Starting phenix.real_space_refine
on Wed Mar  4 12:43:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yae_10747/03_2026/6yae_10747.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.151
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    8767      2.51       5
     N    2336      2.21       5
     O    2532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13707
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4737
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 22, 'TRANS': 577}
    Chain: "B"
      Number of atoms: 4578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4578
          Classifications: {'peptide': 579}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 26, 'TRANS': 552}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "M"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3192
          Classifications: {'peptide': 396}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 378}
          Chain breaks: 3
    Chain: "S"
      Number of atoms: 1200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1200
          Classifications: {'peptide': 142}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 141}
  Time building chain proxies: 2.76, per 1000 atoms: 0.20
  Number of scatterers: 13707
  At special positions: 0
  Unit cell: (97.37, 109.14, 125.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    2532      8.00
     N    2336      7.00
     C    8767      6.00
    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: 1.01
  Conformation dependent library (CDL) restraints added in 588.9 milliseconds
  

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3318

  Finding SS restraints...
    Secondary structure from input PDB file:
      86 helices and 8 sheets defined
      62.8% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
    Processing helix  chain 'A' and resid 25 through 46
    Processing helix  chain 'A' and resid 51 through 69
      removed outlier: 3.578A  pdb=" N   GLY A  69 " --> pdb=" O   ILE A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 82
    Processing helix  chain 'A' and resid 87 through 101
    Processing helix  chain 'A' and resid 105 through 122
    Processing helix  chain 'A' and resid 124 through 139
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 161 through 179
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 200 through 216
      removed outlier: 3.589A  pdb=" N   VAL A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 4.347A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 238
      removed outlier: 4.689A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.507A  pdb=" N   CYS A 267 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 299 through 321
      removed outlier: 3.950A  pdb=" N   SER A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 338
    Processing helix  chain 'A' and resid 342 through 357
      removed outlier: 3.649A  pdb=" N   THR A 355 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 369
      removed outlier: 3.964A  pdb=" N   HIS A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 380
      removed outlier: 3.582A  pdb=" N   THR A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 396
      removed outlier: 3.776A  pdb=" N   ARG A 386 " --> pdb=" O   ASP A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 414
    Processing helix  chain 'A' and resid 417 through 436
      removed outlier: 3.757A  pdb=" N   ARG A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   GLU A 422 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 454
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 472
      removed outlier: 4.318A  pdb=" N   TRP A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR A 463 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 489
    Processing helix  chain 'A' and resid 493 through 508
    Processing helix  chain 'A' and resid 509 through 511
      No H-bonds generated for 'chain 'A' and resid 509 through 511'
    Processing helix  chain 'A' and resid 518 through 531
      removed outlier: 3.670A  pdb=" N   HIS A 531 " --> pdb=" O   HIS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 552
      removed outlier: 3.508A  pdb=" N   ILE A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 564
      removed outlier: 3.718A  pdb=" N   GLN A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 570
      removed outlier: 3.550A  pdb=" N   LYS A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 588
      removed outlier: 4.199A  pdb=" N   GLN A 577 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'B' and resid 13 through 22
    Processing helix  chain 'B' and resid 26 through 44
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 62 through 78
      removed outlier: 3.659A  pdb=" N   LYS B  66 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS B  78 " --> pdb=" O   MET B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 86
      removed outlier: 3.565A  pdb=" N   ALA B  84 " --> pdb=" O   GLN B  80 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET B  86 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 93
    Processing helix  chain 'B' and resid 99 through 113
      removed outlier: 3.701A  pdb=" N   ARG B 103 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
      removed outlier: 3.677A  pdb=" N   TYR B 121 " --> pdb=" O   LYS B 117 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   GLU B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      Proline residue:  B 125  - end of helix
      removed outlier: 4.520A  pdb=" N   LYS B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
      removed outlier: 3.646A  pdb=" N   ARG B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL B 143 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B 146 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 170
      removed outlier: 4.152A  pdb=" N   GLY B 160 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA B 170 " --> pdb=" O   ARG B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 190
      removed outlier: 3.569A  pdb=" N   VAL B 177 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 214
      removed outlier: 4.266A  pdb=" N   ASN B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLU B 213 " --> pdb=" O   THR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 229
      removed outlier: 3.966A  pdb=" N   PHE B 221 " --> pdb=" O   TRP B 217 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TYR B 229 " --> pdb=" O   CYS B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 245
    Processing helix  chain 'B' and resid 251 through 266
      removed outlier: 3.844A  pdb=" N   VAL B 256 " --> pdb=" O   ASN B 252 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU B 257 " --> pdb=" O   SER B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 284
    Processing helix  chain 'B' and resid 284 through 291
    Processing helix  chain 'B' and resid 295 through 313
      removed outlier: 4.002A  pdb=" N   LEU B 308 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 346
      removed outlier: 4.363A  pdb=" N   GLU B 337 " --> pdb=" O   TYR B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 362
      removed outlier: 4.029A  pdb=" N   ALA B 356 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B 359 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 381
    Processing helix  chain 'B' and resid 382 through 383
      No H-bonds generated for 'chain 'B' and resid 382 through 383'
