Starting phenix.real_space_refine
on Thu Jul 31 18:00:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_10747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_10747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_10747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_10747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yae_10747/07_2025/6yae_10747.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.151
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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.89, per 1000 atoms: 0.58
  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: 3.46
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.46
  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: 3.90

  Time building geometry restraints manager: 4.06 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:             0.690
  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:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     31.600
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.020
-------------------------------------------------------------------------------
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 : 17.68
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.015   0.002   TRP A 462 
 HIS   0.010   0.002   HIS S  85 
 PHE   0.026   0.002   PHE A 523 
 TYR   0.024   0.002   TYR B 524 
 ARG   0.009   0.001   ARG A 177 

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

*********************** 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  : 1.674 
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: 0.8712 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: B   86 MET cc_start: 0.9175 (mtm) cc_final: 0.8607 (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: 0.8742 (tp)
REVERT: M  118 PHE cc_start: 0.8110 (t80) cc_final: 0.7410 (t80)
REVERT: M  277 TYR cc_start: 0.8195 (p90) cc_final: 0.7257 (p90)
REVERT: M  361 MET cc_start: 0.9007 (mmt) cc_final: 0.8660 (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: 0.2920
  time to fit residues: 120.6589
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  : 1.493 
-------------------------------------------------------------------------------
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 143 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0470
   chunk 86 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 133 optimal weight:   20.0000
   chunk 51 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 154 optimal weight:   10.0000
   overall best weight:    0.7680

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.097335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.079705 restraints weight = 30537.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.082741 restraints weight = 16258.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.084798 restraints weight = 10511.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13951  Z= 0.139
  Angle     :  0.634  10.784  18886  Z= 0.332
  Chirality :  0.043   0.230   2198
  Planarity :  0.004   0.036   2403
  Dihedral  :  5.301  50.523   1870
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.05 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.71 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.20), residues: 1703
  helix:  0.09 (0.16), residues: 954
  sheet: -0.76 (0.36), residues: 191
  loop : -2.05 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 462 
 HIS   0.006   0.001   HIS S  85 
 PHE   0.020   0.002   PHE B 492 
 TYR   0.017   0.001   TYR A 583 
 ARG   0.005   0.001   ARG S 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  789)
  hydrogen bonds       : angle       4.75891 ( 2295)
  covalent geometry    : bond        0.00299 (13951)
  covalent geometry    : angle       0.63381 (18886)

*********************** 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
  320 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 290
  time to evaluate  : 1.577 
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: 0.8705 (t0) cc_final: 0.8388 (t0)
REVERT: A   71 ASP cc_start: 0.8181 (t0) cc_final: 0.7901 (t0)
REVERT: A   77 MET cc_start: 0.8064 (tpp) cc_final: 0.7764 (tpp)
REVERT: A   92 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8559 (tp-100)
REVERT: A  142 GLU cc_start: 0.9049 (mp0) cc_final: 0.8756 (mp0)
REVERT: A  341 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7575 (ttm170)
REVERT: A  372 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8599 (t)
REVERT: A  396 MET cc_start: 0.8982 (ptt) cc_final: 0.8725 (ptp)
REVERT: A  401 ASN cc_start: 0.8583 (t0) cc_final: 0.8275 (t0)
REVERT: A  492 CYS cc_start: 0.7675 (t) cc_final: 0.7438 (t)
REVERT: B  110 MET cc_start: 0.8605 (mtm) cc_final: 0.8250 (ptp)
REVERT: B  330 ASP cc_start: 0.8350 (m-30) cc_final: 0.8018 (m-30)
REVERT: B  385 GLU cc_start: 0.8074 (tt0) cc_final: 0.7524 (tm-30)
REVERT: B  406 VAL cc_start: 0.9302 (t) cc_final: 0.9091 (p)
REVERT: B  441 GLU cc_start: 0.7702 (mp0) cc_final: 0.7443 (mp0)
REVERT: B  448 MET cc_start: 0.8791 (tpt) cc_final: 0.8298 (tpt)
REVERT: B  509 LEU cc_start: 0.9060 (tp) cc_final: 0.8555 (tp)
REVERT: B  524 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8118 (m-10)
REVERT: B  536 THR cc_start: 0.8923 (p) cc_final: 0.8688 (t)
REVERT: M   35 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8389 (t0)
REVERT: M   41 GLN cc_start: 0.8289 (mp10) cc_final: 0.8054 (mp10)
REVERT: M   99 GLU cc_start: 0.8497 (mp0) cc_final: 0.8293 (mp0)
REVERT: M  118 PHE cc_start: 0.7925 (t80) cc_final: 0.7690 (t80)
REVERT: M  277 TYR cc_start: 0.8465 (p90) cc_final: 0.7776 (p90)
REVERT: S    8 GLN cc_start: 0.8181 (tp40) cc_final: 0.7944 (tp40)
REVERT: S   15 ARG cc_start: 0.8731 (mmt90) cc_final: 0.8467 (mmt90)
REVERT: S   56 LYS cc_start: 0.8351 (ptpp) cc_final: 0.8131 (ptpp)
REVERT: S   74 ASN cc_start: 0.9051 (p0) cc_final: 0.8838 (p0)
REVERT: S   93 GLU cc_start: 0.9160 (tp30) cc_final: 0.8876 (tm-30)
REVERT: S  112 THR cc_start: 0.9013 (m) cc_final: 0.8723 (p)
  outliers start: 30
  outliers final: 11
  residues processed: 304
  average time/residue: 0.2519
  time to fit residues: 112.3780
Evaluate side-chains
  251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 237
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
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 S residue  136 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   chunk 147 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 163 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 109 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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**
A 471 ASN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 ASN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 ASN
B 319 GLN
B 566 HIS
M  35 ASN
S  36 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.091925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.074773 restraints weight = 31800.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.077586 restraints weight = 17296.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.079523 restraints weight = 11335.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13951  Z= 0.260
  Angle     :  0.672  10.148  18886  Z= 0.352
  Chirality :  0.044   0.242   2198
  Planarity :  0.005   0.088   2403
  Dihedral  :  5.256  33.075   1868
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.58 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.12 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.20), residues: 1703
  helix:  0.28 (0.16), residues: 972
  sheet: -0.81 (0.36), residues: 195
  loop : -1.93 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 462 
 HIS   0.006   0.001   HIS S  85 
 PHE   0.016   0.002   PHE A 484 
 TYR   0.022   0.002   TYR A 583 
 ARG   0.003   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04581 (  789)
  hydrogen bonds       : angle       4.93350 ( 2295)
  covalent geometry    : bond        0.00601 (13951)
  covalent geometry    : angle       0.67209 (18886)

