Starting phenix.real_space_refine
on Fri Aug  7 01:42:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2026/8wha_37537_neut.cif"
  }
  resolution = 4.05
  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=   0.000 sd=   0.002
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: 7
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      48      5.16       5
     Be      2      3.05       5
     C   11190      2.51       5
     N    3499      2.21       5
     O    4051      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 19084
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 755
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "B"
      Number of atoms: 692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 692
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "C"
      Number of atoms: 768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 768
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 799
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 688
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 750
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2893
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "J"
      Number of atoms: 2929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2929
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "K"
      Number of atoms: 3669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3669
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 16, 'TRANS': 435}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 3669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3669
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 16, 'TRANS': 435}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "L"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.38, per 1000 atoms: 0.18
  Number of scatterers: 19084
  At special positions: 0
  Unit cell: (145.35, 170.145, 123.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      48     16.00
     P     288     15.00
     F       6      9.00
     O    4051      8.00
     N    3499      7.00
     C   11190      6.00
     Be      2      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 711.0 milliseconds
  

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3078

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 16 sheets defined
      61.5% alpha, 6.6% beta
      108 base pairs and 229 stacking pairs defined.
    Time for finding SS restraints: 3.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 4.182A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 74
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.639A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.746A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.696A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.908A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 109
      removed outlier: 3.535A  pdb=" N   GLY D  85 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASN D 109 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.732A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN D 120 " --> pdb=" O   SER D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 149
      removed outlier: 3.743A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
      removed outlier: 3.606A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.586A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.792A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ILE E 112 " --> pdb=" O   ASN E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 130
      removed outlier: 3.803A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.845A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.870A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.689A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.453A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU G  59 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU G  66 " --> pdb=" O   GLU G  62 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.601A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
      removed outlier: 3.786A  pdb=" N   ASN H 109 " --> pdb=" O   LEU H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 127
      removed outlier: 3.878A  pdb=" N   THR H 121 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 128 through 148
      removed outlier: 3.667A  pdb=" N   ALA H 132 " --> pdb=" O   PRO H 128 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   HIS H 134 " --> pdb=" O   GLU H 130 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER H 137 " --> pdb=" O   LYS H 133 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 204 through 220
    Processing helix  chain 'K' and resid 233 through 246
      removed outlier: 6.307A  pdb=" N   GLY K 239 " --> pdb=" O   ILE K 235 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 258 through 273
      removed outlier: 3.912A  pdb=" N   SER K 263 " --> pdb=" O   LEU K 259 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN K 264 " --> pdb=" O   SER K 260 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 286 through 291
      removed outlier: 3.956A  pdb=" N   GLU K 290 " --> pdb=" O   ASN K 286 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 311 through 317
    Processing helix  chain 'K' and resid 317 through 323
      removed outlier: 4.068A  pdb=" N   ILE K 321 " --> pdb=" O   ASP K 317 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG K 323 " --> pdb=" O   LYS K 319 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 334 through 339
    Processing helix  chain 'K' and resid 343 through 352
      removed outlier: 3.874A  pdb=" N   HIS K 351 " --> pdb=" O   ARG K 347 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LEU K 352 " --> pdb=" O   GLU K 348 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 369 through 380
    Processing helix  chain 'K' and resid 416 through 425
      removed outlier: 3.650A  pdb=" N   ILE K 423 " --> pdb=" O   LYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 453 through 465
    Processing helix  chain 'K' and resid 467 through 472
    Processing helix  chain 'K' and resid 473 through 475
      No H-bonds generated for 'chain 'K' and resid 473 through 475'
    Processing helix  chain 'K' and resid 489 through 499
      removed outlier: 3.789A  pdb=" N   ARG K 494 " --> pdb=" O   VAL K 490 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   LYS K 495 " --> pdb=" O   ILE K 491 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 500 through 508
      removed outlier: 3.796A  pdb=" N   GLN K 506 " --> pdb=" O   LEU K 502 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 519 through 522
    Processing helix  chain 'K' and resid 523 through 536
    Processing helix  chain 'K' and resid 550 through 564
      removed outlier: 3.564A  pdb=" N   LYS K 563 " --> pdb=" O   TYR K 559 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 575 through 587
    Processing helix  chain 'K' and resid 599 through 604
    Processing helix  chain 'K' and resid 623 through 635
      removed outlier: 4.112A  pdb=" N   ASP K 627 " --> pdb=" O   ASN K 623 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN K 629 " --> pdb=" O   GLN K 625 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA K 630 " --> pdb=" O   MET K 626 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG K 633 " --> pdb=" O   GLN K 629 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS K 634 " --> pdb=" O   ALA K 630 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 653 through 676