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 387 through 401
    Processing helix  chain 'B' and resid 403 through 421
      removed outlier: 4.654A  pdb=" N   GLU B 409 " --> pdb=" O   TYR B 405 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 435
      removed outlier: 3.512A  pdb=" N   CYS B 433 " --> pdb=" O   ILE B 429 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU B 434 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ASN B 435 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 454
    Processing helix  chain 'B' and resid 455 through 459
    Processing helix  chain 'B' and resid 461 through 472
      removed outlier: 3.923A  pdb=" N   PHE B 469 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU B 471 " --> pdb=" O   GLU B 467 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   GLY B 472 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 495
    Processing helix  chain 'B' and resid 499 through 512
      removed outlier: 3.593A  pdb=" N   GLN B 504 " --> pdb=" O   GLN B 500 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLN B 505 " --> pdb=" O   GLU B 501 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B 507 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 533
      removed outlier: 3.528A  pdb=" N   ASP B 533 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 542
      removed outlier: 4.536A  pdb=" N   GLU B 539 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 566
    Processing helix  chain 'B' and resid 569 through 575
      removed outlier: 4.347A  pdb=" N   VAL B 573 " --> pdb=" O   SER B 569 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TYR B 574 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   HIS B 575 " --> pdb=" O   ALA B 571 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 569 through 575'
    Processing helix  chain 'B' and resid 577 through 581
    Processing helix  chain 'M' and resid 25 through 36
      removed outlier: 3.909A  pdb=" N   VAL M  29 " --> pdb=" O   GLY M  25 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL M  36 " --> pdb=" O   PHE M  32 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 74 through 94
      removed outlier: 3.595A  pdb=" N   VAL M  78 " --> pdb=" O   ASN M  74 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE M  79 " --> pdb=" O   ALA M  75 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 97 through 104
    Processing helix  chain 'M' and resid 104 through 115
    Processing helix  chain 'M' and resid 125 through 129
    Processing helix  chain 'M' and resid 414 through 418
    Processing helix  chain 'S' and resid 24 through 40
    Processing helix  chain 'S' and resid 77 through 95
    Processing helix  chain 'S' and resid 99 through 106
    Processing helix  chain 'S' and resid 106 through 117
      removed outlier: 4.136A  pdb=" N   THR S 112 " --> pdb=" O   TYR S 108 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 127 through 139
    Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249
    Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19
    Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117
    Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248
      removed outlier: 5.620A  pdb=" N   GLU M 271 " --> pdb=" O   SER M 204 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   SER M 204 " --> pdb=" O   GLU M 271 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   GLU M 273 " --> pdb=" O   MET M 202 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   MET M 202 " --> pdb=" O   GLU M 273 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   MET M 275 " --> pdb=" O   VAL M 200 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU M 173 " --> pdb=" O   TRP M 421 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   ARG M 423 " --> pdb=" O   LEU M 173 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LEU M 175 " --> pdb=" O   ARG M 423 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   ILE M 425 " --> pdb=" O   LEU M 175 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL M 177 " --> pdb=" O   ILE M 425 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ARG M 427 " --> pdb=" O   VAL M 177 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   GLU M 179 " --> pdb=" O   ARG M 427 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLY M 429 " --> pdb=" O   GLU M 179 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL M 181 " --> pdb=" O   GLY M 429 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   TYR M 431 " --> pdb=" O   VAL M 181 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LEU M 183 " --> pdb=" O   TYR M 431 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   THR M 433 " --> pdb=" O   LEU M 183 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   MET M 185 " --> pdb=" O   THR M 433 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   ARG M 427 " --> pdb=" O   VAL M 392 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   VAL M 392 " --> pdb=" O   ARG M 427 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   GLY M 429 " --> pdb=" O   PHE M 390 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   PHE M 390 " --> pdb=" O   GLY M 429 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   TYR M 431 " --> pdb=" O   MET M 388 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   SER M 387 " --> pdb=" O   VAL M 322 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   VAL M 322 " --> pdb=" O   SER M 387 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ASN M 389 " --> pdb=" O   ILE M 320 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ILE M 320 " --> pdb=" O   ASN M 389 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLN M 318 " --> pdb=" O   ARG M 357 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ARG M 357 " --> pdb=" O   GLN M 318 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'M' and resid 263 through 265
    Processing sheet with id=AA6, first strand: chain 'M' and resid 287 through 294
      removed outlier: 3.552A  pdb=" N   GLU M 371 " --> pdb=" O   GLY M 332 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY M 332 " --> pdb=" O   GLU M 371 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'S' and resid 14 through 19
      removed outlier: 6.488A  pdb=" N   THR S  14 " --> pdb=" O   ASN S   9 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASN S   9 " --> pdb=" O   THR S  14 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS S  70 " --> pdb=" O   ARG S   3 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ILE S   5 " --> pdb=" O   CYS S  68 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   CYS S  68 " --> pdb=" O   ILE S   5 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ILE S   7 " --> pdb=" O   TYR S  66 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   TYR S  66 " --> pdb=" O   ILE S   7 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 118 through 119

    789 hydrogen bonds defined for protein.
    2295 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.20

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4482
        1.34 -     1.46: 2500
        1.46 -     1.57: 6858
        1.57 -     1.69: 0
        1.69 -     1.81: 111
  Bond restraints: 13951
  Sorted by residual:
  bond pdb=" CA  ALA B 178 "
       pdb=" C   ALA B 178 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.056 1.41e-02 5.03e+03 1.60e+01
  bond pdb=" C   ALA B 178 "
       pdb=" N   ASN B 179 "
    ideal  model  delta    sigma   weight residual
