Starting phenix.real_space_refine
on Sat Aug 23 17:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fx4_29523/08_2025/8fx4_29523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fx4_29523/08_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_29523/08_2025/8fx4_29523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fx4_29523/08_2025/8fx4_29523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fx4_29523/08_2025/8fx4_29523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fx4_29523/08_2025/8fx4_29523.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.56, per 1000 atoms: 0.19
  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: 0.96
  Conformation dependent library (CDL) restraints added in 549.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.27
  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: 1.52

  Time building geometry restraints manager: 1.21 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 801))
  selection = (chain 'B' and (resid 12 through 218 or resid 278 through 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.690
-------------------------------------------------------------------------------
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 : 13.85
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG B 475 
 TYR   0.021   0.001   TYR A 430 
 PHE   0.016   0.001   PHE A  39 
 TRP   0.038   0.002   TRP D 623 
 HIS   0.007   0.001   HIS A 149 

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

*********************** 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  : 0.683 
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: 0.1534
  time to fit residues: 88.6061
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  : 0.547 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    0.0970
   chunk 122 optimal weight:    0.1980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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
** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.144543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116550 restraints weight = 25075.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.120428 restraints weight = 13576.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.123056 restraints weight = 8580.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124577 restraints weight = 6083.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125973 restraints weight = 4763.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  13708  Z= 0.137
  Angle     :  0.700  10.136  18433  Z= 0.370
  Chirality :  0.044   0.193   2030
  Planarity :  0.004   0.059   2345
  Dihedral  :  7.735  88.076   1867
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.41 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.84 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.21), residues: 1619
  helix:  0.54 (0.20), residues: 692
  sheet:  0.45 (0.40), residues: 190
  loop : -2.75 (0.21), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 338 
 TYR   0.027   0.001   TYR B 305 
 PHE   0.024   0.001   PHE C 125 
 TRP   0.022   0.001   TRP D 623 
 HIS   0.006   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13708)
  covalent geometry    : angle       0.70010 (18433)
  hydrogen bonds       : bond        0.04768 (  574)
  hydrogen bonds       : angle       4.78741 ( 1617)

*********************** 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
  484 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 426
  time to evaluate  : 0.541 
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   53 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8010 (mtpp)
REVERT: A  153 GLU cc_start: 0.7413 (mp0) cc_final: 0.7153 (mp0)
REVERT: A  195 GLU cc_start: 0.7528 (tp30) cc_final: 0.7115 (tp30)
REVERT: A  303 GLU cc_start: 0.7068 (pp20) cc_final: 0.6731 (pp20)
REVERT: A  397 GLN cc_start: 0.7343 (tt0) cc_final: 0.6578 (tm-30)
REVERT: A  400 ILE cc_start: 0.8711 (mm) cc_final: 0.8136 (mm)
REVERT: A  430 TYR cc_start: 0.7636 (t80) cc_final: 0.7382 (t80)
REVERT: A  449 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7658 (tpp80)
REVERT: A  481 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8439 (mmtt)
REVERT: A  501 GLU cc_start: 0.7374 (mp0) cc_final: 0.7054 (mp0)
REVERT: A  513 MET cc_start: 0.7311 (ttm) cc_final: 0.7029 (mtp)
REVERT: A  526 LYS cc_start: 0.7575 (pptt) cc_final: 0.7239 (pptt)
REVERT: A  527 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6171 (mt-10)
REVERT: B   55 ARG cc_start: 0.8286 (ttt180) cc_final: 0.7339 (ttp-170)
REVERT: B   80 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7382 (tm-30)
REVERT: B  154 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7117 (mm-40)
REVERT: B  279 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6793 (mm110)
REVERT: B  294 ASP cc_start: 0.7948 (t0) cc_final: 0.7521 (t0)
REVERT: B  312 TRP cc_start: 0.7506 (p-90) cc_final: 0.7186 (p-90)
REVERT: B  356 TYR cc_start: 0.8353 (m-80) cc_final: 0.7839 (m-80)
REVERT: B  493 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8019 (tp40)
REVERT: B  513 MET cc_start: 0.6613 (mmt) cc_final: 0.6248 (mmt)
REVERT: B  559 LYS cc_start: 0.7717 (ttpp) cc_final: 0.7276 (ttpp)
REVERT: B  569 GLU cc_start: 0.7608 (pm20) cc_final: 0.7183 (pm20)
REVERT: C   16 GLU cc_start: 0.7269 (pp20) cc_final: 0.7000 (tm-30)
REVERT: C   20 HIS cc_start: 0.8075 (t-90) cc_final: 0.7840 (t70)
REVERT: C   36 ARG cc_start: 0.7637 (ttp-170) cc_final: 0.7373 (ttp-170)
REVERT: C  107 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7574 (mtt-85)
REVERT: D  627 GLU cc_start: 0.7232 (pp20) cc_final: 0.6996 (pp20)
REVERT: D  724 LYS cc_start: 0.8244 (tmmt) cc_final: 0.8020 (tmmt)
  outliers start: 58
  outliers final: 35
  residues processed: 459
  average time/residue: 0.1478
  time to fit residues: 93.0508
Evaluate side-chains
  443 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 406
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
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  617 MET
Chi-restraints excluded: chain A residue  632 HIS
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  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  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  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  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 44 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0070
   chunk 100 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0470
   chunk 128 optimal weight:   10.0000
   chunk 134 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.2696

-------------------------------------------------------------------------------
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**
** 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 = 0.146752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.118671 restraints weight = 25324.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122605 restraints weight = 13627.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125205 restraints weight = 8572.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.127034 restraints weight = 6063.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128334 restraints weight = 4698.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13708  Z= 0.120
  Angle     :  0.659  11.006  18433  Z= 0.342
