Starting phenix.real_space_refine
on Thu Jun 12 06:22:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fx4_29523/06_2025/8fx4_29523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fx4_29523/06_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_29523/06_2025/8fx4_29523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fx4_29523/06_2025/8fx4_29523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fx4_29523/06_2025/8fx4_29523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fx4_29523/06_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-5710/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: 8.07, per 1000 atoms: 0.60
  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: 3.18
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.59
  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: 3.78

  Time building geometry restraints manager: 3.77 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:             0.320
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.220
  Find NCS groups from input model:        0.540
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.440
-------------------------------------------------------------------------------
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  : 1.664 
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: 0.3259
  time to fit residues: 186.9794
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  : 1.629 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116850 restraints weight = 25057.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.120702 restraints weight = 13574.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123308 restraints weight = 8600.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
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  : 1.396 
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: 0.7529 (tp30) cc_final: 0.7116 (tp30)
REVERT: A  300 GLU cc_start: 0.6788 (pp20) cc_final: 0.6306 (pt0)
REVERT: A  303 GLU cc_start: 0.7118 (pp20) cc_final: 0.6782 (pp20)
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: 0.7667 (tpp80)
REVERT: A  481 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8445 (mmtt)
REVERT: A  501 GLU cc_start: 0.7400 (mp0) cc_final: 0.7050 (mp0)
REVERT: A  509 GLU cc_start: 0.6977 (tp30) cc_final: 0.6511 (tp30)
REVERT: A  526 LYS cc_start: 0.7531 (pptt) cc_final: 0.7191 (pptt)
REVERT: A  527 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6090 (mt-10)
REVERT: A  553 MET cc_start: 0.7162 (mmm) cc_final: 0.6959 (mmm)
REVERT: B   55 ARG cc_start: 0.8302 (ttt180) cc_final: 0.7396 (ttp-170)
REVERT: B  154 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7077 (mm-40)
REVERT: B  279 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6873 (mm110)
REVERT: B  294 ASP cc_start: 0.7974 (t0) cc_final: 0.7514 (t0)
REVERT: B  312 TRP cc_start: 0.7501 (p-90) cc_final: 0.7174 (p-90)
REVERT: B  356 TYR cc_start: 0.8354 (m-80) cc_final: 0.7851 (m-80)
REVERT: B  359 ARG cc_start: 0.7962 (mpp80) cc_final: 0.7572 (mpp80)
REVERT: B  424 GLU cc_start: 0.6945 (pm20) cc_final: 0.6720 (pm20)
REVERT: B  426 TYR cc_start: 0.8358 (t80) cc_final: 0.8105 (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: 0.8028 (tp40)
REVERT: B  513 MET cc_start: 0.6611 (mmt) cc_final: 0.6317 (mmt)
REVERT: B  559 LYS cc_start: 0.7831 (ttpp) cc_final: 0.7382 (ttpp)
REVERT: B  627 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7277 (mm-30)
REVERT: C   16 GLU cc_start: 0.7183 (pp20) cc_final: 0.6952 (tm-30)
REVERT: C   20 HIS cc_start: 0.8079 (t-90) cc_final: 0.7855 (t70)
REVERT: C   30 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7076 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8496 (m-10) cc_final: 0.7870 (m100)
REVERT: C   36 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7429 (ttp-170)
REVERT: C  107 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7655 (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: 0.7598 (mmmm)
REVERT: D  627 GLU cc_start: 0.7259 (pp20) cc_final: 0.7048 (pp20)
REVERT: D  724 LYS cc_start: 0.8256 (tmmt) cc_final: 0.8015 (tmmt)
  outliers start: 59
  outliers final: 34
  residues processed: 463
  average time/residue: 0.3067
  time to fit residues: 193.0754
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  : 1.415 
-------------------------------------------------------------------------------
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:    4.9990
   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:    2.9990
   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 = 0.3846 r_free = 0.3846 target = 0.144565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116292 restraints weight = 25088.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.120125 restraints weight = 13636.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122698 restraints weight = 8678.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.1552

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= 0.145
  Angle     :  0.670  10.912  18433  Z= 0.354
  Chirality :  0.044   0.196   2030
  Planarity :  0.004   0.053   2345
  Dihedral  :  6.923  86.746   1854
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.91 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 28.31 %
    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: -1.22 (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   0.012   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  574)
  hydrogen bonds       : angle       4.61076 ( 1617)
  covalent geometry    : bond        0.00317 (13708)
  covalent geometry    : angle       0.67016 (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
  506 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 420
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.7835 (tppp) cc_final: 0.7522 (tptp)
REVERT: A  195 GLU cc_start: 0.7406 (tp30) cc_final: 0.6079 (tp30)
REVERT: A  199 LYS cc_start: 0.8551 (pttm) cc_final: 0.7630 (ptpp)
REVERT: A  300 GLU cc_start: 0.6808 (pp20) cc_final: 0.6516 (pp20)
REVERT: A  303 GLU cc_start: 0.7180 (pp20) cc_final: 0.6777 (pp20)
REVERT: A  397 GLN cc_start: 0.7258 (tt0) cc_final: 0.6674 (tm-30)
REVERT: A  400 ILE cc_start: 0.8749 (mm) cc_final: 0.8419 (mm)
REVERT: A  449 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7668 (tpp80)
REVERT: A  481 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8502 (mmtt)
REVERT: A  509 GLU cc_start: 0.6716 (tp30) cc_final: 0.6349 (tp30)
REVERT: A  526 LYS cc_start: 0.7497 (pptt) cc_final: 0.7189 (pptt)
REVERT: A  527 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6082 (mt-10)
REVERT: A  553 MET cc_start: 0.7225 (mmm) cc_final: 0.6919 (mmp)
REVERT: B   55 ARG cc_start: 0.8339 (ttt180) cc_final: 0.7410 (ttp-170)
REVERT: B  101 ASN cc_start: 0.8059 (t0) cc_final: 0.7633 (t0)
REVERT: B  128 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7075 (mp-120)
REVERT: B  154 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7119 (mm-40)
REVERT: B  279 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6816 (mm110)
REVERT: B  294 ASP cc_start: 0.8006 (t0) cc_final: 0.7597 (t0)
REVERT: B  312 TRP cc_start: 0.7515 (p-90) cc_final: 0.7190 (p-90)