    1.332  1.289  0.043 1.35e-02 5.49e+03 1.01e+01
  bond pdb=" CB  TRP A 256 "
       pdb=" CG  TRP A 256 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.07e+00
  bond pdb=" CB  TRP M  64 "
       pdb=" CG  TRP M  64 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.87e+00
  bond pdb=" C   PRO A 604 "
       pdb=" N   PHE A 605 "
    ideal  model  delta    sigma   weight residual
    1.326  1.299  0.027 1.84e-02 2.95e+03 2.17e+00
  ... (remaining 13946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 18686
        2.95 -     5.91: 175
        5.91 -     8.86: 23
        8.86 -    11.82: 1
       11.82 -    14.77: 1
  Bond angle restraints: 18886
  Sorted by residual:
  angle pdb=" C   GLN A 488 "
        pdb=" N   ALA A 489 "
        pdb=" CA  ALA A 489 "
      ideal   model   delta    sigma   weight residual
     120.69  105.92   14.77 2.95e+00 1.15e-01 2.51e+01
  angle pdb=" N   ILE A 511 "
        pdb=" CA  ILE A 511 "
        pdb=" C   ILE A 511 "
      ideal   model   delta    sigma   weight residual
     113.71  109.62    4.09 9.50e-01 1.11e+00 1.85e+01
  angle pdb=" C   VAL S  39 "
        pdb=" N   THR S  40 "
        pdb=" CA  THR S  40 "
      ideal   model   delta    sigma   weight residual
     122.31  115.93    6.38 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" N   HIS B 191 "
        pdb=" CA  HIS B 191 "
        pdb=" C   HIS B 191 "
      ideal   model   delta    sigma   weight residual
     108.59  114.68   -6.09 1.96e+00 2.60e-01 9.64e+00
  angle pdb=" C   PHE S  49 "
        pdb=" N   VAL S  50 "
        pdb=" CA  VAL S  50 "
      ideal   model   delta    sigma   weight residual
     123.14  119.23    3.91 1.31e+00 5.83e-01 8.89e+00
  ... (remaining 18881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 7681
       17.40 -    34.80: 748
       34.80 -    52.20: 114
       52.20 -    69.60: 22
       69.60 -    86.99: 15
  Dihedral angle restraints: 8580
    sinusoidal: 3488
      harmonic: 5092
  Sorted by residual:
  dihedral pdb=" CA  SER B 190 "
           pdb=" C   SER B 190 "
           pdb=" N   HIS B 191 "
           pdb=" CA  HIS B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.22  -35.78     0      5.00e+00 4.00e-02 5.12e+01
  dihedral pdb=" CA  HIS A 493 "
           pdb=" C   HIS A 493 "
           pdb=" N   GLU A 494 "
           pdb=" CA  GLU A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.80  -31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral pdb=" CA  HIS B 191 "
           pdb=" C   HIS B 191 "
           pdb=" N   PRO B 192 "
           pdb=" CA  PRO B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.92   29.08     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 8577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1232
       0.034 -    0.068: 659
       0.068 -    0.102: 233
       0.102 -    0.137: 61
       0.137 -    0.171: 13
  Chirality restraints: 2198
  Sorted by residual:
  chirality pdb=" CA  TRP A 462 "
            pdb=" N   TRP A 462 "
            pdb=" C   TRP A 462 "
            pdb=" CB  TRP A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.29e-01
  chirality pdb=" CA  ASP A 474 "
            pdb=" N   ASP A 474 "
            pdb=" C   ASP A 474 "
            pdb=" CB  ASP A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.62e-01
  chirality pdb=" CA  ILE M 263 "
            pdb=" N   ILE M 263 "
            pdb=" C   ILE M 263 "
            pdb=" CB  ILE M 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.57e-01
  ... (remaining 2195 not shown)

  Planarity restraints: 2403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 295 "   -0.030 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 296 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE M 290 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   ILE M 290 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ILE M 290 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PRO M 291 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 556 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO B 557 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 557 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 557 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 2400 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 339
        2.65 -     3.22: 14575
        3.22 -     3.78: 20637
        3.78 -     4.34: 27703
        4.34 -     4.90: 44080
  Nonbonded interactions: 107334
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 229 "
            pdb=" OE2 GLU B 236 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" O   MET B 155 "
            pdb=" N   ASP B 158 "
     model   vdw
     2.105 3.120
  nonbonded pdb=" OG  SER A 322 "
            pdb=" OE2 GLU A 323 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OD1 ASP A 444 "
            pdb=" OH  TYR A 478 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   HIS A 369 "
            pdb=" OG1 THR A 372 "
     model   vdw
     2.146 3.040
  ... (remaining 107329 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.470
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
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      :  0.009   0.056  13951  Z= 0.386
  Angle     :  0.820  14.773  18886  Z= 0.450
  Chirality :  0.046   0.171   2198
  Planarity :  0.004   0.045   2403
  Dihedral  : 14.185  86.995   5262
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.34 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  8.78 %
    Favored  : 91.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.17), residues: 1703
  helix: -1.83 (0.13), residues: 958
  sheet: -1.48 (0.34), residues: 190
  loop : -2.89 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.024   0.002   TYR B 524 
 PHE   0.026   0.002   PHE A 523 
 TRP   0.015   0.002   TRP A 462 
 HIS   0.010   0.002   HIS S  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00862 (13951)
  covalent geometry    : angle       0.82037 (18886)
  hydrogen bonds       : bond        0.13562 (  789)
  hydrogen bonds       : angle       6.46429 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 294
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8457 (t0) cc_final: 0.8076 (t0)
REVERT: A   77 MET cc_start: 0.8085 (tpp) cc_final: 0.7738 (tpp)
REVERT: A  161 MET cc_start: 0.7078 (ttt) cc_final: 0.6607 (ttt)
REVERT: A  162 ASP cc_start: 0.8466 (p0) cc_final: 0.8235 (p0)
REVERT: A  396 MET cc_start: 0.9039 (ptt) cc_final: 0.8716 (ptp)
REVERT: A  401 ASN cc_start: 0.8672 (t0) cc_final: 0.8334 (t0)
REVERT: A  578 GLN cc_start: 0.8676 (tp40) cc_final: 0.8457 (tt0)
REVERT: B   32 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: B   86 MET cc_start: 0.9175 (mtm) cc_final: 0.8606 (mpp)
REVERT: B  297 GLU cc_start: 0.8389 (mp0) cc_final: 0.7982 (mp0)
REVERT: B  322 LYS cc_start: 0.9368 (mttt) cc_final: 0.9118 (mttp)
REVERT: B  330 ASP cc_start: 0.8540 (m-30) cc_final: 0.8281 (m-30)
REVERT: B  366 ASP cc_start: 0.8272 (t0) cc_final: 0.7816 (t70)
REVERT: B  385 GLU cc_start: 0.8159 (tt0) cc_final: 0.7801 (mm-30)
REVERT: B  485 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8719 (mm)
REVERT: B  509 LEU cc_start: 0.9187 (tp) cc_final: 0.8743 (tp)
REVERT: M  118 PHE cc_start: 0.8111 (t80) cc_final: 0.7410 (t80)
REVERT: M  277 TYR cc_start: 0.8196 (p90) cc_final: 0.7257 (p90)
REVERT: M  361 MET cc_start: 0.9007 (mmt) cc_final: 0.8661 (mmm)
REVERT: S   74 ASN cc_start: 0.8727 (p0) cc_final: 0.8503 (p0)
