Starting phenix.real_space_refine
on Wed Feb  4 10:45:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jxh_61863/02_2026/9jxh_61863.map"
  }
  resolution = 3.15
  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=   0.005 sd=   0.107
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      32      5.49       5
     S      40      5.16       5
     C    6498      2.51       5
     N    1614      2.21       5
     O    1802      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9986
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4903
          Classifications: {'peptide': 590}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 571}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4903
          Classifications: {'peptide': 590}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 571}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 88
          Unusual residues: {'I8P': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 88
          Unusual residues: {'I8P': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.22
  Number of scatterers: 9986
  At special positions: 0
  Unit cell: (110.775, 110.775, 102.335, 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      40     16.00
     P      32     15.00
     O    1802      8.00
     N    1614      7.00
     C    6498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  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: 0.85
  Conformation dependent library (CDL) restraints added in 321.2 milliseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      75.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 5.400A  pdb=" N   LYS A  17 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR A  19 " --> pdb=" O   ARG A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 35
    Processing helix  chain 'A' and resid 43 through 98
      removed outlier: 4.395A  pdb=" N   GLU A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP A  96 " --> pdb=" O   GLN A  92 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 3.652A  pdb=" N   LEU A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.784A  pdb=" N   ILE A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASN A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 3.750A  pdb=" N   LEU A 160 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 179
    Processing helix  chain 'A' and resid 180 through 183
    Processing helix  chain 'A' and resid 190 through 206
      removed outlier: 3.677A  pdb=" N   THR A 203 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.521A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN A 227 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 223 through 227'
    Processing helix  chain 'A' and resid 230 through 241
      removed outlier: 3.578A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.785A  pdb=" N   ILE A 245 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 273
    Processing helix  chain 'A' and resid 273 through 296
      removed outlier: 3.656A  pdb=" N   LEU A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 295 " --> pdb=" O   GLY A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.800A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 358
      removed outlier: 3.804A  pdb=" N   VAL A 356 " --> pdb=" O   TYR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 380
    Processing helix  chain 'A' and resid 391 through 396
    Processing helix  chain 'A' and resid 404 through 420
      removed outlier: 3.879A  pdb=" N   MET A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR A 417 " --> pdb=" O   MET A 413 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 453
      removed outlier: 3.589A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   CYS A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 3.761A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 4.061A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 502
      removed outlier: 3.846A  pdb=" N   VAL A 490 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   PHE A 492 " --> pdb=" O   PHE A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 527
      removed outlier: 3.721A  pdb=" N   ILE A 519 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A 520 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   THR A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 532
      removed outlier: 3.848A  pdb=" N   MET A 532 " --> pdb=" O   TRP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 4.347A  pdb=" N   GLY A 542 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 569
      removed outlier: 3.930A  pdb=" N   VAL A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 580
      removed outlier: 3.640A  pdb=" N   THR A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 617
      removed outlier: 3.932A  pdb=" N   VAL A 595 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 3.556A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU A 615 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 10
    Processing helix  chain 'B' and resid 12 through 19
      removed outlier: 5.402A  pdb=" N   LYS B  17 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR B  19 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 35
    Processing helix  chain 'B' and resid 43 through 98
      removed outlier: 4.396A  pdb=" N   GLU B  55 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR B  86 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN B  88 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   LEU B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASP B  96 " --> pdb=" O   GLN B  92 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLN B  98 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 136
      removed outlier: 3.652A  pdb=" N   LEU B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 154
      removed outlier: 3.785A  pdb=" N   ILE B 143 " --> pdb=" O   TYR B 139 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASN B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN B 152 " --> pdb=" O   TYR B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 3.750A  pdb=" N   LEU B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 179
    Processing helix  chain 'B' and resid 180 through 183
    Processing helix  chain 'B' and resid 190 through 206
      removed outlier: 3.679A  pdb=" N   THR B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 215
    Processing helix  chain 'B' and resid 223 through 227
      removed outlier: 3.522A  pdb=" N   ALA B 226 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN B 227 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 227'
    Processing helix  chain 'B' and resid 230 through 241
