Starting phenix.real_space_refine
on Thu May 15 21:25:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fx4_29523/05_2025/8fx4_29523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fx4_29523/05_2025/8fx4_29523.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/8fx4_29523/05_2025/8fx4_29523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fx4_29523/05_2025/8fx4_29523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fx4_29523/05_2025/8fx4_29523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fx4_29523/05_2025/8fx4_29523.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=   0.002 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      68      5.16       5
     C    8530      2.51       5
     N    2271      2.21       5
     O    2599      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13474
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 623, 5039
          Classifications: {'peptide': 623}
          Link IDs: {'PTRANS': 17, 'TRANS': 605}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 5011
          Classifications: {'peptide': 619}
          Link IDs: {'PTRANS': 17, 'TRANS': 601}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1699
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 4, 'TRANS': 195}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1663
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 8, 'TRANS': 194}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.90, per 1000 atoms: 0.59
  Number of scatterers: 13474
  At special positions: 0
  Unit cell: (99.4671, 130.806, 138.981, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      68     16.00
     P       6     15.00
     O    2599      8.00
     N    2271      7.00
     C    8530      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: 3.17
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3146

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 14 sheets defined
      47.3% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 31
    Processing helix  chain 'A' and resid 37 through 61
      removed outlier: 4.228A  pdb=" N   ARG A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ALA A  50 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   THR A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASP A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 3.591A  pdb=" N   ASP A  66 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   SER A  67 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 101
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.731A  pdb=" N   ALA A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 138
    Processing helix  chain 'A' and resid 188 through 193
      removed outlier: 4.263A  pdb=" N   GLU A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 4.219A  pdb=" N   VAL A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS A 199 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 309
    Processing helix  chain 'A' and resid 400 through 420
      removed outlier: 4.326A  pdb=" N   ILE A 404 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ARG A 405 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS A 406 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LYS A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 444
      removed outlier: 6.552A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ASN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 452
    Processing helix  chain 'A' and resid 469 through 475
    Processing helix  chain 'A' and resid 490 through 496
      removed outlier: 3.885A  pdb=" N   VAL A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ASN A 496 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 515 through 525
      removed outlier: 3.884A  pdb=" N   GLN A 523 " --> pdb=" O   GLU A 519 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLN A 524 " --> pdb=" O   TYR A 520 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 525 " --> pdb=" O   CYS A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 570
      removed outlier: 3.729A  pdb=" N   LYS A 550 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 561 " --> pdb=" O   LYS A 557 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ASN A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LEU A 563 " --> pdb=" O   LYS A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 615 through 621
    Processing helix  chain 'A' and resid 632 through 645
    Processing helix  chain 'A' and resid 649 through 667
      removed outlier: 3.959A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 688
      removed outlier: 4.502A  pdb=" N   HIS A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 31
      removed outlier: 3.699A  pdb=" N   SER B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE B  29 " --> pdb=" O   MET B  25 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 61
      removed outlier: 3.758A  pdb=" N   LEU B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   THR B  60 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASP B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 66
    Processing helix  chain 'B' and resid 94 through 101
      removed outlier: 3.724A  pdb=" N   ASN B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.041A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 140
      removed outlier: 3.879A  pdb=" N   VAL B 139 " --> pdb=" O   ALA B 136 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B 140 " --> pdb=" O   TYR B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
      removed outlier: 3.584A  pdb=" N   TYR B 192 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 206
      removed outlier: 3.604A  pdb=" N   VAL B 198 " --> pdb=" O   GLU B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 310
    Processing helix  chain 'B' and resid 371 through 375
    Processing helix  chain 'B' and resid 398 through 419
      removed outlier: 3.714A  pdb=" N   LYS B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL B 403 " --> pdb=" O   LYS B 399 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE B 404 " --> pdb=" O   ILE B 400 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ARG B 405 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS B 406 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   LYS B 410 " --> pdb=" O   LYS B 406 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS B 411 " --> pdb=" O   ASN B 407 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 415 " --> pdb=" O   LYS B 411 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE B 416 " --> pdb=" O   CYS B 412 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER B 417 " --> pdb=" O   LEU B 413 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU B 418 " --> pdb=" O   GLU B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 444
      removed outlier: 3.889A  pdb=" N   TYR B 426 " --> pdb=" O   ASP B 422 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ALA B 432 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE B 433 " --> pdb=" O   PHE B 429 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LYS B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   ASN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 452
    Processing helix  chain 'B' and resid 469 through 474
    Processing helix  chain 'B' and resid 490 through 496
      removed outlier: 3.579A  pdb=" N   VAL B 494 " --> pdb=" O   SER B 490 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN B 496 " --> pdb=" O   GLU B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 506
    Processing helix  chain 'B' and resid 517 through 525
      removed outlier: 3.621A  pdb=" N   CYS B 521 " --> pdb=" O   ILE B 517 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN B 523 " --> pdb=" O   GLU B 519 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 558
      removed outlier: 3.731A  pdb=" N   ALA B 558 " --> pdb=" O   GLU B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 572
      removed outlier: 3.520A  pdb=" N   LYS B 565 " --> pdb=" O   GLU B 561 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET B 567 " --> pdb=" O   LEU B 563 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   LYS B 568 " --> pdb=" O   CYS B 564 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU B 569 " --> pdb=" O   LYS B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 609
    Processing helix  chain 'B' and resid 632 through 645
      removed outlier: 3.879A  pdb=" N   GLU B 636 " --> pdb=" O   HIS B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 665
      removed outlier: 3.949A  pdb=" N   LYS B 652 " --> pdb=" O   ASP B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 689
      removed outlier: 4.318A  pdb=" N   HIS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY B 689 " --> pdb=" O   LYS B 685 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 58
      removed outlier: 3.886A  pdb=" N   ARG C  30 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS C  54 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 113
    Processing helix  chain 'C' and resid 143 through 160
      removed outlier: 3.665A  pdb=" N   PHE C 152 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 183
    Processing helix  chain 'C' and resid 184 through 199
    Processing helix  chain 'C' and resid 207 through 228
    Processing helix  chain 'C' and resid 230 through 234
      removed outlier: 3.606A  pdb=" N   ALA C 233 " --> pdb=" O   ASP C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.814A  pdb=" N   PHE C 239 " --> pdb=" O   PHE C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 266
    Processing helix  chain 'D' and resid 547 through 551
    Processing helix  chain 'D' and resid 564 through 582
    Processing helix  chain 'D' and resid 625 through 631
      removed outlier: 3.523A  pdb=" N   LEU D 629 " --> pdb=" O   ALA D 625 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLN D 631 " --> pdb=" O   GLU D 627 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 635 through 653
    Processing helix  chain 'D' and resid 664 through 674
    Processing helix  chain 'D' and resid 694 through 704
    Processing helix  chain 'D' and resid 714 through 729
      removed outlier: 4.386A  pdb=" N   ILE D 718 " --> pdb=" O   ASP D 714 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15
      removed outlier: 4.539A  pdb=" N   GLU A  13 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL B 167 " --> pdb=" O   GLU A  13 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A  15 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   PHE B 165 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   GLU B 153 " --> pdb=" O   HIS B 149 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   HIS B 149 " --> pdb=" O   GLU B 153 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   ILE B  73 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ILE B 213 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 215 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU B 280 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
      removed outlier: 7.359A  pdb=" N   GLN A  18 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 78
      removed outlier: 3.793A  pdb=" N   LYS A 142 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   PHE A 165 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE B  15 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 323
      removed outlier: 4.357A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS A 354 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 381 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A 356 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER A 383 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   ASP A 364 " --> pdb=" O   ILE A 353 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LEU A 355 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457
    Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485
      removed outlier: 5.957A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.562A  pdb=" N   ILE A 628 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 363
      removed outlier: 5.891A  pdb=" N   PHE B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL B 357 " --> pdb=" O   PHE B 361 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LYS B 354 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   PHE B 329 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   VAL B 318 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   SER C 128 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   HIS B 320 " --> pdb=" O   SER C 126 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   SER C 126 " --> pdb=" O   HIS B 320 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   SER B 322 " --> pdb=" O   GLY C 124 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 456 through 457
    Processing sheet with id=AB2, first strand: chain 'B' and resid 482 through 483
    Processing sheet with id=AB3, first strand: chain 'B' and resid 486 through 487
      removed outlier: 6.815A  pdb=" N   ILE B 486 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 577 through 580
      removed outlier: 4.367A  pdb=" N   LYS B 577 " --> pdb=" O   LYS B 624 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU B 626 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR B 579 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   CYS B 590 " --> pdb=" O   GLU B 627 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 597 through 599

    574 hydrogen bonds defined for protein.