REVERT: B  376 PHE cc_start: 0.8809 (p90) cc_final: 0.7901 (p90)
REVERT: B  395 LEU cc_start: 0.8098 (tp) cc_final: 0.7784 (tt)
REVERT: B  410 LYS cc_start: 0.8136 (tttt) cc_final: 0.7899 (tmmt)
REVERT: B  476 MET cc_start: 0.6345 (mmm) cc_final: 0.5845 (mmm)
REVERT: B  493 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8028 (mm-40)
REVERT: B  513 MET cc_start: 0.6602 (mmt) cc_final: 0.6081 (mmt)
REVERT: B  559 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7311 (ttpt)
REVERT: B  569 GLU cc_start: 0.7662 (pm20) cc_final: 0.7373 (pm20)
REVERT: B  572 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6568 (p0)
REVERT: C    8 ASP cc_start: 0.6972 (m-30) cc_final: 0.6547 (m-30)
REVERT: C   22 ASN cc_start: 0.7727 (m-40) cc_final: 0.7406 (m-40)
REVERT: C   30 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7115 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.7439 (m-10)
REVERT: C   36 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7514 (ttp-170)
REVERT: C   38 GLU cc_start: 0.7617 (pt0) cc_final: 0.7294 (pt0)
REVERT: C   40 MET cc_start: 0.8067 (tpt) cc_final: 0.7833 (tpt)
REVERT: C   46 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7113 (mm-30)
REVERT: C  104 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7894 (mm-30)
REVERT: C  107 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7765 (mtt-85)
REVERT: D  578 MET cc_start: 0.7870 (mmm) cc_final: 0.7549 (mmm)
REVERT: D  582 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.6153 (t-90)
REVERT: D  585 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7575 (mmmm)
REVERT: D  606 LYS cc_start: 0.6884 (mmmt) cc_final: 0.6564 (mmmt)
REVERT: D  674 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7357 (t0)
REVERT: D  724 LYS cc_start: 0.8308 (tmmt) cc_final: 0.7938 (tmmt)
  outliers start: 86
  outliers final: 54
  residues processed: 468
  average time/residue: 0.2921
  time to fit residues: 186.3846
Evaluate side-chains
  470 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 408
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
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   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  632 HIS
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  357 VAL
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  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
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:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 142 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 89 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0370
   chunk 62 optimal weight:    0.4980
   chunk 63 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 352 ASN
** C  20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 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 = 0.3855 r_free = 0.3855 target = 0.145103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116887 restraints weight = 24897.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120752 restraints weight = 13485.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.123271 restraints weight = 8530.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13708  Z= 0.129
  Angle     :  0.658  11.402  18433  Z= 0.345
  Chirality :  0.044   0.193   2030
  Planarity :  0.004   0.050   2345
  Dihedral  :  6.712  87.322   1854
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.72 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 27.78 %
    Favored  : 66.73 %
  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: -1.12 (0.21), residues: 1619
  helix:  0.74 (0.20), residues: 696
  sheet:  0.43 (0.40), residues: 181
  loop : -2.64 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 289 
 HIS   0.005   0.001   HIS A 149 
 PHE   0.024   0.001   PHE C  29 
 TYR   0.017   0.001   TYR B 305 
 ARG   0.011   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  574)
  hydrogen bonds       : angle       4.45721 ( 1617)
  covalent geometry    : bond        0.00284 (13708)
  covalent geometry    : angle       0.65822 (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
  508 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 426
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.7827 (tppp) cc_final: 0.7514 (tptp)
REVERT: A  195 GLU cc_start: 0.7413 (tp30) cc_final: 0.6119 (tp30)
REVERT: A  199 LYS cc_start: 0.8617 (pttm) cc_final: 0.7741 (pttm)
REVERT: A  300 GLU cc_start: 0.6778 (pp20) cc_final: 0.6469 (pp20)
REVERT: A  303 GLU cc_start: 0.7316 (pp20) cc_final: 0.7049 (pp20)
REVERT: A  397 GLN cc_start: 0.7161 (tt0) cc_final: 0.6596 (tm-30)
REVERT: A  400 ILE cc_start: 0.8751 (mm) cc_final: 0.8425 (mm)
REVERT: A  449 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7646 (tpp80)
REVERT: A  450 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7858 (mmp80)
REVERT: A  481 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8358 (mmtt)
REVERT: A  527 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6057 (mm-30)
REVERT: A  553 MET cc_start: 0.7326 (mmm) cc_final: 0.7025 (mmp)
REVERT: B   55 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7451 (ttp-170)
REVERT: B  101 ASN cc_start: 0.8067 (t0) cc_final: 0.7623 (t0)
REVERT: B  128 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7077 (mp-120)
REVERT: B  154 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7064 (mm-40)
REVERT: B  279 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6864 (mm110)
REVERT: B  294 ASP cc_start: 0.7979 (t0) cc_final: 0.7562 (t0)
REVERT: B  312 TRP cc_start: 0.7465 (p-90) cc_final: 0.7145 (p-90)
REVERT: B  376 PHE cc_start: 0.8771 (p90) cc_final: 0.7958 (p90)
REVERT: B  395 LEU cc_start: 0.8084 (tp) cc_final: 0.7774 (tt)
REVERT: B  410 LYS cc_start: 0.8142 (tttt) cc_final: 0.7922 (tmmt)
REVERT: B  476 MET cc_start: 0.6430 (mmm) cc_final: 0.6025 (mmm)
REVERT: B  481 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8426 (mmtt)
REVERT: B  493 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8126 (mm-40)
REVERT: B  513 MET cc_start: 0.6731 (mmt) cc_final: 0.6488 (mmt)
REVERT: B  559 LYS cc_start: 0.7773 (ttpp) cc_final: 0.7346 (ttpp)
REVERT: B  569 GLU cc_start: 0.7622 (pm20) cc_final: 0.7411 (pm20)
REVERT: B  572 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6598 (p0)
REVERT: B  683 MET cc_start: 0.7885 (mmm) cc_final: 0.7666 (mmm)
REVERT: C    8 ASP cc_start: 0.6915 (m-30) cc_final: 0.6462 (m-30)
REVERT: C   22 ASN cc_start: 0.7772 (m-40) cc_final: 0.7416 (m-40)
REVERT: C   30 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7145 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.7573 (m-10)
REVERT: C   38 GLU cc_start: 0.7613 (pt0) cc_final: 0.7349 (pt0)
REVERT: C   40 MET cc_start: 0.8047 (tpt) cc_final: 0.7774 (tpt)
REVERT: C   48 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7256 (mm-30)
REVERT: C  104 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7838 (mm-30)
REVERT: C  107 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7902 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5592 (ptmm)
REVERT: D  578 MET cc_start: 0.7745 (mmm) cc_final: 0.7349 (mmm)
