix:  0.90 (0.25), residues: 426
  sheet: -0.08 (0.33), residues: 269
  loop : -1.55 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 425 
 TYR   0.022   0.002   TYR B 284 
 PHE   0.019   0.002   PHE A 282 
 TRP   0.010   0.001   TRP A 396 
 HIS   0.006   0.001   HIS B 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9474)
  covalent geometry    : angle       0.61199 (12780)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.72730 (    8)
  hydrogen bonds       : bond        0.03085 (  402)
  hydrogen bonds       : angle       5.13210 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.7749 (mp0) cc_final: 0.7405 (mp0)
REVERT: A  216 PHE cc_start: 0.6680 (t80) cc_final: 0.6341 (t80)
REVERT: A  299 GLN cc_start: 0.6621 (tp-100) cc_final: 0.5965 (mt0)
REVERT: A  412 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.4528 (mp0)
REVERT: B   89 VAL cc_start: 0.4366 (OUTLIER) cc_final: 0.4108 (t)
REVERT: B  268 MET cc_start: 0.5434 (mtt) cc_final: 0.4872 (ptp)
REVERT: B  277 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5462 (mp)
REVERT: B  337 ARG cc_start: 0.7518 (mmt-90) cc_final: 0.6962 (ttm170)
REVERT: B  741 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5674 (tt)
REVERT: B  825 LEU cc_start: 0.8450 (pp) cc_final: 0.8121 (mp)
  outliers start: 33
  outliers final: 25
  residues processed: 171
  average time/residue: 0.1025
  time to fit residues: 24.2682
Evaluate side-chains
  171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 57 optimal weight:    0.3980
   chunk 115 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 107 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.180961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.165720 restraints weight = 25856.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4561 rms_B_bonded: 3.57
r_work: 0.4463 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4467 r_free = 0.4467    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4467 r_free = 0.4467    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6125
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9478  Z= 0.119
  Angle     :  0.597  15.111  12788  Z= 0.295
  Chirality :  0.043   0.190   1482
  Planarity :  0.003   0.038   1629
  Dihedral  :  5.027  42.851   1293
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.77 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.24), residues: 1186
  helix:  1.02 (0.25), residues: 421
  sheet: -0.02 (0.33), residues: 269
  loop : -1.57 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 425 
 TYR   0.022   0.002   TYR A 268 
 PHE   0.018   0.001   PHE B 706 
 TRP   0.010   0.001   TRP A 396 
 HIS   0.006   0.001   HIS B 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9474)
  covalent geometry    : angle       0.59665 (12780)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       0.62994 (    8)
  hydrogen bonds       : bond        0.03011 (  402)
  hydrogen bonds       : angle       5.04705 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 PHE cc_start: 0.6737 (t80) cc_final: 0.6430 (t80)
REVERT: A  299 GLN cc_start: 0.6557 (tp-100) cc_final: 0.5886 (mt0)
REVERT: A  412 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.4516 (mp0)
REVERT: B   89 VAL cc_start: 0.4337 (OUTLIER) cc_final: 0.3983 (t)
REVERT: B  268 MET cc_start: 0.5297 (mtt) cc_final: 0.4784 (ptp)
REVERT: B  277 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5427 (mp)
REVERT: B  741 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5612 (tt)
REVERT: B  777 ARG cc_start: 0.7378 (ptp90) cc_final: 0.6998 (mmt180)
REVERT: B  825 LEU cc_start: 0.8487 (pp) cc_final: 0.8112 (mp)
  outliers start: 35
  outliers final: 26
  residues processed: 163
  average time/residue: 0.0961
  time to fit residues: 22.0901
Evaluate side-chains
  166 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  827 CYS
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   chunk 82 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.181163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.165937 restraints weight = 25953.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4562 rms_B_bonded: 3.58
r_work: 0.4464 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4467 r_free = 0.4467    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4467 r_free = 0.4467    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9478  Z= 0.118
  Angle     :  0.604  14.339  12788  Z= 0.300
  Chirality :  0.043   0.179   1482
  Planarity :  0.004   0.052   1629
  Dihedral  :  4.987  42.804   1293
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.17 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.24), residues: 1186
  helix:  1.02 (0.25), residues: 421
  sheet:  0.04 (0.33), residues: 271
  loop : -1.53 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 392 
 TYR   0.020   0.002   TYR A 268 
 PHE   0.022   0.001   PHE B 706 
 TRP   0.009   0.001   TRP A 396 
 HIS   0.008   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9474)
  covalent geometry    : angle       0.60415 (12780)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       0.59601 (    8)
  hydrogen bonds       : bond        0.03011 (  402)
  hydrogen bonds       : angle       5.06464 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 PHE cc_start: 0.6749 (t80) cc_final: 0.6445 (t80)
REVERT: A  233 GLN cc_start: 0.5176 (mm110) cc_final: 0.4879 (mm110)
REVERT: A  299 GLN cc_start: 0.6514 (tp-100) cc_final: 0.5975 (mt0)
