Starting phenix.real_space_refine
on Fri Feb  6 04:51:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h85_51931/02_2026/9h85_51931.map"
  }
  resolution = 4.2
  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=   0.001 sd=   0.014
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7228      2.51       5
     N    1956      2.21       5
     O    2274      1.98       5
     H   10770      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22260
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 11008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 723, 11008
          Classifications: {'peptide': 723}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 695}
    Chain: "B"
      Number of atoms: 5446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 5446
          Classifications: {'peptide': 370}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 358}
    Chain: "C"
      Number of atoms: 919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 919
          Classifications: {'peptide': 65}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 57}
    Chain: "D"
      Number of atoms: 3498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 3498
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 210}
    Chain: "E"
      Number of atoms: 1389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1389
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 85}
  Time building chain proxies: 3.53, per 1000 atoms: 0.16
  Number of scatterers: 22260
  At special positions: 0
  Unit cell: (120.06, 104.4, 134.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2274      8.00
     N    1956      7.00
     C    7228      6.00
     H   10770      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 681.9 milliseconds
  

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2686

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 17 sheets defined
      25.5% alpha, 28.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 96
      removed outlier: 4.145A  pdb=" N   LYS A  89 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 122
      removed outlier: 4.237A  pdb=" N   ASP A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 173
      removed outlier: 3.746A  pdb=" N   LEU A 171 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 211
      removed outlier: 3.627A  pdb=" N   LEU A 197 " --> pdb=" O   GLN A 193 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLY A 199 " --> pdb=" O   GLN A 195 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 204 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 266
      removed outlier: 3.514A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 292
    Processing helix  chain 'A' and resid 339 through 345
      removed outlier: 3.590A  pdb=" N   LEU A 343 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 3.853A  pdb=" N   GLY A 411 " --> pdb=" O   PHE A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 3.520A  pdb=" N   GLY A 433 " --> pdb=" O   ASN A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 482
    Processing helix  chain 'A' and resid 524 through 534
      removed outlier: 3.966A  pdb=" N   TRP A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 626
      No H-bonds generated for 'chain 'A' and resid 624 through 626'
    Processing helix  chain 'A' and resid 629 through 633
    Processing helix  chain 'A' and resid 637 through 642
    Processing helix  chain 'A' and resid 673 through 677
    Processing helix  chain 'A' and resid 732 through 736
    Processing helix  chain 'B' and resid 217 through 222
    Processing helix  chain 'C' and resid 40 through 44
    Processing helix  chain 'C' and resid 54 through 58
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 25 through 40
    Processing helix  chain 'D' and resid 45 through 60
    Processing helix  chain 'D' and resid 62 through 77
    Processing helix  chain 'D' and resid 82 through 97
      removed outlier: 3.581A  pdb=" N   VAL D  86 " --> pdb=" O   ASN D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 107
    Processing helix  chain 'D' and resid 115 through 132
    Processing helix  chain 'D' and resid 137 through 167
    Processing helix  chain 'D' and resid 168 through 182
    Processing helix  chain 'D' and resid 186 through 203
      Proline residue:  D 194  - end of helix
      removed outlier: 3.608A  pdb=" N   GLU D 197 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 220
      removed outlier: 3.786A  pdb=" N   ILE D 215 " --> pdb=" O   LYS D 211 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER D 220 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 22
    Processing helix  chain 'E' and resid 29 through 38
    Processing helix  chain 'E' and resid 59 through 62
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 76
      removed outlier: 6.210A  pdb=" N   VAL A 141 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A  74 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 161
      removed outlier: 6.325A  pdb=" N   GLU A 154 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL A 234 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
      removed outlier: 8.415A  pdb=" N   GLN A 156 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 12.777A  pdb=" N   VAL A 236 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
      removed outlier: 9.951A  pdb=" N   ILE A 158 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 12.161A  pdb=" N   ILE A 238 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   ILE A 160 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   THR A 239 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   ILE A 218 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 254
      removed outlier: 4.552A  pdb=" N   LEU A 246 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   LEU A 315 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLY A 248 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   VAL A 317 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU A 250 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   VAL A 319 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   SER A 252 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 254
      removed outlier: 4.552A  pdb=" N   LEU A 246 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   LEU A 315 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLY A 248 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   VAL A 317 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU A 250 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   VAL A 319 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   SER A 252 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 333
      removed outlier: 6.292A  pdb=" N   TYR A 326 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   VAL A 392 " --> pdb=" O   TYR A 326 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ARG A 328 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 12.409A  pdb=" N   TYR A 394 " --> pdb=" O   ARG A 328 " (cutoff:3.500A)
      removed outlier: 9.720A  pdb=" N   ILE A 330 " --> pdb=" O   TYR A 394 " (cutoff:3.500A)
      removed outlier: 11.754A  pdb=" N   VAL A 396 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   PHE A 332 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
      removed outlier: 11.190A  pdb=" N   GLU A 398 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL A 393 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   THR A 378 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS A 395 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   VAL A 376 " --> pdb=" O   LYS A 395 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415
      removed outlier: 4.147A  pdb=" N   VAL A 766 " --> pdb=" O   ASN A 787 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR A 717 " --> pdb=" O   THR A 702 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   TYR A 590 " --> pdb=" O   THR A 582 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TRP A 558 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU A 471 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ASP A 475 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   THR A 449 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LYS A 444 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 653 through 656
      removed outlier: 5.661A  pdb=" N   ASP A 686 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   TYR A 656 " --> pdb=" O   SER A 684 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   SER A 684 " --> pdb=" O   TYR A 656 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 23 through 29
      removed outlier: 4.857A  pdb=" N   THR B  24 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   THR B 369 " --> pdb=" O   THR B  24 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TRP B  26 " --> pdb=" O   SER B 367 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 46
      removed outlier: 6.694A  pdb=" N   VAL B  59 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   SER B  72 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA B  61 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 89 through 96
      removed outlier: 6.631A  pdb=" N   GLY B  92 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   TYR B 101 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   THR B  94 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   HIS B  99 " --> pdb=" O   THR B  94 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLN B 108 " --> pdb=" O   SER B 104 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASN B 113 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL B 119 " --> pdb=" O   ASN B 113 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 136
      removed outlier: 3.679A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU B 149 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 162 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA B 151 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 179 through 181
      removed outlier: 6.286A  pdb=" N   LEU B 198 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   MET B 204 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 230 through 232
      removed outlier: 6.519A  pdb=" N   ALA B 247 " --> pdb=" O   MET B 256 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 270
      removed outlier: 3.943A  pdb=" N   VAL B 283 " --> pdb=" O   GLN B 297 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP B 295 " --> pdb=" O   ALA B 285 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   THR B 287 " --> pdb=" O   THR B 293 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   THR B 293 " --> pdb=" O   THR B 287 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 309 through 311
      removed outlier: 3.755A  pdb=" N   ALA B 336 " --> pdb=" O   TRP B 326 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ASN B 328 " --> pdb=" O   PHE B 334 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   PHE B 334 " --> pdb=" O   ASN B 328 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.826A  pdb=" N   ILE E  10 " --> pdb=" O   GLN E  58 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE E  52 " --> pdb=" O   MET E  42 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   MET E  42 " --> pdb=" O   PHE E  52 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.826A  pdb=" N   ILE E  10 " --> pdb=" O   GLN E  58 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   GLN E  66 " --> pdb=" O   PRO E  86 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   THR E  68 " --> pdb=" O   ASN E  84 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ASN E  84 " --> pdb=" O   THR E  68 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   THR E  70 " --> pdb=" O   ILE E  82 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE E  82 " --> pdb=" O   THR E  70 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   THR E  72 " --> pdb=" O   THR E  80 " (cutoff:3.500A)

    491 hydrogen bonds defined for protein.