      removed outlier: 3.579A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.786A  pdb=" N   ILE B 245 " --> pdb=" O   CYS B 241 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 273
    Processing helix  chain 'B' and resid 273 through 296
      removed outlier: 3.655A  pdb=" N   LEU B 282 " --> pdb=" O   LEU B 278 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU B 284 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B 295 " --> pdb=" O   GLY B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.801A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 358
      removed outlier: 3.803A  pdb=" N   VAL B 356 " --> pdb=" O   TYR B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 380
    Processing helix  chain 'B' and resid 391 through 396
    Processing helix  chain 'B' and resid 404 through 420
      removed outlier: 3.878A  pdb=" N   MET B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ILE B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR B 417 " --> pdb=" O   MET B 413 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 453
      removed outlier: 3.589A  pdb=" N   ILE B 450 " --> pdb=" O   GLY B 446 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   CYS B 453 " --> pdb=" O   ALA B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 471
    Processing helix  chain 'B' and resid 472 through 477
      removed outlier: 3.762A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 486
      removed outlier: 4.061A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 502
      removed outlier: 3.847A  pdb=" N   VAL B 490 " --> pdb=" O   THR B 486 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   PHE B 492 " --> pdb=" O   PHE B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 527
      removed outlier: 3.721A  pdb=" N   ILE B 519 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE B 520 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   THR B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 532
      removed outlier: 3.847A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
      removed outlier: 4.348A  pdb=" N   GLY B 542 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 569
      removed outlier: 3.931A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 3.640A  pdb=" N   THR B 580 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 617
      removed outlier: 3.932A  pdb=" N   VAL B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.555A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU B 615 " --> pdb=" O   ARG B 611 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1587 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: 1.44

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1500
        1.29 -     1.42: 2959
        1.42 -     1.55: 5699
        1.55 -     1.68: 42
        1.68 -     1.81: 56
  Bond restraints: 10256
  Sorted by residual:
  bond pdb=" C   PRO B 221 "
       pdb=" O   PRO B 221 "
    ideal  model  delta    sigma   weight residual
    1.240  1.165  0.076 1.12e-02 7.97e+03 4.56e+01
  bond pdb=" C   PRO A 221 "
       pdb=" O   PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.240  1.165  0.075 1.12e-02 7.97e+03 4.49e+01
  bond pdb=" O45 I8P A 702 "
       pdb=" PB5 I8P A 702 "
    ideal  model  delta    sigma   weight residual
    1.695  1.579  0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" CA  ALA A 337 "
       pdb=" CB  ALA A 337 "
    ideal  model  delta    sigma   weight residual
    1.522  1.486  0.036 7.00e-03 2.04e+04 2.71e+01
  bond pdb=" CA  ALA B 337 "
       pdb=" CB  ALA B 337 "
    ideal  model  delta    sigma   weight residual
    1.522  1.486  0.036 7.00e-03 2.04e+04 2.70e+01
  ... (remaining 10251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 13262
        2.80 -     5.60: 563
        5.60 -     8.40: 91
        8.40 -    11.20: 25
       11.20 -    14.00: 11
  Bond angle restraints: 13952
  Sorted by residual:
  angle pdb=" CA  PRO A 221 "
        pdb=" C   PRO A 221 "
        pdb=" N   PRO A 222 "
      ideal   model   delta    sigma   weight residual
     117.93  128.92  -10.99 1.20e+00 6.94e-01 8.38e+01
  angle pdb=" CA  PRO B 221 "
        pdb=" C   PRO B 221 "
        pdb=" N   PRO B 222 "
      ideal   model   delta    sigma   weight residual
     117.93  128.91  -10.98 1.20e+00 6.94e-01 8.38e+01
  angle pdb=" N   HIS A 476 "
        pdb=" CA  HIS A 476 "
        pdb=" C   HIS A 476 "
      ideal   model   delta    sigma   weight residual
     112.45  124.86  -12.41 1.39e+00 5.18e-01 7.97e+01
  angle pdb=" N   HIS B 476 "
        pdb=" CA  HIS B 476 "
        pdb=" C   HIS B 476 "
      ideal   model   delta    sigma   weight residual
     112.45  124.85  -12.40 1.39e+00 5.18e-01 7.96e+01
  angle pdb=" N   PRO A 221 "
        pdb=" CA  PRO A 221 "
        pdb=" CB  PRO A 221 "
      ideal   model   delta    sigma   weight residual
     103.08   94.55    8.53 9.70e-01 1.06e+00 7.73e+01
  ... (remaining 13947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 5858
       34.98 -    69.96: 214
       69.96 -   104.93: 47
      104.93 -   139.91: 10
      139.91 -   174.89: 3
  Dihedral angle restraints: 6132
    sinusoidal: 2638
      harmonic: 3494
  Sorted by residual:
  dihedral pdb=" CA  PHE B 474 "
           pdb=" C   PHE B 474 "
           pdb=" N   PRO B 475 "
           pdb=" CA  PRO B 475 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   38.97  -38.97     0      5.00e+00 4.00e-02 6.08e+01
  dihedral pdb=" CA  PHE A 474 "
           pdb=" C   PHE A 474 "
           pdb=" N   PRO A 475 "
           pdb=" CA  PRO A 475 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   38.96  -38.96     0      5.00e+00 4.00e-02 6.07e+01
  dihedral pdb=" CA  ALA A 384 "
           pdb=" C   ALA A 384 "
           pdb=" N   PRO A 385 "
           pdb=" CA  PRO A 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.40   31.60     0      5.00e+00 4.00e-02 3.99e+01
  ... (remaining 6129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.006: 1512
       1.006 -    2.012: 0
       2.012 -    3.019: 0
       3.019 -    4.025: 0
       4.025 -    5.031: 4
  Chirality restraints: 1516
  Sorted by residual:
  chirality pdb=" C6  I8P A 701 "
            pdb=" C1  I8P A 701 "
            pdb=" C5  I8P A 701 "
            pdb=" O16 I8P A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53    2.50   -5.03 2.00e-01 2.50e+01 6.33e+02
  chirality pdb=" C6  I8P B 702 "
            pdb=" C1  I8P B 702 "
            pdb=" C5  I8P B 702 "
            pdb=" O16 I8P B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53    2.48   -5.01 2.00e-01 2.50e+01 6.28e+02
  chirality pdb=" C3  I8P B 701 "