  Chirality :  0.043   0.188   2030
  Planarity :  0.004   0.055   2345
  Dihedral  :  6.839  86.884   1854
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.23 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 28.71 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.21), residues: 1619
  helix:  0.73 (0.20), residues: 688
  sheet:  0.37 (0.39), residues: 193
  loop : -2.62 (0.22), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 338 
 TYR   0.018   0.001   TYR B 305 
 PHE   0.017   0.001   PHE A 304 
 TRP   0.016   0.001   TRP B 598 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (13708)
  covalent geometry    : angle       0.65919 (18433)
  hydrogen bonds       : bond        0.03827 (  574)
  hydrogen bonds       : angle       4.47359 ( 1617)

*********************** 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
  485 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 421
  time to evaluate  : 0.546 
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  107 LYS cc_start: 0.7769 (tppp) cc_final: 0.7497 (tptp)
REVERT: A  115 GLU cc_start: 0.7712 (tp30) cc_final: 0.7484 (tp30)
REVERT: A  195 GLU cc_start: 0.7398 (tp30) cc_final: 0.6991 (tp30)
REVERT: A  199 LYS cc_start: 0.8299 (ptpp) cc_final: 0.7843 (mtmm)
REVERT: A  300 GLU cc_start: 0.6630 (pp20) cc_final: 0.6199 (pt0)
REVERT: A  303 GLU cc_start: 0.7116 (pp20) cc_final: 0.6719 (pp20)
REVERT: A  324 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6289 (tm-30)
REVERT: A  328 GLU cc_start: 0.7218 (mp0) cc_final: 0.6792 (mp0)
REVERT: A  397 GLN cc_start: 0.7166 (tt0) cc_final: 0.6624 (tm-30)
REVERT: A  400 ILE cc_start: 0.8720 (mm) cc_final: 0.8278 (mm)
REVERT: A  449 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7637 (tpp80)
REVERT: A  481 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8387 (mmtt)
REVERT: A  509 GLU cc_start: 0.6714 (tp30) cc_final: 0.6413 (tp30)
REVERT: A  513 MET cc_start: 0.7215 (ttm) cc_final: 0.6896 (mtp)
REVERT: A  527 GLU cc_start: 0.7039 (mt-10) cc_final: 0.5981 (mt-10)
REVERT: A  553 MET cc_start: 0.7128 (mmm) cc_final: 0.6836 (mmp)
REVERT: A  567 MET cc_start: 0.5745 (mmt) cc_final: 0.5468 (tpp)
REVERT: B   42 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7170 (mm-30)
REVERT: B   55 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7366 (ttp-170)
REVERT: B  101 ASN cc_start: 0.8031 (t0) cc_final: 0.7663 (t0)
REVERT: B  128 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7020 (mp-120)
REVERT: B  154 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7157 (mm-40)
REVERT: B  279 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6765 (mm110)
REVERT: B  280 GLU cc_start: 0.7465 (pt0) cc_final: 0.7161 (tm-30)
REVERT: B  294 ASP cc_start: 0.7956 (t0) cc_final: 0.7479 (t0)
REVERT: B  312 TRP cc_start: 0.7413 (p-90) cc_final: 0.7051 (p-90)
REVERT: B  329 PHE cc_start: 0.8274 (p90) cc_final: 0.7700 (p90)
REVERT: B  476 MET cc_start: 0.6196 (mmm) cc_final: 0.5730 (mmm)
REVERT: B  493 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8073 (mm-40)
REVERT: B  513 MET cc_start: 0.6490 (mmt) cc_final: 0.6178 (mmt)
REVERT: B  519 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6851 (tm-30)
REVERT: B  559 LYS cc_start: 0.7650 (ttpp) cc_final: 0.7403 (ttpp)
REVERT: B  569 GLU cc_start: 0.7529 (pm20) cc_final: 0.7187 (pm20)
REVERT: B  572 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6448 (p0)
REVERT: B  602 MET cc_start: 0.7066 (tpt) cc_final: 0.6805 (tpt)
REVERT: C    8 ASP cc_start: 0.6823 (m-30) cc_final: 0.6433 (m-30)
REVERT: C   31 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7510 (m-10)
REVERT: C   36 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7437 (ttp-170)
REVERT: C   38 GLU cc_start: 0.7472 (pt0) cc_final: 0.7186 (pt0)
REVERT: C   40 MET cc_start: 0.8082 (tpt) cc_final: 0.7828 (tpt)
REVERT: C  104 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: C  107 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7516 (mtt-85)
REVERT: C  110 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7541 (tm-30)
REVERT: D  585 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7603 (mmmm)
REVERT: D  674 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7281 (t0)
REVERT: D  688 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: D  724 LYS cc_start: 0.8302 (tmmt) cc_final: 0.7944 (tmmt)
  outliers start: 64
  outliers final: 36
  residues processed: 457
  average time/residue: 0.1305
  time to fit residues: 82.4669
Evaluate side-chains
  442 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 399
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  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  441 ILE
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  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  182 ILE
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  381 VAL
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  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  619 TYR
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 D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  674 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 2 optimal weight:    0.0020
   chunk 9 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 129 optimal weight:    6.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN
B 352 ASN
C  20 HIS
** C  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.146315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.118061 restraints weight = 25082.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121897 restraints weight = 13604.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.124519 restraints weight = 8645.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126014 restraints weight = 6161.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.127528 restraints weight = 4868.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13708  Z= 0.123
  Angle     :  0.653  11.357  18433  Z= 0.339
  Chirality :  0.043   0.180   2030
  Planarity :  0.004   0.052   2345
  Dihedral  :  6.646  85.914   1854
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.23 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 28.78 %
    Favored  : 66.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.21), residues: 1619
  helix:  0.73 (0.20), residues: 697
  sheet:  0.49 (0.39), residues: 193
  loop : -2.62 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 506 
 TYR   0.018   0.001   TYR A 305 
 PHE   0.012   0.001   PHE C  29 
 TRP   0.014   0.001   TRP B 598 
 HIS   0.005   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13708)
  covalent geometry    : angle       0.65255 (18433)
  hydrogen bonds       : bond        0.03898 (  574)
  hydrogen bonds       : angle       4.40154 ( 1617)

*********************** 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
  479 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 407
  time to evaluate  : 0.375 
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: 0.7786 (tppp) cc_final: 0.7585 (tptp)
REVERT: A  300 GLU cc_start: 0.6602 (pp20) cc_final: 0.6153 (pt0)
REVERT: A  303 GLU cc_start: 0.7189 (pp20) cc_final: 0.6753 (pp20)
REVERT: A  397 GLN cc_start: 0.7143 (tt0) cc_final: 0.6605 (tm-30)