*********************** 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
  293 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 242
  time to evaluate  : 1.489 
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: 0.8742 (t0) cc_final: 0.8402 (t0)
REVERT: A   71 ASP cc_start: 0.8334 (t0) cc_final: 0.8058 (t0)
REVERT: A   77 MET cc_start: 0.8119 (tpp) cc_final: 0.7805 (tpp)
REVERT: A  323 GLU cc_start: 0.8868 (mp0) cc_final: 0.8638 (mp0)
REVERT: A  341 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7570 (ttm170)
REVERT: A  372 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8642 (t)
REVERT: A  401 ASN cc_start: 0.8696 (t0) cc_final: 0.8366 (t0)
REVERT: A  433 GLU cc_start: 0.9104 (tp30) cc_final: 0.8806 (tm-30)
REVERT: A  561 ASP cc_start: 0.8142 (t0) cc_final: 0.7842 (t70)
REVERT: B   74 MET cc_start: 0.9055 (mmt) cc_final: 0.8617 (mmm)
REVERT: B  330 ASP cc_start: 0.8474 (m-30) cc_final: 0.8198 (m-30)
REVERT: B  385 GLU cc_start: 0.8070 (tt0) cc_final: 0.7538 (tm-30)
REVERT: B  441 GLU cc_start: 0.7793 (mp0) cc_final: 0.7436 (mp0)
REVERT: B  448 MET cc_start: 0.8777 (tpt) cc_final: 0.8220 (tpt)
REVERT: B  509 LEU cc_start: 0.9130 (tp) cc_final: 0.8648 (tp)
REVERT: B  524 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8267 (m-10)
REVERT: M   99 GLU cc_start: 0.8519 (mp0) cc_final: 0.8264 (mp0)
REVERT: M  118 PHE cc_start: 0.8029 (t80) cc_final: 0.6901 (t80)
REVERT: M  183 LEU cc_start: 0.9327 (tp) cc_final: 0.9118 (tp)
REVERT: M  277 TYR cc_start: 0.8519 (p90) cc_final: 0.7746 (p90)
REVERT: S    8 GLN cc_start: 0.8321 (tp40) cc_final: 0.8117 (tp40)
REVERT: S   13 LYS cc_start: 0.8831 (tttt) cc_final: 0.7985 (tttt)
REVERT: S   15 ARG cc_start: 0.8773 (mmt90) cc_final: 0.8273 (mmt-90)
REVERT: S   89 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8499 (mm-30)
REVERT: S   93 GLU cc_start: 0.9167 (tp30) cc_final: 0.8864 (tm-30)
  outliers start: 51
  outliers final: 30
  residues processed: 268
  average time/residue: 0.2409
  time to fit residues: 96.5585
Evaluate side-chains
  246 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 214
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
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 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  215 THR
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  451 ILE
Chi-restraints excluded: chain B residue  452 VAL
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  540 VAL
Chi-restraints excluded: chain M residue   43 VAL
Chi-restraints excluded: chain M residue  252 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  305 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   84 ILE
Chi-restraints excluded: chain S residue  103 LEU
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 6 optimal weight:    3.9990
   chunk 167 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 158 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 169 optimal weight:    2.9990
   chunk 149 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 ASN
M 188 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.094296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.077031 restraints weight = 31216.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.079926 restraints weight = 16868.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.081933 restraints weight = 10995.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13951  Z= 0.155
  Angle     :  0.599  10.443  18886  Z= 0.315
  Chirality :  0.042   0.262   2198
  Planarity :  0.004   0.054   2403
  Dihedral  :  5.047  32.009   1868
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.70 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.35 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.20), residues: 1703
  helix:  0.65 (0.16), residues: 979
  sheet: -0.58 (0.36), residues: 194
  loop : -1.67 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 462 
 HIS   0.005   0.001   HIS S  85 
 PHE   0.024   0.001   PHE M  32 
 TYR   0.016   0.001   TYR A  88 
 ARG   0.009   0.000   ARG M 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04083 (  789)
  hydrogen bonds       : angle       4.60919 ( 2295)
  covalent geometry    : bond        0.00362 (13951)
  covalent geometry    : angle       0.59902 (18886)