    1617 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: 3.80

  Time building geometry restraints manager: 3.70 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: 4377
        1.34 -     1.46: 2243
        1.46 -     1.58: 6962
        1.58 -     1.70: 12
        1.70 -     1.82: 114
  Bond restraints: 13708
  Sorted by residual:
  bond pdb=" CB  PRO A  79 "
       pdb=" CG  PRO A  79 "
    ideal  model  delta    sigma   weight residual
    1.492  1.667 -0.175 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" CA  ASN A 582 "
       pdb=" CB  ASN A 582 "
    ideal  model  delta    sigma   weight residual
    1.536  1.634 -0.098 4.10e-02 5.95e+02 5.71e+00
  bond pdb=" CB  GLN B 397 "
       pdb=" CG  GLN B 397 "
    ideal  model  delta    sigma   weight residual
    1.520  1.572 -0.052 3.00e-02 1.11e+03 3.00e+00
  bond pdb=" N   PRO A  79 "
       pdb=" CD  PRO A  79 "
    ideal  model  delta    sigma   weight residual
    1.473  1.495 -0.022 1.40e-02 5.10e+03 2.49e+00
  bond pdb=" CA  ASN A  46 "
       pdb=" C   ASN A  46 "
    ideal  model  delta    sigma   weight residual
    1.522  1.544 -0.021 1.37e-02 5.33e+03 2.46e+00
  ... (remaining 13703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.92: 18099
        2.92 -     5.85: 271
        5.85 -     8.77: 47
        8.77 -    11.69: 13
       11.69 -    14.62: 3
  Bond angle restraints: 18433
  Sorted by residual:
  angle pdb=" CA  PRO A  79 "
        pdb=" N   PRO A  79 "
        pdb=" CD  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     112.00   97.38   14.62 1.40e+00 5.10e-01 1.09e+02
  angle pdb=" CA  GLN B 397 "
        pdb=" CB  GLN B 397 "
        pdb=" CG  GLN B 397 "
      ideal   model   delta    sigma   weight residual
     114.10  125.22  -11.12 2.00e+00 2.50e-01 3.09e+01
  angle pdb=" CA  GLN C  44 "
        pdb=" CB  GLN C  44 "
        pdb=" CG  GLN C  44 "
      ideal   model   delta    sigma   weight residual
     114.10  123.20   -9.10 2.00e+00 2.50e-01 2.07e+01
  angle pdb=" CA  LYS B 557 "
        pdb=" CB  LYS B 557 "
        pdb=" CG  LYS B 557 "
      ideal   model   delta    sigma   weight residual
     114.10  123.18   -9.08 2.00e+00 2.50e-01 2.06e+01
  angle pdb=" C   LYS B 552 "
        pdb=" N   MET B 553 "
        pdb=" CA  MET B 553 "
      ideal   model   delta    sigma   weight residual
     121.14  113.29    7.85 1.75e+00 3.27e-01 2.01e+01
  ... (remaining 18428 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 7047
       17.93 -    35.86: 1084
       35.86 -    53.78: 276
       53.78 -    71.71: 49
       71.71 -    89.64: 22
  Dihedral angle restraints: 8478
    sinusoidal: 3640
      harmonic: 4838
  Sorted by residual:
  dihedral pdb=" CA  GLU C  16 "
           pdb=" C   GLU C  16 "
           pdb=" N   ASP C  17 "
           pdb=" CA  ASP C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.71  -21.29     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  ALA D 632 "
           pdb=" C   ALA D 632 "
           pdb=" N   ASN D 633 "
           pdb=" CA  ASN D 633 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.73   21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LYS B 477 "
           pdb=" C   LYS B 477 "
           pdb=" N   GLU B 478 "
           pdb=" CA  GLU B 478 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.26   20.74     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 8475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1777
       0.069 -    0.139: 238
       0.139 -    0.208: 11
       0.208 -    0.278: 3
       0.278 -    0.347: 1
  Chirality restraints: 2030
  Sorted by residual:
  chirality pdb=" CA  PRO A  79 "
            pdb=" N   PRO A  79 "
            pdb=" C   PRO A  79 "
            pdb=" CB  PRO A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CB  ILE D 607 "
            pdb=" CA  ILE D 607 "
            pdb=" CG1 ILE D 607 "
            pdb=" CG2 ILE D 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  VAL A 656 "
            pdb=" CA  VAL A 656 "
            pdb=" CG1 VAL A 656 "
            pdb=" CG2 VAL A 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 2027 not shown)

  Planarity restraints: 2345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  78 "    0.061 5.00e-02 4.00e+02   8.36e-02 1.12e+01
        pdb=" N   PRO A  79 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A  79 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  79 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 370 "   -0.038 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO B 371 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B 371 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 371 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 623 "   -0.019 2.00e-02 2.50e+03   1.45e-02 5.29e+00
        pdb=" CG  TRP D 623 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 623 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 623 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 623 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 623 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2342 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 351
        2.67 -     3.23: 13395
        3.23 -     3.79: 19965
        3.79 -     4.34: 24887
        4.34 -     4.90: 39435
  Nonbonded interactions: 98033
  Sorted by model distance:
  nonbonded pdb=" O   ARG B  55 "
            pdb=" OG  SER B  58 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OD1 ASP B 546 "
            pdb=" N   GLU B 547 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   GLY B 132 "
            pdb=" OG  SER B 135 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASN C 116 "
            pdb=" OG1 THR C 119 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   VAL D 672 "
            pdb=" OG  SER D 675 "
     model   vdw
     2.217 3.040
  ... (remaining 98028 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 12 through 218 or resid 278 through 613 or resid 617 throu \ 
gh 690 or resid 801))
  selection = (chain 'B' and (resid 12 through 218 or resid 278 through 690 or resid 801))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:                    0.130
  Process input model:                     30.260
  Find NCS groups from input model:        0.470
  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:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
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      :  0.004   0.175  13708  Z= 0.171
  Angle     :  0.915  14.618  18433  Z= 0.490
  Chirality :  0.046   0.347   2030
  Planarity :  0.004   0.084   2345
  Dihedral  : 18.476  89.640   5332
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.66 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 33.00 %
    Favored  : 66.20 %
  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: -1.50 (0.21), residues: 1619
  helix:  0.35 (0.20), residues: 678
  sheet:  0.51 (0.42), residues: 181
  loop : -2.77 (0.20), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP D 623 
 HIS   0.007   0.001   HIS A 149 
 PHE   0.016   0.001   PHE A  39 
 TYR   0.021   0.001   TYR A 430 
 ARG   0.006   0.001   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14478 (  574)
  hydrogen bonds       : angle       5.69773 ( 1617)
  covalent geometry    : bond        0.00392 (13708)
  covalent geometry    : angle       0.91488 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 421
  time to evaluate  : 1.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8221 (mtpp)
REVERT: A  430 TYR cc_start: 0.7491 (t80) cc_final: 0.7214 (t80)
REVERT: A  481 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8632 (mmtt)
REVERT: A  501 GLU cc_start: 0.7593 (mp0) cc_final: 0.7364 (mp0)
REVERT: A  509 GLU cc_start: 0.6405 (tp30) cc_final: 0.5402 (tp30)
REVERT: A  551 LYS cc_start: 0.7642 (ptpp) cc_final: 0.7439 (pttm)
REVERT: B   57 GLU cc_start: 0.7862 (tp30) cc_final: 0.7506 (tp30)
REVERT: B  279 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6632 (mm-40)
REVERT: B  280 GLU cc_start: 0.7697 (pt0) cc_final: 0.6946 (tm-30)
REVERT: B  300 GLU cc_start: 0.7555 (mp0) cc_final: 0.7264 (mp0)
REVERT: B  304 PHE cc_start: 0.8536 (t80) cc_final: 0.8127 (t80)
REVERT: B  312 TRP cc_start: 0.7418 (p-90) cc_final: 0.7136 (p-90)
REVERT: B  393 GLU cc_start: 0.7260 (mp0) cc_final: 0.6909 (mp0)
REVERT: B  395 LEU cc_start: 0.8045 (tp) cc_final: 0.7720 (tt)
REVERT: B  471 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6813 (tm-30)
REVERT: B  476 MET cc_start: 0.6600 (mmm) cc_final: 0.6071 (mmm)
REVERT: B  553 MET cc_start: 0.7549 (ppp) cc_final: 0.7228 (ppp)
REVERT: B  559 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7577 (ttpp)
REVERT: B  627 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: C   20 HIS cc_start: 0.7635 (t-90) cc_final: 0.7363 (t70)
REVERT: C   29 PHE cc_start: 0.7187 (m-10) cc_final: 0.6975 (m-80)
REVERT: C   36 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.6894 (tmm-80)