REVERT: A  400 ILE cc_start: 0.8727 (mm) cc_final: 0.8371 (mm)
REVERT: A  449 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7635 (tpp80)
REVERT: A  450 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7864 (mmp80)
REVERT: A  481 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8487 (mmtt)
REVERT: A  509 GLU cc_start: 0.6655 (tp30) cc_final: 0.6322 (tp30)
REVERT: A  527 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6505 (mt-10)
REVERT: A  553 MET cc_start: 0.7164 (mmm) cc_final: 0.6955 (mmp)
REVERT: A  567 MET cc_start: 0.5701 (mmt) cc_final: 0.5383 (tpp)
REVERT: B   55 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7394 (ttp-170)
REVERT: B  101 ASN cc_start: 0.8033 (t0) cc_final: 0.7589 (t0)
REVERT: B  128 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7042 (mp-120)
REVERT: B  154 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7112 (mm-40)
REVERT: B  279 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6826 (mm110)
REVERT: B  294 ASP cc_start: 0.7930 (t0) cc_final: 0.7512 (t0)
REVERT: B  312 TRP cc_start: 0.7435 (p-90) cc_final: 0.7045 (p-90)
REVERT: B  476 MET cc_start: 0.6319 (mmm) cc_final: 0.5926 (mmm)
REVERT: B  481 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8427 (mmtt)
REVERT: B  493 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7983 (mm-40)
REVERT: B  499 PHE cc_start: 0.7976 (m-80) cc_final: 0.7701 (m-80)
REVERT: B  559 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7397 (ttpp)
REVERT: B  569 GLU cc_start: 0.7508 (pm20) cc_final: 0.7256 (pm20)
REVERT: B  572 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6496 (p0)
REVERT: B  627 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7188 (mm-30)
REVERT: B  683 MET cc_start: 0.7839 (mmm) cc_final: 0.7626 (mmm)
REVERT: C    8 ASP cc_start: 0.6831 (m-30) cc_final: 0.6408 (m-30)
REVERT: C   31 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7507 (m-10)
REVERT: C   36 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7405 (ttp-170)
REVERT: C   40 MET cc_start: 0.8077 (tpt) cc_final: 0.7735 (tpt)
REVERT: C  107 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7549 (mtt-85)
REVERT: D  585 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7600 (mmmm)
REVERT: D  674 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7232 (t0)
REVERT: D  724 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7938 (tmmt)
  outliers start: 72
  outliers final: 46
  residues processed: 446
  average time/residue: 0.1153
  time to fit residues: 71.0898
Evaluate side-chains
  453 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 401
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   85 THR
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  308 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  441 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  623 LYS
Chi-restraints excluded: chain A residue  632 HIS
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  150 ASN
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  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  574 LYS
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  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  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  674 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 143 optimal weight:    0.3980
   chunk 81 optimal weight:    0.0370
   chunk 157 optimal weight:    0.1980
   chunk 93 optimal weight:    2.9990
   chunk 140 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 160 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9990
   chunk 132 optimal weight:    4.9990
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
B 150 ASN
B 189 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 674 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.147296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.119001 restraints weight = 25132.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122877 restraints weight = 13622.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125486 restraints weight = 8658.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127366 restraints weight = 6117.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128664 restraints weight = 4720.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  13708  Z= 0.121
  Angle     :  0.665  11.761  18433  Z= 0.342
  Chirality :  0.043   0.184   2030
  Planarity :  0.004   0.051   2345
  Dihedral  :  6.439  84.888   1852
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.92 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 28.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.21), residues: 1619
  helix:  0.82 (0.20), residues: 691
  sheet:  0.55 (0.39), residues: 193
  loop : -2.59 (0.22), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 506 
 TYR   0.018   0.001   TYR B 305 
 PHE   0.027   0.001   PHE A 361 
 TRP   0.010   0.001   TRP B 598 
 HIS   0.006   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13708)
  covalent geometry    : angle       0.66453 (18433)
  hydrogen bonds       : bond        0.03601 (  574)
  hydrogen bonds       : angle       4.34686 ( 1617)

*********************** 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
  492 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 417
  time to evaluate  : 0.353 
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   30 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7861 (t0)
REVERT: A  303 GLU cc_start: 0.7278 (pp20) cc_final: 0.7002 (pp20)
REVERT: A  397 GLN cc_start: 0.7010 (tt0) cc_final: 0.6515 (tm-30)
REVERT: A  400 ILE cc_start: 0.8734 (mm) cc_final: 0.8418 (mm)
REVERT: A  424 GLU cc_start: 0.7408 (pm20) cc_final: 0.6929 (pm20)
REVERT: A  450 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7847 (mmp80)
REVERT: A  528 PHE cc_start: 0.8538 (t80) cc_final: 0.8136 (t80)
REVERT: A  553 MET cc_start: 0.7172 (mmm) cc_final: 0.6930 (mmp)
REVERT: A  567 MET cc_start: 0.5662 (mmt) cc_final: 0.5389 (tpp)
REVERT: A  623 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7724 (mtmm)
REVERT: B   55 ARG cc_start: 0.8227 (ttt180) cc_final: 0.7391 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7745 (tp30) cc_final: 0.7458 (tp30)
REVERT: B   95 LYS cc_start: 0.8486 (tttt) cc_final: 0.8267 (ttmm)
REVERT: B  101 ASN cc_start: 0.8028 (t0) cc_final: 0.7627 (t0)
REVERT: B  104 THR cc_start: 0.7763 (m) cc_final: 0.7422 (p)
REVERT: B  128 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7020 (mp-120)
REVERT: B  154 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7100 (mm-40)
REVERT: B  279 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6837 (mm110)
REVERT: B  294 ASP cc_start: 0.7772 (t0) cc_final: 0.7273 (t0)
REVERT: B  300 GLU cc_start: 0.7413 (mp0) cc_final: 0.7201 (mp0)
REVERT: B  312 TRP cc_start: 0.7370 (p-90) cc_final: 0.7037 (p-90)
REVERT: B  376 PHE cc_start: 0.8695 (p90) cc_final: 0.7992 (p90)
REVERT: B  493 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8155 (mm-40)
REVERT: B  499 PHE cc_start: 0.7947 (m-80) cc_final: 0.7647 (m-80)
REVERT: B  513 MET cc_start: 0.6632 (mmt) cc_final: 0.6279 (mmt)
REVERT: B  559 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7287 (ttpp)
REVERT: B  569 GLU cc_start: 0.7450 (pm20) cc_final: 0.7226 (pm20)