*********************** 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
  294 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 252
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.8039 (tpp) cc_final: 0.7770 (tpp)
REVERT: A  323 GLU cc_start: 0.8764 (mp0) cc_final: 0.8525 (mp0)
REVERT: A  341 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7560 (ttm170)
REVERT: A  372 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8541 (t)
REVERT: A  396 MET cc_start: 0.8458 (ptt) cc_final: 0.7965 (ptm)
REVERT: A  401 ASN cc_start: 0.8559 (t0) cc_final: 0.8294 (t0)
REVERT: A  427 LYS cc_start: 0.9440 (mttt) cc_final: 0.8970 (mttm)
REVERT: A  433 GLU cc_start: 0.9061 (tp30) cc_final: 0.8818 (tm-30)
REVERT: A  561 ASP cc_start: 0.8053 (t0) cc_final: 0.7773 (t70)
REVERT: A  583 TYR cc_start: 0.8807 (m-80) cc_final: 0.8542 (m-80)
REVERT: B   74 MET cc_start: 0.8925 (mmt) cc_final: 0.8471 (mmm)
REVERT: B   83 MET cc_start: 0.9367 (mtp) cc_final: 0.9039 (mpp)
REVERT: B  330 ASP cc_start: 0.8432 (m-30) cc_final: 0.8145 (m-30)
REVERT: B  385 GLU cc_start: 0.8020 (tt0) cc_final: 0.7528 (tm-30)
REVERT: B  396 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8532 (tt)
REVERT: B  448 MET cc_start: 0.8705 (tpt) cc_final: 0.8163 (tpt)
REVERT: B  524 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8159 (m-10)
REVERT: M    1 MET cc_start: 0.8507 (ttm) cc_final: 0.7326 (mtp)
REVERT: M   15 LEU cc_start: 0.9543 (mp) cc_final: 0.9316 (mp)
REVERT: M   41 GLN cc_start: 0.8247 (mp10) cc_final: 0.7968 (mp10)
REVERT: M   99 GLU cc_start: 0.8528 (mp0) cc_final: 0.8299 (mp0)
REVERT: M  120 TYR cc_start: 0.8026 (m-10) cc_final: 0.7568 (m-10)
REVERT: M  277 TYR cc_start: 0.8447 (p90) cc_final: 0.7836 (p90)
REVERT: S    8 GLN cc_start: 0.8361 (tp40) cc_final: 0.8140 (tp40)
REVERT: S   13 LYS cc_start: 0.8852 (tttt) cc_final: 0.8623 (tttt)
REVERT: S   18 LYS cc_start: 0.8606 (tppt) cc_final: 0.8367 (tppt)
REVERT: S   89 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8404 (mm-30)
REVERT: S   93 GLU cc_start: 0.9084 (tp30) cc_final: 0.8793 (tm-30)
  outliers start: 42
  outliers final: 26
  residues processed: 270
  average time/residue: 0.2493
  time to fit residues: 101.0575
Evaluate side-chains
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 228
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
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  535 VAL
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  558 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  195 ASN
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  264 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  396 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 B residue  566 HIS
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 150 optimal weight:    0.9980
   chunk 145 optimal weight:    6.9990
   chunk 118 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  92 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 = 0.3331 r_free = 0.3331 target = 0.095877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.078473 restraints weight = 31102.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.081453 restraints weight = 16701.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.083509 restraints weight = 10790.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2732

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= 0.125
  Angle     :  0.584  10.909  18886  Z= 0.302
  Chirality :  0.042   0.281   2198
  Planarity :  0.004   0.039   2403
  Dihedral  :  4.873  31.230   1868
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.70 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.33 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.20), residues: 1703
  helix:  0.92 (0.17), residues: 976
  sheet: -0.29 (0.37), residues: 189
  loop : -1.48 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 462 
 HIS   0.004   0.001   HIS S  85 
 PHE   0.017   0.001   PHE M  32 
 TYR   0.015   0.001   TYR A  88 
 ARG   0.005   0.000   ARG M 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  789)
  hydrogen bonds       : angle       4.44436 ( 2295)
  covalent geometry    : bond        0.00285 (13951)
  covalent geometry    : angle       0.58398 (18886)