REVERT: D  582 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.6243 (t-90)
REVERT: D  585 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7567 (mmmm)
REVERT: D  606 LYS cc_start: 0.6918 (mmmt) cc_final: 0.6563 (mmmt)
REVERT: D  674 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7317 (t0)
REVERT: D  724 LYS cc_start: 0.8298 (tmmt) cc_final: 0.7886 (tmmt)
  outliers start: 82
  outliers final: 55
  residues processed: 470
  average time/residue: 0.3184
  time to fit residues: 203.1229
Evaluate side-chains
  477 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 414
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
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   73 ILE
Chi-restraints excluded: chain A residue   75 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  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
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  536 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  634 ILE
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  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  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  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  493 GLN
Chi-restraints excluded: chain B residue  494 VAL
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  611 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  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  582 HIS
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  654 LYS
Chi-restraints excluded: chain D residue  674 ASN
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:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 131 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0770
   chunk 77 optimal weight:    0.2980
   chunk 111 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.5340

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** C  20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3874 r_free = 0.3874 target = 0.146806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117838 restraints weight = 24864.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.121726 restraints weight = 13528.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.124362 restraints weight = 8598.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13708  Z= 0.121
  Angle     :  0.662  11.518  18433  Z= 0.343
  Chirality :  0.043   0.183   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.535  86.125   1854
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.54 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 28.65 %
    Favored  : 65.86 %
  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: -1.02 (0.21), residues: 1619
  helix:  0.80 (0.20), residues: 701
  sheet:  0.44 (0.39), residues: 192
  loop : -2.62 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 289 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.020   0.001   PHE B 304 
 TYR   0.022   0.001   TYR A 305 
 ARG   0.010   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  574)
  hydrogen bonds       : angle       4.35963 ( 1617)
  covalent geometry    : bond        0.00270 (13708)
  covalent geometry    : angle       0.66224 (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
  507 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 425
  time to evaluate  : 1.564 
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   41 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (tmm-80)
REVERT: A  107 LYS cc_start: 0.7812 (tppp) cc_final: 0.7581 (tptp)
REVERT: A  199 LYS cc_start: 0.8621 (pttm) cc_final: 0.8212 (pttm)
REVERT: A  300 GLU cc_start: 0.6725 (pp20) cc_final: 0.6460 (pp20)
REVERT: A  303 GLU cc_start: 0.7323 (pp20) cc_final: 0.7029 (pp20)
REVERT: A  334 PHE cc_start: 0.7630 (m-10) cc_final: 0.7294 (m-80)
REVERT: A  361 PHE cc_start: 0.7377 (t80) cc_final: 0.7100 (t80)
REVERT: A  397 GLN cc_start: 0.7125 (tt0) cc_final: 0.6464 (tm-30)
REVERT: A  400 ILE cc_start: 0.8756 (mm) cc_final: 0.8481 (mm)
REVERT: A  449 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7972 (mtp85)
REVERT: A  450 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7891 (mmp80)
REVERT: A  471 GLU cc_start: 0.7382 (mp0) cc_final: 0.7171 (mp0)
REVERT: A  492 GLU cc_start: 0.7397 (mp0) cc_final: 0.7179 (mm-30)
REVERT: B   55 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7433 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7735 (tp30) cc_final: 0.7462 (tp30)
REVERT: B   95 LYS cc_start: 0.8480 (tttt) cc_final: 0.8245 (ttmm)
REVERT: B  101 ASN cc_start: 0.8050 (t0) cc_final: 0.7630 (t0)
REVERT: B  128 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7105 (mp-120)
REVERT: B  154 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7036 (mm-40)
REVERT: B  188 ASP cc_start: 0.8150 (p0) cc_final: 0.7901 (p0)
REVERT: B  279 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6972 (mm-40)
REVERT: B  294 ASP cc_start: 0.7997 (t0) cc_final: 0.7588 (t0)
REVERT: B  312 TRP cc_start: 0.7440 (p-90) cc_final: 0.7109 (p-90)
REVERT: B  352 ASN cc_start: 0.8241 (m-40) cc_final: 0.7928 (m-40)
REVERT: B  376 PHE cc_start: 0.8724 (p90) cc_final: 0.8092 (p90)
REVERT: B  395 LEU cc_start: 0.8047 (tp) cc_final: 0.7742 (tt)
REVERT: B  410 LYS cc_start: 0.8136 (tttt) cc_final: 0.7904 (ttmt)
REVERT: B  476 MET cc_start: 0.6423 (mmm) cc_final: 0.6049 (mmm)
REVERT: B  493 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8131 (mm-40)
REVERT: B  513 MET cc_start: 0.6780 (mmt) cc_final: 0.6511 (mmt)
REVERT: B  559 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7321 (ttpp)
REVERT: B  569 GLU cc_start: 0.7615 (pm20) cc_final: 0.7383 (pm20)
REVERT: B  572 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6638 (p0)
REVERT: B  683 MET cc_start: 0.7913 (mmm) cc_final: 0.7666 (mmm)
REVERT: C    8 ASP cc_start: 0.6832 (m-30) cc_final: 0.6393 (m-30)
REVERT: C   14 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6942 (p0)
REVERT: C   22 ASN cc_start: 0.7760 (m-40) cc_final: 0.7324 (m-40)
REVERT: C   31 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7634 (m-10)
REVERT: C   38 GLU cc_start: 0.7569 (pt0) cc_final: 0.7321 (pt0)
REVERT: C   40 MET cc_start: 0.8098 (tpt) cc_final: 0.7786 (tpt)
REVERT: C  107 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7821 (mtt-85)
REVERT: D  578 MET cc_start: 0.7745 (mmm) cc_final: 0.7311 (mmm)
REVERT: D  585 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7582 (mmmm)
REVERT: D  606 LYS cc_start: 0.6834 (mmmt) cc_final: 0.6529 (mmmt)
REVERT: D  674 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7348 (t0)
REVERT: D  724 LYS cc_start: 0.8316 (tmmt) cc_final: 0.7863 (tmmt)
  outliers start: 82
  outliers final: 49
  residues processed: 470
  average time/residue: 0.3311
  time to fit residues: 217.8549
Evaluate side-chains
  473 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 416
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   63 SER
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  307 SER
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  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  468 SER
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  634 ILE