REVERT: D  627 GLU cc_start: 0.7252 (pp20) cc_final: 0.7026 (pp20)
  outliers start: 12
  outliers final: 8
  residues processed: 424
  average time/residue: 0.3022
  time to fit residues: 172.5198
Evaluate side-chains
  412 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 403
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  196 ARG
Chi-restraints excluded: chain A residue  397 GLN
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  519 GLU
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain D residue  634 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0970
   chunk 95 optimal weight:    2.9990
   chunk 148 optimal weight:    0.0970
   overall best weight:    0.5976

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

Flipped N/Q/H residues before XYZ refinement:
A 458 HIS
B 150 ASN
B 396 GLN
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116857 restraints weight = 25057.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.120708 restraints weight = 13562.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123307 restraints weight = 8593.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13708  Z= 0.133
  Angle     :  0.682   9.825  18433  Z= 0.361
  Chirality :  0.044   0.182   2030
  Planarity :  0.004   0.059   2345
  Dihedral  :  7.578  87.234   1867
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.41 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 27.51 %
    Favored  : 68.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.29 (0.21), residues: 1619
  helix:  0.55 (0.20), residues: 694
  sheet:  0.38 (0.40), residues: 192
  loop : -2.71 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D 623 
 HIS   0.006   0.001   HIS A 149 
 PHE   0.024   0.001   PHE C 125 
 TYR   0.028   0.001   TYR B 305 
 ARG   0.006   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  574)
  hydrogen bonds       : angle       4.71344 ( 1617)
  covalent geometry    : bond        0.00289 (13708)
  covalent geometry    : angle       0.68216 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  487 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 428
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8013 (mtpp)
REVERT: A  153 GLU cc_start: 0.7417 (mp0) cc_final: 0.7150 (mp0)
REVERT: A  195 GLU cc_start: 0.7530 (tp30) cc_final: 0.7118 (tp30)
REVERT: A  300 GLU cc_start: 0.6790 (pp20) cc_final: 0.6308 (pt0)
REVERT: A  303 GLU cc_start: 0.7118 (pp20) cc_final: 0.6781 (pp20)
REVERT: A  364 ASP cc_start: 0.7587 (p0) cc_final: 0.7387 (p0)
REVERT: A  397 GLN cc_start: 0.7322 (tt0) cc_final: 0.6632 (tm-30)
REVERT: A  400 ILE cc_start: 0.8724 (mm) cc_final: 0.8196 (mm)
REVERT: A  449 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7668 (tpp80)
REVERT: A  481 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8445 (mmtt)
REVERT: A  501 GLU cc_start: 0.7402 (mp0) cc_final: 0.7051 (mp0)
REVERT: A  509 GLU cc_start: 0.6978 (tp30) cc_final: 0.6511 (tp30)
REVERT: A  526 LYS cc_start: 0.7534 (pptt) cc_final: 0.7192 (pptt)
REVERT: A  527 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6091 (mt-10)
REVERT: A  553 MET cc_start: 0.7162 (mmm) cc_final: 0.6960 (mmm)
REVERT: B   55 ARG cc_start: 0.8302 (ttt180) cc_final: 0.7397 (ttp-170)
REVERT: B  101 ASN cc_start: 0.8086 (t0) cc_final: 0.7619 (t0)
REVERT: B  154 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7080 (mm-40)
REVERT: B  279 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6871 (mm110)
REVERT: B  294 ASP cc_start: 0.7974 (t0) cc_final: 0.7514 (t0)
REVERT: B  312 TRP cc_start: 0.7502 (p-90) cc_final: 0.7177 (p-90)
REVERT: B  356 TYR cc_start: 0.8353 (m-80) cc_final: 0.7850 (m-80)
REVERT: B  359 ARG cc_start: 0.7962 (mpp80) cc_final: 0.7573 (mpp80)
REVERT: B  424 GLU cc_start: 0.6947 (pm20) cc_final: 0.6722 (pm20)
REVERT: B  426 TYR cc_start: 0.8360 (t80) cc_final: 0.8108 (t80)
REVERT: B  427 LYS cc_start: 0.8789 (mttt) cc_final: 0.8467 (mtmm)
REVERT: B  493 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8029 (tp40)
REVERT: B  513 MET cc_start: 0.6611 (mmt) cc_final: 0.6318 (mmt)
REVERT: B  559 LYS cc_start: 0.7833 (ttpp) cc_final: 0.7383 (ttpp)
REVERT: B  627 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7275 (mm-30)
REVERT: C   16 GLU cc_start: 0.7186 (pp20) cc_final: 0.6955 (tm-30)
REVERT: C   20 HIS cc_start: 0.8080 (t-90) cc_final: 0.7855 (t70)
REVERT: C   30 ARG cc_start: 0.7367 (mtm180) cc_final: 0.7077 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8494 (m-10) cc_final: 0.7870 (m100)
REVERT: C   36 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7428 (ttp-170)
REVERT: C  107 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7657 (mtt-85)
REVERT: D  578 MET cc_start: 0.7702 (mmm) cc_final: 0.7488 (mmm)
REVERT: D  582 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.6077 (t-90)
REVERT: D  585 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7599 (mmmm)
REVERT: D  627 GLU cc_start: 0.7258 (pp20) cc_final: 0.7048 (pp20)
REVERT: D  724 LYS cc_start: 0.8252 (tmmt) cc_final: 0.8011 (tmmt)
  outliers start: 59
  outliers final: 34
  residues processed: 463
  average time/residue: 0.3023
  time to fit residues: 189.9877
Evaluate side-chains
  444 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 407
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  683 MET
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  566 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  582 HIS
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  598 VAL
Chi-restraints excluded: chain D residue  634 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 77 optimal weight:    0.1980
   chunk 8 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 51 optimal weight:    0.8980
   chunk 139 optimal weight:   10.0000
   chunk 153 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0340

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.144597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116388 restraints weight = 25074.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.120193 restraints weight = 13608.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122788 restraints weight = 8650.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13708  Z= 0.146
  Angle     :  0.670  10.985  18433  Z= 0.353
  Chirality :  0.044   0.191   2030
  Planarity :  0.004   0.053   2345
  Dihedral  :  6.944  88.212   1854
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.97 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 28.11 %
    Favored  : 66.00 %
  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: -1.21 (0.21), residues: 1619
  helix:  0.67 (0.20), residues: 695
  sheet:  0.51 (0.42), residues: 174
  loop : -2.70 (0.21), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 289 
 HIS   0.006   0.001   HIS B 320 
 PHE   0.024   0.001   PHE A 361 
 TYR   0.016   0.001   TYR B 356 
 ARG   0.009   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  574)
  hydrogen bonds       : angle       4.60100 ( 1617)
  covalent geometry    : bond        0.00320 (13708)
  covalent geometry    : angle       0.67039 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  510 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 422
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.7839 (tppp) cc_final: 0.7520 (tptp)
REVERT: A  189 GLN cc_start: 0.8338 (mm110) cc_final: 0.8078 (mm-40)
REVERT: A  195 GLU cc_start: 0.7427 (tp30) cc_final: 0.7073 (tp30)
REVERT: A  199 LYS cc_start: 0.8550 (pttm) cc_final: 0.8128 (pttm)
REVERT: A  300 GLU cc_start: 0.6818 (pp20) cc_final: 0.6525 (pp20)
REVERT: A  303 GLU cc_start: 0.7189 (pp20) cc_final: 0.6782 (pp20)
REVERT: A  397 GLN cc_start: 0.7232 (tt0) cc_final: 0.6617 (tm-30)
REVERT: A  400 ILE cc_start: 0.8750 (mm) cc_final: 0.8419 (mm)
REVERT: A  449 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7677 (tpp80)
REVERT: A  481 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8482 (mmtt)
REVERT: A  509 GLU cc_start: 0.6705 (tp30) cc_final: 0.6338 (tp30)
REVERT: A  526 LYS cc_start: 0.7504 (pptt) cc_final: 0.7192 (pptt)
REVERT: A  527 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6077 (mt-10)
REVERT: A  553 MET cc_start: 0.7237 (mmm) cc_final: 0.6922 (mmp)
REVERT: B   55 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7414 (ttp-170)
REVERT: B   82 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7924 (mtp180)
REVERT: B  101 ASN cc_start: 0.8055 (t0) cc_final: 0.7551 (t0)
REVERT: B  128 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7076 (mp-120)
REVERT: B  154 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7113 (mm-40)
REVERT: B  279 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6820 (mm110)
REVERT: B  294 ASP cc_start: 0.8009 (t0) cc_final: 0.7603 (t0)
REVERT: B  312 TRP cc_start: 0.7515 (p-90) cc_final: 0.7185 (p-90)
REVERT: B  376 PHE cc_start: 0.8803 (p90) cc_final: 0.7913 (p90)
REVERT: B  395 LEU cc_start: 0.8083 (tp) cc_final: 0.7771 (tt)