    1335 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: 5.24

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10767
        1.03 -     1.23: 91
        1.23 -     1.43: 5008
        1.43 -     1.62: 6588
        1.62 -     1.82: 61
  Bond restraints: 22515
  Sorted by residual:
  bond pdb=" N   CYS C   3 "
       pdb=" H1  CYS C   3 "
    ideal  model  delta    sigma   weight residual
    0.960  0.861  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C   ASN A 139 "
       pdb=" O   ASN A 139 "
    ideal  model  delta    sigma   weight residual
    1.239  1.204  0.035 1.47e-02 4.63e+03 5.63e+00
  bond pdb=" CA  PRO A 137 "
       pdb=" CB  PRO A 137 "
    ideal  model  delta    sigma   weight residual
    1.533  1.508  0.025 1.42e-02 4.96e+03 3.06e+00
  bond pdb=" N   LEU E   1 "
       pdb=" CA  LEU E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   PHE B   1 "
       pdb=" CA  PHE B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  ... (remaining 22510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 36066
        1.75 -     3.49: 3993
        3.49 -     5.24: 260
        5.24 -     6.98: 44
        6.98 -     8.73: 7
  Bond angle restraints: 40370
  Sorted by residual:
  angle pdb=" N   HIS B 143 "
        pdb=" CA  HIS B 143 "
        pdb=" C   HIS B 143 "
      ideal   model   delta    sigma   weight residual
     110.59  101.86    8.73 1.45e+00 4.76e-01 3.62e+01
  angle pdb=" N   TYR D 163 "
        pdb=" CA  TYR D 163 "
        pdb=" C   TYR D 163 "
      ideal   model   delta    sigma   weight residual
     111.69  105.84    5.85 1.23e+00 6.61e-01 2.26e+01
  angle pdb=" N   PHE A 706 "
        pdb=" CA  PHE A 706 "
        pdb=" C   PHE A 706 "
      ideal   model   delta    sigma   weight residual
     110.80  118.92   -8.12 2.13e+00 2.20e-01 1.45e+01
  angle pdb=" CA  TYR D 162 "
        pdb=" CB  TYR D 162 "
        pdb=" CG  TYR D 162 "
      ideal   model   delta    sigma   weight residual
     113.90  107.24    6.66 1.80e+00 3.09e-01 1.37e+01
  angle pdb=" CA  TRP A 528 "
        pdb=" CB  TRP A 528 "
        pdb=" CG  TRP A 528 "
      ideal   model   delta    sigma   weight residual
     113.60  107.26    6.34 1.90e+00 2.77e-01 1.11e+01
  ... (remaining 40365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 9708
       16.99 -    33.98: 736
       33.98 -    50.97: 239
       50.97 -    67.96: 76
       67.96 -    84.95: 18
  Dihedral angle restraints: 10777
    sinusoidal: 5771
      harmonic: 5006
  Sorted by residual:
  dihedral pdb=" CA  VAL A 420 "
           pdb=" C   VAL A 420 "
           pdb=" N   SER A 421 "
           pdb=" CA  SER A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  ARG C   8 "
           pdb=" C   ARG C   8 "
           pdb=" N   TYR C   9 "
           pdb=" CA  TYR C   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.99   28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  ASN A 163 "
           pdb=" C   ASN A 163 "
           pdb=" N   HIS A 164 "
           pdb=" CA  HIS A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.21   27.79     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 10774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1113
       0.038 -    0.076: 423
       0.076 -    0.115: 149
       0.115 -    0.153: 43
       0.153 -    0.191: 3
  Chirality restraints: 1731
  Sorted by residual:
  chirality pdb=" CA  TRP A 528 "
            pdb=" N   TRP A 528 "
            pdb=" C   TRP A 528 "
            pdb=" CB  TRP A 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CA  TYR D 162 "
            pdb=" N   TYR D 162 "
            pdb=" C   TYR D 162 "
            pdb=" CB  TYR D 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.99e-01
  chirality pdb=" CA  HIS B 143 "
            pdb=" N   HIS B 143 "
            pdb=" C   HIS B 143 "
            pdb=" CB  HIS B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.73e-01
  ... (remaining 1728 not shown)

  Planarity restraints: 3514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 528 "    0.034 2.00e-02 2.50e+03   3.64e-02 5.30e+01
        pdb=" CG  TRP A 528 "   -0.100 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 528 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 528 "   -0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 528 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 528 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 528 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 528 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 528 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 528 "    0.015 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 528 "    0.066 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 528 "   -0.029 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 528 "    0.032 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 528 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 528 "   -0.040 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 528 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 302 "    0.051 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" CG  HIS B 302 "   -0.004 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 302 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 302 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 302 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 302 "    0.015 2.00e-02 2.50e+03
        pdb=" HD2 HIS B 302 "   -0.041 2.00e-02 2.50e+03
        pdb=" HE1 HIS B 302 "    0.004 2.00e-02 2.50e+03
        pdb=" HE2 HIS B 302 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 524 "    0.027 2.00e-02 2.50e+03   2.39e-02 8.53e+00
        pdb=" CD  GLN A 524 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 524 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 524 "   -0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN A 524 "   -0.023 2.00e-02 2.50e+03
        pdb="HE22 GLN A 524 "    0.034 2.00e-02 2.50e+03
  ... (remaining 3511 not shown)

  Histogram of nonbonded interaction distances:
        1.10 -     1.80: 76
        1.80 -     2.50: 16143
        2.50 -     3.20: 67650
        3.20 -     3.90: 85895
        3.90 -     4.60: 135338
  Nonbonded interactions: 305102
  Sorted by model distance:
  nonbonded pdb=" HG  SER A 697 "
            pdb=" OD1 ASP A 722 "
     model   vdw
     1.102 2.450
  nonbonded pdb=" HH  TYR D  14 "
            pdb=" OD1 ASP D  52 "