*********************** 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
  305 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 258
  time to evaluate  : 1.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7989 (tpp) cc_final: 0.7677 (tpp)
REVERT: A   92 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8594 (tp-100)
REVERT: A  341 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7543 (ttm170)
REVERT: A  372 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8582 (t)
REVERT: A  396 MET cc_start: 0.8608 (ptt) cc_final: 0.8125 (ptm)
REVERT: A  401 ASN cc_start: 0.8530 (t0) cc_final: 0.8283 (t0)
REVERT: A  427 LYS cc_start: 0.9418 (mttt) cc_final: 0.9015 (mttm)
REVERT: A  433 GLU cc_start: 0.9030 (tp30) cc_final: 0.8760 (tm-30)
REVERT: A  561 ASP cc_start: 0.8121 (t0) cc_final: 0.7864 (t70)
REVERT: B   74 MET cc_start: 0.8877 (mmt) cc_final: 0.8436 (mmm)
REVERT: B  110 MET cc_start: 0.8537 (mtm) cc_final: 0.8115 (ptp)
REVERT: B  330 ASP cc_start: 0.8409 (m-30) cc_final: 0.8151 (m-30)
REVERT: B  385 GLU cc_start: 0.7985 (tt0) cc_final: 0.7505 (tm-30)
REVERT: B  441 GLU cc_start: 0.7587 (mp0) cc_final: 0.7275 (mp0)
REVERT: B  448 MET cc_start: 0.8725 (tpt) cc_final: 0.8514 (tpt)
REVERT: B  509 LEU cc_start: 0.9056 (tp) cc_final: 0.8682 (tp)
REVERT: B  524 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8238 (m-10)
REVERT: M   15 LEU cc_start: 0.9556 (mp) cc_final: 0.9318 (mp)
REVERT: M   41 GLN cc_start: 0.8263 (mp10) cc_final: 0.7974 (mp10)
REVERT: M   99 GLU cc_start: 0.8525 (mp0) cc_final: 0.8304 (mp0)
REVERT: M  277 TYR cc_start: 0.8417 (p90) cc_final: 0.7792 (p90)
REVERT: S   13 LYS cc_start: 0.8890 (tttt) cc_final: 0.8677 (tttt)
REVERT: S   18 LYS cc_start: 0.8520 (tppt) cc_final: 0.8274 (tppt)
REVERT: S   53 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8148 (mtp85)
REVERT: S   89 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8436 (mm-30)
REVERT: S   93 GLU cc_start: 0.9059 (tp30) cc_final: 0.8742 (tm-30)
  outliers start: 47
  outliers final: 29
  residues processed: 283
  average time/residue: 0.2403
  time to fit residues: 101.7975
Evaluate side-chains
  268 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
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  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  535 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain B residue    9 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
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  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   73 VAL
Chi-restraints excluded: chain M residue  289 VAL
Chi-restraints excluded: chain M residue  338 MET
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 132 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   chunk 118 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.096871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.079290 restraints weight = 31329.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.082275 restraints weight = 16934.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.084346 restraints weight = 10982.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13951  Z= 0.123
  Angle     :  0.590  11.038  18886  Z= 0.303
  Chirality :  0.042   0.276   2198
  Planarity :  0.004   0.045   2403
  Dihedral  :  4.780  30.143   1868
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.40 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.72 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.54 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.21), residues: 1703
  helix:  0.96 (0.17), residues: 991
  sheet: -0.10 (0.37), residues: 189
  loop : -1.41 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.027   0.001   PHE M 118 
 TYR   0.019   0.001   TYR A 583 
 ARG   0.004   0.000   ARG M 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  789)
  hydrogen bonds       : angle       4.38913 ( 2295)
  covalent geometry    : bond        0.00281 (13951)
  covalent geometry    : angle       0.59012 (18886)