REVERT: B  572 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6513 (p0)
REVERT: B  602 MET cc_start: 0.7245 (tpt) cc_final: 0.6646 (tpt)
REVERT: B  683 MET cc_start: 0.7861 (mmm) cc_final: 0.7619 (mmm)
REVERT: C    8 ASP cc_start: 0.6808 (m-30) cc_final: 0.6391 (m-30)
REVERT: C   31 TRP cc_start: 0.8526 (OUTLIER) cc_final: 0.7529 (m-10)
REVERT: C   36 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7425 (ttp-170)
REVERT: C   40 MET cc_start: 0.8058 (tpt) cc_final: 0.7782 (tpt)
REVERT: C   46 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6997 (mm-30)
REVERT: C  107 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7804 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5560 (ptmm)
REVERT: D  578 MET cc_start: 0.7746 (mmm) cc_final: 0.7443 (mmm)
REVERT: D  585 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7610 (mmmm)
REVERT: D  724 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7906 (tmmt)
  outliers start: 75
  outliers final: 49
  residues processed: 457
  average time/residue: 0.1239
  time to fit residues: 78.0277
Evaluate side-chains
  460 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 402
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  632 HIS
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   99 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  189 GLN
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  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  543 LEU
Chi-restraints excluded: chain B residue  572 ASP
Chi-restraints excluded: chain B residue  574 LYS
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  619 TYR
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  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
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 121 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   chunk 160 optimal weight:    8.9990
   chunk 157 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 155 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0170
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
B 150 ASN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.143801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115755 restraints weight = 25141.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.119621 restraints weight = 13589.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122219 restraints weight = 8589.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.124027 restraints weight = 6074.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125175 restraints weight = 4705.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13708  Z= 0.151
  Angle     :  0.698  11.205  18433  Z= 0.365
  Chirality :  0.045   0.174   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.490  84.320   1852
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.97 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 29.12 %
    Favored  : 65.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.21), residues: 1619
  helix:  0.80 (0.20), residues: 691
  sheet:  0.59 (0.41), residues: 181
  loop : -2.55 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 506 
 TYR   0.022   0.001   TYR A 305 
 PHE   0.021   0.001   PHE B 304 
 TRP   0.016   0.001   TRP A 289 
 HIS   0.006   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13708)
  covalent geometry    : angle       0.69793 (18433)
  hydrogen bonds       : bond        0.04445 (  574)
  hydrogen bonds       : angle       4.47324 ( 1617)

*********************** 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
  489 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 411
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7894 (t0)
REVERT: A   53 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8149 (mtpp)
REVERT: A  108 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7621 (p)
REVERT: A  301 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: A  303 GLU cc_start: 0.7325 (pp20) cc_final: 0.7007 (pp20)
REVERT: A  330 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6722 (mtm-85)
REVERT: A  363 MET cc_start: 0.6645 (ptt) cc_final: 0.6444 (ppp)
REVERT: A  397 GLN cc_start: 0.7193 (tt0) cc_final: 0.6534 (tm-30)
REVERT: A  400 ILE cc_start: 0.8745 (mm) cc_final: 0.8470 (mm)
REVERT: A  427 LYS cc_start: 0.7102 (mttt) cc_final: 0.6661 (mtmm)
REVERT: A  443 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7242 (tp30)
REVERT: A  450 ARG cc_start: 0.8218 (tpp80) cc_final: 0.7932 (mmp80)
REVERT: A  567 MET cc_start: 0.5892 (mmt) cc_final: 0.5603 (tpp)
REVERT: A  607 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8144 (mtpt)
REVERT: A  623 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7858 (mtmm)
REVERT: B   55 ARG cc_start: 0.8245 (ttt180) cc_final: 0.7505 (ttp-170)
REVERT: B   70 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7160 (mp0)
REVERT: B   95 LYS cc_start: 0.8536 (tttt) cc_final: 0.8268 (ttmm)
REVERT: B  101 ASN cc_start: 0.8059 (t0) cc_final: 0.7615 (t0)
REVERT: B  128 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7051 (mp-120)
REVERT: B  154 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7102 (mm-40)
REVERT: B  186 LYS cc_start: 0.7387 (mmtt) cc_final: 0.7169 (mmtp)
REVERT: B  294 ASP cc_start: 0.7833 (t0) cc_final: 0.7364 (t0)
REVERT: B  300 GLU cc_start: 0.7415 (mp0) cc_final: 0.7169 (mp0)
REVERT: B  312 TRP cc_start: 0.7463 (p-90) cc_final: 0.7097 (p-90)
REVERT: B  352 ASN cc_start: 0.8317 (m-40) cc_final: 0.8027 (m-40)
REVERT: B  363 MET cc_start: 0.7228 (mmm) cc_final: 0.6832 (tpt)
REVERT: B  376 PHE cc_start: 0.8644 (p90) cc_final: 0.8130 (p90)
REVERT: B  395 LEU cc_start: 0.8079 (tp) cc_final: 0.7764 (tt)
REVERT: B  410 LYS cc_start: 0.8136 (tttt) cc_final: 0.7902 (ttmt)
REVERT: B  492 GLU cc_start: 0.7726 (pm20) cc_final: 0.7333 (pm20)
REVERT: B  493 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8083 (mm-40)
REVERT: B  513 MET cc_start: 0.6691 (mmt) cc_final: 0.6167 (mmt)
REVERT: B  548 GLU cc_start: 0.7992 (pm20) cc_final: 0.7481 (pm20)
REVERT: B  559 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7348 (ttpp)
REVERT: B  569 GLU cc_start: 0.7536 (pm20) cc_final: 0.7331 (pm20)
REVERT: B  660 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7849 (tp30)
REVERT: B  683 MET cc_start: 0.7960 (mmm) cc_final: 0.7706 (mmm)
REVERT: C    8 ASP cc_start: 0.6941 (m-30) cc_final: 0.6496 (m-30)
REVERT: C   30 ARG cc_start: 0.7501 (mtm180) cc_final: 0.7204 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.7389 (m-90)
REVERT: C   40 MET cc_start: 0.8102 (tpt) cc_final: 0.7782 (tpt)
REVERT: C   46 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6694 (mt-10)
REVERT: C  107 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7672 (mtt-85)
REVERT: D  529 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5700 (ptmm)
REVERT: D  578 MET cc_start: 0.7858 (mmm) cc_final: 0.7624 (mmm)
REVERT: D  585 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7588 (mmmm)
REVERT: D  724 LYS cc_start: 0.8323 (tmmt) cc_final: 0.7867 (tmmt)
  outliers start: 78
  outliers final: 52
  residues processed: 457
  average time/residue: 0.1314
  time to fit residues: 82.3437
Evaluate side-chains
  467 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 405
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   54 ILE