     model   vdw
     1.256 2.450
  nonbonded pdb="HG22 THR B 287 "
            pdb=" H   ASP B 289 "
     model   vdw
     1.470 2.270
  nonbonded pdb=" OE2 GLU A 417 "
            pdb=" H   SER A 639 "
     model   vdw
     1.483 2.450
  nonbonded pdb=" OE1 GLU B 128 "
            pdb=" HG  SER B 145 "
     model   vdw
     1.490 2.450
  ... (remaining 305097 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  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:             0.150
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     21.450
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11745  Z= 0.169
  Angle     :  0.752   8.730  15968  Z= 0.428
  Chirality :  0.047   0.191   1731
  Planarity :  0.006   0.072   2109
  Dihedral  : 13.250  84.951   4250
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.20 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  0.89 %
    Favored  : 98.62 %
  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: -1.35 (0.21), residues: 1462
  helix: -0.32 (0.27), residues: 301
  sheet: -0.66 (0.26), residues: 375
  loop : -1.21 (0.22), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 716 
 TYR   0.031   0.002   TYR D 162 
 PHE   0.016   0.002   PHE A 408 
 TRP   0.087   0.003   TRP A 528 
 HIS   0.019   0.002   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11745)
  covalent geometry    : angle       0.75153 (15968)
  hydrogen bonds       : bond        0.18700 (  488)
  hydrogen bonds       : angle       9.23620 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  421 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 415
  time to evaluate  : 0.553 
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: 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: 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: 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: 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: 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  196 LYS cc_start: 0.8905 (mttp) cc_final: 0.8675 (tppt)
REVERT: A  230 LYS cc_start: 0.8796 (pttp) cc_final: 0.8542 (pttm)
REVERT: A  274 TYR cc_start: 0.8611 (t80) cc_final: 0.8379 (t80)
REVERT: A  283 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8273 (mm-30)
REVERT: A  292 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7499 (mtp-110)
REVERT: A  337 THR cc_start: 0.8448 (m) cc_final: 0.8219 (p)
REVERT: A  504 TYR cc_start: 0.7794 (m-80) cc_final: 0.7449 (m-80)
REVERT: A  578 THR cc_start: 0.7182 (m) cc_final: 0.6881 (m)
REVERT: A  650 ILE cc_start: 0.8954 (mm) cc_final: 0.8600 (mm)
REVERT: A  723 MET cc_start: 0.5465 (mtp) cc_final: 0.5121 (mtm)
REVERT: A  769 TYR cc_start: 0.8157 (t80) cc_final: 0.7409 (t80)
REVERT: A  786 PHE cc_start: 0.7605 (p90) cc_final: 0.7371 (p90)
REVERT: B   51 TYR cc_start: 0.9250 (m-80) cc_final: 0.8859 (m-80)
REVERT: B   94 THR cc_start: 0.8192 (m) cc_final: 0.7621 (m)
REVERT: B  106 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8239 (mmtt)
REVERT: B  110 TYR cc_start: 0.8888 (m-80) cc_final: 0.8679 (m-80)
REVERT: B  124 LYS cc_start: 0.8710 (tttm) cc_final: 0.8334 (ttpt)
REVERT: B  219 ILE cc_start: 0.6485 (mt) cc_final: 0.6027 (mt)
REVERT: B  248 LEU cc_start: 0.8783 (mt) cc_final: 0.8451 (mp)
REVERT: D    8 ASN cc_start: 0.7421 (m-40) cc_final: 0.7043 (m-40)
REVERT: D   20 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8379 (mmmm)
REVERT: D   27 ARG cc_start: 0.7923 (mtt180) cc_final: 0.6975 (mtp180)
REVERT: D  109 ASP cc_start: 0.7122 (m-30) cc_final: 0.6838 (p0)
REVERT: D  112 ASP cc_start: 0.8031 (p0) cc_final: 0.7807 (p0)
REVERT: D  166 ARG cc_start: 0.8447 (tpp80) cc_final: 0.7868 (ttm110)
REVERT: E   28 MET cc_start: 0.7470 (tpp) cc_final: 0.7025 (mmm)
REVERT: E   58 GLN cc_start: 0.8314 (tt0) cc_final: 0.7647 (mt0)
REVERT: E   70 THR cc_start: 0.9360 (m) cc_final: 0.9137 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 419
  average time/residue: 0.2643
  time to fit residues: 152.6419
Evaluate side-chains
  262 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN
B 302 HIS
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.124138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.092661 restraints weight = 90396.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.096996 restraints weight = 41632.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.099775 restraints weight = 25761.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101533 restraints weight = 19148.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.102511 restraints weight = 15879.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11745  Z= 0.250
  Angle     :  0.700   7.157  15968  Z= 0.394
  Chirality :  0.046   0.156   1731
  Planarity :  0.006   0.054   2109
  Dihedral  :  7.172  69.988   1617
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.29 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.33 %
    Favored  : 96.59 %
  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: -1.40 (0.21), residues: 1462
  helix:  0.09 (0.27), residues: 307
  sheet: -0.81 (0.26), residues: 354
  loop : -1.39 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 470 
 TYR   0.029   0.002   TYR D 162 
 PHE   0.017   0.002   PHE A 552 
 TRP   0.032   0.002   TRP A 528 
 HIS   0.015   0.002   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (11745)
  covalent geometry    : angle       0.69963 (15968)
  hydrogen bonds       : bond        0.05319 (  488)
  hydrogen bonds       : angle       7.09339 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  297 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 296
  time to evaluate  : 0.689 
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: 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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7773 (mtp85)
REVERT: A  422 PHE cc_start: 0.6234 (m-80) cc_final: 0.5918 (m-10)
REVERT: A  671 GLU cc_start: 0.6846 (tp30) cc_final: 0.6618 (tp30)
REVERT: A  680 ASP cc_start: 0.6229 (t0) cc_final: 0.5534 (p0)
REVERT: A  786 PHE cc_start: 0.7275 (p90) cc_final: 0.6879 (p90)
REVERT: B   51 TYR cc_start: 0.9041 (m-80) cc_final: 0.8715 (m-80)
REVERT: B  106 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8563 (mptt)
REVERT: B  124 LYS cc_start: 0.8785 (tttm) cc_final: 0.8338 (ttpt)
REVERT: B  167 MET cc_start: 0.8941 (tpp) cc_final: 0.8726 (tpp)
REVERT: B  204 MET cc_start: 0.7743 (mmp) cc_final: 0.7335 (pmm)