*********************** 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
  292 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 247
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7984 (tpp) cc_final: 0.7645 (tpp)
REVERT: A  341 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7587 (ttm170)
REVERT: A  372 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8590 (t)
REVERT: A  396 MET cc_start: 0.8644 (ptt) cc_final: 0.8088 (ptm)
REVERT: A  401 ASN cc_start: 0.8541 (t0) cc_final: 0.8294 (t0)
REVERT: A  427 LYS cc_start: 0.9408 (mttt) cc_final: 0.9044 (mttm)
REVERT: A  433 GLU cc_start: 0.9090 (tp30) cc_final: 0.8806 (tm-30)
REVERT: A  533 CYS cc_start: 0.9328 (m) cc_final: 0.8806 (m)
REVERT: A  561 ASP cc_start: 0.8140 (t0) cc_final: 0.7919 (t70)
REVERT: A  583 TYR cc_start: 0.8807 (m-80) cc_final: 0.8568 (m-80)
REVERT: B   74 MET cc_start: 0.8860 (mmt) cc_final: 0.8435 (mmm)
REVERT: B   83 MET cc_start: 0.9237 (mtp) cc_final: 0.8513 (mpp)
REVERT: B   86 MET cc_start: 0.8849 (mtm) cc_final: 0.8272 (mpp)
REVERT: B  330 ASP cc_start: 0.8458 (m-30) cc_final: 0.8207 (m-30)
REVERT: B  385 GLU cc_start: 0.7941 (tt0) cc_final: 0.7515 (tm-30)
REVERT: B  509 LEU cc_start: 0.9026 (tp) cc_final: 0.8667 (tp)
REVERT: M   15 LEU cc_start: 0.9496 (mp) cc_final: 0.9270 (mp)
REVERT: M   41 GLN cc_start: 0.8241 (mp10) cc_final: 0.7910 (mp10)
REVERT: M   99 GLU cc_start: 0.8480 (mp0) cc_final: 0.8274 (mp0)
REVERT: M  277 TYR cc_start: 0.8421 (p90) cc_final: 0.7820 (p90)
REVERT: S   13 LYS cc_start: 0.8970 (tttt) cc_final: 0.8519 (tttt)
REVERT: S   61 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8297 (ttp-110)
REVERT: S   89 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8452 (mm-30)
REVERT: S   93 GLU cc_start: 0.8991 (tp30) cc_final: 0.8669 (tp30)
REVERT: S  109 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8710 (ttmm)
  outliers start: 45
  outliers final: 28
  residues processed: 272
  average time/residue: 0.2375
  time to fit residues: 97.3803
Evaluate side-chains
  262 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
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    9 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 VAL
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  480 VAL
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  555 ILE
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 58 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 158 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 142 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 121 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.097392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.079919 restraints weight = 31024.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.082920 restraints weight = 16761.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.084989 restraints weight = 10856.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13951  Z= 0.124
  Angle     :  0.595  11.167  18886  Z= 0.302
  Chirality :  0.043   0.373   2198
  Planarity :  0.004   0.055   2403
  Dihedral  :  4.661  29.827   1868
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.35 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.84 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.21), residues: 1703
  helix:  1.05 (0.17), residues: 996
  sheet:  0.06 (0.38), residues: 188
  loop : -1.34 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 462 
 HIS   0.004   0.001   HIS S  85 
 PHE   0.018   0.001   PHE M  93 
 TYR   0.013   0.001   TYR A 247 
 ARG   0.004   0.000   ARG M 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03607 (  789)
  hydrogen bonds       : angle       4.36552 ( 2295)
  covalent geometry    : bond        0.00285 (13951)
  covalent geometry    : angle       0.59465 (18886)

*********************** 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
  299 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 257
  time to evaluate  : 1.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.6346 (mtm-85)
REVERT: A   77 MET cc_start: 0.7970 (tpp) cc_final: 0.7640 (tpp)
REVERT: A  119 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8417 (m-30)
REVERT: A  161 MET cc_start: 0.7531 (tpp) cc_final: 0.7239 (tpp)
REVERT: A  341 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7583 (ttm170)
REVERT: A  372 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (t)
REVERT: A  396 MET cc_start: 0.8691 (ptt) cc_final: 0.8300 (ptm)
REVERT: A  401 ASN cc_start: 0.8521 (t0) cc_final: 0.8286 (t0)
REVERT: A  427 LYS cc_start: 0.9394 (mttt) cc_final: 0.9051 (mttm)
REVERT: A  433 GLU cc_start: 0.9150 (tp30) cc_final: 0.8816 (tm-30)
REVERT: A  533 CYS cc_start: 0.9310 (m) cc_final: 0.8828 (m)
REVERT: A  583 TYR cc_start: 0.8851 (m-80) cc_final: 0.8589 (m-80)
REVERT: B   74 MET cc_start: 0.8862 (mmt) cc_final: 0.8439 (mmm)
REVERT: B   83 MET cc_start: 0.9212 (mtp) cc_final: 0.8537 (ptp)
REVERT: B   86 MET cc_start: 0.8879 (mtm) cc_final: 0.8303 (mpp)
REVERT: B  213 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8543 (pt0)
REVERT: B  297 GLU cc_start: 0.8528 (mp0) cc_final: 0.8005 (mp0)
REVERT: B  330 ASP cc_start: 0.8468 (m-30) cc_final: 0.8216 (m-30)
REVERT: B  385 GLU cc_start: 0.7900 (tt0) cc_final: 0.7522 (tm-30)
REVERT: B  508 SER cc_start: 0.9236 (m) cc_final: 0.8877 (p)
REVERT: B  509 LEU cc_start: 0.9020 (tp) cc_final: 0.8729 (tp)
REVERT: M   15 LEU cc_start: 0.9489 (mp) cc_final: 0.9247 (mp)
REVERT: M   41 GLN cc_start: 0.8266 (mp10) cc_final: 0.7941 (mp10)
REVERT: M  277 TYR cc_start: 0.8412 (p90) cc_final: 0.7740 (p90)
REVERT: M  302 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: M  358 MET cc_start: 0.8584 (ttt) cc_final: 0.8298 (ttm)
REVERT: S   13 LYS cc_start: 0.8976 (tttt) cc_final: 0.8751 (tttt)
REVERT: S   60 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8179 (ttm-80)
REVERT: S   61 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8275 (ttp-110)
REVERT: S   89 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8433 (mm-30)
REVERT: S   93 GLU cc_start: 0.9035 (tp30) cc_final: 0.8720 (tp30)
REVERT: S  109 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8723 (ttmm)
  outliers start: 42
  outliers final: 27
  residues processed: 277
  average time/residue: 0.2379
  time to fit residues: 98.3879
Evaluate side-chains
  257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 227
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
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  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    9 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  244 VAL
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  480 VAL
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  555 ILE
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 153 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 164 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 266 GLN
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.079316 restraints weight = 31289.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.082313 restraints weight = 16848.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.084381 restraints weight = 10883.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13951  Z= 0.141
  Angle     :  0.615  11.299  18886  Z= 0.311
  Chirality :  0.043   0.273   2198
  Planarity :  0.004   0.049   2403
  Dihedral  :  4.629  29.850   1868
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.58 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.23 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.21), residues: 1703
  helix:  1.11 (0.17), residues: 990
  sheet:  0.05 (0.38), residues: 193
  loop : -1.27 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 462 
 HIS   0.004   0.001   HIS A 320 
 PHE   0.016   0.001   PHE M  93 
 TYR   0.012   0.001   TYR A  88 
 ARG   0.008   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  789)
  hydrogen bonds       : angle       4.43799 ( 2295)
  covalent geometry    : bond        0.00329 (13951)
  covalent geometry    : angle       0.61516 (18886)