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  279 GLN
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  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  493 GLN
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  617 MET
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  240 THR
Chi-restraints excluded: chain C residue  257 LEU
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  674 ASN
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:    0.0770
   chunk 130 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 154 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 147 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7544

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.145368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116706 restraints weight = 25128.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.120676 restraints weight = 13548.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123344 restraints weight = 8551.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13708  Z= 0.131
  Angle     :  0.680  11.400  18433  Z= 0.353
  Chirality :  0.044   0.181   2030
  Planarity :  0.004   0.048   2345
  Dihedral  :  6.514  86.176   1852
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.84 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 29.05 %
    Favored  : 65.33 %
  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: -1.05 (0.21), residues: 1619
  helix:  0.77 (0.20), residues: 702
  sheet:  0.51 (0.40), residues: 181
  loop : -2.60 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 289 
 HIS   0.004   0.001   HIS B 320 
 PHE   0.017   0.001   PHE B 304 
 TYR   0.021   0.001   TYR B 305 
 ARG   0.013   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  574)
  hydrogen bonds       : angle       4.39826 ( 1617)
  covalent geometry    : bond        0.00293 (13708)
  covalent geometry    : angle       0.68032 (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: 84
    poor density    : 432
  time to evaluate  : 1.573 
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   72 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6594 (mtmm)
REVERT: A  107 LYS cc_start: 0.7830 (tppp) cc_final: 0.7567 (tptp)
REVERT: A  199 LYS cc_start: 0.8560 (pttm) cc_final: 0.7867 (pttm)
REVERT: A  280 GLU cc_start: 0.6987 (tp30) cc_final: 0.6487 (tp30)
REVERT: A  300 GLU cc_start: 0.6863 (pp20) cc_final: 0.6586 (pp20)
REVERT: A  303 GLU cc_start: 0.7377 (pp20) cc_final: 0.7035 (pp20)
REVERT: A  330 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6713 (mtm-85)
REVERT: A  397 GLN cc_start: 0.7167 (tt0) cc_final: 0.6464 (tm-30)
REVERT: A  400 ILE cc_start: 0.8749 (mm) cc_final: 0.8478 (mm)
REVERT: A  449 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.8036 (mtp85)
REVERT: A  450 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7895 (mmp80)
REVERT: A  492 GLU cc_start: 0.7446 (mp0) cc_final: 0.7224 (mm-30)
REVERT: A  501 GLU cc_start: 0.7171 (mp0) cc_final: 0.6884 (mp0)
REVERT: A  509 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6857 (tm-30)
REVERT: A  567 MET cc_start: 0.5842 (mmt) cc_final: 0.5497 (tpp)
REVERT: A  582 ASN cc_start: 0.8001 (p0) cc_final: 0.7698 (p0)
REVERT: A  599 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6427 (t)
REVERT: A  621 MET cc_start: 0.3917 (mmt) cc_final: 0.3607 (mmt)
REVERT: B   55 ARG cc_start: 0.8243 (ttt180) cc_final: 0.7471 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7772 (tp30) cc_final: 0.7358 (tp30)
REVERT: B   70 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7187 (mp0)
REVERT: B   95 LYS cc_start: 0.8492 (tttt) cc_final: 0.8220 (ttmm)
REVERT: B  101 ASN cc_start: 0.8058 (t0) cc_final: 0.7607 (t0)
REVERT: B  128 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7110 (mp-120)
REVERT: B  154 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6816 (mm-40)
REVERT: B  188 ASP cc_start: 0.8186 (p0) cc_final: 0.7976 (p0)
REVERT: B  279 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6989 (mm-40)
REVERT: B  294 ASP cc_start: 0.7983 (t0) cc_final: 0.7573 (t0)
REVERT: B  312 TRP cc_start: 0.7456 (p-90) cc_final: 0.7150 (p-90)
REVERT: B  320 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7638 (t70)
REVERT: B  352 ASN cc_start: 0.8315 (m-40) cc_final: 0.7933 (m-40)
REVERT: B  376 PHE cc_start: 0.8701 (p90) cc_final: 0.8198 (p90)
REVERT: B  395 LEU cc_start: 0.8068 (tp) cc_final: 0.7754 (tt)
REVERT: B  410 LYS cc_start: 0.8146 (tttt) cc_final: 0.7923 (ttmt)
REVERT: B  461 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8064 (mm-40)
REVERT: B  493 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (mm-40)
REVERT: B  513 MET cc_start: 0.6836 (mmt) cc_final: 0.6499 (mmt)
REVERT: B  548 GLU cc_start: 0.8022 (pm20) cc_final: 0.7567 (pm20)
REVERT: B  559 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7336 (ttpp)
REVERT: B  683 MET cc_start: 0.7971 (mmm) cc_final: 0.7704 (mmm)
REVERT: C    8 ASP cc_start: 0.6893 (m-30) cc_final: 0.6420 (m-30)
REVERT: C   14 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6870 (p0)
REVERT: C   22 ASN cc_start: 0.7796 (m-40) cc_final: 0.7400 (m-40)
REVERT: C   31 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7569 (m-10)
REVERT: C   38 GLU cc_start: 0.7644 (pt0) cc_final: 0.7390 (pt0)
REVERT: C   40 MET cc_start: 0.8108 (tpt) cc_final: 0.7785 (tpt)
REVERT: C   46 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6762 (mt-10)
REVERT: C  107 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7789 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5646 (ptmm)
REVERT: D  578 MET cc_start: 0.7716 (mmm) cc_final: 0.7399 (mmm)
REVERT: D  585 LYS cc_start: 0.7792 (mmmm) cc_final: 0.7574 (mmmm)
REVERT: D  606 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6583 (mmmt)
REVERT: D  674 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7373 (t0)
REVERT: D  724 LYS cc_start: 0.8375 (tmmt) cc_final: 0.7984 (tmmt)
  outliers start: 84
  outliers final: 56
  residues processed: 480
  average time/residue: 0.3000
  time to fit residues: 196.0144
Evaluate side-chains
  494 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 426
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
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  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  307 SER
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  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  683 MET
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  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  320 HIS
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  406 LYS
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  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   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  579 SER
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  674 ASN
Chi-restraints excluded: chain D residue  686 PHE
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:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0570
   chunk 29 optimal weight:    0.3980
   chunk 154 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0040