            pdb=" C2  I8P B 701 "
            pdb=" C4  I8P B 701 "
            pdb=" O13 I8P B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    2.29   -4.71 2.00e-01 2.50e+01 5.54e+02
  ... (remaining 1513 not shown)

  Planarity restraints: 1694
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 468 "   -0.029 2.00e-02 2.50e+03   5.85e-02 3.42e+01
        pdb=" C   ARG A 468 "    0.101 2.00e-02 2.50e+03
        pdb=" O   ARG A 468 "   -0.038 2.00e-02 2.50e+03
        pdb=" N   ASP A 469 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 468 "    0.029 2.00e-02 2.50e+03   5.83e-02 3.40e+01
        pdb=" C   ARG B 468 "   -0.101 2.00e-02 2.50e+03
        pdb=" O   ARG B 468 "    0.038 2.00e-02 2.50e+03
        pdb=" N   ASP B 469 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 254 "   -0.024 2.00e-02 2.50e+03   4.64e-02 2.15e+01
        pdb=" C   ALA A 254 "    0.080 2.00e-02 2.50e+03
        pdb=" O   ALA A 254 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ALA A 255 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1691 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 821
        2.71 -     3.25: 10918
        3.25 -     3.80: 16384
        3.80 -     4.35: 20481
        4.35 -     4.90: 32928
  Nonbonded interactions: 81532
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 559 "
            pdb=" OE1 GLU B 613 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OH  TYR A 272 "
            pdb=" OG  SER A 330 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OH  TYR A 559 "
            pdb=" OE1 GLU A 613 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OH  TYR B 272 "
            pdb=" OG  SER B 330 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" NH2 ARG A 548 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     2.171 3.120
  ... (remaining 81527 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.050
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
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      :  0.012   0.116  10258  Z= 0.625
  Angle     :  1.375  14.001  13956  Z= 0.841
  Chirality :  0.258   5.031   1516
  Planarity :  0.007   0.077   1694
  Dihedral  : 20.150 174.888   3858
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 21.02
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 10.59 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.03 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.35 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.14 (0.19), residues: 1162
  helix: -2.96 (0.13), residues: 840
  sheet:  None (None), residues: 0
  loop : -4.11 (0.29), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 604 
 TYR   0.016   0.002   TYR B 368 
 PHE   0.019   0.002   PHE A  84 
 TRP   0.022   0.002   TRP B 607 
 HIS   0.009   0.002   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.01224 (10256)
  covalent geometry    : angle       1.37512 (13952)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.71217 (    4)
  hydrogen bonds       : bond        0.19391 (  539)
  hydrogen bonds       : angle       8.45341 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 255
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.7903 (t) cc_final: 0.7375 (m)
REVERT: A   63 GLU cc_start: 0.7593 (tp30) cc_final: 0.7301 (mm-30)
REVERT: A   83 ARG cc_start: 0.6233 (tpp80) cc_final: 0.6016 (ttt180)
REVERT: A  143 ILE cc_start: 0.8017 (tt) cc_final: 0.7689 (tt)
REVERT: A  189 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7764 (mmtt)
REVERT: A  216 LYS cc_start: 0.8412 (tttt) cc_final: 0.8048 (ttpp)
REVERT: A  217 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6901 (mtm110)
REVERT: A  227 GLN cc_start: 0.6675 (pt0) cc_final: 0.6441 (pm20)
REVERT: A  259 LEU cc_start: 0.7850 (tt) cc_final: 0.7580 (tt)
REVERT: A  261 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5925 (p)
REVERT: A  280 GLU cc_start: 0.8054 (tt0) cc_final: 0.7053 (tt0)
REVERT: A  468 ARG cc_start: 0.6265 (tmm160) cc_final: 0.5914 (ttm170)
REVERT: B    8 SER cc_start: 0.8066 (t) cc_final: 0.7600 (m)
REVERT: B   59 PHE cc_start: 0.6866 (m-10) cc_final: 0.6565 (m-10)
REVERT: B   83 ARG cc_start: 0.6432 (tpp80) cc_final: 0.6112 (ttt180)
REVERT: B   86 THR cc_start: 0.8440 (p) cc_final: 0.7960 (p)
REVERT: B  143 ILE cc_start: 0.7718 (tt) cc_final: 0.7500 (tt)
REVERT: B  189 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7556 (mmtt)
REVERT: B  210 ASP cc_start: 0.7657 (t0) cc_final: 0.7327 (t0)
REVERT: B  216 LYS cc_start: 0.8237 (tttt) cc_final: 0.7985 (ttpp)
REVERT: B  227 GLN cc_start: 0.6484 (pt0) cc_final: 0.6164 (pm20)
REVERT: B  468 ARG cc_start: 0.6576 (tmm160) cc_final: 0.5567 (mtp180)
REVERT: B  533 ASP cc_start: 0.6904 (m-30) cc_final: 0.6672 (m-30)
REVERT: B  548 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7143 (ttm110)
  outliers start: 10
  outliers final: 2
  residues processed: 261
  average time/residue: 0.1326
  time to fit residues: 44.2295
Evaluate side-chains
  157 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 117 optimal weight:    8.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  18 GLN
A  21 GLN
A  70 ASN
A 125 HIS
A 152 ASN
A 163 HIS
A 204 ASN
A 288 ASN
A 399 GLN
A 462 GLN
A 476 HIS
A 479 ASN
A 619 ASN
B  60 GLN
B  70 ASN
B 125 HIS
B 152 ASN
B 163 HIS
B 204 ASN
B 288 ASN
B 399 GLN
B 462 GLN
B 476 HIS
B 479 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.189028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157294 restraints weight = 11062.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.14
r_work: 0.3262 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10258  Z= 0.166
  Angle     :  0.760  13.454  13956  Z= 0.383
  Chirality :  0.046   0.323   1516
  Planarity :  0.005   0.042   1694
  Dihedral  : 18.307 167.769   1559
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.66 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.24), residues: 1162
  helix: -0.99 (0.17), residues: 848
  sheet:  None (None), residues: 0
  loop : -3.55 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 217 
 TYR   0.017   0.002   TYR B 139 
 PHE   0.040   0.002   PHE A   3 
 TRP   0.016   0.002   TRP B 528 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10256)
  covalent geometry    : angle       0.76037 (13952)
  SS BOND              : bond        0.00011 (    2)
  SS BOND              : angle       0.51766 (    4)
  hydrogen bonds       : bond        0.04607 (  539)
  hydrogen bonds       : angle       4.82161 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.8617 (t) cc_final: 0.8222 (m)
REVERT: A   23 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7990 (mm-30)