*********************** 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
  296 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 248
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.6270 (mtm-85)
REVERT: A   77 MET cc_start: 0.8009 (tpp) cc_final: 0.7724 (tpp)
REVERT: A  119 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8447 (m-30)
REVERT: A  341 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7595 (ttm170)
REVERT: A  372 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (t)
REVERT: A  401 ASN cc_start: 0.8530 (t0) cc_final: 0.8287 (t0)
REVERT: A  427 LYS cc_start: 0.9414 (mttt) cc_final: 0.8976 (mttm)
REVERT: A  433 GLU cc_start: 0.9145 (tp30) cc_final: 0.8804 (tm-30)
REVERT: A  533 CYS cc_start: 0.9316 (m) cc_final: 0.8821 (m)
REVERT: A  583 TYR cc_start: 0.8796 (m-80) cc_final: 0.8579 (m-80)
REVERT: B   74 MET cc_start: 0.8876 (mmt) cc_final: 0.8455 (mmm)
REVERT: B   83 MET cc_start: 0.9172 (mtp) cc_final: 0.8378 (mpp)
REVERT: B   86 MET cc_start: 0.8925 (mtm) cc_final: 0.8342 (mpp)
REVERT: B  297 GLU cc_start: 0.8575 (mp0) cc_final: 0.8025 (mp0)
REVERT: B  330 ASP cc_start: 0.8480 (m-30) cc_final: 0.8240 (m-30)
REVERT: B  342 MET cc_start: 0.8280 (mtt) cc_final: 0.7890 (mtt)
REVERT: B  385 GLU cc_start: 0.7953 (tt0) cc_final: 0.7573 (tm-30)
REVERT: B  508 SER cc_start: 0.9234 (m) cc_final: 0.8878 (p)
REVERT: B  509 LEU cc_start: 0.9037 (tp) cc_final: 0.8738 (tp)
REVERT: M    1 MET cc_start: 0.8481 (mtp) cc_final: 0.8246 (ptp)
REVERT: M   15 LEU cc_start: 0.9500 (mp) cc_final: 0.9235 (mp)
REVERT: M   41 GLN cc_start: 0.8268 (mp10) cc_final: 0.7949 (mp10)
REVERT: M  120 TYR cc_start: 0.8040 (m-10) cc_final: 0.7678 (m-10)
REVERT: M  277 TYR cc_start: 0.8446 (p90) cc_final: 0.7743 (p90)
REVERT: M  302 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8055 (tm-30)
REVERT: M  358 MET cc_start: 0.8625 (ttt) cc_final: 0.8360 (ttm)
REVERT: S   18 LYS cc_start: 0.8530 (tppt) cc_final: 0.8305 (tppt)
REVERT: S   60 ARG cc_start: 0.8609 (ttm170) cc_final: 0.8203 (ttm-80)
REVERT: S   61 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8253 (ttp-110)
REVERT: S   89 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8417 (mm-30)
REVERT: S   93 GLU cc_start: 0.9039 (tp30) cc_final: 0.8731 (tp30)
REVERT: S  109 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8787 (ttmm)
  outliers start: 48
  outliers final: 33
  residues processed: 272
  average time/residue: 0.2343
  time to fit residues: 95.0632
Evaluate side-chains
  272 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 236
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  353 MET
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  592 THR
Chi-restraints excluded: chain B residue    9 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  177 VAL
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  451 ILE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  501 GLU
Chi-restraints excluded: chain B residue  555 ILE
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  207 SER
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 160 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0670
   chunk 141 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 12 optimal weight:    8.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    0.8124