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  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  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  574 LYS
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  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   90 GLN
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  659 THR
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 161 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 676 HIS
** C  90 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.144046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115342 restraints weight = 25006.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119220 restraints weight = 13523.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121779 restraints weight = 8557.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.123540 restraints weight = 6094.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.124726 restraints weight = 4778.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13708  Z= 0.163
  Angle     :  0.740  13.057  18433  Z= 0.384
  Chirality :  0.045   0.181   2030
  Planarity :  0.004   0.051   2345
  Dihedral  :  6.578  86.074   1849
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.46 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 28.92 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.21), residues: 1619
  helix:  0.69 (0.20), residues: 698
  sheet:  0.69 (0.43), residues: 167
  loop : -2.57 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 338 
 TYR   0.027   0.002   TYR B 305 
 PHE   0.030   0.001   PHE C  29 
 TRP   0.016   0.001   TRP A 289 
 HIS   0.007   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13708)
  covalent geometry    : angle       0.73990 (18433)
  hydrogen bonds       : bond        0.04722 (  574)
  hydrogen bonds       : angle       4.57039 ( 1617)

*********************** 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: 83
    poor density    : 431
  time to evaluate  : 0.543 
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: 0.8584 (OUTLIER) cc_final: 0.8257 (tmm-80)
REVERT: A  195 GLU cc_start: 0.7353 (tp30) cc_final: 0.7075 (tp30)
REVERT: A  199 LYS cc_start: 0.8510 (pttm) cc_final: 0.8216 (pttm)
REVERT: A  280 GLU cc_start: 0.6937 (tp30) cc_final: 0.6323 (tp30)
REVERT: A  300 GLU cc_start: 0.6861 (pp20) cc_final: 0.6219 (pp20)
REVERT: A  301 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7709 (t80)
REVERT: A  303 GLU cc_start: 0.7367 (pp20) cc_final: 0.7017 (pp20)
REVERT: A  330 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6866 (mtm-85)
REVERT: A  386 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: A  397 GLN cc_start: 0.7240 (tt0) cc_final: 0.6562 (tm-30)
REVERT: A  400 ILE cc_start: 0.8734 (mm) cc_final: 0.8472 (mm)
REVERT: A  443 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7532 (tp30)
REVERT: A  450 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7941 (mmp80)
REVERT: A  553 MET cc_start: 0.7203 (mmp) cc_final: 0.6989 (mmm)
REVERT: A  567 MET cc_start: 0.5920 (mmt) cc_final: 0.5637 (tpp)
REVERT: A  582 ASN cc_start: 0.8126 (p0) cc_final: 0.7853 (p0)
REVERT: A  607 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8150 (mtpt)
REVERT: A  623 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7898 (mtmm)
REVERT: B   55 ARG cc_start: 0.8271 (ttt180) cc_final: 0.7524 (ttp-170)
REVERT: B   95 LYS cc_start: 0.8541 (tttt) cc_final: 0.8293 (ttmm)
REVERT: B  101 ASN cc_start: 0.8066 (t0) cc_final: 0.7621 (t0)
REVERT: B  154 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7076 (mm-40)
REVERT: B  294 ASP cc_start: 0.7825 (t0) cc_final: 0.7351 (t0)
REVERT: B  300 GLU cc_start: 0.7411 (mp0) cc_final: 0.7181 (mp0)
REVERT: B  312 TRP cc_start: 0.7518 (p-90) cc_final: 0.7177 (p-90)
REVERT: B  352 ASN cc_start: 0.8218 (m-40) cc_final: 0.7967 (m-40)
REVERT: B  363 MET cc_start: 0.7226 (mmm) cc_final: 0.6890 (tpt)
REVERT: B  376 PHE cc_start: 0.8635 (p90) cc_final: 0.8140 (p90)
REVERT: B  395 LEU cc_start: 0.8139 (tp) cc_final: 0.7905 (tt)
REVERT: B  410 LYS cc_start: 0.8170 (tttt) cc_final: 0.7929 (ttmt)
REVERT: B  492 GLU cc_start: 0.7698 (pm20) cc_final: 0.7328 (pm20)
REVERT: B  493 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7911 (tp40)
REVERT: B  513 MET cc_start: 0.6687 (mmt) cc_final: 0.6173 (mmt)
REVERT: B  519 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6197 (tm-30)
REVERT: B  559 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7452 (ttpp)
REVERT: B  569 GLU cc_start: 0.7590 (pm20) cc_final: 0.7377 (pm20)
REVERT: B  572 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6695 (p0)
REVERT: B  602 MET cc_start: 0.7224 (tpt) cc_final: 0.6977 (tpt)
REVERT: B  660 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7888 (tp30)
REVERT: B  683 MET cc_start: 0.8012 (mmm) cc_final: 0.7753 (mmm)
REVERT: C    8 ASP cc_start: 0.7034 (m-30) cc_final: 0.6536 (m-30)
REVERT: C   14 ASP cc_start: 0.7427 (p0) cc_final: 0.6910 (p0)
REVERT: C   22 ASN cc_start: 0.7938 (m-40) cc_final: 0.7345 (m-40)
REVERT: C   30 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7277 (mtm-85)
REVERT: C   31 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7463 (m-10)
REVERT: C   38 GLU cc_start: 0.7638 (pt0) cc_final: 0.7321 (pt0)
REVERT: C   40 MET cc_start: 0.8109 (tpt) cc_final: 0.7790 (tpt)
REVERT: C   46 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7024 (mm-30)
REVERT: C  107 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7563 (mtt-85)
REVERT: C  110 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7556 (tm-30)
REVERT: D  578 MET cc_start: 0.7780 (mmm) cc_final: 0.7461 (mmm)
REVERT: D  585 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7576 (mmmm)
REVERT: D  606 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6511 (mmmt)
REVERT: D  724 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7976 (tmmt)
  outliers start: 83
  outliers final: 63
  residues processed: 478
  average time/residue: 0.1317
  time to fit residues: 86.3624
Evaluate side-chains
  495 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 423
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  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  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  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   99 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  280 GLU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  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  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  594 SER
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   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   90 GLN
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  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  659 THR
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 118 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 151 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0040
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0040
   overall best weight:    0.4204

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