REVERT: A   55 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: A   63 GLU cc_start: 0.8193 (tp30) cc_final: 0.7891 (mm-30)
REVERT: A   82 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.8133 (mtm110)
REVERT: A   83 ARG cc_start: 0.7204 (tpp80) cc_final: 0.6901 (ttt180)
REVERT: A  124 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6568 (tm-30)
REVERT: A  133 LEU cc_start: 0.8511 (tp) cc_final: 0.8231 (tt)
REVERT: A  143 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8052 (tt)
REVERT: A  196 SER cc_start: 0.8509 (t) cc_final: 0.8029 (m)
REVERT: A  227 GLN cc_start: 0.7174 (pt0) cc_final: 0.6808 (pm20)
REVERT: A  259 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: A  357 PHE cc_start: 0.7502 (t80) cc_final: 0.7285 (t80)
REVERT: A  468 ARG cc_start: 0.6707 (tmm160) cc_final: 0.6264 (ttm170)
REVERT: A  543 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: A  624 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7715 (ttp80)
REVERT: B    8 SER cc_start: 0.8676 (t) cc_final: 0.8229 (m)
REVERT: B   83 ARG cc_start: 0.7342 (tpp80) cc_final: 0.6917 (ttt180)
REVERT: B  143 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7830 (tt)
REVERT: B  196 SER cc_start: 0.8647 (t) cc_final: 0.8009 (m)
REVERT: B  210 ASP cc_start: 0.7991 (t0) cc_final: 0.7694 (t70)
REVERT: B  216 LYS cc_start: 0.8519 (tttt) cc_final: 0.8289 (ttpp)
REVERT: B  270 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7304 (mtt90)
REVERT: B  276 PHE cc_start: 0.8481 (t80) cc_final: 0.8209 (t80)
REVERT: B  294 GLN cc_start: 0.8054 (tp40) cc_final: 0.7831 (mm-40)
REVERT: B  468 ARG cc_start: 0.6805 (tmm160) cc_final: 0.6240 (ttm170)
REVERT: B  489 MET cc_start: 0.7804 (ttp) cc_final: 0.7592 (ttm)
REVERT: B  500 LYS cc_start: 0.6700 (tmmt) cc_final: 0.5832 (tttp)
REVERT: B  624 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7515 (ttp80)
  outliers start: 29
  outliers final: 14
  residues processed: 191
  average time/residue: 0.1130
  time to fit residues: 28.4410
Evaluate side-chains
  159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  532 MET
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
B 149 GLN
B 476 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.178898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.129976 restraints weight = 10800.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.69
r_work: 0.3039 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10258  Z= 0.159
  Angle     :  0.660  12.779  13956  Z= 0.335
  Chirality :  0.042   0.242   1516
  Planarity :  0.004   0.059   1694
  Dihedral  : 16.468 133.689   1558
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.80 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.25), residues: 1162
  helix: -0.06 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -2.98 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  82 
 TYR   0.026   0.002   TYR B 417 
 PHE   0.030   0.002   PHE A 610 
 TRP   0.013   0.002   TRP B 232 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10256)
  covalent geometry    : angle       0.66026 (13952)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.30975 (    4)
  hydrogen bonds       : bond        0.03924 (  539)
  hydrogen bonds       : angle       4.19135 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.8643 (t) cc_final: 0.8243 (m)
REVERT: A   17 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7250 (mmtm)
REVERT: A   23 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: A   59 PHE cc_start: 0.7074 (m-10) cc_final: 0.6758 (m-10)
REVERT: A   63 GLU cc_start: 0.8142 (tp30) cc_final: 0.7644 (mm-30)
REVERT: A   82 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7836 (mtp180)
REVERT: A   83 ARG cc_start: 0.7085 (tpp80) cc_final: 0.6645 (ttt180)
REVERT: A  133 LEU cc_start: 0.8370 (tp) cc_final: 0.8024 (tt)
REVERT: A  203 THR cc_start: 0.7972 (m) cc_final: 0.7765 (m)
REVERT: A  253 LEU cc_start: 0.8254 (mm) cc_final: 0.8048 (mt)
REVERT: A  259 LEU cc_start: 0.7986 (tt) cc_final: 0.7749 (tt)
REVERT: A  288 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8947 (m-40)
REVERT: A  357 PHE cc_start: 0.7434 (t80) cc_final: 0.7106 (t80)
REVERT: A  394 PHE cc_start: 0.8375 (t80) cc_final: 0.8098 (t80)
REVERT: A  468 ARG cc_start: 0.6822 (tmm160) cc_final: 0.5723 (mtp180)
REVERT: A  543 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: A  624 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7635 (ttp80)
REVERT: B    8 SER cc_start: 0.8583 (t) cc_final: 0.8166 (m)
REVERT: B   83 ARG cc_start: 0.7301 (tpp80) cc_final: 0.6951 (ttt180)
REVERT: B  210 ASP cc_start: 0.8065 (t0) cc_final: 0.7487 (t0)
REVERT: B  212 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: B  216 LYS cc_start: 0.8824 (tttt) cc_final: 0.8539 (ttpp)
REVERT: B  288 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (m-40)
REVERT: B  294 GLN cc_start: 0.8274 (tp40) cc_final: 0.7998 (mm-40)
REVERT: B  468 ARG cc_start: 0.6736 (tmm160) cc_final: 0.5587 (mtp180)
REVERT: B  500 LYS cc_start: 0.6465 (tmmt) cc_final: 0.5655 (tttp)
REVERT: B  508 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5908 (mmm)
  outliers start: 39
  outliers final: 18
  residues processed: 181
  average time/residue: 0.1115
  time to fit residues: 26.7534
Evaluate side-chains
  159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  340 SER
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  508 MET
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
B  70 ASN
B 127 ASN
B 619 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.161779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.109943 restraints weight = 10964.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.72
r_work: 0.2955 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10258  Z= 0.165
  Angle     :  0.632  14.310  13956  Z= 0.319
  Chirality :  0.042   0.244   1516
  Planarity :  0.004   0.044   1694
  Dihedral  : 15.736 114.808   1558
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.86 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.25), residues: 1162
  helix:  0.28 (0.18), residues: 856
  sheet:  None (None), residues: 0
  loop : -2.46 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 171 
 TYR   0.012   0.002   TYR A 518 
 PHE   0.025   0.002   PHE A 610 
 TRP   0.013   0.002   TRP B 528 
 HIS   0.004   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (10256)
  covalent geometry    : angle       0.63243 (13952)
  SS BOND              : bond        0.00077 (    2)
  SS BOND              : angle       0.21814 (    4)
  hydrogen bonds       : bond        0.03626 (  539)
  hydrogen bonds       : angle       3.98767 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.8745 (t) cc_final: 0.8353 (m)