REVERT: B  410 LYS cc_start: 0.8139 (tttt) cc_final: 0.7902 (tmmt)
REVERT: B  476 MET cc_start: 0.6347 (mmm) cc_final: 0.5843 (mmm)
REVERT: B  481 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8349 (mmtt)
REVERT: B  493 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8037 (mm-40)
REVERT: B  513 MET cc_start: 0.6609 (mmt) cc_final: 0.6079 (mmt)
REVERT: B  559 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7319 (ttpt)
REVERT: B  569 GLU cc_start: 0.7674 (pm20) cc_final: 0.7383 (pm20)
REVERT: B  572 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6575 (p0)
REVERT: C    8 ASP cc_start: 0.6966 (m-30) cc_final: 0.6543 (m-30)
REVERT: C   30 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7124 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.7435 (m-10)
REVERT: C   36 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7520 (ttp-170)
REVERT: C   38 GLU cc_start: 0.7616 (pt0) cc_final: 0.7318 (pt0)
REVERT: C   40 MET cc_start: 0.8069 (tpt) cc_final: 0.7836 (tpt)
REVERT: C   46 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7040 (mm-30)
REVERT: C  104 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7632 (mm-30)
REVERT: C  107 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7536 (mtt-85)
REVERT: D  578 MET cc_start: 0.7873 (mmm) cc_final: 0.7559 (mmm)
REVERT: D  585 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7590 (mmmm)
REVERT: D  674 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (t0)
REVERT: D  724 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7937 (tmmt)
  outliers start: 88
  outliers final: 57
  residues processed: 470
  average time/residue: 0.2948
  time to fit residues: 188.7636
Evaluate side-chains
  474 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 410
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  406 LYS
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  566 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  571 LEU
Chi-restraints excluded: chain D residue  579 SER
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  598 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  674 ASN
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 142 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  30 ASN
B 352 ASN
C  20 HIS
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.141069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.112779 restraints weight = 24929.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.116592 restraints weight = 13502.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.119184 restraints weight = 8581.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13708  Z= 0.247
  Angle     :  0.756  11.091  18433  Z= 0.408
  Chirality :  0.048   0.216   2030
  Planarity :  0.005   0.051   2345
  Dihedral  :  7.250  84.330   1854
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.50 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 26.91 %
    Favored  : 65.93 %
  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: -1.49 (0.21), residues: 1619
  helix:  0.36 (0.20), residues: 698
  sheet:  0.37 (0.41), residues: 179
  loop : -2.79 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 289 
 HIS   0.008   0.002   HIS B 315 
 PHE   0.029   0.002   PHE A 329 
 TYR   0.021   0.002   TYR B 356 
 ARG   0.012   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06500 (  574)
  hydrogen bonds       : angle       5.02923 ( 1617)
  covalent geometry    : bond        0.00527 (13708)
  covalent geometry    : angle       0.75604 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  539 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 432
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8339 (mtpp)
REVERT: A   72 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6671 (pttm)
REVERT: A  115 GLU cc_start: 0.7811 (tp30) cc_final: 0.7540 (tp30)
REVERT: A  153 GLU cc_start: 0.7523 (mp0) cc_final: 0.7157 (mp0)
REVERT: A  155 TYR cc_start: 0.7523 (m-80) cc_final: 0.6973 (m-80)
REVERT: A  195 GLU cc_start: 0.7564 (tp30) cc_final: 0.6376 (tp30)
REVERT: A  199 LYS cc_start: 0.8673 (pttm) cc_final: 0.7905 (pttm)
REVERT: A  300 GLU cc_start: 0.6983 (pp20) cc_final: 0.6638 (pp20)
REVERT: A  301 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7850 (t80)
REVERT: A  303 GLU cc_start: 0.7396 (pp20) cc_final: 0.7141 (pp20)
REVERT: A  305 TYR cc_start: 0.8074 (t80) cc_final: 0.7433 (t80)
REVERT: A  366 CYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7456 (m)
REVERT: A  386 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (mp)
REVERT: A  397 GLN cc_start: 0.7436 (tt0) cc_final: 0.6690 (tm-30)
REVERT: A  400 ILE cc_start: 0.8764 (mm) cc_final: 0.8536 (mm)
REVERT: A  443 GLU cc_start: 0.7875 (tp30) cc_final: 0.7524 (tp30)
REVERT: A  449 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7713 (tpp80)
REVERT: A  481 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8259 (mmmm)
REVERT: A  487 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7852 (p)
REVERT: A  501 GLU cc_start: 0.7938 (mp0) cc_final: 0.7710 (mp0)
REVERT: A  513 MET cc_start: 0.7412 (mtp) cc_final: 0.7146 (tpp)
REVERT: A  526 LYS cc_start: 0.7671 (pptt) cc_final: 0.7315 (pptt)
REVERT: A  527 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6075 (mt-10)
REVERT: A  553 MET cc_start: 0.7352 (mmm) cc_final: 0.7110 (mmp)
REVERT: A  582 ASN cc_start: 0.8113 (p0) cc_final: 0.7883 (p0)
REVERT: B   58 SER cc_start: 0.8493 (p) cc_final: 0.8180 (p)
REVERT: B   93 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7717 (mmt)
REVERT: B  101 ASN cc_start: 0.8063 (t0) cc_final: 0.7567 (t0)
REVERT: B  117 LEU cc_start: 0.8329 (tp) cc_final: 0.8095 (tp)
REVERT: B  128 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7047 (mp-120)
REVERT: B  154 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6905 (mm-40)
REVERT: B  158 GLU cc_start: 0.6855 (pp20) cc_final: 0.6594 (pp20)
REVERT: B  186 LYS cc_start: 0.7475 (mmtt) cc_final: 0.7175 (mmtm)
REVERT: B  279 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6887 (mm110)
REVERT: B  294 ASP cc_start: 0.7921 (t0) cc_final: 0.7530 (t0)
REVERT: B  300 GLU cc_start: 0.7573 (mp0) cc_final: 0.7088 (mp0)
REVERT: B  312 TRP cc_start: 0.7606 (p-90) cc_final: 0.7229 (p-90)
REVERT: B  329 PHE cc_start: 0.8566 (p90) cc_final: 0.8022 (p90)
REVERT: B  356 TYR cc_start: 0.8508 (m-80) cc_final: 0.8058 (m-80)
REVERT: B  364 ASP cc_start: 0.6895 (p0) cc_final: 0.6662 (p0)
REVERT: B  376 PHE cc_start: 0.8756 (p90) cc_final: 0.8082 (p90)
REVERT: B  397 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7138 (tm-30)
REVERT: B  476 MET cc_start: 0.6501 (mmm) cc_final: 0.6099 (mmm)
REVERT: B  493 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (mm-40)
REVERT: B  513 MET cc_start: 0.6973 (mmt) cc_final: 0.6751 (mmt)
REVERT: B  514 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7628 (p)
REVERT: B  542 GLU cc_start: 0.7383 (tp30) cc_final: 0.7180 (tp30)
REVERT: B  559 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7735 (ttpp)
REVERT: B  627 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7259 (mm-30)
REVERT: B  660 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7821 (tp30)
REVERT: C    8 ASP cc_start: 0.7149 (m-30) cc_final: 0.6641 (m-30)
REVERT: C   22 ASN cc_start: 0.7943 (m-40) cc_final: 0.7598 (m-40)
REVERT: C   30 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7205 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.7406 (m-10)
REVERT: C   36 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7578 (ttp-170)
REVERT: C   38 GLU cc_start: 0.7763 (pt0) cc_final: 0.7475 (pt0)
REVERT: C   40 MET cc_start: 0.8091 (tpt) cc_final: 0.7790 (tpt)
REVERT: C  104 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: C  107 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7547 (mtt-85)
REVERT: C  222 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7682 (pm20)
REVERT: D  529 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5600 (ptmm)
REVERT: D  578 MET cc_start: 0.7752 (mmm) cc_final: 0.7501 (mmm)
REVERT: D  585 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7574 (mmmm)
REVERT: D  678 MET cc_start: 0.6228 (ppp) cc_final: 0.5997 (ppp)
REVERT: D  724 LYS cc_start: 0.8307 (tmmt) cc_final: 0.7846 (tmmt)
  outliers start: 107
  outliers final: 67
  residues processed: 493
  average time/residue: 0.2879
  time to fit residues: 194.7604
Evaluate side-chains
  496 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 417
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  684 ILE
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  566 LEU
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  571 LEU
Chi-restraints excluded: chain D residue  579 SER
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  598 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  608 THR
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0870
   chunk 131 optimal weight:    0.0060