B 189 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** 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 = 0.3880 r_free = 0.3880 target = 0.146571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.117989 restraints weight = 24781.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121916 restraints weight = 13323.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.124402 restraints weight = 8415.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126307 restraints weight = 6061.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127326 restraints weight = 4673.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13708  Z= 0.131
  Angle     :  0.730  12.349  18433  Z= 0.374
  Chirality :  0.044   0.207   2030
  Planarity :  0.004   0.049   2345
  Dihedral  :  6.435  85.806   1849
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.54 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 29.85 %
    Favored  : 65.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.21), residues: 1619
  helix:  0.77 (0.20), residues: 694
  sheet:  0.63 (0.40), residues: 192
  loop : -2.52 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 338 
 TYR   0.023   0.001   TYR B 305 
 PHE   0.020   0.001   PHE B 329 
 TRP   0.012   0.001   TRP B 598 
 HIS   0.007   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (13708)
  covalent geometry    : angle       0.72999 (18433)
  hydrogen bonds       : bond        0.03826 (  574)
  hydrogen bonds       : angle       4.43163 ( 1617)

*********************** 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
  501 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 425
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8162 (tmm-80)
REVERT: A  199 LYS cc_start: 0.8510 (pttm) cc_final: 0.8064 (mtmm)
REVERT: A  280 GLU cc_start: 0.7012 (tp30) cc_final: 0.6433 (tp30)
REVERT: A  301 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7607 (t80)
REVERT: A  303 GLU cc_start: 0.7383 (pp20) cc_final: 0.6998 (pp20)
REVERT: A  330 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6633 (mtm-85)
REVERT: A  386 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: A  397 GLN cc_start: 0.7165 (tt0) cc_final: 0.6508 (tm-30)
REVERT: A  400 ILE cc_start: 0.8729 (mm) cc_final: 0.8445 (mm)
REVERT: A  443 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7399 (tp30)
REVERT: A  450 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7810 (mmp80)
REVERT: A  481 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8393 (mmtt)
REVERT: A  509 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7037 (tm-30)
REVERT: A  553 MET cc_start: 0.7202 (mmp) cc_final: 0.6993 (mmm)
REVERT: A  623 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7744 (mtmm)
REVERT: B   55 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7447 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7700 (tp30) cc_final: 0.7306 (tp30)
REVERT: B   95 LYS cc_start: 0.8514 (tttt) cc_final: 0.8254 (ttmm)
REVERT: B  101 ASN cc_start: 0.8042 (t0) cc_final: 0.7605 (t0)
REVERT: B  128 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7059 (mp-120)
REVERT: B  142 LYS cc_start: 0.8260 (mttt) cc_final: 0.7658 (mtmm)
REVERT: B  154 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7015 (mm-40)
REVERT: B  294 ASP cc_start: 0.7785 (t0) cc_final: 0.7303 (t0)
REVERT: B  312 TRP cc_start: 0.7448 (p-90) cc_final: 0.7118 (p-90)
REVERT: B  352 ASN cc_start: 0.8270 (m-40) cc_final: 0.7974 (m-40)
REVERT: B  363 MET cc_start: 0.7133 (mmm) cc_final: 0.6904 (tpt)
REVERT: B  376 PHE cc_start: 0.8666 (p90) cc_final: 0.8192 (p90)
REVERT: B  410 LYS cc_start: 0.8105 (tttt) cc_final: 0.7879 (ttmt)
REVERT: B  427 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8432 (mtmm)
REVERT: B  492 GLU cc_start: 0.7698 (pm20) cc_final: 0.7335 (pm20)
REVERT: B  493 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7930 (mm-40)
REVERT: B  513 MET cc_start: 0.6591 (mmt) cc_final: 0.6041 (mmt)
REVERT: B  519 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6278 (tm-30)
REVERT: B  559 LYS cc_start: 0.7658 (ttpp) cc_final: 0.7384 (ttpp)
REVERT: B  569 GLU cc_start: 0.7505 (pm20) cc_final: 0.7273 (pm20)
REVERT: B  572 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6687 (p0)
REVERT: B  602 MET cc_start: 0.6978 (tpt) cc_final: 0.6750 (tpt)
REVERT: B  660 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7879 (tp30)
REVERT: C    8 ASP cc_start: 0.6900 (m-30) cc_final: 0.6404 (m-30)
REVERT: C   14 ASP cc_start: 0.7499 (p0) cc_final: 0.7029 (p0)
REVERT: C   22 ASN cc_start: 0.7916 (m-40) cc_final: 0.7336 (m-40)
REVERT: C   31 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.7521 (m-10)
REVERT: C   38 GLU cc_start: 0.7521 (pt0) cc_final: 0.7174 (pt0)
REVERT: C   40 MET cc_start: 0.8068 (tpt) cc_final: 0.7728 (tpt)
REVERT: C   46 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6706 (mt-10)
REVERT: C  107 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7693 (mtt-85)
REVERT: C  118 ASP cc_start: 0.6956 (t0) cc_final: 0.6688 (t0)
REVERT: D  578 MET cc_start: 0.7699 (mmm) cc_final: 0.7393 (mmm)
REVERT: D  585 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7563 (mmmm)
REVERT: D  606 LYS cc_start: 0.6904 (mmmt) cc_final: 0.6575 (mmmt)
REVERT: D  699 LEU cc_start: 0.7226 (mm) cc_final: 0.6949 (mm)
REVERT: D  724 LYS cc_start: 0.8382 (tmmt) cc_final: 0.7991 (tmmt)
  outliers start: 76
  outliers final: 53
  residues processed: 468
  average time/residue: 0.1285
  time to fit residues: 82.9204
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  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  301 TYR
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  330 ARG
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  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  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
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   99 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  189 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  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  459 THR
Chi-restraints excluded: chain B residue  466 MET
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  536 VAL
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  632 HIS
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   18 GLU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   90 GLN
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  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 157 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0570
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** 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 = 0.3880 r_free = 0.3880 target = 0.146690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117928 restraints weight = 25091.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121860 restraints weight = 13526.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.124540 restraints weight = 8563.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126419 restraints weight = 6058.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127434 restraints weight = 4677.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13708  Z= 0.137
  Angle     :  0.765  13.716  18433  Z= 0.390
  Chirality :  0.045   0.230   2030
  Planarity :  0.004   0.054   2345
  Dihedral  :  6.442  85.684   1849
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.78 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 30.92 %