REVERT: A   17 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7447 (mmtm)
REVERT: A   50 TYR cc_start: 0.8579 (t80) cc_final: 0.8241 (t80)
REVERT: A   63 GLU cc_start: 0.8192 (tp30) cc_final: 0.7702 (mm-30)
REVERT: A   83 ARG cc_start: 0.7223 (tpp80) cc_final: 0.6830 (ttt180)
REVERT: A  133 LEU cc_start: 0.8466 (tp) cc_final: 0.8144 (tt)
REVERT: A  143 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7860 (tt)
REVERT: A  186 TYR cc_start: 0.8052 (t80) cc_final: 0.7651 (t80)
REVERT: A  253 LEU cc_start: 0.8461 (mm) cc_final: 0.8210 (mt)
REVERT: A  357 PHE cc_start: 0.7535 (t80) cc_final: 0.7277 (t80)
REVERT: A  414 ILE cc_start: 0.8277 (mt) cc_final: 0.8027 (mm)
REVERT: A  468 ARG cc_start: 0.6918 (tmm160) cc_final: 0.5901 (mtp180)
REVERT: A  502 ARG cc_start: 0.6883 (mtp85) cc_final: 0.6682 (mtt-85)
REVERT: A  520 ILE cc_start: 0.7970 (mm) cc_final: 0.7691 (mt)
REVERT: A  543 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: A  624 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7494 (ttp80)
REVERT: B    8 SER cc_start: 0.8721 (t) cc_final: 0.8293 (m)
REVERT: B   17 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7278 (mmtm)
REVERT: B   18 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8017 (mm-40)
REVERT: B   83 ARG cc_start: 0.7335 (tpp80) cc_final: 0.7049 (ttt180)
REVERT: B  143 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: B  154 THR cc_start: 0.8523 (t) cc_final: 0.8283 (t)
REVERT: B  156 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8358 (t80)
REVERT: B  203 THR cc_start: 0.8560 (m) cc_final: 0.8143 (m)
REVERT: B  212 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: B  216 LYS cc_start: 0.8894 (tttt) cc_final: 0.8641 (ttpp)
REVERT: B  314 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8527 (mm-40)
REVERT: B  414 ILE cc_start: 0.8259 (mt) cc_final: 0.7939 (mm)
REVERT: B  468 ARG cc_start: 0.6911 (tmm160) cc_final: 0.5697 (mtp180)
REVERT: B  508 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5980 (mmm)
REVERT: B  529 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8264 (t0)
REVERT: B  624 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7513 (ttp80)
  outliers start: 31
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1154
  time to fit residues: 23.3511
Evaluate side-chains
  153 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  508 MET
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:    0.0270
   chunk 4 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 114 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 124 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 = 0.3744 r_free = 0.3744 target = 0.162114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.110580 restraints weight = 10949.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.71
r_work: 0.2960 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10258  Z= 0.127
  Angle     :  0.573   8.008  13956  Z= 0.292
  Chirality :  0.040   0.224   1516
  Planarity :  0.004   0.052   1694
  Dihedral  : 15.142  96.535   1558
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.34 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.26), residues: 1162
  helix:  0.65 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -2.13 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 171 
 TYR   0.014   0.001   TYR B 518 
 PHE   0.021   0.001   PHE A 610 
 TRP   0.013   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10256)
  covalent geometry    : angle       0.57275 (13952)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       0.16307 (    4)
  hydrogen bonds       : bond        0.03406 (  539)
  hydrogen bonds       : angle       3.86803 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.8703 (t) cc_final: 0.8276 (m)
REVERT: A   17 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7704 (mmtm)
REVERT: A   50 TYR cc_start: 0.8571 (t80) cc_final: 0.8246 (t80)
REVERT: A   59 PHE cc_start: 0.7654 (m-10) cc_final: 0.7452 (m-10)
REVERT: A   63 GLU cc_start: 0.8028 (tp30) cc_final: 0.7493 (mm-30)
REVERT: A   83 ARG cc_start: 0.7306 (tpp80) cc_final: 0.6844 (ttt180)
REVERT: A  133 LEU cc_start: 0.8433 (tp) cc_final: 0.8138 (tt)
REVERT: A  143 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7866 (tt)
REVERT: A  186 TYR cc_start: 0.8175 (t80) cc_final: 0.7760 (t80)
REVERT: A  253 LEU cc_start: 0.8474 (mm) cc_final: 0.8249 (mt)
REVERT: A  357 PHE cc_start: 0.7531 (t80) cc_final: 0.7295 (t80)
REVERT: A  414 ILE cc_start: 0.8339 (mt) cc_final: 0.8087 (mm)
REVERT: A  468 ARG cc_start: 0.7057 (tmm160) cc_final: 0.5868 (mtp180)
REVERT: A  520 ILE cc_start: 0.8068 (mm) cc_final: 0.7780 (mt)
REVERT: A  529 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8268 (t0)
REVERT: B    8 SER cc_start: 0.8783 (t) cc_final: 0.8375 (m)
REVERT: B   17 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7335 (mmtm)
REVERT: B   18 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8039 (mm-40)
REVERT: B   83 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7201 (ttt180)
REVERT: B  143 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7703 (tt)
REVERT: B  156 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8284 (t80)
REVERT: B  171 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7274 (ttt180)
REVERT: B  210 ASP cc_start: 0.8519 (t0) cc_final: 0.7931 (t70)
REVERT: B  212 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: B  216 LYS cc_start: 0.8924 (tttt) cc_final: 0.8685 (ttpp)
REVERT: B  294 GLN cc_start: 0.8402 (tp40) cc_final: 0.8056 (mm-40)
REVERT: B  414 ILE cc_start: 0.8215 (mt) cc_final: 0.7863 (mm)
REVERT: B  468 ARG cc_start: 0.6920 (tmm160) cc_final: 0.5682 (mtp180)
REVERT: B  508 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5955 (mmm)
REVERT: B  520 ILE cc_start: 0.8301 (mm) cc_final: 0.7991 (mt)
REVERT: B  529 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8229 (t0)
REVERT: B  624 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7593 (ttp80)
  outliers start: 27
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1159
  time to fit residues: 22.3746
Evaluate side-chains
  148 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  508 MET
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0060
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B   6 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.161890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.111086 restraints weight = 10903.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 1.65
r_work: 0.2964 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.5233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10258  Z= 0.123
  Angle     :  0.570  10.414  13956  Z= 0.287