   chunk 26 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 111 optimal weight:    0.3980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN
B 632 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.144655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.116347 restraints weight = 24864.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120183 restraints weight = 13456.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122836 restraints weight = 8504.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13708  Z= 0.127
  Angle     :  0.686  11.676  18433  Z= 0.357
  Chirality :  0.044   0.211   2030
  Planarity :  0.004   0.050   2345
  Dihedral  :  6.666  84.435   1850
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.54 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 30.52 %
    Favored  : 65.26 %
  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: -1.19 (0.21), residues: 1619
  helix:  0.62 (0.20), residues: 703
  sheet:  0.38 (0.40), residues: 191
  loop : -2.68 (0.22), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 623 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.028   0.001   PHE A 361 
 TYR   0.026   0.001   TYR B 305 
 ARG   0.012   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04085 (  574)
  hydrogen bonds       : angle       4.49793 ( 1617)
  covalent geometry    : bond        0.00282 (13708)
  covalent geometry    : angle       0.68623 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  489 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 426
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7973 (mpp) cc_final: 0.7533 (mpp)
REVERT: A  107 LYS cc_start: 0.7879 (tppp) cc_final: 0.7558 (tptp)
REVERT: A  199 LYS cc_start: 0.8601 (pttm) cc_final: 0.8061 (ptpp)
REVERT: A  214 THR cc_start: 0.8376 (t) cc_final: 0.8008 (p)
REVERT: A  300 GLU cc_start: 0.6748 (pp20) cc_final: 0.6370 (pp20)
REVERT: A  301 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7760 (t80)
REVERT: A  303 GLU cc_start: 0.7274 (pp20) cc_final: 0.6977 (pp20)
REVERT: A  397 GLN cc_start: 0.7331 (tt0) cc_final: 0.6654 (tm-30)
REVERT: A  400 ILE cc_start: 0.8765 (mm) cc_final: 0.8461 (mm)
REVERT: A  449 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7653 (tpp80)
REVERT: A  493 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7590 (mt0)
REVERT: A  509 GLU cc_start: 0.6446 (tp30) cc_final: 0.5979 (tp30)
REVERT: A  527 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6084 (mm-30)
REVERT: B   55 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7428 (ttp-170)
REVERT: B  117 LEU cc_start: 0.8300 (tp) cc_final: 0.8073 (tp)
REVERT: B  128 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7055 (mp-120)
REVERT: B  154 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6925 (mm-40)
REVERT: B  279 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6889 (mm110)
REVERT: B  294 ASP cc_start: 0.7975 (t0) cc_final: 0.7552 (t0)
REVERT: B  312 TRP cc_start: 0.7480 (p-90) cc_final: 0.7198 (p-90)
REVERT: B  329 PHE cc_start: 0.8400 (p90) cc_final: 0.7869 (p90)
REVERT: B  376 PHE cc_start: 0.8760 (p90) cc_final: 0.8081 (p90)
REVERT: B  476 MET cc_start: 0.6389 (mmm) cc_final: 0.5991 (mmm)
REVERT: B  481 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8306 (mmtt)
REVERT: B  493 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8119 (mm-40)
REVERT: B  559 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7399 (ttpp)
REVERT: B  572 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6660 (p0)
REVERT: C    8 ASP cc_start: 0.6983 (m-30) cc_final: 0.6455 (m-30)
REVERT: C   14 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6541 (p0)
REVERT: C   22 ASN cc_start: 0.7861 (m-40) cc_final: 0.7547 (m-40)
REVERT: C   31 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.7614 (m-10)
REVERT: C   36 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7526 (ttp-170)
REVERT: C   38 GLU cc_start: 0.7620 (pt0) cc_final: 0.7362 (pt0)
REVERT: C   40 MET cc_start: 0.8052 (tpt) cc_final: 0.7746 (tpt)
REVERT: C   46 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7076 (mm-30)
REVERT: C  107 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7726 (mtt-85)
REVERT: C  133 LYS cc_start: 0.6660 (mtpt) cc_final: 0.6289 (mmtm)
REVERT: D  529 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5658 (ptmm)
REVERT: D  578 MET cc_start: 0.7658 (mmm) cc_final: 0.7293 (mmm)
REVERT: D  699 LEU cc_start: 0.7152 (mm) cc_final: 0.6932 (mm)
REVERT: D  724 LYS cc_start: 0.8394 (tmmt) cc_final: 0.8032 (tmmt)
  outliers start: 63
  outliers final: 40
  residues processed: 458
  average time/residue: 0.2927
  time to fit residues: 184.2051
Evaluate side-chains
  469 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 420
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  683 MET
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain C residue   14 ASP
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  686 PHE
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 130 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 154 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 147 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 632 HIS
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 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 = 0.3797 r_free = 0.3797 target = 0.141402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.112955 restraints weight = 25151.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.116757 restraints weight = 13582.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.119318 restraints weight = 8642.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  13708  Z= 0.246
  Angle     :  0.781  10.521  18433  Z= 0.418
  Chirality :  0.048   0.208   2030
  Planarity :  0.005   0.058   2345
  Dihedral  :  7.133  85.070   1850
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.69 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 29.85 %
    Favored  : 63.86 %
  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: -1.47 (0.21), residues: 1619
  helix:  0.36 (0.20), residues: 700
  sheet:  0.26 (0.41), residues: 180
  loop : -2.75 (0.22), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 289 
 HIS   0.007   0.001   HIS D 582 
 PHE   0.030   0.002   PHE A 329 
 TYR   0.032   0.002   TYR B 305 
 ARG   0.013   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06403 (  574)
  hydrogen bonds       : angle       5.00479 ( 1617)
  covalent geometry    : bond        0.00529 (13708)
  covalent geometry    : angle       0.78120 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  516 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 422
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6650 (pttm)
REVERT: A  115 GLU cc_start: 0.7754 (tp30) cc_final: 0.7517 (tp30)
REVERT: A  155 TYR cc_start: 0.7511 (m-80) cc_final: 0.6987 (m-80)
REVERT: A  199 LYS cc_start: 0.8637 (pttm) cc_final: 0.7763 (pttm)
REVERT: A  219 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5065 (pttm)
REVERT: A  301 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7811 (t80)
REVERT: A  303 GLU cc_start: 0.7455 (pp20) cc_final: 0.7140 (pp20)
REVERT: A  305 TYR cc_start: 0.8079 (t80) cc_final: 0.7443 (t80)
REVERT: A  329 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7407 (p90)
REVERT: A  363 MET cc_start: 0.6575 (ptt) cc_final: 0.6119 (ppp)
REVERT: A  366 CYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7573 (m)
REVERT: A  386 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8045 (mp)
REVERT: A  397 GLN cc_start: 0.7415 (tt0) cc_final: 0.6664 (tm-30)
REVERT: A  443 GLU cc_start: 0.7972 (tp30) cc_final: 0.7628 (tp30)
REVERT: A  449 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8036 (mtp85)
REVERT: A  493 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7897 (mt0)
REVERT: A  501 GLU cc_start: 0.7976 (mp0) cc_final: 0.7635 (mp0)
REVERT: A  513 MET cc_start: 0.7477 (mtp) cc_final: 0.6279 (tpp)
REVERT: A  527 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6631 (mt-10)
REVERT: A  582 ASN cc_start: 0.7914 (p0) cc_final: 0.7612 (p0)
REVERT: A  602 MET cc_start: 0.8151 (tpp) cc_final: 0.7937 (mmm)
REVERT: A  649 LYS cc_start: 0.7889 (pptt) cc_final: 0.7250 (mmtm)
REVERT: A  668 PHE cc_start: 0.8115 (m-80) cc_final: 0.7869 (m-80)
REVERT: B   58 SER cc_start: 0.8445 (p) cc_final: 0.8109 (p)
REVERT: B   70 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7140 (mp0)
REVERT: B  117 LEU cc_start: 0.8372 (tp) cc_final: 0.8137 (tp)
REVERT: B  128 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7030 (mp-120)
REVERT: B  142 LYS cc_start: 0.8362 (mttt) cc_final: 0.7771 (mtmm)
REVERT: B  154 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6828 (mm-40)
REVERT: B  158 GLU cc_start: 0.6757 (pp20) cc_final: 0.6517 (pp20)
REVERT: B  195 GLU cc_start: 0.6941 (pm20) cc_final: 0.6652 (pp20)
REVERT: B  279 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6996 (mm-40)
REVERT: B  294 ASP cc_start: 0.7928 (t0) cc_final: 0.7526 (t0)