    Favored  : 64.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.21), residues: 1619
  helix:  0.70 (0.20), residues: 701
  sheet:  0.60 (0.40), residues: 194
  loop : -2.54 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 338 
 TYR   0.022   0.001   TYR D 658 
 PHE   0.020   0.001   PHE B 329 
 TRP   0.011   0.001   TRP A 289 
 HIS   0.008   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13708)
  covalent geometry    : angle       0.76468 (18433)
  hydrogen bonds       : bond        0.03941 (  574)
  hydrogen bonds       : angle       4.38185 ( 1617)

*********************** 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
  486 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 416
  time to evaluate  : 0.374 
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   39 PHE cc_start: 0.7983 (p90) cc_final: 0.7762 (p90)
REVERT: A   41 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8167 (tmm-80)
REVERT: A  195 GLU cc_start: 0.7585 (tp30) cc_final: 0.7182 (tp30)
REVERT: A  280 GLU cc_start: 0.7018 (tp30) cc_final: 0.6410 (tp30)
REVERT: A  301 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7640 (t80)
REVERT: A  303 GLU cc_start: 0.7395 (pp20) cc_final: 0.7004 (pp20)
REVERT: A  330 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6602 (mtm-85)
REVERT: A  386 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7828 (mp)
REVERT: A  397 GLN cc_start: 0.7164 (tt0) cc_final: 0.6503 (tm-30)
REVERT: A  400 ILE cc_start: 0.8750 (mm) cc_final: 0.8494 (mm)
REVERT: A  443 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7374 (tp30)
REVERT: A  450 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7828 (mmp80)
REVERT: A  509 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7023 (tm-30)
REVERT: A  528 PHE cc_start: 0.8376 (t80) cc_final: 0.8052 (t80)
REVERT: A  553 MET cc_start: 0.7189 (mmp) cc_final: 0.6979 (mmm)
REVERT: A  567 MET cc_start: 0.5713 (mmt) cc_final: 0.5408 (tpp)
REVERT: A  623 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7754 (mtmm)
REVERT: B   55 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7461 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7691 (tp30) cc_final: 0.7297 (tp30)
REVERT: B   95 LYS cc_start: 0.8510 (tttt) cc_final: 0.8272 (ttmm)
REVERT: B  101 ASN cc_start: 0.8060 (t0) cc_final: 0.7582 (t0)
REVERT: B  114 MET cc_start: 0.8281 (tpp) cc_final: 0.7424 (tmm)
REVERT: B  128 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7075 (mp-120)
REVERT: B  142 LYS cc_start: 0.8258 (mttt) cc_final: 0.7656 (mtmm)
REVERT: B  154 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6975 (mm-40)
REVERT: B  294 ASP cc_start: 0.7676 (t0) cc_final: 0.7213 (t0)
REVERT: B  300 GLU cc_start: 0.7292 (mp0) cc_final: 0.6881 (pm20)
REVERT: B  312 TRP cc_start: 0.7475 (p-90) cc_final: 0.7134 (p-90)
REVERT: B  352 ASN cc_start: 0.8246 (m-40) cc_final: 0.7971 (m-40)
REVERT: B  363 MET cc_start: 0.7090 (mmm) cc_final: 0.6815 (tpt)
REVERT: B  376 PHE cc_start: 0.8624 (p90) cc_final: 0.8236 (p90)
REVERT: B  393 GLU cc_start: 0.7441 (mp0) cc_final: 0.7148 (mp0)
REVERT: B  410 LYS cc_start: 0.8114 (tttt) cc_final: 0.7900 (ttmt)
REVERT: B  427 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8410 (mtmm)
REVERT: B  492 GLU cc_start: 0.7685 (pm20) cc_final: 0.7292 (pm20)
REVERT: B  493 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7872 (mm-40)
REVERT: B  513 MET cc_start: 0.6666 (mmt) cc_final: 0.6269 (mmp)
REVERT: B  519 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6788 (tm-30)
REVERT: B  559 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7421 (ttpp)
REVERT: B  569 GLU cc_start: 0.7475 (pm20) cc_final: 0.7238 (pm20)
REVERT: B  572 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6656 (p0)
REVERT: B  612 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7152 (mmm-85)
REVERT: C    8 ASP cc_start: 0.6868 (m-30) cc_final: 0.6360 (m-30)
REVERT: C   14 ASP cc_start: 0.7537 (p0) cc_final: 0.7179 (p0)
REVERT: C   22 ASN cc_start: 0.7939 (m-40) cc_final: 0.7722 (m-40)
REVERT: C   31 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.7496 (m-10)
REVERT: C   38 GLU cc_start: 0.7509 (pt0) cc_final: 0.7182 (pt0)
REVERT: C   40 MET cc_start: 0.8072 (tpt) cc_final: 0.7741 (tpt)
REVERT: C   46 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7052 (mm-30)
REVERT: C  107 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7639 (mtt-85)
REVERT: C  111 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8043 (mttt)
REVERT: C  118 ASP cc_start: 0.6952 (t0) cc_final: 0.6680 (t0)
REVERT: D  529 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5695 (ptmm)
REVERT: D  578 MET cc_start: 0.7746 (mmm) cc_final: 0.7419 (mmm)
REVERT: D  585 LYS cc_start: 0.7868 (mmmm) cc_final: 0.7536 (mmmm)
REVERT: D  724 LYS cc_start: 0.8336 (tmmt) cc_final: 0.7972 (tmmt)
  outliers start: 70
  outliers final: 54
  residues processed: 454
  average time/residue: 0.1263
  time to fit residues: 78.7325
Evaluate side-chains
  478 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 413
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  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  511 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  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  536 VAL
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  594 SER
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   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   90 GLN
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 84 optimal weight:    0.4980
   chunk 124 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 136 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9980
   chunk 114 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 71 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.146090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.117396 restraints weight = 24858.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121244 restraints weight = 13460.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.123916 restraints weight = 8568.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125704 restraints weight = 6082.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.126828 restraints weight = 4722.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13708  Z= 0.144
  Angle     :  0.773  13.825  18433  Z= 0.395
  Chirality :  0.045   0.228   2030
  Planarity :  0.004   0.057   2345
  Dihedral  :  6.479  85.540   1849
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.28 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 31.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.21), residues: 1619
  helix:  0.70 (0.20), residues: 698
  sheet:  0.50 (0.40), residues: 192
  loop : -2.56 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG A 338 
 TYR   0.035   0.002   TYR D 658 
 PHE   0.021   0.001   PHE B 329 
 TRP   0.013   0.001   TRP A 289 
 HIS   0.008   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13708)
  covalent geometry    : angle       0.77293 (18433)
  hydrogen bonds       : bond        0.04129 (  574)
  hydrogen bonds       : angle       4.42762 ( 1617)

********************** 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
  476 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 409