   chunk 85 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.6712

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.146600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118009 restraints weight = 24839.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121890 restraints weight = 13504.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.124545 restraints weight = 8581.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.2222

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= 0.130
  Angle     :  0.702  13.083  18433  Z= 0.360
  Chirality :  0.044   0.189   2030
  Planarity :  0.004   0.047   2345
  Dihedral  :  6.525  86.155   1852
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.47 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 29.12 %
    Favored  : 64.99 %
  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: -1.06 (0.21), residues: 1619
  helix:  0.70 (0.20), residues: 708
  sheet:  0.51 (0.40), residues: 193
  loop : -2.62 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 289 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.021   0.001   PHE B 304 
 TYR   0.019   0.001   TYR A 305 
 ARG   0.017   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (  574)
  hydrogen bonds       : angle       4.41557 ( 1617)
  covalent geometry    : bond        0.00292 (13708)
  covalent geometry    : angle       0.70234 (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
  514 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 426
  time to evaluate  : 1.508 
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: 0.8495 (OUTLIER) cc_final: 0.8220 (tmm-80)
REVERT: A   72 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6543 (mtmm)
REVERT: A  107 LYS cc_start: 0.7825 (tppp) cc_final: 0.7589 (tptp)
REVERT: A  189 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8167 (mm-40)
REVERT: A  199 LYS cc_start: 0.8558 (pttm) cc_final: 0.8239 (pttm)
REVERT: A  300 GLU cc_start: 0.6754 (pp20) cc_final: 0.6511 (pp20)
REVERT: A  301 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7667 (t80)
REVERT: A  303 GLU cc_start: 0.7352 (pp20) cc_final: 0.7018 (pp20)
REVERT: A  330 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6716 (mtm-85)
REVERT: A  397 GLN cc_start: 0.7136 (tt0) cc_final: 0.6523 (tm-30)
REVERT: A  400 ILE cc_start: 0.8753 (mm) cc_final: 0.8504 (mm)
REVERT: A  449 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.8002 (mtp85)
REVERT: A  450 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7887 (mmp80)
REVERT: A  509 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6500 (tm-30)
REVERT: A  528 PHE cc_start: 0.8558 (t80) cc_final: 0.8194 (t80)
REVERT: A  567 MET cc_start: 0.5856 (mmt) cc_final: 0.5504 (tpp)
REVERT: A  582 ASN cc_start: 0.7969 (p0) cc_final: 0.7708 (p0)
REVERT: A  599 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6455 (t)
REVERT: B   55 ARG cc_start: 0.8206 (ttt180) cc_final: 0.7482 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7697 (tp30) cc_final: 0.7409 (tp30)
REVERT: B   70 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7165 (mp0)
REVERT: B   95 LYS cc_start: 0.8492 (tttt) cc_final: 0.8255 (ttmm)
REVERT: B  101 ASN cc_start: 0.8066 (t0) cc_final: 0.7622 (t0)
REVERT: B  128 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7088 (mp-120)
REVERT: B  142 LYS cc_start: 0.8349 (mttt) cc_final: 0.7753 (mtmm)
REVERT: B  154 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6819 (mm-40)
REVERT: B  188 ASP cc_start: 0.8178 (p0) cc_final: 0.7958 (p0)
REVERT: B  279 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.7056 (mm-40)
REVERT: B  294 ASP cc_start: 0.7980 (t0) cc_final: 0.7563 (t0)
REVERT: B  312 TRP cc_start: 0.7445 (p-90) cc_final: 0.7136 (p-90)
REVERT: B  320 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (t70)
REVERT: B  352 ASN cc_start: 0.8235 (m-40) cc_final: 0.7917 (m-40)
REVERT: B  376 PHE cc_start: 0.8650 (p90) cc_final: 0.8245 (p90)
REVERT: B  395 LEU cc_start: 0.8057 (tp) cc_final: 0.7733 (tt)
REVERT: B  410 LYS cc_start: 0.8156 (tttt) cc_final: 0.7943 (ttmt)
REVERT: B  461 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8051 (mm-40)
REVERT: B  493 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8140 (mm-40)
REVERT: B  513 MET cc_start: 0.6826 (mmt) cc_final: 0.6486 (mmt)
REVERT: B  559 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7330 (ttpp)
REVERT: B  569 GLU cc_start: 0.7535 (pm20) cc_final: 0.7154 (pm20)
REVERT: B  572 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6722 (p0)
REVERT: B  683 MET cc_start: 0.7943 (mmm) cc_final: 0.7666 (mmm)
REVERT: C    8 ASP cc_start: 0.6914 (m-30) cc_final: 0.6447 (m-30)
REVERT: C   14 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6832 (p0)
REVERT: C   22 ASN cc_start: 0.7826 (m-40) cc_final: 0.7463 (m-40)
REVERT: C   31 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.7585 (m-10)
REVERT: C   40 MET cc_start: 0.8099 (tpt) cc_final: 0.7770 (tpt)
REVERT: C   46 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6779 (mt-10)
REVERT: C  107 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7743 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5640 (ptmm)
REVERT: D  578 MET cc_start: 0.7683 (mmm) cc_final: 0.7369 (mmm)
REVERT: D  585 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7580 (mmmm)
REVERT: D  606 LYS cc_start: 0.6898 (mmmt) cc_final: 0.6613 (mmmt)
REVERT: D  674 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7400 (t0)
REVERT: D  724 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8010 (tmmt)
  outliers start: 88
  outliers final: 62
  residues processed: 475
  average time/residue: 0.3061
  time to fit residues: 198.0581
Evaluate side-chains
  497 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 420
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   63 SER
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  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  301 TYR
Chi-restraints excluded: chain A residue  307 SER
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  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 ASP
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 A residue  599 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  683 MET
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  279 GLN
Chi-restraints excluded: chain B residue  320 HIS
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  406 LYS
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  611 LEU
Chi-restraints excluded: chain B residue  617 MET
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   14 ASP
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  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  605 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 115 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.145351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.116857 restraints weight = 24878.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.120779 restraints weight = 13348.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123458 restraints weight = 8414.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.2389