REVERT: B  275 TYR cc_start: 0.8074 (m-80) cc_final: 0.7829 (m-80)
REVERT: C   17 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7964 (pm20)
REVERT: D   27 ARG cc_start: 0.7917 (mtt180) cc_final: 0.6828 (mtp180)
REVERT: D  112 ASP cc_start: 0.8255 (p0) cc_final: 0.7825 (p0)
REVERT: D  166 ARG cc_start: 0.8703 (tpp80) cc_final: 0.7503 (mtt180)
REVERT: E   22 SER cc_start: 0.8934 (m) cc_final: 0.8506 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 297
  average time/residue: 0.2551
  time to fit residues: 104.6714
Evaluate side-chains
  235 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   chunk 124 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 108 optimal weight:   10.0000
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 ASN
B 279 GLN
B 297 GLN
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.123525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092043 restraints weight = 89692.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096304 restraints weight = 41476.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099048 restraints weight = 25716.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.100771 restraints weight = 19104.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.101850 restraints weight = 15896.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11745  Z= 0.173
  Angle     :  0.600   5.257  15968  Z= 0.334
  Chirality :  0.044   0.155   1731
  Planarity :  0.005   0.053   2109
  Dihedral  :  6.627  68.088   1617
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.50 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  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: -1.35 (0.21), residues: 1462
  helix:  0.45 (0.28), residues: 307
  sheet: -0.93 (0.26), residues: 355
  loop : -1.42 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 173 
 TYR   0.039   0.002   TYR D  57 
 PHE   0.023   0.001   PHE A 634 
 TRP   0.015   0.001   TRP A 528 
 HIS   0.014   0.002   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (11745)
  covalent geometry    : angle       0.60014 (15968)
  hydrogen bonds       : bond        0.04684 (  488)
  hydrogen bonds       : angle       6.59604 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  273 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.600 
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: 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: 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: 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  251 VAL cc_start: 0.8716 (p) cc_final: 0.8306 (p)
REVERT: A  274 TYR cc_start: 0.8479 (t80) cc_final: 0.8053 (t80)
REVERT: A  292 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7736 (mtp-110)
REVERT: A  349 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8835 (tp-100)
REVERT: A  422 PHE cc_start: 0.6280 (m-80) cc_final: 0.5903 (m-80)
REVERT: A  494 ASP cc_start: 0.7649 (m-30) cc_final: 0.7371 (t0)
REVERT: A  551 ASP cc_start: 0.7784 (m-30) cc_final: 0.7420 (m-30)
REVERT: A  576 ASN cc_start: 0.8740 (t0) cc_final: 0.8469 (t0)
REVERT: A  596 ASP cc_start: 0.8596 (t0) cc_final: 0.8323 (t0)
REVERT: A  680 ASP cc_start: 0.6335 (t0) cc_final: 0.5502 (p0)
REVERT: A  681 LEU cc_start: 0.8106 (mp) cc_final: 0.7502 (mt)
REVERT: B   51 TYR cc_start: 0.9023 (m-80) cc_final: 0.8685 (m-80)
REVERT: B   75 LEU cc_start: 0.7427 (mt) cc_final: 0.7016 (mp)
REVERT: B  106 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8565 (mptt)
REVERT: B  124 LYS cc_start: 0.8870 (tttm) cc_final: 0.8392 (ttpt)
REVERT: B  167 MET cc_start: 0.8902 (tpp) cc_final: 0.8621 (tpp)
REVERT: B  204 MET cc_start: 0.7664 (mmp) cc_final: 0.7343 (pmm)
REVERT: B  275 TYR cc_start: 0.7933 (m-80) cc_final: 0.7697 (m-80)
REVERT: C   56 LYS cc_start: 0.8543 (pttm) cc_final: 0.8034 (mmtt)
REVERT: D   27 ARG cc_start: 0.7839 (mtt180) cc_final: 0.6712 (mtp180)
REVERT: D   57 TYR cc_start: 0.8970 (m-80) cc_final: 0.8743 (m-80)
REVERT: D  166 ARG cc_start: 0.8711 (tpp80) cc_final: 0.7420 (mtt180)
REVERT: D  185 ASP cc_start: 0.8353 (m-30) cc_final: 0.7653 (p0)
REVERT: E   22 SER cc_start: 0.8987 (m) cc_final: 0.8509 (p)
REVERT: E   82 ILE cc_start: 0.8612 (mt) cc_final: 0.8102 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2465
  time to fit residues: 94.7207
Evaluate side-chains
  216 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 125 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 GLN
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.120923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.089345 restraints weight = 90266.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.093525 restraints weight = 41506.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096198 restraints weight = 25671.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097845 restraints weight = 19118.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.098729 restraints weight = 15981.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11745  Z= 0.234
  Angle     :  0.616   5.382  15968  Z= 0.343
  Chirality :  0.044   0.151   1731
  Planarity :  0.006   0.126   2109
  Dihedral  :  6.391  65.578   1617
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.32 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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: -1.46 (0.21), residues: 1462
  helix:  0.46 (0.28), residues: 313
  sheet: -1.12 (0.25), residues: 376
  loop : -1.48 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E   7 
 TYR   0.019   0.002   TYR D  57 
 PHE   0.022   0.002   PHE A 784 
 TRP   0.016   0.001   TRP A 558 
 HIS   0.011   0.002   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (11745)
  covalent geometry    : angle       0.61558 (15968)
  hydrogen bonds       : bond        0.04248 (  488)
  hydrogen bonds       : angle       6.35799 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  258 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.607 
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: 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: 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: 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  292 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7868 (mtp85)
REVERT: A  422 PHE cc_start: 0.6495 (m-80) cc_final: 0.6129 (m-80)
REVERT: A  494 ASP cc_start: 0.7831 (m-30) cc_final: 0.7551 (t0)
REVERT: A  504 TYR cc_start: 0.8439 (m-80) cc_final: 0.8113 (m-80)