  time to evaluate  : 0.379 
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   39 PHE cc_start: 0.8061 (p90) cc_final: 0.7849 (p90)
REVERT: A   41 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8185 (tmm-80)
REVERT: A  280 GLU cc_start: 0.6997 (tp30) cc_final: 0.6397 (tp30)
REVERT: A  301 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7659 (t80)
REVERT: A  303 GLU cc_start: 0.7406 (pp20) cc_final: 0.7005 (pp20)
REVERT: A  328 GLU cc_start: 0.7476 (mp0) cc_final: 0.7104 (mm-30)
REVERT: A  330 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6574 (mtm-85)
REVERT: A  338 ARG cc_start: 0.7917 (mmp80) cc_final: 0.7586 (mmp80)
REVERT: A  386 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: A  397 GLN cc_start: 0.7179 (tt0) cc_final: 0.6528 (tm-30)
REVERT: A  400 ILE cc_start: 0.8750 (mm) cc_final: 0.8494 (mm)
REVERT: A  443 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7399 (tp30)
REVERT: A  450 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7943 (mmp80)
REVERT: A  526 LYS cc_start: 0.7868 (tptt) cc_final: 0.7406 (tppt)
REVERT: A  528 PHE cc_start: 0.8464 (t80) cc_final: 0.8047 (t80)
REVERT: A  551 LYS cc_start: 0.7462 (pttm) cc_final: 0.7190 (pttm)
REVERT: A  553 MET cc_start: 0.7249 (mmp) cc_final: 0.7032 (mmm)
REVERT: A  567 MET cc_start: 0.5758 (mmt) cc_final: 0.5448 (tpp)
REVERT: A  607 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8155 (mtpt)
REVERT: A  640 GLN cc_start: 0.7811 (pp30) cc_final: 0.7476 (pp30)
REVERT: B   55 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7464 (ttp-170)
REVERT: B   57 GLU cc_start: 0.7704 (tp30) cc_final: 0.7310 (tp30)
REVERT: B   95 LYS cc_start: 0.8549 (tttt) cc_final: 0.8300 (ttmm)
REVERT: B  101 ASN cc_start: 0.8067 (t0) cc_final: 0.7598 (t0)
REVERT: B  114 MET cc_start: 0.8288 (tpp) cc_final: 0.7437 (tmm)
REVERT: B  128 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7078 (mp-120)
REVERT: B  142 LYS cc_start: 0.8245 (mttt) cc_final: 0.7690 (mtmm)
REVERT: B  154 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6933 (mm-40)
REVERT: B  294 ASP cc_start: 0.7651 (t0) cc_final: 0.7093 (t0)
REVERT: B  300 GLU cc_start: 0.7289 (mp0) cc_final: 0.6887 (pm20)
REVERT: B  312 TRP cc_start: 0.7502 (p-90) cc_final: 0.7134 (p-90)
REVERT: B  352 ASN cc_start: 0.8299 (m-40) cc_final: 0.7996 (m-40)
REVERT: B  363 MET cc_start: 0.7192 (mmm) cc_final: 0.6848 (tpt)
REVERT: B  376 PHE cc_start: 0.8638 (p90) cc_final: 0.8244 (p90)
REVERT: B  393 GLU cc_start: 0.7409 (mp0) cc_final: 0.7097 (mp0)
REVERT: B  410 LYS cc_start: 0.8149 (tttt) cc_final: 0.7946 (ttmt)
REVERT: B  427 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8456 (mtmm)
REVERT: B  492 GLU cc_start: 0.7692 (pm20) cc_final: 0.7293 (pm20)
REVERT: B  493 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7878 (mm-40)
REVERT: B  513 MET cc_start: 0.6733 (mmt) cc_final: 0.6334 (mmp)
REVERT: B  559 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7471 (ttpp)
REVERT: B  569 GLU cc_start: 0.7492 (pm20) cc_final: 0.7239 (pm20)
REVERT: B  572 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6669 (p0)
REVERT: B  612 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7313 (mmm-85)
REVERT: C    8 ASP cc_start: 0.6904 (m-30) cc_final: 0.6412 (m-30)
REVERT: C   14 ASP cc_start: 0.7467 (p0) cc_final: 0.7238 (p0)
REVERT: C   22 ASN cc_start: 0.7958 (m-40) cc_final: 0.7694 (m-40)
REVERT: C   31 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7509 (m-10)
REVERT: C   40 MET cc_start: 0.8059 (tpt) cc_final: 0.7730 (tpt)
REVERT: C  107 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7764 (mtt-85)
REVERT: C  111 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8040 (mttt)
REVERT: C  118 ASP cc_start: 0.6975 (t0) cc_final: 0.6738 (t0)
REVERT: D  529 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5608 (ptmm)
REVERT: D  533 MET cc_start: 0.7880 (ptp) cc_final: 0.7454 (ptp)
REVERT: D  578 MET cc_start: 0.7744 (mmm) cc_final: 0.7419 (mmm)
REVERT: D  724 LYS cc_start: 0.8331 (tmmt) cc_final: 0.7969 (tmmt)
  outliers start: 67
  outliers final: 53
  residues processed: 448
  average time/residue: 0.1264
  time to fit residues: 77.6447
Evaluate side-chains
  471 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 409
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  301 TYR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  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  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  611 LEU
Chi-restraints excluded: chain A residue  676 HIS
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   99 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  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  536 VAL
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  632 HIS
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain C residue   18 GLU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   31 TRP
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain D residue  529 LYS
Chi-restraints excluded: chain D residue  534 ILE
Chi-restraints excluded: chain D residue  586 THR
Chi-restraints excluded: chain D residue  588 VAL
Chi-restraints excluded: chain D residue  605 VAL
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  634 ILE
Chi-restraints excluded: chain D residue  652 LEU
Chi-restraints excluded: chain D residue  708 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 107 optimal weight:    0.0570
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0970
   chunk 95 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 52 optimal weight:    0.3980
   chunk 151 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** 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 = 0.3880 r_free = 0.3880 target = 0.145947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117557 restraints weight = 25007.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121408 restraints weight = 13561.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124052 restraints weight = 8618.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125802 restraints weight = 6140.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.127065 restraints weight = 4773.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.122  13708  Z= 0.142
  Angle     :  0.786  14.187  18433  Z= 0.400
  Chirality :  0.045   0.224   2030
  Planarity :  0.004   0.061   2345
  Dihedral  :  6.426  86.091   1849
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.84 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 31.73 %
    Favored  : 63.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.21), residues: 1619
  helix:  0.66 (0.20), residues: 704
  sheet:  0.49 (0.40), residues: 192
  loop : -2.52 (0.22), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 338 
 TYR   0.044   0.001   TYR D 658 
 PHE   0.037   0.001   PHE A 361 
 TRP   0.013   0.001   TRP D 623 
 HIS   0.004   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (13708)
  covalent geometry    : angle       0.78555 (18433)
  hydrogen bonds       : bond        0.03843 (  574)
  hydrogen bonds       : angle       4.39178 ( 1617)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2446.91 seconds
wall clock time: 42 minutes 55.77 seconds (2575.77 seconds total)