  Chirality :  0.039   0.218   1516
  Planarity :  0.004   0.048   1694
  Dihedral  : 14.468  95.054   1558
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.72 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.26), residues: 1162
  helix:  0.95 (0.19), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.93 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  82 
 TYR   0.011   0.001   TYR B 518 
 PHE   0.019   0.001   PHE A 610 
 TRP   0.012   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10256)
  covalent geometry    : angle       0.56956 (13952)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       0.69805 (    4)
  hydrogen bonds       : bond        0.03256 (  539)
  hydrogen bonds       : angle       3.76976 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7430 (mt-10)
REVERT: A    8 SER cc_start: 0.8682 (t) cc_final: 0.8297 (m)
REVERT: A   17 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7689 (mmtm)
REVERT: A   83 ARG cc_start: 0.7436 (tpp80) cc_final: 0.6985 (ttt180)
REVERT: A  133 LEU cc_start: 0.8350 (tp) cc_final: 0.8083 (tt)
REVERT: A  143 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7880 (tt)
REVERT: A  186 TYR cc_start: 0.8169 (t80) cc_final: 0.7668 (t80)
REVERT: A  203 THR cc_start: 0.8037 (m) cc_final: 0.7788 (m)
REVERT: A  253 LEU cc_start: 0.8479 (mm) cc_final: 0.8261 (mt)
REVERT: A  357 PHE cc_start: 0.7541 (t80) cc_final: 0.7293 (t80)
REVERT: A  414 ILE cc_start: 0.8247 (mt) cc_final: 0.7993 (mm)
REVERT: A  468 ARG cc_start: 0.7000 (tmm160) cc_final: 0.5800 (mtp180)
REVERT: A  520 ILE cc_start: 0.8143 (mm) cc_final: 0.7873 (mt)
REVERT: A  525 THR cc_start: 0.9029 (t) cc_final: 0.8529 (p)
REVERT: A  529 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8297 (t0)
REVERT: A  594 THR cc_start: 0.9236 (t) cc_final: 0.8941 (m)
REVERT: B    8 SER cc_start: 0.8794 (t) cc_final: 0.8394 (m)
REVERT: B   17 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7498 (mmtm)
REVERT: B   18 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8087 (mm-40)
REVERT: B   83 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7215 (ttt180)
REVERT: B  143 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7763 (tt)
REVERT: B  154 THR cc_start: 0.8383 (t) cc_final: 0.8140 (t)
REVERT: B  156 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8252 (t80)
REVERT: B  210 ASP cc_start: 0.8531 (t0) cc_final: 0.8053 (t0)
REVERT: B  212 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: B  216 LYS cc_start: 0.8926 (tttt) cc_final: 0.8691 (ttpp)
REVERT: B  288 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8871 (m-40)
REVERT: B  294 GLN cc_start: 0.8354 (tp40) cc_final: 0.8032 (mm110)
REVERT: B  468 ARG cc_start: 0.6934 (tmm160) cc_final: 0.5666 (mtp180)
REVERT: B  520 ILE cc_start: 0.8355 (mm) cc_final: 0.8048 (mt)
REVERT: B  529 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8313 (t0)
REVERT: B  624 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7498 (ttp80)
  outliers start: 29
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1180
  time to fit residues: 22.9731
Evaluate side-chains
  143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 86 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 124 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 = 0.3715 r_free = 0.3715 target = 0.159420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.107996 restraints weight = 10858.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.68
r_work: 0.2928 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.5517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10258  Z= 0.147
  Angle     :  0.582   8.393  13956  Z= 0.294
  Chirality :  0.041   0.225   1516
  Planarity :  0.004   0.059   1694
  Dihedral  : 13.617  95.952   1558
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.62 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1162
  helix:  1.04 (0.18), residues: 850
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  82 
 TYR   0.012   0.001   TYR B 518 
 PHE   0.019   0.002   PHE A 610 
 TRP   0.012   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10256)
  covalent geometry    : angle       0.58233 (13952)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.22236 (    4)
  hydrogen bonds       : bond        0.03315 (  539)
  hydrogen bonds       : angle       3.77578 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7438 (mt-10)
REVERT: A    8 SER cc_start: 0.8678 (t) cc_final: 0.8309 (m)
REVERT: A   17 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7709 (mmtm)
REVERT: A   34 ASP cc_start: 0.8619 (t70) cc_final: 0.8418 (m-30)
REVERT: A   83 ARG cc_start: 0.7443 (tpp80) cc_final: 0.6975 (ttt180)
REVERT: A  133 LEU cc_start: 0.8315 (tp) cc_final: 0.8046 (tt)
REVERT: A  143 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7923 (tt)
REVERT: A  171 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7483 (ttt180)
REVERT: A  186 TYR cc_start: 0.8318 (t80) cc_final: 0.7813 (t80)
REVERT: A  203 THR cc_start: 0.8058 (m) cc_final: 0.7833 (m)
REVERT: A  212 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: A  253 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8263 (mt)
REVERT: A  288 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8897 (m-40)
REVERT: A  414 ILE cc_start: 0.8252 (mt) cc_final: 0.8052 (mm)
REVERT: A  468 ARG cc_start: 0.7020 (tmm160) cc_final: 0.5800 (mtp180)
REVERT: A  520 ILE cc_start: 0.8338 (mm) cc_final: 0.8072 (mt)
REVERT: A  525 THR cc_start: 0.9064 (t) cc_final: 0.8593 (p)
REVERT: A  529 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8317 (t0)
REVERT: A  594 THR cc_start: 0.9232 (t) cc_final: 0.8967 (m)
REVERT: B    8 SER cc_start: 0.8749 (t) cc_final: 0.8339 (m)
REVERT: B   17 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7544 (mmtm)
REVERT: B   18 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8130 (mm-40)
REVERT: B   83 ARG cc_start: 0.7439 (tpp80) cc_final: 0.7197 (ttt180)
REVERT: B  143 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7747 (tt)
REVERT: B  154 THR cc_start: 0.8472 (t) cc_final: 0.8250 (t)
REVERT: B  156 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8125 (t80)
REVERT: B  186 TYR cc_start: 0.8526 (t80) cc_final: 0.7955 (t80)
REVERT: B  210 ASP cc_start: 0.8533 (t0) cc_final: 0.8054 (t0)
REVERT: B  212 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: B  216 LYS cc_start: 0.8993 (tttt) cc_final: 0.8761 (ttpp)
REVERT: B  294 GLN cc_start: 0.8399 (tp40) cc_final: 0.8083 (mm110)
REVERT: B  318 GLU cc_start: 0.8926 (tt0) cc_final: 0.8068 (tt0)
REVERT: B  414 ILE cc_start: 0.8323 (mt) cc_final: 0.8003 (mm)
REVERT: B  468 ARG cc_start: 0.6789 (tmm160) cc_final: 0.5570 (mtp180)