REVERT: B  312 TRP cc_start: 0.7623 (p-90) cc_final: 0.7248 (p-90)
REVERT: B  329 PHE cc_start: 0.8565 (p90) cc_final: 0.8020 (p90)
REVERT: B  376 PHE cc_start: 0.8688 (p90) cc_final: 0.8139 (p90)
REVERT: B  476 MET cc_start: 0.6448 (mmm) cc_final: 0.6071 (mmm)
REVERT: B  481 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8348 (mmtt)
REVERT: B  493 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8104 (mm-40)
REVERT: B  513 MET cc_start: 0.6825 (mmt) cc_final: 0.6223 (mmt)
REVERT: B  559 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7753 (ttpp)
REVERT: B  569 GLU cc_start: 0.7676 (pm20) cc_final: 0.7243 (pm20)
REVERT: B  572 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6742 (p0)
REVERT: B  606 MET cc_start: 0.7483 (mmm) cc_final: 0.7156 (mpp)
REVERT: C    8 ASP cc_start: 0.7142 (m-30) cc_final: 0.6652 (m-30)
REVERT: C   14 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6558 (p0)
REVERT: C   22 ASN cc_start: 0.7950 (m-40) cc_final: 0.7609 (m-40)
REVERT: C   29 PHE cc_start: 0.6976 (m-10) cc_final: 0.6710 (m-10)
REVERT: C   30 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7206 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7423 (m-10)
REVERT: C   38 GLU cc_start: 0.7825 (pt0) cc_final: 0.7617 (pt0)
REVERT: C   40 MET cc_start: 0.8101 (tpt) cc_final: 0.7737 (tpt)
REVERT: C  107 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7615 (mtt-85)
REVERT: D  529 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.5683 (ptmm)
REVERT: D  578 MET cc_start: 0.7803 (mmm) cc_final: 0.7470 (mmm)
REVERT: D  724 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8008 (tmmt)
  outliers start: 94
  outliers final: 63
  residues processed: 478
  average time/residue: 0.2835
  time to fit residues: 185.7023
Evaluate side-chains
  497 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 421
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   14 ASP
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  598 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 154 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0870
   chunk 0 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
B 632 HIS
** C  22 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 = 0.3840 r_free = 0.3840 target = 0.143731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115046 restraints weight = 24810.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118926 restraints weight = 13396.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.121553 restraints weight = 8461.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13708  Z= 0.147
  Angle     :  0.745  15.381  18433  Z= 0.384
  Chirality :  0.045   0.195   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.842  84.118   1850
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.09 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 32.13 %
    Favored  : 63.05 %
  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: -1.31 (0.21), residues: 1619
  helix:  0.50 (0.20), residues: 705
  sheet:  0.42 (0.42), residues: 177
  loop : -2.69 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 289 
 HIS   0.005   0.001   HIS B 320 
 PHE   0.034   0.001   PHE A 361 
 TYR   0.031   0.001   TYR B 305 
 ARG   0.008   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04730 (  574)
  hydrogen bonds       : angle       4.63587 ( 1617)
  covalent geometry    : bond        0.00327 (13708)
  covalent geometry    : angle       0.74494 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  492 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 420
  time to evaluate  : 1.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7120 (mm-30)
REVERT: A   93 MET cc_start: 0.7925 (mpp) cc_final: 0.7553 (mpp)
REVERT: A  115 GLU cc_start: 0.7700 (tp30) cc_final: 0.7410 (tp30)
REVERT: A  155 TYR cc_start: 0.7414 (m-80) cc_final: 0.6926 (m-80)
REVERT: A  189 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8223 (mm-40)
REVERT: A  195 GLU cc_start: 0.7389 (tp30) cc_final: 0.6236 (tp30)
REVERT: A  199 LYS cc_start: 0.8537 (pttm) cc_final: 0.8250 (ptpp)
REVERT: A  219 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.4926 (pttp)
REVERT: A  301 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7713 (t80)
REVERT: A  303 GLU cc_start: 0.7427 (pp20) cc_final: 0.7068 (pp20)
REVERT: A  324 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5929 (tm-30)
REVERT: A  328 GLU cc_start: 0.7450 (mp0) cc_final: 0.6619 (mm-30)
REVERT: A  363 MET cc_start: 0.6684 (ptt) cc_final: 0.6144 (ppp)
REVERT: A  366 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7475 (m)
REVERT: A  386 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8002 (mp)
REVERT: A  397 GLN cc_start: 0.7449 (tt0) cc_final: 0.6575 (tm-30)
REVERT: A  449 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7938 (mtp85)
REVERT: A  481 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8173 (mmtt)
REVERT: A  493 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7699 (mt0)
REVERT: A  501 GLU cc_start: 0.7867 (mp0) cc_final: 0.7479 (mp0)
REVERT: A  509 GLU cc_start: 0.6628 (tp30) cc_final: 0.6078 (tp30)
REVERT: A  527 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6760 (mm-30)
REVERT: B   58 SER cc_start: 0.8419 (p) cc_final: 0.8067 (p)
REVERT: B   70 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7155 (mp0)
REVERT: B  117 LEU cc_start: 0.8309 (tp) cc_final: 0.8085 (tp)
REVERT: B  128 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7063 (mp-120)
REVERT: B  142 LYS cc_start: 0.8322 (mttt) cc_final: 0.7732 (mtmm)
REVERT: B  154 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6771 (mm-40)
REVERT: B  158 GLU cc_start: 0.6782 (pp20) cc_final: 0.6533 (pp20)
REVERT: B  294 ASP cc_start: 0.7982 (t0) cc_final: 0.7593 (t0)
REVERT: B  300 GLU cc_start: 0.7489 (mp0) cc_final: 0.7285 (mp0)
REVERT: B  312 TRP cc_start: 0.7567 (p-90) cc_final: 0.7176 (p-90)
REVERT: B  329 PHE cc_start: 0.8500 (p90) cc_final: 0.7939 (p90)
REVERT: B  376 PHE cc_start: 0.8694 (p90) cc_final: 0.8115 (p90)
REVERT: B  476 MET cc_start: 0.6432 (mmm) cc_final: 0.6059 (mmm)
REVERT: B  481 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8308 (mmtt)
REVERT: B  493 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8121 (mm-40)
REVERT: B  513 MET cc_start: 0.6843 (mmt) cc_final: 0.6147 (mmt)
REVERT: B  559 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7646 (ttpp)
REVERT: B  569 GLU cc_start: 0.7591 (pm20) cc_final: 0.7230 (pm20)
REVERT: B  572 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6712 (p0)
REVERT: B  602 MET cc_start: 0.7905 (tpt) cc_final: 0.7681 (mmm)
REVERT: B  612 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7718 (mmm-85)
REVERT: C    8 ASP cc_start: 0.7038 (m-30) cc_final: 0.6514 (m-30)
REVERT: C   14 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6544 (p0)
REVERT: C   22 ASN cc_start: 0.7945 (m-40) cc_final: 0.7316 (m-40)
REVERT: C   30 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7147 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7490 (m-10)
REVERT: C   38 GLU cc_start: 0.7763 (pt0) cc_final: 0.7497 (pt0)
REVERT: C   40 MET cc_start: 0.8064 (tpt) cc_final: 0.7752 (tpt)
REVERT: C   46 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7085 (mm-30)
REVERT: C  107 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7693 (mtt-85)
REVERT: D  529 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.5683 (ptmm)
REVERT: D  578 MET cc_start: 0.7711 (mmm) cc_final: 0.7356 (mmm)
REVERT: D  606 LYS cc_start: 0.6955 (mmmt) cc_final: 0.6595 (mmmt)
REVERT: D  693 LYS cc_start: 0.7540 (tttt) cc_final: 0.6882 (tmmt)
REVERT: D  711 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7493 (tmmt)
REVERT: D  724 LYS cc_start: 0.8322 (tmmt) cc_final: 0.8038 (tmmt)
  outliers start: 72
  outliers final: 47
  residues processed: 462
  average time/residue: 0.2914
  time to fit residues: 183.9166
Evaluate side-chains
  478 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 418
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   14 ASP
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  711 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0670
   chunk 33 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 115 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 524 GLN
B 632 HIS
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.144616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116035 restraints weight = 24932.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119899 restraints weight = 13524.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.122477 restraints weight = 8558.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13708  Z= 0.138
  Angle     :  0.736  12.264  18433  Z= 0.380
  Chirality :  0.045   0.201   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.588  83.020   1847
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.08 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 31.86 %
    Favored  : 63.39 %