REVERT: S   93 GLU cc_start: 0.9147 (tp30) cc_final: 0.8576 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 296
  average time/residue: 0.1285
  time to fit residues: 53.3861
Evaluate side-chains
  209 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 107 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 320 HIS
A 339 GLN
A 344 ASN
A 471 ASN
A 571 ASN
B 195 ASN
B 238 GLN
B 252 ASN
B 311 GLN
B 575 HIS
M  27 ASN
M  35 ASN
M  38 HIS
M  72 ASN
M 135 GLN
M 188 GLN
M 195 HIS
M 310 ASN
S  46 HIS
S  48 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.097061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.079347 restraints weight = 30678.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.082385 restraints weight = 16361.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.084477 restraints weight = 10590.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085930 restraints weight = 7702.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.086999 restraints weight = 6091.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13951  Z= 0.135
  Angle     :  0.635  10.928  18886  Z= 0.333
  Chirality :  0.043   0.234   2198
  Planarity :  0.004   0.037   2403
  Dihedral  :  5.305  50.242   1870
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.17 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.78 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

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: -1.12 (0.20), residues: 1703
  helix:  0.08 (0.16), residues: 954
  sheet: -0.76 (0.36), residues: 191
  loop : -2.07 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 585 
 TYR   0.017   0.001   TYR A 583 
 PHE   0.020   0.002   PHE B 492 
 TRP   0.015   0.001   TRP A 462 
 HIS   0.006   0.001   HIS S  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13951)
  covalent geometry    : angle       0.63489 (18886)
  hydrogen bonds       : bond        0.04388 (  789)
  hydrogen bonds       : angle       4.76408 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 291
  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: A   19 ASP cc_start: 0.8661 (t0) cc_final: 0.8351 (t0)
REVERT: A   71 ASP cc_start: 0.8143 (t0) cc_final: 0.7874 (t0)
REVERT: A   77 MET cc_start: 0.8029 (tpp) cc_final: 0.7735 (tpp)
REVERT: A   92 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8548 (tp-100)
REVERT: A  142 GLU cc_start: 0.9002 (mp0) cc_final: 0.8710 (mp0)
REVERT: A  341 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7556 (ttm170)
REVERT: A  372 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8580 (t)
REVERT: A  396 MET cc_start: 0.8978 (ptt) cc_final: 0.8721 (ptp)
REVERT: A  401 ASN cc_start: 0.8526 (t0) cc_final: 0.8227 (t0)
REVERT: A  492 CYS cc_start: 0.7588 (t) cc_final: 0.7368 (t)
REVERT: B  110 MET cc_start: 0.8574 (mtm) cc_final: 0.8233 (ptp)
REVERT: B  330 ASP cc_start: 0.8324 (m-30) cc_final: 0.7999 (m-30)
REVERT: B  385 GLU cc_start: 0.7982 (tt0) cc_final: 0.7485 (tm-30)
REVERT: B  406 VAL cc_start: 0.9266 (t) cc_final: 0.9059 (p)
REVERT: B  448 MET cc_start: 0.8782 (tpt) cc_final: 0.8280 (tpt)
REVERT: B  509 LEU cc_start: 0.9056 (tp) cc_final: 0.8550 (tp)
REVERT: B  524 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8113 (m-10)
REVERT: B  536 THR cc_start: 0.8888 (p) cc_final: 0.8645 (t)
REVERT: M   35 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8386 (t0)
REVERT: M   41 GLN cc_start: 0.8253 (mp10) cc_final: 0.8030 (mp10)
REVERT: M  118 PHE cc_start: 0.7927 (t80) cc_final: 0.7702 (t80)
REVERT: M  277 TYR cc_start: 0.8458 (p90) cc_final: 0.7764 (p90)
REVERT: S    8 GLN cc_start: 0.8172 (tp40) cc_final: 0.7952 (tp40)
REVERT: S   15 ARG cc_start: 0.8732 (mmt90) cc_final: 0.8467 (mmt90)
REVERT: S   74 ASN cc_start: 0.9025 (p0) cc_final: 0.8800 (p0)
REVERT: S   93 GLU cc_start: 0.9161 (tp30) cc_final: 0.8882 (tm-30)
  outliers start: 31
  outliers final: 12
  residues processed: 305
  average time/residue: 0.1098
  time to fit residues: 49.4556
Evaluate side-chains
  250 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 235
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain M residue   35 ASN
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  378 LYS
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0060
   chunk 24 optimal weight:    0.5980
   chunk 153 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.3202

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

Flipped N/Q/H residues before XYZ refinement:
A 200 HIS
** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 ASN
B 195 ASN
B 319 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.096049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.078868 restraints weight = 31105.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.081844 restraints weight = 16503.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.083882 restraints weight = 10616.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.085284 restraints weight = 7691.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.086302 restraints weight = 6071.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13951  Z= 0.138
  Angle     :  0.592  10.763  18886  Z= 0.310
  Chirality :  0.042   0.242   2198
  Planarity :  0.004   0.083   2403
  Dihedral  :  4.977  32.760   1868
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.52 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.12 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

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: -0.52 (0.20), residues: 1703
  helix:  0.52 (0.16), residues: 971
  sheet: -0.57 (0.36), residues: 195
  loop : -1.76 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 170 
 TYR   0.027   0.001   TYR A 583 
 PHE   0.014   0.001   PHE M  32 
 TRP   0.015   0.001   TRP A 462 
 HIS   0.005   0.001   HIS S  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (13951)
  covalent geometry    : angle       0.59190 (18886)
  hydrogen bonds       : bond        0.04048 (  789)
  hydrogen bonds       : angle       4.58103 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 263
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8612 (t0) cc_final: 0.8310 (t0)
REVERT: A   71 ASP cc_start: 0.8198 (t0) cc_final: 0.7927 (t0)
REVERT: A   77 MET cc_start: 0.7999 (tpp) cc_final: 0.7718 (tpp)
REVERT: A  142 GLU cc_start: 0.8865 (mp0) cc_final: 0.8608 (mp0)
REVERT: A  372 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8581 (t)
REVERT: A  396 MET cc_start: 0.8940 (ptt) cc_final: 0.8627 (ptm)
REVERT: A  401 ASN cc_start: 0.8472 (t0) cc_final: 0.8213 (t0)
REVERT: A  427 LYS cc_start: 0.9409 (mttt) cc_final: 0.9037 (mttm)
REVERT: A  433 GLU cc_start: 0.9022 (tp30) cc_final: 0.8720 (tm-30)
REVERT: B   74 MET cc_start: 0.8959 (mmt) cc_final: 0.8479 (mmm)
REVERT: B  264 MET cc_start: 0.9164 (ttm) cc_final: 0.8963 (ttm)
REVERT: B  330 ASP cc_start: 0.8351 (m-30) cc_final: 0.8064 (m-30)
REVERT: B  385 GLU cc_start: 0.7972 (tt0) cc_final: 0.7520 (tm-30)
REVERT: B  406 VAL cc_start: 0.9300 (t) cc_final: 0.9087 (p)
REVERT: B  441 GLU cc_start: 0.7825 (mp0) cc_final: 0.7546 (mp0)
REVERT: B  448 MET cc_start: 0.8730 (tpt) cc_final: 0.8482 (tpt)
REVERT: B  536 THR cc_start: 0.8908 (p) cc_final: 0.8650 (t)
REVERT: M   41 GLN cc_start: 0.8243 (mp10) cc_final: 0.7940 (mp10)
REVERT: M  277 TYR cc_start: 0.8435 (p90) cc_final: 0.7825 (p90)
REVERT: S    8 GLN cc_start: 0.8241 (tp40) cc_final: 0.7896 (tp40)
REVERT: S   13 LYS cc_start: 0.8813 (tttt) cc_final: 0.8261 (tttt)
REVERT: S   89 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8401 (mm-30)