REVERT: A  516 ASN cc_start: 0.8402 (m110) cc_final: 0.8164 (m-40)
REVERT: A  551 ASP cc_start: 0.7840 (m-30) cc_final: 0.7571 (m-30)
REVERT: A  596 ASP cc_start: 0.8647 (t0) cc_final: 0.8344 (t0)
REVERT: A  681 LEU cc_start: 0.8208 (mp) cc_final: 0.7889 (mt)
REVERT: A  754 ILE cc_start: 0.8311 (mt) cc_final: 0.7507 (mt)
REVERT: B   51 TYR cc_start: 0.9162 (m-80) cc_final: 0.8788 (m-80)
REVERT: B  101 TYR cc_start: 0.7567 (m-80) cc_final: 0.7315 (m-80)
REVERT: B  167 MET cc_start: 0.8883 (tpp) cc_final: 0.8371 (tpp)
REVERT: B  204 MET cc_start: 0.7661 (mmp) cc_final: 0.7444 (pmm)
REVERT: B  275 TYR cc_start: 0.8053 (m-80) cc_final: 0.7778 (m-80)
REVERT: C   56 LYS cc_start: 0.8528 (pttm) cc_final: 0.8069 (mmtt)
REVERT: D   27 ARG cc_start: 0.7853 (mtt180) cc_final: 0.6658 (mtp180)
REVERT: D   57 TYR cc_start: 0.9024 (m-80) cc_final: 0.8543 (m-80)
REVERT: D  161 GLU cc_start: 0.8084 (tp30) cc_final: 0.7870 (tm-30)
REVERT: D  165 GLU cc_start: 0.8321 (tp30) cc_final: 0.7656 (tp30)
REVERT: D  166 ARG cc_start: 0.8894 (tpp80) cc_final: 0.7194 (mtt180)
REVERT: D  185 ASP cc_start: 0.8300 (m-30) cc_final: 0.7693 (p0)
REVERT: E   22 SER cc_start: 0.8882 (m) cc_final: 0.8626 (p)
REVERT: E   81 ASN cc_start: 0.7827 (m-40) cc_final: 0.7608 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2461
  time to fit residues: 91.0159
Evaluate side-chains
  203 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 129 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 110 optimal weight:    0.3980
   chunk 128 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 HIS
B 233 ASN
B 328 ASN
D  77 ASN
E  32 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.122393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.090275 restraints weight = 89070.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.094607 restraints weight = 40789.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.097409 restraints weight = 25115.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.099086 restraints weight = 18632.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.100122 restraints weight = 15547.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.5482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11745  Z= 0.128
  Angle     :  0.553   4.617  15968  Z= 0.302
  Chirality :  0.043   0.173   1731
  Planarity :  0.004   0.055   2109
  Dihedral  :  6.035  62.711   1617
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.54 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.97 %
    Favored  : 98.94 %
  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: -1.19 (0.21), residues: 1462
  helix:  0.84 (0.28), residues: 313
  sheet: -1.07 (0.25), residues: 368
  loop : -1.31 (0.22), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 399 
 TYR   0.020   0.001   TYR D  57 
 PHE   0.014   0.001   PHE A 216 
 TRP   0.010   0.001   TRP A 528 
 HIS   0.009   0.001   HIS C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11745)
  covalent geometry    : angle       0.55334 (15968)
  hydrogen bonds       : bond        0.03912 (  488)
  hydrogen bonds       : angle       6.02716 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  263 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 0.641 
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: 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: 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: 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  349 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8810 (tp-100)
REVERT: A  391 ASP cc_start: 0.8681 (m-30) cc_final: 0.8116 (p0)
REVERT: A  422 PHE cc_start: 0.6431 (m-80) cc_final: 0.6056 (m-80)
REVERT: A  494 ASP cc_start: 0.7887 (m-30) cc_final: 0.7625 (t0)
REVERT: A  596 ASP cc_start: 0.8665 (t0) cc_final: 0.8365 (t0)
REVERT: A  681 LEU cc_start: 0.8198 (mp) cc_final: 0.7892 (mt)
REVERT: B   51 TYR cc_start: 0.9090 (m-80) cc_final: 0.8705 (m-80)
REVERT: B  143 HIS cc_start: 0.8076 (t-90) cc_final: 0.7849 (t70)
REVERT: B  275 TYR cc_start: 0.7963 (m-80) cc_final: 0.7738 (m-80)
REVERT: C   56 LYS cc_start: 0.8495 (pttm) cc_final: 0.8000 (mmtt)
REVERT: D   27 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6721 (mtp180)
REVERT: D  161 GLU cc_start: 0.8082 (tp30) cc_final: 0.7877 (tm-30)
REVERT: D  165 GLU cc_start: 0.8252 (tp30) cc_final: 0.7370 (tp30)
REVERT: D  166 ARG cc_start: 0.8855 (tpp80) cc_final: 0.7147 (mtt180)
REVERT: D  185 ASP cc_start: 0.8227 (m-30) cc_final: 0.7474 (p0)
REVERT: E   22 SER cc_start: 0.8838 (m) cc_final: 0.8543 (p)
REVERT: E   81 ASN cc_start: 0.7809 (m-40) cc_final: 0.7597 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2351
  time to fit residues: 89.4667
Evaluate side-chains
  213 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 73 optimal weight:    7.9990
   chunk 137 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.120324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.087945 restraints weight = 89928.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.092173 restraints weight = 41361.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.094851 restraints weight = 25718.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.096541 restraints weight = 19250.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.097291 restraints weight = 16065.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.5874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  11745  Z= 0.216
  Angle     :  0.578   5.152  15968  Z= 0.320
  Chirality :  0.043   0.143   1731
  Planarity :  0.005   0.069   2109
  Dihedral  :  5.969  61.563   1617
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.11 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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: -1.26 (0.21), residues: 1462
  helix:  0.87 (0.29), residues: 311
  sheet: -1.13 (0.25), residues: 374
  loop : -1.39 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 345 
 TYR   0.015   0.002   TYR D  57 
 PHE   0.015   0.002   PHE A 657 
 TRP   0.041   0.002   TRP A 528 
 HIS   0.009   0.002   HIS C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (11745)
  covalent geometry    : angle       0.57840 (15968)
  hydrogen bonds       : bond        0.03959 (  488)
  hydrogen bonds       : angle       6.06028 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  248 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.707 