REVERT: B  520 ILE cc_start: 0.8350 (mm) cc_final: 0.8039 (mt)
REVERT: B  529 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8481 (t0)
REVERT: B  594 THR cc_start: 0.9193 (t) cc_final: 0.8940 (m)
REVERT: B  624 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7491 (ttp80)
  outliers start: 31
  outliers final: 19
  residues processed: 149
  average time/residue: 0.1243
  time to fit residues: 23.8445
Evaluate side-chains
  143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 MET
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.109135 restraints weight = 10796.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.63
r_work: 0.2943 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10258  Z= 0.128
  Angle     :  0.562   7.503  13956  Z= 0.284
  Chirality :  0.040   0.212   1516
  Planarity :  0.004   0.050   1694
  Dihedral  : 13.233  95.694   1558
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.01 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1162
  helix:  1.18 (0.19), residues: 856
  sheet:  None (None), residues: 0
  loop : -1.86 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.011   0.001   TYR B 518 
 PHE   0.022   0.001   PHE B  54 
 TRP   0.012   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10256)
  covalent geometry    : angle       0.56189 (13952)
  SS BOND              : bond        0.00025 (    2)
  SS BOND              : angle       0.28564 (    4)
  hydrogen bonds       : bond        0.03226 (  539)
  hydrogen bonds       : angle       3.68819 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7540 (mt-10)
REVERT: A    8 SER cc_start: 0.8694 (t) cc_final: 0.8323 (m)
REVERT: A   17 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7722 (mmtm)
REVERT: A   83 ARG cc_start: 0.7451 (tpp80) cc_final: 0.6988 (ttt180)
REVERT: A  133 LEU cc_start: 0.8292 (tp) cc_final: 0.8043 (tt)
REVERT: A  143 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: A  203 THR cc_start: 0.8047 (m) cc_final: 0.7814 (m)
REVERT: A  212 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7683 (tm-30)
REVERT: A  253 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8267 (mt)
REVERT: A  288 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8899 (m-40)
REVERT: A  414 ILE cc_start: 0.8316 (mt) cc_final: 0.8045 (mm)
REVERT: A  468 ARG cc_start: 0.7034 (tmm160) cc_final: 0.5813 (mtp180)
REVERT: A  520 ILE cc_start: 0.8401 (mm) cc_final: 0.8149 (mt)
REVERT: A  525 THR cc_start: 0.9025 (t) cc_final: 0.8590 (p)
REVERT: A  529 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8377 (t0)
REVERT: A  594 THR cc_start: 0.9225 (t) cc_final: 0.8968 (m)
REVERT: B    8 SER cc_start: 0.8739 (t) cc_final: 0.8335 (m)
REVERT: B   17 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7565 (mmtm)
REVERT: B   18 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8137 (mm-40)
REVERT: B   82 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7967 (ttp-110)
REVERT: B   83 ARG cc_start: 0.7553 (tpp80) cc_final: 0.7267 (ttt180)
REVERT: B  143 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7769 (tt)
REVERT: B  156 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8215 (t80)
REVERT: B  171 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7524 (ttt180)
REVERT: B  210 ASP cc_start: 0.8542 (t0) cc_final: 0.8163 (t0)
REVERT: B  212 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7564 (tm-30)
REVERT: B  216 LYS cc_start: 0.9018 (tttt) cc_final: 0.8807 (ttpp)
REVERT: B  288 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (m-40)
REVERT: B  294 GLN cc_start: 0.8387 (tp40) cc_final: 0.8041 (mm110)
REVERT: B  414 ILE cc_start: 0.8332 (mt) cc_final: 0.8040 (mm)
REVERT: B  468 ARG cc_start: 0.6890 (tmm160) cc_final: 0.5699 (mtp180)
REVERT: B  520 ILE cc_start: 0.8374 (mm) cc_final: 0.8075 (mt)
REVERT: B  529 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8493 (t0)
REVERT: B  594 THR cc_start: 0.9164 (t) cc_final: 0.8962 (m)
REVERT: B  624 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7541 (ttp80)
  outliers start: 30
  outliers final: 21
  residues processed: 141
  average time/residue: 0.1113
  time to fit residues: 20.6342
Evaluate side-chains
  141 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  340 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.157756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.106967 restraints weight = 10855.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 1.63
r_work: 0.2920 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10258  Z= 0.152
  Angle     :  0.586   9.772  13956  Z= 0.294
  Chirality :  0.041   0.220   1516
  Planarity :  0.004   0.058   1694
  Dihedral  : 12.989  96.584   1558
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.62 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.26), residues: 1162
  helix:  1.04 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.76 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.012   0.001   TYR B 518 
 PHE   0.019   0.001   PHE A 610 
 TRP   0.012   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10256)
  covalent geometry    : angle       0.58638 (13952)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.61377 (    4)
  hydrogen bonds       : bond        0.03346 (  539)
  hydrogen bonds       : angle       3.75702 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7568 (mt-10)
REVERT: A    8 SER cc_start: 0.8673 (t) cc_final: 0.8308 (m)
REVERT: A   17 LYS cc_start: 0.8466 (mtmm) cc_final: 0.7754 (mmtm)
REVERT: A   83 ARG cc_start: 0.7427 (tpp80) cc_final: 0.6926 (ttt180)
REVERT: A  133 LEU cc_start: 0.8292 (tp) cc_final: 0.7969 (tp)
REVERT: A  143 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7925 (tt)
REVERT: A  171 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7550 (ttt180)
REVERT: A  203 THR cc_start: 0.8067 (m) cc_final: 0.7842 (m)
REVERT: A  253 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8255 (mt)
REVERT: A  288 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8925 (m-40)
REVERT: A  468 ARG cc_start: 0.7075 (tmm160) cc_final: 0.5811 (mtp180)
REVERT: A  520 ILE cc_start: 0.8437 (mm) cc_final: 0.8179 (mt)
REVERT: A  525 THR cc_start: 0.9053 (t) cc_final: 0.8623 (p)
REVERT: A  529 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8363 (t0)
REVERT: A  594 THR cc_start: 0.9213 (t) cc_final: 0.8970 (m)
REVERT: B    8 SER cc_start: 0.8735 (t) cc_final: 0.8347 (m)
REVERT: B   17 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7609 (mmtm)
REVERT: B   18 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8165 (mm-40)
REVERT: B   82 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7950 (ttp-110)
REVERT: B   83 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7192 (ttt180)