REVERT: S   93 GLU cc_start: 0.9087 (tp30) cc_final: 0.8815 (tm-30)
  outliers start: 33
  outliers final: 19
  residues processed: 278
  average time/residue: 0.1020
  time to fit residues: 42.5301
Evaluate side-chains
  251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 231
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain S residue   84 ILE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 168 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0170
   chunk 88 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 164 optimal weight:    0.8980
   chunk 159 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 143 optimal weight:    4.9990
   overall best weight:    0.7822

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

Flipped N/Q/H residues before XYZ refinement:
B  24 ASN
B  75 ASN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 ASN
B 566 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.097686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.080094 restraints weight = 30850.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.083112 restraints weight = 16540.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.085162 restraints weight = 10695.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.086656 restraints weight = 7808.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.087713 restraints weight = 6137.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13951  Z= 0.119
  Angle     :  0.576  11.122  18886  Z= 0.301
  Chirality :  0.041   0.267   2198
  Planarity :  0.004   0.059   2403
  Dihedral  :  4.851  31.277   1868
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.11 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.89 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

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: -0.05 (0.20), residues: 1703
  helix:  0.84 (0.17), residues: 973
  sheet: -0.16 (0.37), residues: 188
  loop : -1.52 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M 169 
 TYR   0.023   0.001   TYR A 247 
 PHE   0.017   0.001   PHE A  97 
 TRP   0.014   0.001   TRP A 462 
 HIS   0.005   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (13951)
  covalent geometry    : angle       0.57614 (18886)
  hydrogen bonds       : bond        0.03774 (  789)
  hydrogen bonds       : angle       4.39625 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 265
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ASP cc_start: 0.8680 (t0) cc_final: 0.8386 (t0)
REVERT: A   71 ASP cc_start: 0.8147 (t0) cc_final: 0.7851 (t0)
REVERT: A   77 MET cc_start: 0.8016 (tpp) cc_final: 0.7706 (tpp)
REVERT: A  372 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8602 (t)
REVERT: A  396 MET cc_start: 0.8931 (ptt) cc_final: 0.8625 (ptm)
REVERT: A  401 ASN cc_start: 0.8531 (t0) cc_final: 0.8228 (t0)
REVERT: A  427 LYS cc_start: 0.9389 (mttt) cc_final: 0.9036 (mttm)
REVERT: A  433 GLU cc_start: 0.8984 (tp30) cc_final: 0.8751 (tm-30)
REVERT: A  464 ARG cc_start: 0.8357 (ttm170) cc_final: 0.8139 (ttm170)
REVERT: A  583 TYR cc_start: 0.8778 (m-80) cc_final: 0.8565 (m-80)
REVERT: B   74 MET cc_start: 0.8980 (mmt) cc_final: 0.8504 (mmm)
REVERT: B   83 MET cc_start: 0.9324 (mtp) cc_final: 0.9001 (mpp)
REVERT: B  264 MET cc_start: 0.9189 (ttm) cc_final: 0.8981 (ttm)
REVERT: B  330 ASP cc_start: 0.8348 (m-30) cc_final: 0.8026 (m-30)
REVERT: B  385 GLU cc_start: 0.7850 (tt0) cc_final: 0.7442 (tm-30)
REVERT: B  448 MET cc_start: 0.8754 (tpt) cc_final: 0.8525 (tpt)
REVERT: B  524 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7952 (m-10)
REVERT: B  536 THR cc_start: 0.8937 (p) cc_final: 0.8648 (t)
REVERT: M    1 MET cc_start: 0.8424 (ttp) cc_final: 0.7906 (ttt)
REVERT: M   41 GLN cc_start: 0.8214 (mp10) cc_final: 0.7858 (mp10)
REVERT: M  277 TYR cc_start: 0.8351 (p90) cc_final: 0.7769 (p90)
REVERT: S   89 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8429 (mm-30)
REVERT: S   93 GLU cc_start: 0.9125 (tp30) cc_final: 0.8823 (tm-30)
  outliers start: 41
  outliers final: 21
  residues processed: 285
  average time/residue: 0.1080
  time to fit residues: 46.4009
Evaluate side-chains
  258 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 235
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 146 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 132 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 84 optimal weight:    0.0020
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 488 GLN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 188 GLN
S  97 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.097321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.079908 restraints weight = 31257.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.082921 restraints weight = 16700.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.085016 restraints weight = 10722.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.086441 restraints weight = 7766.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.087300 restraints weight = 6118.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13951  Z= 0.124
  Angle     :  0.585  11.375  18886  Z= 0.300
  Chirality :  0.042   0.263   2198
  Planarity :  0.004   0.041   2403
  Dihedral  :  4.714  30.620   1868
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.40 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.48 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.18 (0.21), residues: 1703
  helix:  0.95 (0.17), residues: 981
  sheet:  0.08 (0.37), residues: 188
  loop : -1.36 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S  15 
 TYR   0.018   0.001   TYR B 405 
 PHE   0.019   0.001   PHE M  93 
 TRP   0.015   0.001   TRP A 462 
 HIS   0.004   0.001   HIS S  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13951)
  covalent geometry    : angle       0.58503 (18886)
  hydrogen bonds       : bond        0.03684 (  789)
  hydrogen bonds       : angle       4.35592 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 268
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7426 (mpp) cc_final: 0.7030 (mmt)
REVERT: A   19 ASP cc_start: 0.8653 (t0) cc_final: 0.8361 (t0)
REVERT: A   77 MET cc_start: 0.8014 (tpp) cc_final: 0.7708 (tpp)
REVERT: A  372 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8601 (t)
REVERT: A  396 MET cc_start: 0.8938 (ptt) cc_final: 0.8295 (ptm)
REVERT: A  401 ASN cc_start: 0.8512 (t0) cc_final: 0.8236 (t0)
REVERT: A  427 LYS cc_start: 0.9385 (mttt) cc_final: 0.9056 (mttm)
REVERT: A  481 LYS cc_start: 0.8751 (tttt) cc_final: 0.8547 (mtmt)
REVERT: A  561 ASP cc_start: 0.7911 (t0) cc_final: 0.7597 (t0)
REVERT: B   74 MET cc_start: 0.8915 (mmt) cc_final: 0.8456 (mmm)
REVERT: B  264 MET cc_start: 0.9205 (ttm) cc_final: 0.8970 (ttm)
REVERT: B  330 ASP cc_start: 0.8359 (m-30) cc_final: 0.8080 (m-30)
REVERT: B  385 GLU cc_start: 0.7890 (tt0) cc_final: 0.7468 (tm-30)
REVERT: B  448 MET cc_start: 0.8746 (tpt) cc_final: 0.8543 (tpt)
REVERT: B  509 LEU cc_start: 0.9022 (tp) cc_final: 0.8653 (tp)
REVERT: B  524 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8013 (m-10)
REVERT: B  536 THR cc_start: 0.8937 (p) cc_final: 0.8645 (t)
REVERT: M    1 MET cc_start: 0.8399 (ttp) cc_final: 0.8085 (ttt)
REVERT: M   26 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7031 (ptp90)
REVERT: M   41 GLN cc_start: 0.8250 (mp10) cc_final: 0.7944 (mp10)
REVERT: M  277 TYR cc_start: 0.8335 (p90) cc_final: 0.7690 (p90)