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: 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: 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: symmetry clash
REVERT: A  200 ASP cc_start: 0.8416 (m-30) cc_final: 0.8162 (t0)
REVERT: A  235 THR cc_start: 0.6609 (m) cc_final: 0.6388 (m)
REVERT: A  349 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8816 (tp-100)
REVERT: A  391 ASP cc_start: 0.8709 (m-30) cc_final: 0.8178 (p0)
REVERT: A  422 PHE cc_start: 0.6486 (m-80) cc_final: 0.6092 (m-80)
REVERT: A  551 ASP cc_start: 0.7980 (m-30) cc_final: 0.7663 (m-30)
REVERT: A  596 ASP cc_start: 0.8709 (t0) cc_final: 0.8443 (t0)
REVERT: A  681 LEU cc_start: 0.8338 (mp) cc_final: 0.8015 (mt)
REVERT: B   51 TYR cc_start: 0.9179 (m-80) cc_final: 0.8763 (m-80)
REVERT: B  143 HIS cc_start: 0.8156 (t-90) cc_final: 0.7910 (t70)
REVERT: B  275 TYR cc_start: 0.8020 (m-80) cc_final: 0.7786 (m-80)
REVERT: C   56 LYS cc_start: 0.8510 (pttm) cc_final: 0.8031 (mmtt)
REVERT: D   27 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6710 (mtp180)
REVERT: D   57 TYR cc_start: 0.8981 (m-80) cc_final: 0.8400 (m-80)
REVERT: D  165 GLU cc_start: 0.8381 (tp30) cc_final: 0.7559 (tp30)
REVERT: D  166 ARG cc_start: 0.8951 (tpp80) cc_final: 0.7187 (mtt180)
REVERT: E   22 SER cc_start: 0.8932 (m) cc_final: 0.8636 (p)
REVERT: E   81 ASN cc_start: 0.7841 (m-40) cc_final: 0.7615 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2133
  time to fit residues: 78.5659
Evaluate side-chains
  200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.121741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089565 restraints weight = 89274.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.093820 restraints weight = 40975.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.096506 restraints weight = 25331.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.098262 restraints weight = 18853.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.099161 restraints weight = 15663.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.6047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11745  Z= 0.126
  Angle     :  0.540   5.486  15968  Z= 0.293
  Chirality :  0.043   0.146   1731
  Planarity :  0.004   0.056   2109
  Dihedral  :  5.706  58.347   1617
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.81 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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: -1.02 (0.22), residues: 1462
  helix:  1.11 (0.29), residues: 311
  sheet: -1.03 (0.25), residues: 366
  loop : -1.22 (0.22), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 345 
 TYR   0.016   0.001   TYR D  57 
 PHE   0.012   0.001   PHE A 499 
 TRP   0.030   0.001   TRP A 528 
 HIS   0.006   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11745)
  covalent geometry    : angle       0.54000 (15968)
  hydrogen bonds       : bond        0.03707 (  488)
  hydrogen bonds       : angle       5.81406 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  250 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.628 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 THR cc_start: 0.6477 (m) cc_final: 0.6262 (m)
REVERT: A  349 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8798 (tp-100)
REVERT: A  350 MET cc_start: 0.8451 (mmp) cc_final: 0.8202 (mmp)
REVERT: A  391 ASP cc_start: 0.8716 (m-30) cc_final: 0.8114 (p0)
REVERT: A  422 PHE cc_start: 0.6534 (m-80) cc_final: 0.6131 (m-80)
REVERT: A  513 TYR cc_start: 0.7679 (t80) cc_final: 0.7318 (t80)
REVERT: A  596 ASP cc_start: 0.8655 (t0) cc_final: 0.8413 (t0)
REVERT: A  681 LEU cc_start: 0.8335 (mp) cc_final: 0.8034 (mt)
REVERT: B   40 ASN cc_start: 0.8256 (t0) cc_final: 0.8007 (t0)
REVERT: B   51 TYR cc_start: 0.9158 (m-80) cc_final: 0.8704 (m-80)
REVERT: B  143 HIS cc_start: 0.8171 (t-90) cc_final: 0.7925 (t70)
REVERT: B  275 TYR cc_start: 0.7994 (m-80) cc_final: 0.7762 (m-80)
REVERT: C   49 ASN cc_start: 0.8711 (p0) cc_final: 0.8479 (p0)
REVERT: C   56 LYS cc_start: 0.8527 (pttm) cc_final: 0.8046 (mmtt)
REVERT: D   27 ARG cc_start: 0.7786 (mtt180) cc_final: 0.6582 (mtp180)
REVERT: D   57 TYR cc_start: 0.8918 (m-80) cc_final: 0.8327 (m-80)
REVERT: D  165 GLU cc_start: 0.8423 (tp30) cc_final: 0.7647 (tp30)
REVERT: D  166 ARG cc_start: 0.8886 (tpp80) cc_final: 0.7294 (mtt90)
REVERT: D  185 ASP cc_start: 0.8153 (m-30) cc_final: 0.7859 (m-30)
REVERT: E   22 SER cc_start: 0.9002 (m) cc_final: 0.8724 (p)
REVERT: E   42 MET cc_start: 0.8415 (mtp) cc_final: 0.8148 (mtp)
REVERT: E   81 ASN cc_start: 0.7844 (m-40) cc_final: 0.7615 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.2325
  time to fit residues: 85.4696
Evaluate side-chains
  203 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0980
   chunk 64 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 129 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 ASN
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.121040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.088150 restraints weight = 90067.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.092398 restraints weight = 42298.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.095129 restraints weight = 26449.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.096845 restraints weight = 19867.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.097920 restraints weight = 16645.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.6242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11745  Z= 0.156
  Angle     :  0.546   7.999  15968  Z= 0.296
  Chirality :  0.043   0.152   1731
  Planarity :  0.004   0.055   2109
  Dihedral  :  5.599  56.184   1617
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.63 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -1.05 (0.22), residues: 1462
  helix:  1.05 (0.29), residues: 311
  sheet: -1.05 (0.25), residues: 373
  loop : -1.22 (0.22), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 151 
 TYR   0.010   0.001   TYR E   6 
 PHE   0.024   0.001   PHE A 175 
 TRP   0.025   0.001   TRP A 528 
 HIS   0.005   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11745)
  covalent geometry    : angle       0.54596 (15968)
  hydrogen bonds       : bond        0.03622 (  488)
  hydrogen bonds       : angle       5.78268 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  243 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.645 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 TYR cc_start: 0.8619 (t80) cc_final: 0.8213 (t80)