-------------------------------------------------------------------------------
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**
B 305 ASN
M  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.081116 restraints weight = 30662.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.084128 restraints weight = 16436.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086230 restraints weight = 10614.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  13951  Z= 0.119
  Angle     :  0.640  15.069  18886  Z= 0.316
  Chirality :  0.043   0.405   2198
  Planarity :  0.004   0.048   2403
  Dihedral  :  4.550  29.061   1868
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.17 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.41 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.21), residues: 1703
  helix:  1.12 (0.17), residues: 1000
  sheet:  0.25 (0.38), residues: 188
  loop : -1.24 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 462 
 HIS   0.005   0.001   HIS A 320 
 PHE   0.015   0.001   PHE M  93 
 TYR   0.012   0.001   TYR S  94 
 ARG   0.009   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  789)
  hydrogen bonds       : angle       4.37150 ( 2295)
  covalent geometry    : bond        0.00275 (13951)
  covalent geometry    : angle       0.63998 (18886)

*********************** 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
  294 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 258
  time to evaluate  : 1.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.6227 (mtm-85)
REVERT: A   77 MET cc_start: 0.7933 (tpp) cc_final: 0.7611 (tpp)
REVERT: A  119 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8413 (m-30)
REVERT: A  341 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7596 (ttm170)
REVERT: A  372 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8582 (t)
REVERT: A  401 ASN cc_start: 0.8454 (t0) cc_final: 0.8230 (t0)
REVERT: A  433 GLU cc_start: 0.9119 (tp30) cc_final: 0.8642 (tm-30)
REVERT: A  533 CYS cc_start: 0.9282 (m) cc_final: 0.8798 (m)
REVERT: B   74 MET cc_start: 0.8876 (mmt) cc_final: 0.8440 (mmm)
REVERT: B   83 MET cc_start: 0.9038 (mtp) cc_final: 0.8410 (mpp)
REVERT: B   86 MET cc_start: 0.8881 (mtm) cc_final: 0.8289 (mpp)
REVERT: B  110 MET cc_start: 0.8531 (mtm) cc_final: 0.8239 (mtm)
REVERT: B  297 GLU cc_start: 0.8532 (mp0) cc_final: 0.7959 (mp0)
REVERT: B  330 ASP cc_start: 0.8451 (m-30) cc_final: 0.8230 (m-30)
REVERT: B  342 MET cc_start: 0.8094 (mtt) cc_final: 0.7705 (mtt)
REVERT: B  385 GLU cc_start: 0.7906 (tt0) cc_final: 0.7532 (tm-30)
REVERT: B  448 MET cc_start: 0.8764 (tpt) cc_final: 0.8295 (tpt)
REVERT: B  508 SER cc_start: 0.9206 (m) cc_final: 0.8838 (p)
REVERT: B  509 LEU cc_start: 0.9015 (tp) cc_final: 0.8728 (tp)
REVERT: M   15 LEU cc_start: 0.9483 (mp) cc_final: 0.9224 (mp)
REVERT: M   41 GLN cc_start: 0.8231 (mp10) cc_final: 0.7916 (mp10)
REVERT: M  120 TYR cc_start: 0.8015 (m-10) cc_final: 0.7638 (m-10)
REVERT: M  277 TYR cc_start: 0.8430 (p90) cc_final: 0.7832 (p90)
REVERT: M  302 GLU cc_start: 0.8206 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: M  358 MET cc_start: 0.8594 (ttt) cc_final: 0.8317 (ttm)
REVERT: S   13 LYS cc_start: 0.8986 (tttt) cc_final: 0.8246 (tttt)
REVERT: S   15 ARG cc_start: 0.8608 (mmt90) cc_final: 0.7547 (mmt-90)
REVERT: S   18 LYS cc_start: 0.8549 (tppt) cc_final: 0.8321 (tppt)
REVERT: S   60 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8160 (ttm-80)
REVERT: S   61 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8220 (ttp-110)
REVERT: S   89 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8431 (mm-30)
REVERT: S  109 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8733 (ttmm)
  outliers start: 36
  outliers final: 22
  residues processed: 275
  average time/residue: 0.2355
  time to fit residues: 96.9758
Evaluate side-chains
  265 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 240
  time to evaluate  : 1.735 
-------------------------------------------------------------------------------
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  353 MET
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  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  499 THR
Chi-restraints excluded: chain B residue  501 GLU
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   53 THR
Chi-restraints excluded: chain M residue  207 SER
Chi-restraints excluded: chain S residue   39 VAL
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 154 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 169 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0570
   chunk 63 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 95 optimal weight:   10.0000
   chunk 100 optimal weight:    1.9990
   chunk 132 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
B  24 ASN
** 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 = 0.3385 r_free = 0.3385 target = 0.099084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.081622 restraints weight = 30629.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.084665 restraints weight = 16558.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086754 restraints weight = 10708.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13951  Z= 0.122
  Angle     :  0.656  14.193  18886  Z= 0.324
  Chirality :  0.043   0.383   2198
  Planarity :  0.004   0.070   2403
  Dihedral  :  4.501  28.954   1868
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.17 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.53 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.21), residues: 1703
  helix:  1.12 (0.17), residues: 997
  sheet:  0.26 (0.38), residues: 189
  loop : -1.16 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 462 
 HIS   0.006   0.001   HIS A 320 
 PHE   0.015   0.001   PHE M  93 
 TYR   0.016   0.001   TYR A 583 
 ARG   0.010   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  789)
  hydrogen bonds       : angle       4.39314 ( 2295)
  covalent geometry    : bond        0.00284 (13951)
  covalent geometry    : angle       0.65642 (18886)