REVERT: B  143 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7655 (tt)
REVERT: B  156 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8133 (t80)
REVERT: B  171 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7612 (ttt180)
REVERT: B  186 TYR cc_start: 0.8594 (t80) cc_final: 0.8114 (t80)
REVERT: B  210 ASP cc_start: 0.8565 (t0) cc_final: 0.8213 (t0)
REVERT: B  212 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7615 (tm-30)
REVERT: B  216 LYS cc_start: 0.9022 (tttt) cc_final: 0.8756 (ttpp)
REVERT: B  288 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8920 (m-40)
REVERT: B  294 GLN cc_start: 0.8395 (tp40) cc_final: 0.8023 (mm-40)
REVERT: B  318 GLU cc_start: 0.8945 (tt0) cc_final: 0.8105 (tt0)
REVERT: B  414 ILE cc_start: 0.8343 (mt) cc_final: 0.8090 (mm)
REVERT: B  468 ARG cc_start: 0.6921 (tmm160) cc_final: 0.5694 (mtp180)
REVERT: B  520 ILE cc_start: 0.8493 (mm) cc_final: 0.8273 (mt)
REVERT: B  529 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8508 (t0)
REVERT: B  624 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7549 (ttp80)
  outliers start: 29
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1103
  time to fit residues: 20.2213
Evaluate side-chains
  140 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  340 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 116 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    0.1980
   chunk 95 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0870
   chunk 108 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.160442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.109829 restraints weight = 10741.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.63
r_work: 0.2957 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10258  Z= 0.108
  Angle     :  0.551   7.683  13956  Z= 0.278
  Chirality :  0.039   0.196   1516
  Planarity :  0.004   0.049   1694
  Dihedral  : 12.528  95.574   1558
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.58 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1162
  helix:  1.31 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.70 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.009   0.001   TYR B 518 
 PHE   0.019   0.001   PHE A   3 
 TRP   0.013   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10256)
  covalent geometry    : angle       0.55137 (13952)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       0.51242 (    4)
  hydrogen bonds       : bond        0.03087 (  539)
  hydrogen bonds       : angle       3.62854 ( 1587)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7724 (mt-10)
REVERT: A    8 SER cc_start: 0.8613 (t) cc_final: 0.8273 (m)
REVERT: A   17 LYS cc_start: 0.8428 (mtmm) cc_final: 0.7735 (mmtm)
REVERT: A   18 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8162 (mm-40)
REVERT: A   83 ARG cc_start: 0.7472 (tpp80) cc_final: 0.7020 (ttt180)
REVERT: A  133 LEU cc_start: 0.8232 (tp) cc_final: 0.7920 (tp)
REVERT: A  143 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7872 (tt)
REVERT: A  203 THR cc_start: 0.8045 (m) cc_final: 0.7814 (m)
REVERT: A  253 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (mt)
REVERT: A  468 ARG cc_start: 0.7112 (tmm160) cc_final: 0.5811 (mtp180)
REVERT: A  525 THR cc_start: 0.8988 (t) cc_final: 0.8631 (p)
REVERT: A  529 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8359 (t0)
REVERT: A  594 THR cc_start: 0.9199 (t) cc_final: 0.8980 (m)
REVERT: B    8 SER cc_start: 0.8725 (t) cc_final: 0.8395 (m)
REVERT: B   17 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7567 (mmtm)
REVERT: B   18 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8151 (mm-40)
REVERT: B   82 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7899 (ttp-110)
REVERT: B   83 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7224 (ttt180)
REVERT: B  143 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7802 (tt)
REVERT: B  153 PHE cc_start: 0.7744 (t80) cc_final: 0.7498 (t80)
REVERT: B  156 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: B  171 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7636 (ttt180)
REVERT: B  210 ASP cc_start: 0.8503 (t0) cc_final: 0.8186 (t0)
REVERT: B  212 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: B  216 LYS cc_start: 0.8969 (tttt) cc_final: 0.8739 (ttpp)
REVERT: B  288 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8829 (m-40)
REVERT: B  294 GLN cc_start: 0.8327 (tp40) cc_final: 0.7969 (mm110)
REVERT: B  414 ILE cc_start: 0.8251 (mt) cc_final: 0.8013 (mm)
REVERT: B  468 ARG cc_start: 0.6983 (tmm160) cc_final: 0.5714 (mtp180)
REVERT: B  508 MET cc_start: 0.6418 (mmp) cc_final: 0.5914 (tpp)
REVERT: B  520 ILE cc_start: 0.8442 (mm) cc_final: 0.8160 (mt)
REVERT: B  529 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8455 (t0)
REVERT: B  624 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7552 (ttp80)
  outliers start: 25
  outliers final: 17
  residues processed: 139
  average time/residue: 0.1129
  time to fit residues: 20.4395
Evaluate side-chains
  137 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  576 GLN
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  288 ASN
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  340 SER
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  631 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0370
   chunk 82 optimal weight:    5.9990
   chunk 116 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.159635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.108875 restraints weight = 10829.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.64
r_work: 0.2938 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.6015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10258  Z= 0.128
  Angle     :  0.564   8.954  13956  Z= 0.283
  Chirality :  0.040   0.207   1516
  Planarity :  0.004   0.054   1694
  Dihedral  : 12.384  95.765   1558
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.39 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.26), residues: 1162
  helix:  1.31 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.64 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.011   0.001   TYR B 518 
 PHE   0.018   0.001   PHE A   3 
 TRP   0.012   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10256)
  covalent geometry    : angle       0.56449 (13952)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.32048 (    4)
  hydrogen bonds       : bond        0.03155 (  539)
  hydrogen bonds       : angle       3.66148 ( 1587)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2677.81 seconds
wall clock time: 46 minutes 20.10 seconds (2780.10 seconds total)