      removed outlier: 3.559A  pdb=" N   ARG K 657 " --> pdb=" O   SER K 653 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 204 through 220
    Processing helix  chain 'L' and resid 232 through 246
      removed outlier: 3.694A  pdb=" N   GLY L 246 " --> pdb=" O   SER L 242 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 258 through 273
      removed outlier: 3.912A  pdb=" N   SER L 263 " --> pdb=" O   LEU L 259 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN L 264 " --> pdb=" O   SER L 260 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 286 through 291
      removed outlier: 3.956A  pdb=" N   GLU L 290 " --> pdb=" O   ASN L 286 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 311 through 317
    Processing helix  chain 'L' and resid 317 through 323
      removed outlier: 4.067A  pdb=" N   ILE L 321 " --> pdb=" O   ASP L 317 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG L 323 " --> pdb=" O   LYS L 319 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 334 through 339
    Processing helix  chain 'L' and resid 343 through 352
      removed outlier: 3.874A  pdb=" N   HIS L 351 " --> pdb=" O   ARG L 347 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LEU L 352 " --> pdb=" O   GLU L 348 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 369 through 380
    Processing helix  chain 'L' and resid 381 through 384
      removed outlier: 3.543A  pdb=" N   PHE L 384 " --> pdb=" O   PRO L 381 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 381 through 384'
    Processing helix  chain 'L' and resid 416 through 425
      removed outlier: 3.652A  pdb=" N   ILE L 423 " --> pdb=" O   LYS L 419 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 453 through 465
    Processing helix  chain 'L' and resid 467 through 472
    Processing helix  chain 'L' and resid 473 through 475
      No H-bonds generated for 'chain 'L' and resid 473 through 475'
    Processing helix  chain 'L' and resid 488 through 499
      removed outlier: 3.846A  pdb=" N   ASN L 496 " --> pdb=" O   GLN L 492 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 500 through 508
      removed outlier: 3.796A  pdb=" N   GLN L 506 " --> pdb=" O   LEU L 502 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE L 507 " --> pdb=" O   LEU L 503 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 518 through 522
    Processing helix  chain 'L' and resid 523 through 536
    Processing helix  chain 'L' and resid 550 through 564
      removed outlier: 3.566A  pdb=" N   LYS L 563 " --> pdb=" O   TYR L 559 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 575 through 587
    Processing helix  chain 'L' and resid 599 through 604
    Processing helix  chain 'L' and resid 623 through 635
      removed outlier: 4.111A  pdb=" N   ASP L 627 " --> pdb=" O   ASN L 623 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN L 629 " --> pdb=" O   GLN L 625 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA L 630 " --> pdb=" O   MET L 626 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG L 633 " --> pdb=" O   GLN L 629 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS L 634 " --> pdb=" O   ALA L 630 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 653 through 676
      removed outlier: 3.559A  pdb=" N   ARG L 657 " --> pdb=" O   SER L 653 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.396A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.266A  pdb=" N   ARG B  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.467A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79
      removed outlier: 3.595A  pdb=" N   ILE C  79 " --> pdb=" O   GLY D  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
      removed outlier: 7.491A  pdb=" N   THR F  96 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.544A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 225
      removed outlier: 4.246A  pdb=" N   GLY K 223 " --> pdb=" O   LYS K 357 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL K 330 " --> pdb=" O   LEU K 358 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   LEU K 360 " --> pdb=" O   VAL K 330 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ILE K 332 " --> pdb=" O   LEU K 360 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU K 254 " --> pdb=" O   TYR K 329 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 444 through 450
      removed outlier: 6.325A  pdb=" N   LYS K 444 " --> pdb=" O   VAL K 645 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ARG K 647 " --> pdb=" O   LYS K 444 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE K 446 " --> pdb=" O   ARG K 647 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   SER K 649 " --> pdb=" O   ILE K 446 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   MET K 448 " --> pdb=" O   SER K 649 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   CYS K 615 " --> pdb=" O   TYR K 646 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU K 648 " --> pdb=" O   CYS K 615 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU K 617 " --> pdb=" O   LEU K 648 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   THR K 650 " --> pdb=" O   LEU K 617 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU K 544 " --> pdb=" O   ILE K 616 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'K' and resid 567 through 570
      removed outlier: 6.351A  pdb=" N   CYS K 568 " --> pdb=" O   LEU K 597 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 223 through 225
      removed outlier: 4.246A  pdb=" N   GLY L 223 " --> pdb=" O   LYS L 357 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL L 330 " --> pdb=" O   LEU L 358 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LEU L 360 " --> pdb=" O   VAL L 330 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ILE L 332 " --> pdb=" O   LEU L 360 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU L 254 " --> pdb=" O   TYR L 329 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 444 through 450
      removed outlier: 6.325A  pdb=" N   LYS L 444 " --> pdb=" O   VAL L 645 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ARG L 647 " --> pdb=" O   LYS L 444 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE L 446 " --> pdb=" O   ARG L 647 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   SER L 649 " --> pdb=" O   ILE L 446 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   MET L 448 " --> pdb=" O   SER L 649 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   CYS L 615 " --> pdb=" O   TYR L 646 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU L 648 " --> pdb=" O   CYS L 615 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU L 617 " --> pdb=" O   LEU L 648 " (cutoff:3.500A)
      removed outlier: 9.077A  pdb=" N   THR L 650 " --> pdb=" O   LEU L 617 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU L 544 " --> pdb=" O   ILE L 616 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'L' and resid 567 through 570
      removed outlier: 6.350A  pdb=" N   CYS L 568 " --> pdb=" O   LEU L 597 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    645 hydrogen bonds defined for protein.