  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: -1.26 (0.21), residues: 1619
  helix:  0.54 (0.20), residues: 706
  sheet:  0.37 (0.42), residues: 180
  loop : -2.66 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 623 
 HIS   0.004   0.001   HIS D 582 
 PHE   0.018   0.001   PHE C 260 
 TYR   0.027   0.001   TYR A 305 
 ARG   0.020   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04334 (  574)
  hydrogen bonds       : angle       4.51751 ( 1617)
  covalent geometry    : bond        0.00309 (13708)
  covalent geometry    : angle       0.73586 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  497 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 426
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6632 (ptpp)
REVERT: A  107 LYS cc_start: 0.7863 (tppp) cc_final: 0.7270 (ttpp)
REVERT: A  155 TYR cc_start: 0.7358 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  189 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8180 (mm-40)
REVERT: A  195 GLU cc_start: 0.7381 (tp30) cc_final: 0.5567 (tp30)
REVERT: A  199 LYS cc_start: 0.8546 (pttm) cc_final: 0.8080 (ptpp)
REVERT: A  219 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.4806 (pttp)
REVERT: A  301 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7798 (t80)
REVERT: A  303 GLU cc_start: 0.7365 (pp20) cc_final: 0.6995 (pp20)
REVERT: A  328 GLU cc_start: 0.7425 (mp0) cc_final: 0.7046 (mm-30)
REVERT: A  330 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6695 (mtm-85)
REVERT: A  386 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7993 (mp)
REVERT: A  397 GLN cc_start: 0.7495 (tt0) cc_final: 0.6655 (tm-30)
REVERT: A  449 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7979 (mtp85)
REVERT: A  493 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7662 (mt0)
REVERT: A  509 GLU cc_start: 0.6608 (tp30) cc_final: 0.6314 (tp30)
REVERT: A  519 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: A  527 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6753 (mm-30)
REVERT: B   70 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7145 (mp0)
REVERT: B  117 LEU cc_start: 0.8325 (tp) cc_final: 0.8103 (tp)
REVERT: B  128 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7087 (mp-120)
REVERT: B  142 LYS cc_start: 0.8321 (mttt) cc_final: 0.7783 (mtmm)
REVERT: B  154 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6904 (mm-40)
REVERT: B  188 ASP cc_start: 0.8078 (p0) cc_final: 0.7828 (p0)
REVERT: B  312 TRP cc_start: 0.7526 (p-90) cc_final: 0.7227 (p-90)
REVERT: B  329 PHE cc_start: 0.8468 (p90) cc_final: 0.7920 (p90)
REVERT: B  344 PHE cc_start: 0.7663 (m-80) cc_final: 0.7428 (m-80)
REVERT: B  376 PHE cc_start: 0.8641 (p90) cc_final: 0.8172 (p90)
REVERT: B  493 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8113 (mm-40)
REVERT: B  513 MET cc_start: 0.6868 (mmt) cc_final: 0.6128 (mmp)
REVERT: B  559 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7333 (ttpp)
REVERT: B  560 PHE cc_start: 0.7476 (m-10) cc_final: 0.6641 (m-10)
REVERT: B  569 GLU cc_start: 0.7536 (pm20) cc_final: 0.7139 (pm20)
REVERT: B  572 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6713 (p0)
REVERT: B  612 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7561 (mmm-85)
REVERT: C    8 ASP cc_start: 0.6970 (m-30) cc_final: 0.6444 (m-30)
REVERT: C   22 ASN cc_start: 0.7909 (m-40) cc_final: 0.7282 (m-40)
REVERT: C   31 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.7574 (m-10)
REVERT: C   32 ARG cc_start: 0.8265 (mtt90) cc_final: 0.8043 (mtt90)
REVERT: C   38 GLU cc_start: 0.7652 (pt0) cc_final: 0.7394 (pt0)
REVERT: C   40 MET cc_start: 0.8024 (tpt) cc_final: 0.7684 (tpt)
REVERT: C   46 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6934 (mt-10)
REVERT: C  104 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7610 (mm-30)
REVERT: C  107 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7591 (mtt-85)
REVERT: C  133 LYS cc_start: 0.6698 (mtpt) cc_final: 0.6360 (mmtm)
REVERT: D  529 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5667 (ptmm)
REVERT: D  578 MET cc_start: 0.7637 (mmm) cc_final: 0.7295 (mmm)
REVERT: D  606 LYS cc_start: 0.6992 (mmmt) cc_final: 0.6645 (mmmt)
REVERT: D  724 LYS cc_start: 0.8356 (tmmt) cc_final: 0.8062 (tmmt)
  outliers start: 71
  outliers final: 47
  residues processed: 467
  average time/residue: 0.2865
  time to fit residues: 182.4293
Evaluate side-chains
  475 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 417
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  662 CYS
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 139 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 143 optimal weight:    0.0040
   chunk 61 optimal weight:    1.9990
   chunk 131 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 156 optimal weight:    1.9990
   chunk 159 optimal weight:    4.9990
   overall best weight:    0.7654

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.144598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.116085 restraints weight = 24551.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.119906 restraints weight = 13149.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.122441 restraints weight = 8317.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13708  Z= 0.146
  Angle     :  0.774  11.985  18433  Z= 0.396
  Chirality :  0.045   0.207   2030
  Planarity :  0.004   0.048   2345
  Dihedral  :  6.572  83.097   1847
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.52 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 32.26 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.27 (0.21), residues: 1619
  helix:  0.50 (0.20), residues: 707
  sheet:  0.43 (0.42), residues: 180
  loop : -2.64 (0.22), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 623 
 HIS   0.005   0.001   HIS B 632 
 PHE   0.029   0.001   PHE C  29 
 TYR   0.030   0.001   TYR D 658 
 ARG   0.007   0.000   ARG B 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  574)
  hydrogen bonds       : angle       4.51219 ( 1617)
  covalent geometry    : bond        0.00328 (13708)
  covalent geometry    : angle       0.77353 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  496 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 429
  time to evaluate  : 1.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8194 (tmm-80)
REVERT: A   72 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6625 (mtmm)
REVERT: A  107 LYS cc_start: 0.7851 (tppp) cc_final: 0.7251 (ttpp)
REVERT: A  155 TYR cc_start: 0.7347 (m-80) cc_final: 0.6819 (m-80)
REVERT: A  189 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8164 (mm-40)
REVERT: A  195 GLU cc_start: 0.7467 (tp30) cc_final: 0.6363 (tp30)
REVERT: A  199 LYS cc_start: 0.8577 (pttm) cc_final: 0.7769 (pttm)
REVERT: A  219 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.4852 (pttp)
REVERT: A  301 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7751 (t80)
REVERT: A  303 GLU cc_start: 0.7435 (pp20) cc_final: 0.7048 (pp20)
REVERT: A  328 GLU cc_start: 0.7419 (mp0) cc_final: 0.7021 (mm-30)
REVERT: A  330 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6710 (mtm-85)
REVERT: A  361 PHE cc_start: 0.7400 (t80) cc_final: 0.7169 (t80)
REVERT: A  386 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7905 (mp)
REVERT: A  397 GLN cc_start: 0.7535 (tt0) cc_final: 0.6649 (tm-30)
REVERT: A  449 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.8033 (mtp85)
REVERT: A  493 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7670 (mt0)
REVERT: A  501 GLU cc_start: 0.7701 (mp0) cc_final: 0.7378 (mp0)
REVERT: A  527 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6746 (mm-30)
REVERT: A  582 ASN cc_start: 0.7960 (p0) cc_final: 0.7678 (p0)
REVERT: A  640 GLN cc_start: 0.7955 (pp30) cc_final: 0.7575 (pp30)
REVERT: B   70 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7157 (mp0)
REVERT: B  117 LEU cc_start: 0.8317 (tp) cc_final: 0.8111 (tp)
REVERT: B  142 LYS cc_start: 0.8341 (mttt) cc_final: 0.7760 (mtmm)
REVERT: B  154 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6909 (mm-40)
REVERT: B  188 ASP cc_start: 0.8118 (p0) cc_final: 0.7809 (p0)
REVERT: B  312 TRP cc_start: 0.7558 (p-90) cc_final: 0.7253 (p-90)
REVERT: B  329 PHE cc_start: 0.8454 (p90) cc_final: 0.7890 (p90)
REVERT: B  376 PHE cc_start: 0.8662 (p90) cc_final: 0.8126 (p90)
REVERT: B  481 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8374 (mmtt)
REVERT: B  493 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8027 (tp40)
REVERT: B  513 MET cc_start: 0.7017 (mmt) cc_final: 0.6635 (mmt)
REVERT: B  559 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7415 (ttpp)
REVERT: B  560 PHE cc_start: 0.7538 (m-10) cc_final: 0.6699 (m-10)
REVERT: B  569 GLU cc_start: 0.7564 (pm20) cc_final: 0.7168 (pm20)
REVERT: B  572 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6839 (p0)
REVERT: C    8 ASP cc_start: 0.6938 (m-30) cc_final: 0.6411 (m-30)
REVERT: C   22 ASN cc_start: 0.7992 (m-40) cc_final: 0.7383 (m-40)