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= 0.139
  Angle     :  0.715  12.022  18433  Z= 0.369
  Chirality :  0.044   0.191   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.578  85.661   1852
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.03 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 29.12 %
    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: -1.09 (0.21), residues: 1619
  helix:  0.68 (0.20), residues: 708
  sheet:  0.47 (0.40), residues: 193
  loop : -2.63 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 289 
 HIS   0.006   0.001   HIS B 632 
 PHE   0.026   0.001   PHE C  29 
 TYR   0.033   0.001   TYR D 658 
 ARG   0.020   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  574)
  hydrogen bonds       : angle       4.41915 ( 1617)
  covalent geometry    : bond        0.00315 (13708)
  covalent geometry    : angle       0.71477 (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
  498 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 414
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (tmm-80)
REVERT: A   72 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6596 (mtmm)
REVERT: A  107 LYS cc_start: 0.7848 (tppp) cc_final: 0.7576 (tptp)
REVERT: A  189 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8161 (mm-40)
REVERT: A  199 LYS cc_start: 0.8479 (pttm) cc_final: 0.8137 (pttm)
REVERT: A  300 GLU cc_start: 0.6867 (pp20) cc_final: 0.6595 (pp20)
REVERT: A  301 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7775 (t80)
REVERT: A  303 GLU cc_start: 0.7411 (pp20) cc_final: 0.7042 (pp20)
REVERT: A  328 GLU cc_start: 0.7428 (mp0) cc_final: 0.7066 (mm-30)
REVERT: A  330 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6631 (mtm-85)
REVERT: A  363 MET cc_start: 0.6935 (ptt) cc_final: 0.6379 (ppp)
REVERT: A  397 GLN cc_start: 0.7182 (tt0) cc_final: 0.6504 (tm-30)
REVERT: A  400 ILE cc_start: 0.8743 (mm) cc_final: 0.8469 (mm)
REVERT: A  449 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7982 (mtp85)
REVERT: A  450 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7829 (mmp80)
REVERT: A  501 GLU cc_start: 0.7708 (mp0) cc_final: 0.7472 (mp0)
REVERT: A  509 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6666 (tm-30)
REVERT: A  528 PHE cc_start: 0.8573 (t80) cc_final: 0.8213 (t80)
REVERT: A  582 ASN cc_start: 0.8023 (p0) cc_final: 0.7715 (p0)
REVERT: A  599 THR cc_start: 0.6843 (OUTLIER) cc_final: 0.6399 (t)
REVERT: A  623 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7766 (mtmm)
REVERT: B   57 GLU cc_start: 0.7731 (tp30) cc_final: 0.7322 (tp30)
REVERT: B   70 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7149 (mp0)
REVERT: B   95 LYS cc_start: 0.8505 (tttt) cc_final: 0.8268 (tttt)
REVERT: B  101 ASN cc_start: 0.8079 (t0) cc_final: 0.7606 (t0)
REVERT: B  128 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7087 (mp-120)
REVERT: B  142 LYS cc_start: 0.8331 (mttt) cc_final: 0.7717 (mtmm)
REVERT: B  154 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6723 (mm-40)
REVERT: B  186 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7442 (mmtp)
REVERT: B  188 ASP cc_start: 0.8172 (p0) cc_final: 0.7946 (p0)
REVERT: B  279 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7022 (mm-40)
REVERT: B  294 ASP cc_start: 0.7981 (t0) cc_final: 0.7595 (t0)
REVERT: B  300 GLU cc_start: 0.7366 (mp0) cc_final: 0.7049 (mp0)
REVERT: B  312 TRP cc_start: 0.7510 (p-90) cc_final: 0.7182 (p-90)
REVERT: B  352 ASN cc_start: 0.8321 (m-40) cc_final: 0.7970 (m-40)
REVERT: B  376 PHE cc_start: 0.8709 (p90) cc_final: 0.8173 (p90)
REVERT: B  395 LEU cc_start: 0.8081 (tp) cc_final: 0.7782 (tt)
REVERT: B  410 LYS cc_start: 0.8175 (tttt) cc_final: 0.7952 (ttmt)
REVERT: B  461 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8051 (mm-40)
REVERT: B  493 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8173 (mm-40)
REVERT: B  513 MET cc_start: 0.6803 (mmt) cc_final: 0.6432 (mmt)
REVERT: B  514 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7048 (p)
REVERT: B  559 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7474 (ttpp)
REVERT: B  569 GLU cc_start: 0.7557 (pm20) cc_final: 0.7196 (pm20)
REVERT: B  572 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6734 (p0)
REVERT: B  683 MET cc_start: 0.8014 (mmm) cc_final: 0.7742 (mmm)
REVERT: C    8 ASP cc_start: 0.6944 (m-30) cc_final: 0.6452 (m-30)
REVERT: C   14 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6826 (p0)
REVERT: C   16 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6846 (tm-30)
REVERT: C   22 ASN cc_start: 0.7879 (m-40) cc_final: 0.7507 (m-40)
REVERT: C   31 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7607 (m-10)
REVERT: C   40 MET cc_start: 0.8077 (tpt) cc_final: 0.7761 (tpt)
REVERT: C   46 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6795 (mt-10)
REVERT: C  107 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7710 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5666 (ptmm)
REVERT: D  578 MET cc_start: 0.7680 (mmm) cc_final: 0.7342 (mmm)
REVERT: D  585 LYS cc_start: 0.7794 (mmmm) cc_final: 0.7585 (mmmm)
REVERT: D  606 LYS cc_start: 0.6902 (mmmt) cc_final: 0.6616 (mmmt)
REVERT: D  674 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7462 (t0)
REVERT: D  724 LYS cc_start: 0.8391 (tmmt) cc_final: 0.8003 (tmmt)
  outliers start: 84
  outliers final: 62
  residues processed: 462
  average time/residue: 0.3025
  time to fit residues: 190.5758
Evaluate side-chains
  486 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 408
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   63 SER
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  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  301 TYR
Chi-restraints excluded: chain A residue  307 SER
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  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 ASP
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  683 MET
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  279 GLN
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  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  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  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  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   14 ASP
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  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  605 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 139 optimal weight:    0.0060
   chunk 23 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 143 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 131 optimal weight:    0.0980
   chunk 85 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 156 optimal weight:    9.9990
   chunk 159 optimal weight:    4.9990
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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**
D 674 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.146568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117982 restraints weight = 24660.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.121908 restraints weight = 13244.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.124568 restraints weight = 8341.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13708  Z= 0.134