********************** 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
  289 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 253
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6183 (mtm-85)
REVERT: A   77 MET cc_start: 0.7940 (tpp) cc_final: 0.7610 (tpp)
REVERT: A  119 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8400 (m-30)
REVERT: A  372 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (t)
REVERT: A  433 GLU cc_start: 0.8795 (tp30) cc_final: 0.8507 (tm-30)
REVERT: A  533 CYS cc_start: 0.9223 (m) cc_final: 0.8773 (m)
REVERT: B   74 MET cc_start: 0.8872 (mmt) cc_final: 0.8431 (mmm)
REVERT: B   83 MET cc_start: 0.9001 (mtp) cc_final: 0.8434 (mpp)
REVERT: B   86 MET cc_start: 0.8878 (mtm) cc_final: 0.8395 (mpp)
REVERT: B  297 GLU cc_start: 0.8522 (mp0) cc_final: 0.7954 (mp0)
REVERT: B  330 ASP cc_start: 0.8456 (m-30) cc_final: 0.8220 (m-30)
REVERT: B  342 MET cc_start: 0.8190 (mtt) cc_final: 0.7776 (mtt)
REVERT: B  385 GLU cc_start: 0.8081 (tt0) cc_final: 0.7641 (mm-30)
REVERT: B  448 MET cc_start: 0.8675 (tpt) cc_final: 0.8359 (tpt)
REVERT: B  508 SER cc_start: 0.9208 (m) cc_final: 0.8842 (p)
REVERT: B  509 LEU cc_start: 0.8970 (tp) cc_final: 0.8688 (tp)
REVERT: M   15 LEU cc_start: 0.9472 (mp) cc_final: 0.9206 (mp)
REVERT: M   41 GLN cc_start: 0.8201 (mp10) cc_final: 0.7875 (mp10)
REVERT: M  277 TYR cc_start: 0.8412 (p90) cc_final: 0.7822 (p90)
REVERT: M  302 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: M  358 MET cc_start: 0.8619 (ttt) cc_final: 0.8360 (ttm)
REVERT: S   13 LYS cc_start: 0.8999 (tttt) cc_final: 0.8622 (tttt)
REVERT: S   18 LYS cc_start: 0.8503 (tppt) cc_final: 0.8300 (tppt)
REVERT: S   60 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8174 (ttm-80)
REVERT: S   61 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8166 (ttp-110)
REVERT: S   89 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8429 (mm-30)
REVERT: S   93 GLU cc_start: 0.8879 (tp30) cc_final: 0.8605 (tp30)
  outliers start: 36
  outliers final: 26
  residues processed: 270
  average time/residue: 0.2414
  time to fit residues: 97.7825
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  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  353 MET
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  592 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  401 THR
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  501 GLU
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   53 THR
Chi-restraints excluded: chain M residue  207 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 158 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0170
   chunk 18 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 157 optimal weight:    6.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 ASN
** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 203 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.099453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.081953 restraints weight = 31116.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.085006 restraints weight = 16755.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.087119 restraints weight = 10825.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13951  Z= 0.121
  Angle     :  0.653  13.907  18886  Z= 0.324
  Chirality :  0.043   0.380   2198
  Planarity :  0.004   0.050   2403
  Dihedral  :  4.476  28.675   1868
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.17 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.72 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.21), residues: 1703
  helix:  1.15 (0.17), residues: 997
  sheet:  0.29 (0.38), residues: 191
  loop : -1.11 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 462 
 HIS   0.005   0.001   HIS A 320 
 PHE   0.015   0.001   PHE M  93 
 TYR   0.012   0.001   TYR S  94 
 ARG   0.007   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  789)
  hydrogen bonds       : angle       4.36011 ( 2295)
  covalent geometry    : bond        0.00279 (13951)
  covalent geometry    : angle       0.65307 (18886)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3928.01 seconds
wall clock time: 69 minutes 26.67 seconds (4166.67 seconds total)