REVERT: S   15 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8413 (mmt-90)
REVERT: S   53 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8204 (mtp85)
REVERT: S   60 ARG cc_start: 0.8545 (ttm170) cc_final: 0.8136 (ttm-80)
REVERT: S   89 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8645 (mm-30)
REVERT: S   93 GLU cc_start: 0.8980 (tp30) cc_final: 0.8643 (tp30)
  outliers start: 45
  outliers final: 29
  residues processed: 289
  average time/residue: 0.1086
  time to fit residues: 47.2130
Evaluate side-chains
  267 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 235
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue   84 ILE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 114 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.097327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.079984 restraints weight = 31178.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.083012 restraints weight = 16715.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.085067 restraints weight = 10767.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.086554 restraints weight = 7809.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087617 restraints weight = 6134.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13951  Z= 0.131
  Angle     :  0.608  13.056  18886  Z= 0.308
  Chirality :  0.042   0.281   2198
  Planarity :  0.004   0.045   2403
  Dihedral  :  4.689  30.655   1868
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.29 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.13 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.26 (0.21), residues: 1703
  helix:  0.98 (0.17), residues: 990
  sheet:  0.21 (0.38), residues: 188
  loop : -1.34 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 169 
 TYR   0.019   0.001   TYR A 583 
 PHE   0.025   0.001   PHE A 523 
 TRP   0.014   0.001   TRP A 462 
 HIS   0.006   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13951)
  covalent geometry    : angle       0.60821 (18886)
  hydrogen bonds       : bond        0.03671 (  789)
  hydrogen bonds       : angle       4.36875 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 253
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7496 (mpp) cc_final: 0.7065 (mmt)
REVERT: A   19 ASP cc_start: 0.8629 (t0) cc_final: 0.8320 (t0)
REVERT: A   77 MET cc_start: 0.7964 (tpp) cc_final: 0.7682 (tpp)
REVERT: A  161 MET cc_start: 0.7290 (tpp) cc_final: 0.6940 (tpp)
REVERT: A  372 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8575 (t)
REVERT: A  396 MET cc_start: 0.8923 (ptt) cc_final: 0.8299 (ptm)
REVERT: A  401 ASN cc_start: 0.8454 (t0) cc_final: 0.8227 (t0)
REVERT: A  427 LYS cc_start: 0.9400 (mttt) cc_final: 0.9076 (mttm)
REVERT: A  533 CYS cc_start: 0.9298 (m) cc_final: 0.8868 (m)
REVERT: A  561 ASP cc_start: 0.7789 (t0) cc_final: 0.7534 (t70)
REVERT: A  583 TYR cc_start: 0.8825 (m-80) cc_final: 0.8617 (m-80)
REVERT: B   74 MET cc_start: 0.8879 (mmt) cc_final: 0.8425 (mmm)
REVERT: B   83 MET cc_start: 0.9243 (mtp) cc_final: 0.8512 (mtm)
REVERT: B   86 MET cc_start: 0.8855 (mtm) cc_final: 0.8290 (mpp)
REVERT: B  297 GLU cc_start: 0.8507 (mp0) cc_final: 0.8013 (mp0)
REVERT: B  330 ASP cc_start: 0.8352 (m-30) cc_final: 0.8101 (m-30)
REVERT: B  385 GLU cc_start: 0.7778 (tt0) cc_final: 0.7444 (tm-30)
REVERT: B  509 LEU cc_start: 0.9003 (tp) cc_final: 0.8652 (tp)
REVERT: B  524 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8008 (m-10)
REVERT: B  536 THR cc_start: 0.8913 (p) cc_final: 0.8630 (t)
REVERT: M    1 MET cc_start: 0.8404 (ttp) cc_final: 0.8116 (ttt)
REVERT: M   26 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7024 (ptp90)
REVERT: M   41 GLN cc_start: 0.8257 (mp10) cc_final: 0.7948 (mp10)
REVERT: M  277 TYR cc_start: 0.8382 (p90) cc_final: 0.7781 (p90)
REVERT: S   13 LYS cc_start: 0.8962 (tttt) cc_final: 0.8219 (tmtt)
REVERT: S   15 ARG cc_start: 0.8657 (mmt90) cc_final: 0.8367 (mmt-90)
REVERT: S   60 ARG cc_start: 0.8576 (ttm170) cc_final: 0.8158 (ttm-80)
REVERT: S   87 PHE cc_start: 0.8961 (t80) cc_final: 0.8753 (t80)
REVERT: S   89 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8649 (mm-30)
REVERT: S   93 GLU cc_start: 0.8961 (tp30) cc_final: 0.8622 (tp30)
  outliers start: 45
  outliers final: 30
  residues processed: 273
  average time/residue: 0.1094
  time to fit residues: 45.0247
Evaluate side-chains
  271 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 238
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  480 VAL
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue   49 PHE
Chi-restraints excluded: chain S residue   84 ILE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Chi-restraints excluded: chain S residue  136 LEU
Chi-restraints excluded: chain S residue  138 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 68 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 133 optimal weight:   20.0000
   chunk 164 optimal weight:    2.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.079346 restraints weight = 31018.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.082326 restraints weight = 16770.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084372 restraints weight = 10883.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.085839 restraints weight = 7941.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.086836 restraints weight = 6256.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13951  Z= 0.148
  Angle     :  0.612  11.285  18886  Z= 0.312
  Chirality :  0.043   0.231   2198
  Planarity :  0.004   0.053   2403
  Dihedral  :  4.666  30.930   1868
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.64 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.92 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    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:  0.34 (0.21), residues: 1703
  helix:  1.03 (0.17), residues: 986
  sheet:  0.24 (0.38), residues: 188
  loop : -1.24 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 169 
 TYR   0.016   0.001   TYR A 439 
 PHE   0.022   0.001   PHE A 523 
 TRP   0.013   0.001   TRP A 462 
 HIS   0.010   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13951)
  covalent geometry    : angle       0.61201 (18886)
  hydrogen bonds       : bond        0.03729 (  789)
  hydrogen bonds       : angle       4.40266 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 254
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7967 (tpp) cc_final: 0.7687 (tpp)
REVERT: A  161 MET cc_start: 0.7495 (tpp) cc_final: 0.7188 (tpp)
REVERT: A  372 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (t)
REVERT: A  396 MET cc_start: 0.8935 (ptt) cc_final: 0.8278 (ptm)
REVERT: A  401 ASN cc_start: 0.8500 (t0) cc_final: 0.8263 (t0)
REVERT: A  427 LYS cc_start: 0.9392 (mttt) cc_final: 0.9046 (mttm)
REVERT: A  459 GLU cc_start: 0.8084 (tp30) cc_final: 0.7810 (tp30)
REVERT: A  533 CYS cc_start: 0.9283 (m) cc_final: 0.8764 (m)
REVERT: A  561 ASP cc_start: 0.8039 (t0) cc_final: 0.7810 (t70)
REVERT: A  583 TYR cc_start: 0.8868 (m-80) cc_final: 0.8605 (m-80)
REVERT: B   74 MET cc_start: 0.8880 (mmt) cc_final: 0.8447 (mmm)
REVERT: B   83 MET cc_start: 0.9247 (mtp) cc_final: 0.8283 (mtm)
REVERT: B   86 MET cc_start: 0.8904 (mtm) cc_final: 0.8329 (mpp)
REVERT: B  297 GLU cc_start: 0.8560 (mp0) cc_final: 0.8030 (mp0)
REVERT: B  330 ASP cc_start: 0.8412 (m-30) cc_final: 0.8165 (m-30)
REVERT: B  385 GLU cc_start: 0.7838 (tt0) cc_final: 0.7537 (tm-30)
REVERT: B  509 LEU cc_start: 0.9011 (tp) cc_final: 0.8678 (tp)