  Angle     :  0.751  13.994  18433  Z= 0.381
  Chirality :  0.045   0.200   2030
  Planarity :  0.004   0.048   2345
  Dihedral  :  6.526  86.066   1852
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.29 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 30.39 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.21), residues: 1619
  helix:  0.64 (0.20), residues: 707
  sheet:  0.45 (0.40), residues: 193
  loop : -2.60 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 289 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.023   0.001   PHE A  39 
 TYR   0.037   0.001   TYR D 658 
 ARG   0.025   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  574)
  hydrogen bonds       : angle       4.36815 ( 1617)
  covalent geometry    : bond        0.00308 (13708)
  covalent geometry    : angle       0.75051 (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
  494 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 414
  time to evaluate  : 2.003 
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   41 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8199 (tmm-80)
REVERT: A   72 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6474 (ptpp)
REVERT: A  107 LYS cc_start: 0.7839 (tppp) cc_final: 0.7570 (tptp)
REVERT: A  189 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8180 (mm-40)
REVERT: A  199 LYS cc_start: 0.8490 (pttm) cc_final: 0.8127 (pttm)
REVERT: A  300 GLU cc_start: 0.6817 (pp20) cc_final: 0.6557 (pp20)
REVERT: A  301 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7781 (t80)
REVERT: A  303 GLU cc_start: 0.7397 (pp20) cc_final: 0.7024 (pp20)
REVERT: A  328 GLU cc_start: 0.7416 (mp0) cc_final: 0.7039 (mm-30)
REVERT: A  330 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6551 (mtm-85)
REVERT: A  338 ARG cc_start: 0.7865 (mmp80) cc_final: 0.7511 (mmp80)
REVERT: A  397 GLN cc_start: 0.7150 (tt0) cc_final: 0.6484 (tm-30)
REVERT: A  400 ILE cc_start: 0.8758 (mm) cc_final: 0.8511 (mm)
REVERT: A  450 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7791 (mmp80)
REVERT: A  487 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7517 (p)
REVERT: A  501 GLU cc_start: 0.7650 (mp0) cc_final: 0.7423 (mp0)
REVERT: A  509 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6611 (tm-30)
REVERT: A  528 PHE cc_start: 0.8563 (t80) cc_final: 0.8337 (t80)
REVERT: A  567 MET cc_start: 0.5803 (mmt) cc_final: 0.5501 (tpp)
REVERT: A  582 ASN cc_start: 0.8004 (p0) cc_final: 0.7729 (p0)
REVERT: A  599 THR cc_start: 0.6708 (OUTLIER) cc_final: 0.6336 (t)
REVERT: A  623 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7779 (mtmm)
REVERT: A  640 GLN cc_start: 0.7852 (pp30) cc_final: 0.7541 (pp30)
REVERT: B   57 GLU cc_start: 0.7714 (tp30) cc_final: 0.7299 (tp30)
REVERT: B   95 LYS cc_start: 0.8476 (tttt) cc_final: 0.8255 (tttt)
REVERT: B  101 ASN cc_start: 0.8067 (t0) cc_final: 0.7600 (t0)
REVERT: B  128 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7094 (mp-120)
REVERT: B  142 LYS cc_start: 0.8318 (mttt) cc_final: 0.7734 (mtmm)
REVERT: B  154 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6691 (mm-40)
REVERT: B  188 ASP cc_start: 0.8194 (p0) cc_final: 0.7949 (p0)
REVERT: B  279 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7029 (mm110)
REVERT: B  294 ASP cc_start: 0.7998 (t0) cc_final: 0.7609 (t0)
REVERT: B  300 GLU cc_start: 0.7371 (mp0) cc_final: 0.7029 (mp0)
REVERT: B  312 TRP cc_start: 0.7483 (p-90) cc_final: 0.7179 (p-90)
REVERT: B  352 ASN cc_start: 0.8284 (m-40) cc_final: 0.7964 (m-40)
REVERT: B  376 PHE cc_start: 0.8706 (p90) cc_final: 0.8242 (p90)
REVERT: B  395 LEU cc_start: 0.8035 (tp) cc_final: 0.7709 (tt)
REVERT: B  410 LYS cc_start: 0.8138 (tttt) cc_final: 0.7928 (ttmt)
REVERT: B  433 PHE cc_start: 0.7989 (m-10) cc_final: 0.7746 (m-10)
REVERT: B  481 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8379 (mmtt)
REVERT: B  493 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8132 (mm-40)
REVERT: B  513 MET cc_start: 0.6816 (mmt) cc_final: 0.6482 (mmt)
REVERT: B  569 GLU cc_start: 0.7537 (pm20) cc_final: 0.7150 (pm20)
REVERT: B  572 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6732 (p0)
REVERT: B  683 MET cc_start: 0.7965 (mmm) cc_final: 0.7678 (mmm)
REVERT: C    8 ASP cc_start: 0.6906 (m-30) cc_final: 0.6410 (m-30)
REVERT: C   31 TRP cc_start: 0.8613 (OUTLIER) cc_final: 0.7651 (m-10)
REVERT: C   40 MET cc_start: 0.8069 (tpt) cc_final: 0.7729 (tpt)
REVERT: C   46 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6780 (mt-10)
REVERT: C  107 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7868 (mtt-85)
REVERT: D  529 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5755 (ptmm)
REVERT: D  578 MET cc_start: 0.7639 (mmm) cc_final: 0.7313 (mmm)
REVERT: D  585 LYS cc_start: 0.7794 (mmmm) cc_final: 0.7593 (mmmm)
REVERT: D  724 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7979 (tmmt)
  outliers start: 80
  outliers final: 58
  residues processed: 458
  average time/residue: 0.3276
  time to fit residues: 205.8791
Evaluate side-chains
  480 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 408
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   63 SER
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  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  301 TYR
Chi-restraints excluded: chain A residue  307 SER
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  366 CYS
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  468 SER
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  522 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  683 MET
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  279 GLN
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  406 LYS
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  497 SER
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  611 LEU
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  626 LEU
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  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  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  708 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 137 optimal weight:   20.0000
   chunk 74 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0030
   chunk 93 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0870
   overall best weight:    0.5168

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.146729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.118237 restraints weight = 24641.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122141 restraints weight = 13305.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124810 restraints weight = 8424.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13708  Z= 0.136
  Angle     :  0.761  13.996  18433  Z= 0.387
  Chirality :  0.044   0.196   2030
  Planarity :  0.004   0.058   2345
  Dihedral  :  6.515  85.786   1852
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.41 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 30.39 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.21), residues: 1619