REVERT: A  412 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.4479 (mp0)
REVERT: B   89 VAL cc_start: 0.4336 (OUTLIER) cc_final: 0.3982 (t)
REVERT: B  268 MET cc_start: 0.5285 (mtt) cc_final: 0.4801 (ptp)
REVERT: B  741 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5613 (tt)
REVERT: B  825 LEU cc_start: 0.8454 (pp) cc_final: 0.8056 (mp)
  outliers start: 30
  outliers final: 25
  residues processed: 161
  average time/residue: 0.0928
  time to fit residues: 21.0845
Evaluate side-chains
  168 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  614 SER
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  734 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  827 CYS
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0020
   chunk 56 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 114 optimal weight:    0.1980
   chunk 77 optimal weight:    0.0470
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 86 optimal weight:    0.4980
   overall best weight:    0.1644

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 299 GLN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4781 r_free = 0.4781 target = 0.182844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.167764 restraints weight = 25802.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 3.60
r_work: 0.4490 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4493 r_free = 0.4493    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4493 r_free = 0.4493    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6069
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9478  Z= 0.106
  Angle     :  0.603  14.448  12788  Z= 0.298
  Chirality :  0.043   0.170   1482
  Planarity :  0.004   0.049   1629
  Dihedral  :  4.687  43.505   1291
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.09 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.25 (0.24), residues: 1186
  helix:  1.06 (0.25), residues: 428
  sheet:  0.13 (0.34), residues: 274
  loop : -1.45 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 392 
 TYR   0.018   0.001   TYR B 511 
 PHE   0.029   0.001   PHE B 706 
 TRP   0.008   0.001   TRP A 396 
 HIS   0.011   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9474)
  covalent geometry    : angle       0.60293 (12780)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       0.35938 (    8)
  hydrogen bonds       : bond        0.02869 (  402)
  hydrogen bonds       : angle       4.91036 ( 1167)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 TYR cc_start: 0.3542 (m-10) cc_final: 0.3340 (m-10)
REVERT: A   97 ARG cc_start: 0.5987 (mmt180) cc_final: 0.5325 (mmt180)
REVERT: A  216 PHE cc_start: 0.6709 (t80) cc_final: 0.6397 (t80)
REVERT: A  299 GLN cc_start: 0.6401 (tp40) cc_final: 0.5976 (mt0)
REVERT: B   89 VAL cc_start: 0.4429 (OUTLIER) cc_final: 0.4041 (t)
REVERT: B  268 MET cc_start: 0.4993 (mtt) cc_final: 0.4638 (ptp)
REVERT: B  741 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5426 (tt)
REVERT: B  777 ARG cc_start: 0.7297 (ptp90) cc_final: 0.7024 (mmt180)
REVERT: B  825 LEU cc_start: 0.8384 (pp) cc_final: 0.7923 (tt)
  outliers start: 27
  outliers final: 23
  residues processed: 164
  average time/residue: 0.0972
  time to fit residues: 22.2076
Evaluate side-chains
  163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   43 TYR
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  412 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  627 SER
Chi-restraints excluded: chain B residue  629 SER
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  757 LEU
Chi-restraints excluded: chain B residue  790 ILE
Chi-restraints excluded: chain B residue  827 CYS
Chi-restraints excluded: chain B residue  847 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 72 optimal weight:    0.0470
   chunk 75 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 110 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 100 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 ASN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.182811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.167901 restraints weight = 25462.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.4589 rms_B_bonded: 3.55
r_work: 0.4491 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4493 r_free = 0.4493    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4493 r_free = 0.4493    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6069
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.140   9478  Z= 0.276
  Angle     :  0.984  59.200  12788  Z= 0.579
  Chirality :  0.047   0.584   1482
  Planarity :  0.006   0.166   1629
  Dihedral  :  4.652  43.402   1289
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.90 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.24), residues: 1186
  helix:  1.05 (0.25), residues: 428
  sheet:  0.13 (0.34), residues: 274
  loop : -1.44 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 392 
 TYR   0.019   0.001   TYR B 511 
 PHE   0.029   0.001   PHE B 706 
 TRP   0.008   0.001   TRP A 396 
 HIS   0.046   0.002   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 9474)
  covalent geometry    : angle       0.98458 (12780)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       0.35751 (    8)
  hydrogen bonds       : bond        0.02915 (  402)
  hydrogen bonds       : angle       4.92485 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2767.56 seconds
wall clock time: 48 minutes 4.66 seconds (2884.66 seconds total)