REVERT: B  536 THR cc_start: 0.8938 (p) cc_final: 0.8653 (t)
REVERT: M    1 MET cc_start: 0.8476 (ttp) cc_final: 0.8192 (ttt)
REVERT: M   41 GLN cc_start: 0.8278 (mp10) cc_final: 0.7974 (mp10)
REVERT: M  277 TYR cc_start: 0.8419 (p90) cc_final: 0.7728 (p90)
REVERT: S   13 LYS cc_start: 0.8917 (tttt) cc_final: 0.8141 (tttt)
REVERT: S   15 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8027 (mmt-90)
REVERT: S   53 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8213 (mtp85)
REVERT: S   60 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8089 (ttm-80)
REVERT: S   89 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8447 (mm-30)
REVERT: S   93 GLU cc_start: 0.9012 (tp30) cc_final: 0.8685 (tp30)
  outliers start: 46
  outliers final: 29
  residues processed: 274
  average time/residue: 0.1060
  time to fit residues: 43.8188
Evaluate side-chains
  269 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   24 ASP
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue   49 PHE
Chi-restraints excluded: chain S residue   84 ILE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 28 optimal weight:    0.0040
   chunk 147 optimal weight:    6.9990
   chunk 169 optimal weight:    5.9990
   chunk 158 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 135 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.099284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.081963 restraints weight = 30473.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.085030 restraints weight = 16335.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086909 restraints weight = 10506.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.088501 restraints weight = 7830.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.089470 restraints weight = 6080.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  13951  Z= 0.117
  Angle     :  0.610  11.414  18886  Z= 0.306
  Chirality :  0.042   0.248   2198
  Planarity :  0.004   0.053   2403
  Dihedral  :  4.555  29.753   1868
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.97 %
    Favored  : 76.74 %
  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:  0.46 (0.21), residues: 1703
  helix:  1.12 (0.17), residues: 992
  sheet:  0.25 (0.38), residues: 189
  loop : -1.19 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 169 
 TYR   0.010   0.001   TYR A 247 
 PHE   0.017   0.001   PHE M  32 
 TRP   0.017   0.001   TRP A 462 
 HIS   0.005   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (13951)
  covalent geometry    : angle       0.61008 (18886)
  hydrogen bonds       : bond        0.03454 (  789)
  hydrogen bonds       : angle       4.32829 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 265
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7363 (mpp) cc_final: 0.6955 (mmt)
REVERT: A   11 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.6276 (mtm-85)
REVERT: A   77 MET cc_start: 0.7873 (tpp) cc_final: 0.7550 (tpp)
REVERT: A  119 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8359 (m-30)
REVERT: A  161 MET cc_start: 0.7501 (tpp) cc_final: 0.7204 (tpp)
REVERT: A  372 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8580 (t)
REVERT: A  396 MET cc_start: 0.8872 (ptt) cc_final: 0.8527 (ptm)
REVERT: A  427 LYS cc_start: 0.9376 (mttt) cc_final: 0.9059 (mttm)
REVERT: A  533 CYS cc_start: 0.9220 (m) cc_final: 0.8714 (m)
REVERT: A  583 TYR cc_start: 0.8832 (m-80) cc_final: 0.8606 (m-80)
REVERT: B   83 MET cc_start: 0.8972 (mtp) cc_final: 0.8213 (mtm)
REVERT: B   86 MET cc_start: 0.8872 (mtm) cc_final: 0.8330 (mpp)
REVERT: B  297 GLU cc_start: 0.8481 (mp0) cc_final: 0.7938 (mp0)
REVERT: B  330 ASP cc_start: 0.8325 (m-30) cc_final: 0.8107 (m-30)
REVERT: B  385 GLU cc_start: 0.7913 (tt0) cc_final: 0.7512 (tm-30)
REVERT: B  448 MET cc_start: 0.8681 (tpt) cc_final: 0.8268 (tpt)
REVERT: B  508 SER cc_start: 0.9183 (m) cc_final: 0.8832 (p)
REVERT: B  509 LEU cc_start: 0.8958 (tp) cc_final: 0.8697 (tp)
REVERT: B  536 THR cc_start: 0.8909 (p) cc_final: 0.8613 (t)
REVERT: M   26 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7029 (ptp90)
REVERT: M   41 GLN cc_start: 0.8209 (mp10) cc_final: 0.7875 (mp10)
REVERT: M  277 TYR cc_start: 0.8373 (p90) cc_final: 0.7833 (p90)
REVERT: M  361 MET cc_start: 0.9015 (mmm) cc_final: 0.8814 (mmm)
REVERT: S   13 LYS cc_start: 0.8922 (tttt) cc_final: 0.8173 (tttt)
REVERT: S   15 ARG cc_start: 0.8634 (mmt90) cc_final: 0.7845 (mmt-90)
REVERT: S   60 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8458 (ttm-80)
REVERT: S   89 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8612 (mm-30)
REVERT: S   93 GLU cc_start: 0.8965 (tp30) cc_final: 0.8643 (tp30)
  outliers start: 35
  outliers final: 22
  residues processed: 280
  average time/residue: 0.1076
  time to fit residues: 45.6471
Evaluate side-chains
  264 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 239
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  139 LYS
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue   49 PHE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 64 optimal weight:    0.0870
   chunk 164 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9980
   chunk 153 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 143 optimal weight:   10.0000
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.7962

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.099815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.082489 restraints weight = 30698.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.085557 restraints weight = 16231.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.087665 restraints weight = 10403.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.089173 restraints weight = 7508.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.090220 restraints weight = 5863.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13951  Z= 0.120
  Angle     :  0.628  13.651  18886  Z= 0.314
  Chirality :  0.042   0.337   2198
  Planarity :  0.004   0.054   2403
  Dihedral  :  4.476  29.722   1868
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.52 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.95 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.21), residues: 1703
  helix:  1.17 (0.17), residues: 980
  sheet:  0.29 (0.38), residues: 189
  loop : -1.15 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG M 169 
 TYR   0.013   0.001   TYR B 405 
 PHE   0.022   0.001   PHE A  97 
 TRP   0.017   0.001   TRP A 462 
 HIS   0.006   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13951)
  covalent geometry    : angle       0.62807 (18886)
  hydrogen bonds       : bond        0.03472 (  789)
  hydrogen bonds       : angle       4.32545 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 259
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7323 (mpp) cc_final: 0.6934 (mmt)
REVERT: A   11 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.6253 (mtm-85)
REVERT: A   77 MET cc_start: 0.7873 (tpp) cc_final: 0.7556 (tpp)
REVERT: A  119 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: A  372 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8550 (t)
REVERT: A  396 MET cc_start: 0.8838 (ptt) cc_final: 0.8562 (ptm)
REVERT: A  433 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8790 (tp30)
REVERT: A  533 CYS cc_start: 0.9224 (m) cc_final: 0.8734 (m)
REVERT: B   74 MET cc_start: 0.9202 (tpp) cc_final: 0.8951 (mmm)
REVERT: B   83 MET cc_start: 0.8936 (mtp) cc_final: 0.8160 (mtm)