    1893 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      269 hydrogen bonds
      530 hydrogen bond angles
      0 basepair planarities
      108 basepair parallelities
      229 stacking parallelities
  Total time for adding SS restraints: 3.23

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2538
        1.31 -     1.44: 6620
        1.44 -     1.57: 10210
        1.57 -     1.70: 582
        1.70 -     1.83: 78
  Bond restraints: 20028
  Sorted by residual:
  bond pdb=" C1'  DT I 134 "
       pdb=" N1   DT I 134 "
    ideal  model  delta    sigma   weight residual
    1.468  1.550 -0.082 1.40e-02 5.10e+03 3.43e+01
  bond pdb=" C4  ADP K 802 "
       pdb=" C5  ADP K 802 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C1'  DC I 125 "
       pdb=" N1   DC I 125 "
    ideal  model  delta    sigma   weight residual
    1.468  1.544 -0.076 1.40e-02 5.10e+03 2.97e+01
  bond pdb=" C4  ADP L 802 "
       pdb=" C5  ADP L 802 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C1'  DC J  34 "
       pdb=" N1   DC J  34 "
    ideal  model  delta    sigma   weight residual
    1.468  1.542 -0.074 1.40e-02 5.10e+03 2.76e+01
  ... (remaining 20023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 27216
        3.21 -     6.43: 944
        6.43 -     9.64: 73
        9.64 -    12.85: 18
       12.85 -    16.07: 2
  Bond angle restraints: 28253
  Sorted by residual:
  angle pdb=" N   THR E 107 "
        pdb=" CA  THR E 107 "
        pdb=" C   THR E 107 "
      ideal   model   delta    sigma   weight residual
     113.18  102.18   11.00 1.21e+00 6.83e-01 8.26e+01
  angle pdb=" N   ARG K 293 "
        pdb=" CA  ARG K 293 "
        pdb=" C   ARG K 293 "
      ideal   model   delta    sigma   weight residual
     113.19  102.98   10.21 1.19e+00 7.06e-01 7.36e+01
  angle pdb=" N   ARG L 293 "
        pdb=" CA  ARG L 293 "
        pdb=" C   ARG L 293 "
      ideal   model   delta    sigma   weight residual
     113.19  103.02   10.17 1.19e+00 7.06e-01 7.30e+01
  angle pdb=" N   HIS G 113 "
        pdb=" CA  HIS G 113 "
        pdb=" C   HIS G 113 "
      ideal   model   delta    sigma   weight residual
     108.78  115.18   -6.40 8.20e-01 1.49e+00 6.09e+01
  angle pdb=" CA  TYR K 513 "
        pdb=" C   TYR K 513 "
        pdb=" O   TYR K 513 "
      ideal   model   delta    sigma   weight residual
     120.23  112.38    7.85 1.02e+00 9.61e-01 5.92e+01
  ... (remaining 28248 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 9936
       35.87 -    71.74: 1333
       71.74 -   107.61: 36
      107.61 -   143.48: 4
      143.48 -   179.35: 7
  Dihedral angle restraints: 11316
    sinusoidal: 6552
      harmonic: 4764
  Sorted by residual:
  dihedral pdb=" C5' ADP L 802 "
           pdb=" O5' ADP L 802 "
           pdb=" PA  ADP L 802 "
           pdb=" O2A ADP L 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  155.31  144.70     1      2.00e+01 2.50e-03 4.36e+01
  dihedral pdb=" C5' ADP K 802 "
           pdb=" O5' ADP K 802 "
           pdb=" PA  ADP K 802 "
           pdb=" O2A ADP K 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  155.36  144.64     1      2.00e+01 2.50e-03 4.36e+01
  dihedral pdb=" O2A ADP L 802 "
           pdb=" O3A ADP L 802 "
           pdb=" PA  ADP L 802 "
           pdb=" PB  ADP L 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   58.10 -118.10     1      2.00e+01 2.50e-03 3.53e+01
  ... (remaining 11313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.186: 3123
       0.186 -    0.371: 58
       0.371 -    0.557: 0
       0.557 -    0.742: 1
       0.742 -    0.928: 3
  Chirality restraints: 3185
  Sorted by residual:
  chirality pdb=" C3'  DG I 101 "
            pdb=" C4'  DG I 101 "
            pdb=" O3'  DG I 101 "
            pdb=" C2'  DG I 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -1.80   -0.93 2.00e-01 2.50e+01 2.15e+01
  chirality pdb=" C3'  DG I 126 "
            pdb=" C4'  DG I 126 "
            pdb=" O3'  DG I 126 "
            pdb=" C2'  DG I 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -1.84   -0.89 2.00e-01 2.50e+01 2.00e+01
  chirality pdb=" C3'  DG J 138 "
            pdb=" C4'  DG J 138 "
            pdb=" O3'  DG J 138 "
            pdb=" C2'  DG J 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -1.90   -0.83 2.00e-01 2.50e+01 1.71e+01
  ... (remaining 3182 not shown)

  Planarity restraints: 2576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP K 250 "    0.023 2.00e-02 2.50e+03   4.61e-02 2.13e+01
        pdb=" C   ASP K 250 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   ASP K 250 "    0.030 2.00e-02 2.50e+03
        pdb=" N   GLY K 251 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR K 550 "   -0.020 2.00e-02 2.50e+03   3.80e-02 1.44e+01
        pdb=" C   THR K 550 "    0.066 2.00e-02 2.50e+03
        pdb=" O   THR K 550 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS K 551 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L 550 "    0.020 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   THR L 550 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   THR L 550 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LYS L 551 "    0.022 2.00e-02 2.50e+03
  ... (remaining 2573 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 2731
        2.75 -     3.29: 18188
        3.29 -     3.83: 33616
        3.83 -     4.36: 42010
        4.36 -     4.90: 61302
  Nonbonded interactions: 157847
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ASP C  91 "