REVERT: A  283 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: A  349 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8819 (tp-100)
REVERT: A  350 MET cc_start: 0.8425 (mmp) cc_final: 0.8206 (mmp)
REVERT: A  391 ASP cc_start: 0.8725 (m-30) cc_final: 0.8158 (p0)
REVERT: A  422 PHE cc_start: 0.6523 (m-80) cc_final: 0.6095 (m-80)
REVERT: A  504 TYR cc_start: 0.8665 (m-80) cc_final: 0.8423 (m-10)
REVERT: A  544 ASP cc_start: 0.7969 (p0) cc_final: 0.7750 (p0)
REVERT: A  596 ASP cc_start: 0.8670 (t0) cc_final: 0.8430 (t0)
REVERT: B   51 TYR cc_start: 0.9203 (m-80) cc_final: 0.8713 (m-80)
REVERT: B  143 HIS cc_start: 0.8147 (t-90) cc_final: 0.7885 (t70)
REVERT: C   49 ASN cc_start: 0.8721 (p0) cc_final: 0.8505 (p0)
REVERT: C   56 LYS cc_start: 0.8503 (pttm) cc_final: 0.8048 (mmtt)
REVERT: D   27 ARG cc_start: 0.7817 (mtt180) cc_final: 0.6618 (mtp180)
REVERT: D  165 GLU cc_start: 0.8437 (tp30) cc_final: 0.7742 (tp30)
REVERT: D  166 ARG cc_start: 0.8900 (tpp80) cc_final: 0.7073 (mtt180)
REVERT: D  185 ASP cc_start: 0.8119 (m-30) cc_final: 0.7637 (p0)
REVERT: E   22 SER cc_start: 0.9032 (m) cc_final: 0.8723 (p)
REVERT: E   81 ASN cc_start: 0.7817 (m-40) cc_final: 0.7607 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2247
  time to fit residues: 80.4989
Evaluate side-chains
  202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 114 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 112 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0970
   chunk 78 optimal weight:    0.5980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.120623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.088111 restraints weight = 89497.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.092346 restraints weight = 41315.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.095014 restraints weight = 25580.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.096539 restraints weight = 19099.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.097757 restraints weight = 16130.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.6438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11745  Z= 0.151
  Angle     :  0.540   6.245  15968  Z= 0.292
  Chirality :  0.043   0.155   1731
  Planarity :  0.004   0.054   2109
  Dihedral  :  5.509  53.313   1617
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.16 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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: -0.97 (0.22), residues: 1462
  helix:  1.20 (0.29), residues: 310
  sheet: -1.07 (0.25), residues: 372
  loop : -1.17 (0.23), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 344 
 TYR   0.027   0.001   TYR D  57 
 PHE   0.013   0.001   PHE A 657 
 TRP   0.021   0.001   TRP A 528 
 HIS   0.005   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (11745)
  covalent geometry    : angle       0.53993 (15968)
  hydrogen bonds       : bond        0.03554 (  488)
  hydrogen bonds       : angle       5.70013 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  242 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.623 
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: 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: 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: 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  235 THR cc_start: 0.6566 (m) cc_final: 0.6350 (m)
REVERT: A  283 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8136 (mm-30)
REVERT: A  349 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8776 (tp-100)
REVERT: A  350 MET cc_start: 0.8423 (mmp) cc_final: 0.8205 (mmp)
REVERT: A  391 ASP cc_start: 0.8714 (m-30) cc_final: 0.8150 (p0)
REVERT: A  422 PHE cc_start: 0.6601 (m-80) cc_final: 0.6178 (m-80)
REVERT: A  596 ASP cc_start: 0.8654 (t0) cc_final: 0.8426 (t0)
REVERT: B   51 TYR cc_start: 0.9215 (m-80) cc_final: 0.8711 (m-80)
REVERT: B  141 LEU cc_start: 0.8985 (mm) cc_final: 0.8628 (mm)
REVERT: B  143 HIS cc_start: 0.8102 (t-90) cc_final: 0.7843 (t70)
REVERT: C   49 ASN cc_start: 0.8664 (p0) cc_final: 0.8456 (p0)
REVERT: C   56 LYS cc_start: 0.8510 (pttm) cc_final: 0.8064 (mmtt)
REVERT: D   27 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6590 (mtp180)
REVERT: D  165 GLU cc_start: 0.8465 (tp30) cc_final: 0.7769 (tp30)
REVERT: D  166 ARG cc_start: 0.8864 (tpp80) cc_final: 0.7172 (mtt180)
REVERT: D  185 ASP cc_start: 0.8055 (m-30) cc_final: 0.7546 (p0)
REVERT: E   22 SER cc_start: 0.8988 (m) cc_final: 0.8695 (p)
REVERT: E   81 ASN cc_start: 0.7768 (m-40) cc_final: 0.7528 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2158
  time to fit residues: 78.0016
Evaluate side-chains
  200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 116 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 91 optimal weight:    8.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 ASN
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.118883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.088773 restraints weight = 89640.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.090769 restraints weight = 39158.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.091887 restraints weight = 25944.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.092473 restraints weight = 23900.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.092522 restraints weight = 21588.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.6752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11745  Z= 0.223
  Angle     :  0.582   5.808  15968  Z= 0.321
  Chirality :  0.043   0.144   1731
  Planarity :  0.004   0.052   2109
  Dihedral  :  5.562  51.429   1617
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.66 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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: -1.20 (0.21), residues: 1462
  helix:  0.89 (0.28), residues: 311
  sheet: -1.15 (0.24), residues: 378
  loop : -1.29 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 151 
 TYR   0.021   0.002   TYR D  14 
 PHE   0.015   0.002   PHE A 657 
 TRP   0.021   0.001   TRP A 528 
 HIS   0.005   0.002   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (11745)
  covalent geometry    : angle       0.58198 (15968)
  hydrogen bonds       : bond        0.03827 (  488)
  hydrogen bonds       : angle       5.85974 ( 1335)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   72 is missing expected H atoms. Skipping.