REVERT: C   31 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.7567 (m-10)
REVERT: C   38 GLU cc_start: 0.7676 (pt0) cc_final: 0.7402 (pt0)
REVERT: C   40 MET cc_start: 0.8072 (tpt) cc_final: 0.7746 (tpt)
REVERT: C   46 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7008 (mm-30)
REVERT: C  107 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7542 (mtt-85)
REVERT: C  111 LYS cc_start: 0.8320 (mmmm) cc_final: 0.7872 (mttt)
REVERT: C  133 LYS cc_start: 0.6790 (mtpt) cc_final: 0.6360 (mmtm)
REVERT: C  222 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8042 (mp0)
REVERT: D  529 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5698 (ptmm)
REVERT: D  578 MET cc_start: 0.7603 (mmm) cc_final: 0.7278 (mmm)
REVERT: D  606 LYS cc_start: 0.7025 (mmmt) cc_final: 0.6713 (mmmt)
REVERT: D  711 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7200 (tptt)
REVERT: D  724 LYS cc_start: 0.8336 (tmmt) cc_final: 0.8043 (tmmt)
  outliers start: 67
  outliers final: 48
  residues processed: 468
  average time/residue: 0.3047
  time to fit residues: 192.1812
Evaluate side-chains
  490 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 430
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  662 CYS
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  711 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 137 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 93 optimal weight:    0.2980
   chunk 145 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.145490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.116861 restraints weight = 24667.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.120717 restraints weight = 13236.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.123367 restraints weight = 8375.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13708  Z= 0.141
  Angle     :  0.778  11.731  18433  Z= 0.396
  Chirality :  0.045   0.212   2030
  Planarity :  0.004   0.055   2345
  Dihedral  :  6.534  83.154   1847
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.59 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 31.73 %
    Favored  : 63.45 %
  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: -1.21 (0.21), residues: 1619
  helix:  0.53 (0.20), residues: 706
  sheet:  0.47 (0.42), residues: 180
  loop : -2.60 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 623 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.040   0.001   PHE C  29 
 TYR   0.023   0.001   TYR B 305 
 ARG   0.014   0.001   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  574)
  hydrogen bonds       : angle       4.45103 ( 1617)
  covalent geometry    : bond        0.00323 (13708)
  covalent geometry    : angle       0.77759 (18433)

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

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

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3238 Ramachandran restraints generated.
    1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  499 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 427
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8219 (tmm-80)
REVERT: A   72 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6491 (ptpp)
REVERT: A  107 LYS cc_start: 0.7858 (tppp) cc_final: 0.7239 (ttpp)
REVERT: A  155 TYR cc_start: 0.7337 (m-80) cc_final: 0.6872 (m-80)
REVERT: A  195 GLU cc_start: 0.7435 (tp30) cc_final: 0.6270 (tp30)
REVERT: A  199 LYS cc_start: 0.8589 (pttm) cc_final: 0.7736 (pttm)
REVERT: A  301 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7796 (t80)
REVERT: A  303 GLU cc_start: 0.7427 (pp20) cc_final: 0.7028 (pp20)
REVERT: A  328 GLU cc_start: 0.7423 (mp0) cc_final: 0.7013 (mm-30)
REVERT: A  330 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6655 (mtm-85)
REVERT: A  350 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8005 (tmtt)
REVERT: A  361 PHE cc_start: 0.7310 (t80) cc_final: 0.7087 (t80)
REVERT: A  386 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: A  397 GLN cc_start: 0.7533 (tt0) cc_final: 0.6633 (tm-30)
REVERT: A  449 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8023 (mtp85)
REVERT: A  493 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7637 (mt0)
REVERT: A  527 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6726 (mm-30)
REVERT: A  567 MET cc_start: 0.5957 (tpp) cc_final: 0.5753 (tpp)
REVERT: A  640 GLN cc_start: 0.7935 (pp30) cc_final: 0.7621 (pp30)
REVERT: B   57 GLU cc_start: 0.7752 (tp30) cc_final: 0.7377 (tp30)
REVERT: B   70 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7137 (mp0)
REVERT: B  104 THR cc_start: 0.7817 (m) cc_final: 0.7466 (p)
REVERT: B  117 LEU cc_start: 0.8368 (tp) cc_final: 0.8165 (tp)
REVERT: B  142 LYS cc_start: 0.8293 (mttt) cc_final: 0.7730 (mtmm)
REVERT: B  154 GLN cc_start: 0.7343 (mm-40) cc_final: 0.6877 (mm-40)
REVERT: B  188 ASP cc_start: 0.8120 (p0) cc_final: 0.7791 (p0)
REVERT: B  312 TRP cc_start: 0.7530 (p-90) cc_final: 0.7219 (p-90)
REVERT: B  344 PHE cc_start: 0.7652 (m-80) cc_final: 0.7431 (m-80)
REVERT: B  354 LYS cc_start: 0.8056 (mttm) cc_final: 0.7829 (mttm)
REVERT: B  376 PHE cc_start: 0.8710 (p90) cc_final: 0.8205 (p90)
REVERT: B  393 GLU cc_start: 0.7470 (mp0) cc_final: 0.7109 (mp0)
REVERT: B  493 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8015 (tp40)
REVERT: B  513 MET cc_start: 0.6913 (mmt) cc_final: 0.6623 (mmt)
REVERT: B  559 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7422 (ttpp)
REVERT: B  560 PHE cc_start: 0.7494 (m-10) cc_final: 0.6673 (m-10)
REVERT: B  569 GLU cc_start: 0.7536 (pm20) cc_final: 0.7129 (pm20)
REVERT: B  572 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6827 (p0)
REVERT: C    8 ASP cc_start: 0.6931 (m-30) cc_final: 0.6430 (m-30)
REVERT: C   14 ASP cc_start: 0.7337 (p0) cc_final: 0.7087 (p0)
REVERT: C   22 ASN cc_start: 0.7940 (m-40) cc_final: 0.7622 (m-40)
REVERT: C   31 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7601 (m-10)
REVERT: C   38 GLU cc_start: 0.7659 (pt0) cc_final: 0.7387 (pt0)
REVERT: C   40 MET cc_start: 0.8075 (tpt) cc_final: 0.7742 (tpt)
REVERT: C   46 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6818 (mt-10)
REVERT: C  107 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7550 (mtt-85)
REVERT: C  111 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7921 (mttt)
REVERT: C  133 LYS cc_start: 0.6729 (mtpt) cc_final: 0.6322 (mmtm)
REVERT: D  529 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5654 (ptmm)
REVERT: D  533 MET cc_start: 0.7849 (ptp) cc_final: 0.7498 (ptp)
REVERT: D  578 MET cc_start: 0.7654 (mmm) cc_final: 0.7314 (mmm)
REVERT: D  711 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7216 (tptt)
REVERT: D  724 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8020 (tmmt)
  outliers start: 72
  outliers final: 51
  residues processed: 469
  average time/residue: 0.2991
  time to fit residues: 191.0985
Evaluate side-chains
  485 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 422
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  350 LYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   18 GLU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  662 CYS
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  711 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 158 optimal weight:    0.0970
   chunk 101 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0000
   chunk 155 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0020
   chunk 28 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
B 632 HIS
** C  22 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 = 0.3884 r_free = 0.3884 target = 0.147103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.118481 restraints weight = 24588.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122257 restraints weight = 13215.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.124966 restraints weight = 8471.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13708  Z= 0.139
  Angle     :  0.783  11.343  18433  Z= 0.397
  Chirality :  0.045   0.265   2030
  Planarity :  0.004   0.048   2345
  Dihedral  :  6.433  82.836   1847
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.60 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 32.26 %
    Favored  : 63.72 %
  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: -1.13 (0.21), residues: 1619
  helix:  0.61 (0.20), residues: 706
  sheet:  0.39 (0.40), residues: 192
  loop : -2.58 (0.22), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 623 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.041   0.001   PHE C  29 
 TYR   0.046   0.001   TYR D 658 
 ARG   0.020   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  574)
  hydrogen bonds       : angle       4.36847 ( 1617)
  covalent geometry    : bond        0.00319 (13708)
  covalent geometry    : angle       0.78291 (18433)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4791.51 seconds
wall clock time: 84 minutes 27.07 seconds (5067.07 seconds total)