            pdb=" OG  SER C  95 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" NH1 ARG G  30 "
            pdb=" O   THR H  61 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" OD1 ASN K 368 "
            pdb=" N   SER K 370 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OD1 ASN L 368 "
            pdb=" N   SER L 370 "
     model   vdw
     2.320 3.120
  ... (remaining 157842 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 41 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 17 through 100)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 18 through 116)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  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:             0.020
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     18.530
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
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      :  0.010   0.110  20028  Z= 0.698
  Angle     :  1.302  16.065  28253  Z= 0.915
  Chirality :  0.074   0.928   3185
  Planarity :  0.007   0.056   2576
  Dihedral  : 24.532 179.348   8238
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.51 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  6.17 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.19), residues: 1622
  helix: -1.34 (0.16), residues: 870
  sheet: -2.76 (0.41), residues: 120
  loop : -2.81 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  89 
 TYR   0.041   0.003   TYR L 329 
 PHE   0.048   0.003   PHE C  26 
 TRP   0.038   0.002   TRP K 217 
 HIS   0.014   0.002   HIS K 541 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01015 /  0.70 (20028)
  covalent geometry    : angle       1.30221 /  0.92 (28253)
  hydrogen bonds       : bond        0.22885 / 15.43 (  914)
  hydrogen bonds       : angle       9.11710 /  6.38 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 541
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8716 (tt0) cc_final: 0.8366 (mt0)
REVERT: B   25 ASN cc_start: 0.7831 (m-40) cc_final: 0.7487 (m110)
REVERT: B   88 TYR cc_start: 0.8317 (m-10) cc_final: 0.7386 (m-10)
REVERT: C   25 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8179 (mm-40)
REVERT: C   73 ASP cc_start: 0.8119 (t0) cc_final: 0.7809 (t0)
REVERT: D   80 SER cc_start: 0.8842 (p) cc_final: 0.8610 (m)
REVERT: D   81 SER cc_start: 0.9099 (t) cc_final: 0.8827 (m)
REVERT: E   58 THR cc_start: 0.7554 (p) cc_final: 0.7251 (p)
REVERT: E  120 MET cc_start: 0.8020 (mpp) cc_final: 0.7776 (mtp)
REVERT: E  126 LEU cc_start: 0.9279 (tp) cc_final: 0.9073 (tp)
REVERT: F   84 MET cc_start: 0.7503 (tpp) cc_final: 0.7275 (tpp)
REVERT: F   88 TYR cc_start: 0.8779 (m-10) cc_final: 0.8003 (m-10)
REVERT: F   96 THR cc_start: 0.8856 (m) cc_final: 0.8541 (t)
REVERT: G   58 TYR cc_start: 0.7832 (t80) cc_final: 0.7326 (t80)
REVERT: H   97 LYS cc_start: 0.8381 (mttt) cc_final: 0.8180 (mptt)
REVERT: H  108 TYR cc_start: 0.7993 (m-10) cc_final: 0.7791 (m-10)
REVERT: K  208 LYS cc_start: 0.8413 (tptt) cc_final: 0.8027 (tttt)
REVERT: K  211 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8746 (tptt)
REVERT: K  229 MET cc_start: 0.4725 (ptt) cc_final: 0.3363 (ptm)
REVERT: K  238 ILE cc_start: 0.6609 (mm) cc_final: 0.5981 (tp)
REVERT: K  259 LEU cc_start: 0.7624 (mt) cc_final: 0.7182 (mp)
REVERT: K  260 SER cc_start: 0.8420 (p) cc_final: 0.7974 (m)
REVERT: K  268 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6200 (mm-30)
REVERT: K  269 ILE cc_start: 0.3059 (OUTLIER) cc_final: 0.2566 (mm)
REVERT: K  272 PHE cc_start: 0.5472 (m-80) cc_final: 0.5134 (m-80)
REVERT: K  312 GLU cc_start: 0.8728 (mp0) cc_final: 0.8405 (mt-10)
REVERT: K  313 VAL cc_start: 0.7729 (t) cc_final: 0.7100 (t)
REVERT: K  348 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6642 (mt-10)
REVERT: K  487 ASN cc_start: 0.7789 (t0) cc_final: 0.7543 (p0)
REVERT: K  491 ILE cc_start: 0.8442 (mm) cc_final: 0.8155 (mm)
REVERT: K  526 PHE cc_start: 0.7698 (t80) cc_final: 0.7337 (t80)
REVERT: K  654 ILE cc_start: 0.8506 (mm) cc_final: 0.8014 (tt)
REVERT: L  229 MET cc_start: 0.7645 (ptt) cc_final: 0.7261 (ptm)
REVERT: L  261 THR cc_start: 0.8687 (p) cc_final: 0.8348 (t)
REVERT: L  268 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: L  269 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8154 (mt)
REVERT: L  279 ILE cc_start: 0.8401 (tp) cc_final: 0.8092 (mt)
REVERT: L  322 LEU cc_start: 0.7295 (tp) cc_final: 0.6538 (mt)
REVERT: L  359 LEU cc_start: 0.8510 (mt) cc_final: 0.8157 (mp)
REVERT: L  379 ILE cc_start: 0.5412 (tp) cc_final: 0.5205 (tp)
REVERT: L  442 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7272 (mtm-85)
REVERT: L  504 GLN cc_start: 0.8117 (tp40) cc_final: 0.7789 (tp40)
REVERT: L  549 TRP cc_start: 0.8417 (m-10) cc_final: 0.7686 (m-10)
REVERT: L  628 LEU cc_start: 0.8520 (mt) cc_final: 0.8214 (tp)
REVERT: L  660 LYS cc_start: 0.8668 (tttt) cc_final: 0.8441 (mttt)
  outliers start: 20
  outliers final: 0
  residues processed: 554
  average time/residue: 0.1735
  time to fit residues: 134.6121
Evaluate side-chains
  270 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 267
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   30.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  88 ASN
E  55 GLN
H  74 HIS
** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 282 HIS
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 488 ASN
K 498 ASN
K 608 ASN
** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.107488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.075749 restraints weight = 70934.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077171 restraints weight = 42968.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.077762 restraints weight = 26508.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.078070 restraints weight = 22512.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.078008 restraints weight = 21722.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  20028  Z= 0.255
  Angle     :  0.907  12.323  28253  Z= 0.486
  Chirality :  0.054   0.345   3185
  Planarity :  0.007   0.089   2576
  Dihedral  : 28.634 179.464   4914
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.41 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.33 %
    Favored  : 94.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.20), residues: 1622
  helix: -0.01 (0.16), residues: 924
  sheet: -2.28 (0.42), residues: 128
  loop : -2.54 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG F  19 
 TYR   0.033   0.003   TYR K 513 
 PHE   0.025   0.002   PHE K 240 
 TRP   0.029   0.003   TRP L 622 
 HIS   0.014   0.002   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00520 /  0.26 (20028)
  covalent geometry    : angle       0.90697 /  0.49 (28253)
  hydrogen bonds       : bond        0.08399 /  5.99 (  914)
  hydrogen bonds       : angle       4.50605 /  3.20 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 325
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8340 (mtmm)
REVERT: A   59 GLU cc_start: 0.8131 (pp20) cc_final: 0.7500 (pp20)
REVERT: A   68 GLN cc_start: 0.8690 (tt0) cc_final: 0.8353 (mt0)
REVERT: B   82 THR cc_start: 0.9385 (t) cc_final: 0.9172 (m)
REVERT: C   25 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8369 (mm-40)
REVERT: D   81 SER cc_start: 0.9067 (t) cc_final: 0.8807 (m)
REVERT: D   84 MET cc_start: 0.9016 (tpp) cc_final: 0.8758 (tpp)
REVERT: E  120 MET cc_start: 0.8304 (mpp) cc_final: 0.8072 (mtp)
REVERT: F   84 MET cc_start: 0.8048 (tpp) cc_final: 0.7547 (tpp)
REVERT: F   88 TYR cc_start: 0.8842 (m-10) cc_final: 0.8335 (m-10)
REVERT: G   57 GLU cc_start: 0.8051 (tt0) cc_final: 0.7823 (mt-10)
REVERT: G   58 TYR cc_start: 0.7753 (t80) cc_final: 0.7506 (t80)
REVERT: G   62 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6933 (mt-10)
REVERT: H   98 LEU cc_start: 0.9194 (mt) cc_final: 0.8959 (mp)
REVERT: K  229 MET cc_start: 0.3632 (ptt) cc_final: 0.3382 (ptm)
REVERT: K  329 TYR cc_start: 0.6046 (m-80) cc_final: 0.5435 (m-80)
REVERT: K  506 GLN cc_start: 0.7876 (pt0) cc_final: 0.7675 (pp30)
REVERT: K  526 PHE cc_start: 0.7719 (t80) cc_final: 0.7517 (t80)
REVERT: K  549 TRP cc_start: 0.7489 (m-10) cc_final: 0.7127 (m-90)
REVERT: K  617 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (tp)
REVERT: K  654 ILE cc_start: 0.8513 (mm) cc_final: 0.8237 (tt)
REVERT: L  229 MET cc_start: 0.7790 (ptt) cc_final: 0.7294 (ptp)
REVERT: L  253 TYR cc_start: 0.5181 (t80) cc_final: 0.4915 (t80)
REVERT: L  315 MET cc_start: 0.8424 (ttt) cc_final: 0.8202 (ttm)
REVERT: L  322 LEU cc_start: 0.7724 (tp) cc_final: 0.6910 (mt)
REVERT: L  442 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7296 (mtm-85)
REVERT: L  452 MET cc_start: 0.6947 (tmm) cc_final: 0.6660 (tmm)
REVERT: L  660 LYS cc_start: 0.8571 (tttt) cc_final: 0.8345 (mttt)
  outliers start: 4
  outliers final: 0
  residues processed: 329
  average time/residue: 0.1443
  time to fit residues: 70.8978
Evaluate side-chains
  228 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 132 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 140 optimal weight:    9.9990
   chunk 176 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 92 optimal weight:   20.0000
   chunk 150 optimal weight:    4.9990
   chunk 107 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.4175 > 50:)
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 341 HIS
** K 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 625 GLN
** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.105855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.074494 restraints weight = 71367.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.075783 restraints weight = 43933.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.076511 restraints weight = 26848.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.076877 restraints weight = 22221.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.076859 restraints weight = 21100.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.4422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  20028  Z= 0.184
  Angle     :  0.726  11.931  28253  Z= 0.399
  Chirality :  0.047   0.249   3185
  Planarity :  0.005   0.079   2576
  Dihedral  : 28.412 178.480   4914
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.98 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.81 (0.21), residues: 1622
  helix:  0.66 (0.17), residues: 937
  sheet: -2.14 (0.41), residues: 148
  loop : -2.16 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  89 
 TYR   0.019   0.002   TYR K 311 
 PHE   0.034   0.002   PHE K 240 
 TRP   0.023   0.002   TRP K 373 
 HIS   0.007   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.18 (20028)
  covalent geometry    : angle       0.72614 /  0.40 (28253)
  hydrogen bonds       : bond        0.06801 /  4.85 (  914)
  hydrogen bonds       : angle       4.07612 /  2.92 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8185 (pp20) cc_final: 0.7423 (pp20)
REVERT: A   68 GLN cc_start: 0.8728 (tt0) cc_final: 0.8427 (mt0)
REVERT: B   82 THR cc_start: 0.9394 (t) cc_final: 0.9188 (m)