REVERT: B   86 MET cc_start: 0.8879 (mtm) cc_final: 0.8369 (mpp)
REVERT: B  297 GLU cc_start: 0.8502 (mp0) cc_final: 0.7944 (mp0)
REVERT: B  330 ASP cc_start: 0.8367 (m-30) cc_final: 0.8155 (m-30)
REVERT: B  385 GLU cc_start: 0.7858 (tt0) cc_final: 0.7531 (tm-30)
REVERT: B  448 MET cc_start: 0.8662 (tpt) cc_final: 0.8358 (tpt)
REVERT: B  508 SER cc_start: 0.9163 (m) cc_final: 0.8809 (p)
REVERT: B  509 LEU cc_start: 0.8920 (tp) cc_final: 0.8662 (tp)
REVERT: B  536 THR cc_start: 0.8927 (p) cc_final: 0.8639 (t)
REVERT: M   26 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7064 (ptp90)
REVERT: M   41 GLN cc_start: 0.8215 (mp10) cc_final: 0.7913 (mp10)
REVERT: M  277 TYR cc_start: 0.8374 (p90) cc_final: 0.7811 (p90)
REVERT: M  361 MET cc_start: 0.8987 (mmm) cc_final: 0.8785 (mmm)
REVERT: S   13 LYS cc_start: 0.8923 (tttt) cc_final: 0.8549 (tttt)
REVERT: S   15 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8112 (mmt90)
REVERT: S   60 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8509 (ttm-80)
REVERT: S   89 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8639 (mm-30)
REVERT: S   93 GLU cc_start: 0.8977 (tp30) cc_final: 0.8538 (tp30)
  outliers start: 33
  outliers final: 23
  residues processed: 277
  average time/residue: 0.1101
  time to fit residues: 45.7042
Evaluate side-chains
  267 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 241
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   49 PHE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Chi-restraints excluded: chain S residue  136 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 137 optimal weight:    0.2980
   chunk 72 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.099838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.082313 restraints weight = 30642.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.085380 restraints weight = 16531.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.087511 restraints weight = 10689.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.088999 restraints weight = 7744.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.090006 restraints weight = 6076.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13951  Z= 0.119
  Angle     :  0.636  13.989  18886  Z= 0.317
  Chirality :  0.042   0.318   2198
  Planarity :  0.004   0.053   2403
  Dihedral  :  4.441  29.398   1868
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.40 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 22.94 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.21), residues: 1703
  helix:  1.14 (0.17), residues: 985
  sheet:  0.31 (0.38), residues: 189
  loop : -1.11 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 177 
 TYR   0.016   0.001   TYR A 583 
 PHE   0.023   0.001   PHE A  97 
 TRP   0.018   0.001   TRP A 462 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13951)
  covalent geometry    : angle       0.63601 (18886)
  hydrogen bonds       : bond        0.03516 (  789)
  hydrogen bonds       : angle       4.32992 ( 2295)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 255
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7194 (mpp) cc_final: 0.6828 (mmt)
REVERT: A   11 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.6229 (mtm-85)
REVERT: A   77 MET cc_start: 0.7876 (tpp) cc_final: 0.7548 (tpp)
REVERT: A  119 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8328 (t70)
REVERT: A  161 MET cc_start: 0.7412 (tpp) cc_final: 0.6936 (tpp)
REVERT: A  162 ASP cc_start: 0.8178 (p0) cc_final: 0.7950 (p0)
REVERT: A  312 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8580 (mm-30)
REVERT: A  372 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (t)
REVERT: A  396 MET cc_start: 0.8889 (ptt) cc_final: 0.8533 (ptm)
REVERT: A  433 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8777 (tp30)
REVERT: A  524 ASN cc_start: 0.8797 (m110) cc_final: 0.8577 (m110)
REVERT: A  533 CYS cc_start: 0.9223 (m) cc_final: 0.8728 (m)
REVERT: B   83 MET cc_start: 0.8905 (mtp) cc_final: 0.8141 (mtm)
REVERT: B   86 MET cc_start: 0.8863 (mtm) cc_final: 0.8373 (mpp)
REVERT: B  297 GLU cc_start: 0.8492 (mp0) cc_final: 0.7941 (mp0)
REVERT: B  330 ASP cc_start: 0.8412 (m-30) cc_final: 0.8198 (m-30)
REVERT: B  385 GLU cc_start: 0.7880 (tt0) cc_final: 0.7556 (tm-30)
REVERT: B  508 SER cc_start: 0.9171 (m) cc_final: 0.8814 (p)
REVERT: B  509 LEU cc_start: 0.8903 (tp) cc_final: 0.8645 (tp)
REVERT: B  536 THR cc_start: 0.8927 (p) cc_final: 0.8650 (t)
REVERT: M   26 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7046 (ptp90)
REVERT: M   41 GLN cc_start: 0.8168 (mp10) cc_final: 0.7839 (mp10)
REVERT: M  277 TYR cc_start: 0.8367 (p90) cc_final: 0.7818 (p90)
REVERT: M  361 MET cc_start: 0.8966 (mmm) cc_final: 0.8759 (mmm)
REVERT: S   13 LYS cc_start: 0.8921 (tttt) cc_final: 0.8094 (tttt)
REVERT: S   15 ARG cc_start: 0.8553 (mmt90) cc_final: 0.7683 (mmt-90)
REVERT: S   60 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8557 (ttm-80)
REVERT: S   89 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8612 (mm-30)
REVERT: S   93 GLU cc_start: 0.8974 (tp30) cc_final: 0.8552 (tp30)
  outliers start: 30
  outliers final: 25
  residues processed: 269
  average time/residue: 0.1096
  time to fit residues: 44.4130
Evaluate side-chains
  270 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  139 LYS
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  566 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   26 ARG
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue   92 TYR
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
Chi-restraints excluded: chain S residue   49 PHE
Chi-restraints excluded: chain S residue  103 LEU
Chi-restraints excluded: chain S residue  109 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 156 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 163 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 146 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 140 optimal weight:    5.9990
   chunk 131 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.099920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.082288 restraints weight = 30870.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.085367 restraints weight = 16585.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.087491 restraints weight = 10729.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.089008 restraints weight = 7793.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.090035 restraints weight = 6110.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13951  Z= 0.125
  Angle     :  0.656  14.535  18886  Z= 0.325
  Chirality :  0.043   0.343   2198
  Planarity :  0.004   0.071   2403
  Dihedral  :  4.427  29.256   1868
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.58 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.39 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.50 (0.21), residues: 1703
  helix:  1.13 (0.17), residues: 979
  sheet:  0.23 (0.38), residues: 191
  loop : -1.06 (0.28), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 177 
 TYR   0.016   0.001   TYR S  94 
 PHE   0.024   0.001   PHE A  97 
 TRP   0.017   0.001   TRP A 462 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13951)
  covalent geometry    : angle       0.65565 (18886)
  hydrogen bonds       : bond        0.03624 (  789)
  hydrogen bonds       : angle       4.35161 ( 2295)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1975.02 seconds
wall clock time: 35 minutes 8.87 seconds (2108.87 seconds total)