Residue ILE   75 is missing expected H atoms. Skipping.
Residue ILE  108 is missing expected H atoms. Skipping.
Residue ILE  111 is missing expected H atoms. Skipping.
Residue ILE  155 is missing expected H atoms. Skipping.
Residue ILE  158 is missing expected H atoms. Skipping.
Residue ILE  160 is missing expected H atoms. Skipping.
Residue ILE  172 is missing expected H atoms. Skipping.
Residue ILE  218 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue ILE  238 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  286 is missing expected H atoms. Skipping.
Residue ILE  306 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue ILE  412 is missing expected H atoms. Skipping.
Residue ILE  440 is missing expected H atoms. Skipping.
Residue ILE  501 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue ILE  603 is missing expected H atoms. Skipping.
Residue ILE  650 is missing expected H atoms. Skipping.
Residue ILE  701 is missing expected H atoms. Skipping.
Residue ILE  707 is missing expected H atoms. Skipping.
Residue ILE  748 is missing expected H atoms. Skipping.
Residue ILE  754 is missing expected H atoms. Skipping.
Residue ILE  788 is missing expected H atoms. Skipping.
Residue ILE   34 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE  102 is missing expected H atoms. Skipping.
Residue ILE  142 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue ILE  210 is missing expected H atoms. Skipping.
Residue ILE  219 is missing expected H atoms. Skipping.
Residue ILE  255 is missing expected H atoms. Skipping.
Residue ILE  268 is missing expected H atoms. Skipping.
Residue ILE  274 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue ILE  327 is missing expected H atoms. Skipping.
Residue ILE  358 is missing expected H atoms. Skipping.
Residue ILE  368 is missing expected H atoms. Skipping.
Residue ILE   35 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue ILE   60 is missing expected H atoms. Skipping.
Residue ILE   13 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue ILE   54 is missing expected H atoms. Skipping.
Residue ILE   70 is missing expected H atoms. Skipping.
Residue ILE   74 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue ILE  215 is missing expected H atoms. Skipping.
Residue ILE  216 is missing expected H atoms. Skipping.
Residue ILE   10 is missing expected H atoms. Skipping.
Residue ILE   24 is missing expected H atoms. Skipping.
Residue ILE   82 is missing expected H atoms. Skipping.
Evaluate side-chains
  234 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.680 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 THR cc_start: 0.6706 (m) cc_final: 0.6490 (m)
REVERT: A  283 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8238 (mm-30)
REVERT: A  349 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8779 (tp-100)
REVERT: A  391 ASP cc_start: 0.8687 (m-30) cc_final: 0.8264 (p0)
REVERT: A  422 PHE cc_start: 0.6795 (m-80) cc_final: 0.6349 (m-80)
REVERT: A  513 TYR cc_start: 0.7765 (t80) cc_final: 0.7482 (t80)
REVERT: A  596 ASP cc_start: 0.8645 (t0) cc_final: 0.8438 (t0)
REVERT: A  605 ASP cc_start: 0.8050 (m-30) cc_final: 0.7554 (p0)
REVERT: B   51 TYR cc_start: 0.9185 (m-80) cc_final: 0.8762 (m-80)
REVERT: B  141 LEU cc_start: 0.9026 (mm) cc_final: 0.8704 (mm)
REVERT: B  143 HIS cc_start: 0.8046 (t-90) cc_final: 0.7802 (t70)
REVERT: C   56 LYS cc_start: 0.8609 (pttm) cc_final: 0.8097 (mmtt)
REVERT: D   27 ARG cc_start: 0.7898 (mtt180) cc_final: 0.6746 (mtp180)
REVERT: D  165 GLU cc_start: 0.8506 (tp30) cc_final: 0.7950 (tp30)
REVERT: D  166 ARG cc_start: 0.8925 (tpp80) cc_final: 0.7616 (ttm110)
REVERT: D  185 ASP cc_start: 0.8047 (m-30) cc_final: 0.7616 (p0)
REVERT: E   22 SER cc_start: 0.9139 (m) cc_final: 0.8823 (p)
REVERT: E   81 ASN cc_start: 0.7947 (m-40) cc_final: 0.7670 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2195
  time to fit residues: 77.1831
Evaluate side-chains
  198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN
E  30 GLN
E  49 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.117475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087822 restraints weight = 89757.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.089505 restraints weight = 37254.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.090180 restraints weight = 25876.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.090795 restraints weight = 25466.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.091035 restraints weight = 22365.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.7085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11745  Z= 0.257
  Angle     :  0.608   8.382  15968  Z= 0.333
  Chirality :  0.044   0.142   1731
  Planarity :  0.005   0.051   2109
  Dihedral  :  5.704  48.761   1617
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.00 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.37 (0.21), residues: 1462
  helix:  0.61 (0.28), residues: 318
  sheet: -1.17 (0.25), residues: 377
  loop : -1.41 (0.22), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 344 
 TYR   0.036   0.002   TYR D  14 
 PHE   0.017   0.002   PHE A 657 
 TRP   0.026   0.002   TRP A 528 
 HIS   0.006   0.002   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (11745)
  covalent geometry    : angle       0.60791 (15968)
  hydrogen bonds       : bond        0.03895 (  488)
  hydrogen bonds       : angle       5.98124 ( 1335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4159.42 seconds
wall clock time: 71 minutes 46.06 seconds (4306.06 seconds total)