REVERT: C   25 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8406 (mm-40)
REVERT: D   81 SER cc_start: 0.8914 (t) cc_final: 0.8707 (m)
REVERT: D   84 MET cc_start: 0.8905 (tpp) cc_final: 0.8471 (tpp)
REVERT: E  120 MET cc_start: 0.8411 (mpp) cc_final: 0.7961 (mtp)
REVERT: G   57 GLU cc_start: 0.8122 (tt0) cc_final: 0.7698 (mt-10)
REVERT: G   62 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7242 (mt-10)
REVERT: H   76 ASP cc_start: 0.8317 (p0) cc_final: 0.7991 (p0)
REVERT: H   98 LEU cc_start: 0.9266 (mt) cc_final: 0.9005 (mp)
REVERT: K  241 LEU cc_start: 0.6399 (mm) cc_final: 0.6121 (pp)
REVERT: K  260 SER cc_start: 0.8527 (m) cc_final: 0.8163 (p)
REVERT: K  329 TYR cc_start: 0.5998 (m-80) cc_final: 0.5333 (m-80)
REVERT: K  348 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6950 (mm-30)
REVERT: K  491 ILE cc_start: 0.8348 (mm) cc_final: 0.8099 (mp)
REVERT: K  549 TRP cc_start: 0.7625 (m-10) cc_final: 0.7257 (m-90)
REVERT: K  559 TYR cc_start: 0.4512 (t80) cc_final: 0.4283 (t80)
REVERT: K  616 ILE cc_start: 0.7262 (tp) cc_final: 0.6924 (tp)
REVERT: L  315 MET cc_start: 0.8424 (ttt) cc_final: 0.8197 (ttm)
REVERT: L  322 LEU cc_start: 0.7812 (tp) cc_final: 0.6999 (mt)
REVERT: L  428 ILE cc_start: 0.7829 (mp) cc_final: 0.7614 (mp)
REVERT: L  442 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7343 (mtm-85)
REVERT: L  660 LYS cc_start: 0.8427 (tttt) cc_final: 0.8213 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.1507
  time to fit residues: 69.4340
Evaluate side-chains
  212 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 137 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 153 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 129 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 182 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN
K 236 GLN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 462 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.102616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.070705 restraints weight = 71243.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.072116 restraints weight = 42739.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.072651 restraints weight = 26905.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.072918 restraints weight = 22778.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.072886 restraints weight = 21808.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.5204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  20028  Z= 0.214
  Angle     :  0.764  12.229  28253  Z= 0.413
  Chirality :  0.048   0.221   3185
  Planarity :  0.005   0.066   2576
  Dihedral  : 28.291 179.104   4914
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.54 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.57 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.21), residues: 1622
  helix:  0.98 (0.17), residues: 936
  sheet: -2.01 (0.43), residues: 132
  loop : -1.92 (0.25), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K 661 
 TYR   0.042   0.003   TYR D 108 
 PHE   0.033   0.002   PHE K 240 
 TRP   0.015   0.002   TRP L 212 
 HIS   0.008   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.21 (20028)
  covalent geometry    : angle       0.76418 /  0.41 (28253)
  hydrogen bonds       : bond        0.06806 /  4.84 (  914)
  hydrogen bonds       : angle       3.98258 /  2.86 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 279
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7913 (pp20) cc_final: 0.7467 (pp20)
REVERT: A   68 GLN cc_start: 0.8769 (tt0) cc_final: 0.8453 (mt0)
REVERT: B   88 TYR cc_start: 0.8643 (m-10) cc_final: 0.8134 (m-10)
REVERT: C   25 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8466 (mm-40)
REVERT: C   62 GLU cc_start: 0.7698 (tp30) cc_final: 0.7449 (tp30)
REVERT: D   84 MET cc_start: 0.8931 (tpp) cc_final: 0.8722 (tpp)
REVERT: E  120 MET cc_start: 0.8585 (mpp) cc_final: 0.8255 (mtp)
REVERT: G   57 GLU cc_start: 0.8183 (tt0) cc_final: 0.7946 (tt0)
REVERT: H   76 ASP cc_start: 0.8212 (p0) cc_final: 0.7979 (p0)
REVERT: K  241 LEU cc_start: 0.6448 (mm) cc_final: 0.6229 (pp)
REVERT: K  260 SER cc_start: 0.8322 (m) cc_final: 0.7978 (m)
REVERT: K  280 ILE cc_start: 0.6909 (mt) cc_final: 0.6694 (mp)
REVERT: K  312 GLU cc_start: 0.8713 (mp0) cc_final: 0.8483 (mt-10)
REVERT: K  329 TYR cc_start: 0.6143 (m-80) cc_final: 0.5252 (m-80)
REVERT: K  350 LYS cc_start: 0.5471 (mtmm) cc_final: 0.5173 (mttp)
REVERT: K  432 MET cc_start: 0.4829 (mpp) cc_final: 0.4454 (ptp)
REVERT: K  469 GLU cc_start: 0.7205 (pt0) cc_final: 0.6830 (tp30)
REVERT: K  549 TRP cc_start: 0.7724 (m-10) cc_final: 0.7246 (m-90)
REVERT: K  559 TYR cc_start: 0.4742 (t80) cc_final: 0.4496 (t80)
REVERT: K  577 ASP cc_start: 0.7803 (t0) cc_final: 0.7396 (p0)
REVERT: L  206 GLN cc_start: 0.8101 (mt0) cc_final: 0.7586 (tm-30)
REVERT: L  268 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8041 (tm-30)
REVERT: L  315 MET cc_start: 0.8543 (ttt) cc_final: 0.8322 (ttm)
  outliers start: 2
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1285
  time to fit residues: 55.2768
Evaluate side-chains
  200 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 143 optimal weight:    5.9990
   chunk 172 optimal weight:    0.0060
   chunk 26 optimal weight:   10.0000
   chunk 139 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 90 optimal weight:   30.0000
   chunk 184 optimal weight:    9.9990
   chunk 120 optimal weight:   30.0000
   chunk 113 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    4.6004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