  helix:  0.65 (0.20), residues: 707
  sheet:  0.50 (0.40), residues: 192
  loop : -2.58 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 289 
 HIS   0.004   0.001   HIS A 149 
 PHE   0.026   0.001   PHE A  39 
 TYR   0.031   0.001   TYR B 305 
 ARG   0.019   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  574)
  hydrogen bonds       : angle       4.37125 ( 1617)
  covalent geometry    : bond        0.00314 (13708)
  covalent geometry    : angle       0.76108 (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
  492 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 416
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8233 (tmm-80)
REVERT: A  107 LYS cc_start: 0.7856 (tppp) cc_final: 0.7586 (tptp)
REVERT: A  180 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7882 (mmtm)
REVERT: A  189 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8180 (mm-40)
REVERT: A  300 GLU cc_start: 0.6756 (pp20) cc_final: 0.6513 (pp20)
REVERT: A  301 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7763 (t80)
REVERT: A  303 GLU cc_start: 0.7396 (pp20) cc_final: 0.7010 (pp20)
REVERT: A  328 GLU cc_start: 0.7423 (mp0) cc_final: 0.7035 (mm-30)
REVERT: A  330 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6659 (mtm-85)
REVERT: A  338 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7523 (mmp80)
REVERT: A  397 GLN cc_start: 0.7119 (tt0) cc_final: 0.6476 (tm-30)
REVERT: A  400 ILE cc_start: 0.8745 (mm) cc_final: 0.8504 (mm)
REVERT: A  450 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7861 (mmp80)
REVERT: A  487 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7682 (p)
REVERT: A  501 GLU cc_start: 0.7631 (mp0) cc_final: 0.7426 (mp0)
REVERT: A  509 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6673 (tm-30)
REVERT: A  528 PHE cc_start: 0.8566 (t80) cc_final: 0.8240 (t80)
REVERT: A  567 MET cc_start: 0.5807 (mmt) cc_final: 0.5485 (tpp)
REVERT: A  582 ASN cc_start: 0.8017 (p0) cc_final: 0.7718 (p0)
REVERT: A  599 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6273 (t)
REVERT: A  602 MET cc_start: 0.8287 (tpp) cc_final: 0.7939 (tpp)
REVERT: A  640 GLN cc_start: 0.7966 (pp30) cc_final: 0.7513 (pp30)
REVERT: B   57 GLU cc_start: 0.7688 (tp30) cc_final: 0.7293 (tp30)
REVERT: B   95 LYS cc_start: 0.8413 (tttt) cc_final: 0.8195 (tttt)
REVERT: B  101 ASN cc_start: 0.8073 (t0) cc_final: 0.7607 (t0)
REVERT: B  128 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7092 (mp-120)
REVERT: B  142 LYS cc_start: 0.8303 (mttt) cc_final: 0.7708 (mtmm)
REVERT: B  154 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6621 (mm-40)
REVERT: B  188 ASP cc_start: 0.8214 (p0) cc_final: 0.7911 (p0)
REVERT: B  279 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7046 (mm110)
REVERT: B  294 ASP cc_start: 0.8016 (t0) cc_final: 0.7590 (t0)
REVERT: B  312 TRP cc_start: 0.7476 (p-90) cc_final: 0.7139 (p-90)
REVERT: B  329 PHE cc_start: 0.8382 (p90) cc_final: 0.7843 (p90)
REVERT: B  352 ASN cc_start: 0.8332 (m-40) cc_final: 0.7930 (m-40)
REVERT: B  376 PHE cc_start: 0.8689 (p90) cc_final: 0.8253 (p90)
REVERT: B  395 LEU cc_start: 0.8028 (tp) cc_final: 0.7714 (tt)
REVERT: B  481 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8390 (mmtt)
REVERT: B  492 GLU cc_start: 0.7760 (pm20) cc_final: 0.7258 (pm20)
REVERT: B  493 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8078 (mm-40)
REVERT: B  513 MET cc_start: 0.6895 (mmt) cc_final: 0.6532 (mmt)
REVERT: B  569 GLU cc_start: 0.7513 (pm20) cc_final: 0.7112 (pm20)
REVERT: B  572 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6713 (p0)
REVERT: B  683 MET cc_start: 0.7923 (mmm) cc_final: 0.7642 (mmm)
REVERT: C    8 ASP cc_start: 0.6877 (m-30) cc_final: 0.6389 (m-30)
REVERT: C   14 ASP cc_start: 0.7219 (p0) cc_final: 0.6738 (p0)
REVERT: C   31 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7608 (m-10)
REVERT: C   40 MET cc_start: 0.8070 (tpt) cc_final: 0.7722 (tpt)
REVERT: C   46 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6843 (mt-10)
REVERT: C  107 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7722 (mtt-85)
REVERT: C  111 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7919 (mttt)
REVERT: C  118 ASP cc_start: 0.6975 (t0) cc_final: 0.6727 (t0)
REVERT: D  529 LYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5750 (ptmm)
REVERT: D  578 MET cc_start: 0.7600 (mmm) cc_final: 0.7283 (mmm)
REVERT: D  724 LYS cc_start: 0.8326 (tmmt) cc_final: 0.7998 (tmmt)
  outliers start: 76
  outliers final: 56
  residues processed: 459
  average time/residue: 0.3073
  time to fit residues: 191.8851
Evaluate side-chains
  476 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 408
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
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  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  307 SER
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  441 ILE
Chi-restraints excluded: chain A residue  468 SER
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  522 VAL
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  683 MET
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  279 GLN
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  406 LYS
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  611 LEU
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  626 LEU
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  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  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  708 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 158 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 114 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 155 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 127 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.144722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.116191 restraints weight = 24639.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120075 restraints weight = 13223.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.122724 restraints weight = 8320.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13708  Z= 0.162
  Angle     :  0.783  13.719  18433  Z= 0.403
  Chirality :  0.046   0.197   2030
  Planarity :  0.004   0.048   2345
  Dihedral  :  6.698  85.024   1852
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.02 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 30.59 %
    Favored  : 64.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.21), residues: 1619
  helix:  0.58 (0.20), residues: 708
  sheet:  0.49 (0.41), residues: 184
  loop : -2.57 (0.22), residues: 727

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   0.031   0.002   PHE A 361 
 TYR   0.028   0.002   TYR B 305 
 ARG   0.019   0.001   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  574)
  hydrogen bonds       : angle       4.52196 ( 1617)
  covalent geometry    : bond        0.00367 (13708)
  covalent geometry    : angle       0.78341 (18433)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5109.55 seconds
wall clock time: 89 minutes 13.57 seconds (5353.57 seconds total)