F  64 ASN
K 264 ASN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 498 ASN
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.100875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.068817 restraints weight = 71792.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.070271 restraints weight = 42636.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.070598 restraints weight = 26573.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.070917 restraints weight = 23777.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.070833 restraints weight = 22532.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.5794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  20028  Z= 0.221
  Angle     :  0.753  12.228  28253  Z= 0.408
  Chirality :  0.048   0.297   3185
  Planarity :  0.005   0.069   2576
  Dihedral  : 28.170 179.231   4914
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.10 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.21), residues: 1622
  helix:  0.98 (0.17), residues: 949
  sheet: -2.13 (0.40), residues: 152
  loop : -2.01 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  83 
 TYR   0.019   0.002   TYR F  88 
 PHE   0.033   0.002   PHE K 240 
 TRP   0.019   0.002   TRP K 265 
 HIS   0.019   0.002   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.22 (20028)
  covalent geometry    : angle       0.75348 /  0.41 (28253)
  hydrogen bonds       : bond        0.06638 /  4.71 (  914)
  hydrogen bonds       : angle       3.94086 /  2.82 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7937 (pp20) cc_final: 0.7439 (pp20)
REVERT: A   68 GLN cc_start: 0.8731 (tt0) cc_final: 0.8445 (mt0)
REVERT: D   84 MET cc_start: 0.8966 (tpp) cc_final: 0.8734 (tpp)
REVERT: E  120 MET cc_start: 0.8713 (mpp) cc_final: 0.8465 (mtp)
REVERT: G   57 GLU cc_start: 0.8102 (tt0) cc_final: 0.7863 (tt0)
REVERT: G   58 TYR cc_start: 0.7923 (t80) cc_final: 0.7232 (t80)
REVERT: K  241 LEU cc_start: 0.6693 (mm) cc_final: 0.6415 (pp)
REVERT: K  280 ILE cc_start: 0.6802 (mt) cc_final: 0.6597 (mp)
REVERT: K  312 GLU cc_start: 0.8739 (mp0) cc_final: 0.8507 (mt-10)
REVERT: K  329 TYR cc_start: 0.6244 (m-80) cc_final: 0.5409 (m-80)
REVERT: K  452 MET cc_start: 0.3023 (mtp) cc_final: 0.2684 (ttm)
REVERT: K  469 GLU cc_start: 0.7338 (pt0) cc_final: 0.6894 (tp30)
REVERT: K  577 ASP cc_start: 0.7954 (t0) cc_final: 0.7478 (p0)
REVERT: K  661 ARG cc_start: 0.8459 (ttt90) cc_final: 0.8114 (ttp80)
REVERT: L  206 GLN cc_start: 0.8190 (mt0) cc_final: 0.7714 (tm-30)
REVERT: L  229 MET cc_start: 0.7549 (ptp) cc_final: 0.7202 (ptp)
REVERT: L  268 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: L  315 MET cc_start: 0.8569 (ttt) cc_final: 0.8366 (ttm)
REVERT: L  322 LEU cc_start: 0.7974 (tp) cc_final: 0.7694 (pp)
REVERT: L  354 MET cc_start: 0.7689 (mpp) cc_final: 0.7460 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1268
  time to fit residues: 51.7707
Evaluate side-chains
  184 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 181 optimal weight:    8.9990
   chunk 163 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 148 optimal weight:    9.9990
   chunk 182 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0060
   chunk 135 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 157 optimal weight:    1.9990
   overall best weight:    1.4004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
F  64 ASN
G 105 ASN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 608 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.102201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.069691 restraints weight = 70946.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.071356 restraints weight = 39138.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.072340 restraints weight = 27628.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.072764 restraints weight = 23076.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 65)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.073123 restraints weight = 21094.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  20028  Z= 0.141
  Angle     :  0.671  11.065  28253  Z= 0.368
  Chirality :  0.045   0.224   3185
  Planarity :  0.004   0.040   2576
  Dihedral  : 28.049 178.545   4914
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.30 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.21), residues: 1622
  helix:  1.41 (0.17), residues: 933
  sheet: -1.86 (0.42), residues: 144
  loop : -1.83 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 494 
 TYR   0.026   0.002   TYR B  88 
 PHE   0.025   0.001   PHE K 240 
 TRP   0.016   0.002   TRP K 265 
 HIS   0.010   0.001   HIS L 455 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (20028)
  covalent geometry    : angle       0.67130 /  0.37 (28253)
  hydrogen bonds       : bond        0.05725 /  4.15 (  914)
  hydrogen bonds       : angle       3.60690 /  2.58 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 VAL cc_start: 0.8667 (m) cc_final: 0.8362 (p)
REVERT: A   59 GLU cc_start: 0.7762 (pp20) cc_final: 0.7349 (pp20)
REVERT: A   64 LYS cc_start: 0.9004 (mptt) cc_final: 0.8577 (mmtp)
REVERT: A   68 GLN cc_start: 0.8624 (tt0) cc_final: 0.8412 (mt0)
REVERT: C   65 GLU cc_start: 0.8458 (pt0) cc_final: 0.7767 (pt0)
REVERT: C   92 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7748 (mm-30)
REVERT: D   72 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: D   84 MET cc_start: 0.8840 (tpp) cc_final: 0.8553 (tpp)
REVERT: E  120 MET cc_start: 0.8682 (mpp) cc_final: 0.8315 (mtp)
REVERT: G   57 GLU cc_start: 0.8075 (tt0) cc_final: 0.7845 (tt0)
REVERT: G   62 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7209 (mt-10)
REVERT: K  241 LEU cc_start: 0.6942 (mm) cc_final: 0.6664 (pp)
REVERT: K  280 ILE cc_start: 0.7045 (mt) cc_final: 0.6831 (mp)
REVERT: K  312 GLU cc_start: 0.8755 (mp0) cc_final: 0.8543 (mt-10)
REVERT: K  432 MET cc_start: 0.4809 (mpp) cc_final: 0.4477 (ptp)
REVERT: K  469 GLU cc_start: 0.7230 (pt0) cc_final: 0.6797 (tp30)
REVERT: K  577 ASP cc_start: 0.8025 (t0) cc_final: 0.7632 (p0)
REVERT: K  661 ARG cc_start: 0.8430 (ttt90) cc_final: 0.8119 (ttp80)
REVERT: L  206 GLN cc_start: 0.8068 (mt0) cc_final: 0.7651 (tm-30)
REVERT: L  238 ILE cc_start: 0.8113 (mm) cc_final: 0.7882 (mm)
REVERT: L  268 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: L  315 MET cc_start: 0.8514 (ttt) cc_final: 0.8311 (ttm)
REVERT: L  322 LEU cc_start: 0.7973 (tp) cc_final: 0.7596 (pp)
REVERT: L  446 ILE cc_start: 0.7575 (mp) cc_final: 0.7177 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1298
  time to fit residues: 52.8409
Evaluate side-chains
  193 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 160 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 148 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 136 optimal weight:    5.9990
   chunk 88 optimal weight:   30.0000
   chunk 34 optimal weight:    1.9990
   chunk 151 optimal weight:    6.9990
   chunk 81 optimal weight:   30.0000
   chunk 72 optimal weight:   30.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
D  88 ASN
D  92 ASN
F  93 GLN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.099934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.068207 restraints weight = 71260.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.069737 restraints weight = 41249.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.070738 restraints weight = 25295.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.070611 restraints weight = 23093.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.070491 restraints weight = 21396.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.6411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  20028  Z= 0.209
  Angle     :  0.739  11.817  28253  Z= 0.396
  Chirality :  0.046   0.213   3185
  Planarity :  0.005   0.044   2576
  Dihedral  : 28.061 177.975   4914
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.47 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.21), residues: 1622
  helix:  1.24 (0.17), residues: 937
  sheet: -1.79 (0.44), residues: 128
  loop : -1.80 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L 293 
 TYR   0.026   0.002   TYR K 513 
 PHE   0.022   0.002   PHE K 240 
 TRP   0.012   0.002   TRP K 373 
 HIS   0.010   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.21 (20028)
  covalent geometry    : angle       0.73949 /  0.40 (28253)
  hydrogen bonds       : bond        0.06557 /  4.63 (  914)
  hydrogen bonds       : angle       3.83688 /  2.73 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7780 (pp20) cc_final: 0.7338 (pp20)
REVERT: A   68 GLN cc_start: 0.8687 (tt0) cc_final: 0.8477 (mt0)
REVERT: B   88 TYR cc_start: 0.8648 (m-10) cc_final: 0.7859 (m-10)
REVERT: C   65 GLU cc_start: 0.8304 (pt0) cc_final: 0.7569 (pt0)
REVERT: C   96 LYS cc_start: 0.8806 (mppt) cc_final: 0.8195 (mtmm)
REVERT: D   72 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: D   84 MET cc_start: 0.8951 (tpp) cc_final: 0.8715 (tpp)
REVERT: E  120 MET cc_start: 0.8761 (mpp) cc_final: 0.8475 (mtp)
REVERT: F   66 ILE cc_start: 0.9420 (mm) cc_final: 0.9217 (mm)
REVERT: G   58 TYR cc_start: 0.7716 (t80) cc_final: 0.7042 (t80)
REVERT: H  108 TYR cc_start: 0.7740 (m-80) cc_final: 0.7386 (m-80)
REVERT: K  241 LEU cc_start: 0.6938 (mm) cc_final: 0.6622 (pp)
REVERT: K  469 GLU cc_start: 0.7485 (pt0) cc_final: 0.6946 (tp30)
REVERT: K  577 ASP cc_start: 0.8025 (t0) cc_final: 0.7686 (p0)
REVERT: K  661 ARG cc_start: 0.8479 (ttt90) cc_final: 0.8179 (ttp80)
REVERT: L  206 GLN cc_start: 0.8216 (mt0) cc_final: 0.7750 (tm-30)
REVERT: L  229 MET cc_start: 0.7422 (ptp) cc_final: 0.7113 (ptp)
REVERT: L  238 ILE cc_start: 0.8179 (mm) cc_final: 0.7963 (mm)
REVERT: L  268 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: L  315 MET cc_start: 0.8542 (ttt) cc_final: 0.8337 (ttm)
REVERT: L  446 ILE cc_start: 0.7669 (mp) cc_final: 0.7219 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1322
  time to fit residues: 49.1143
Evaluate side-chains
  179 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 167 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 156 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 141 optimal weight:    6.9990
   chunk 184 optimal weight:    2.9990
   chunk 163 optimal weight:    5.9990
   chunk 174 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
F  27 GLN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.099676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.068673 restraints weight = 71290.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.069823 restraints weight = 45979.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.069743 restraints weight = 28258.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.070064 restraints weight = 28325.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.070099 restraints weight = 25628.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.6689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  20028  Z= 0.192
  Angle     :  0.710  11.925  28253  Z= 0.386
  Chirality :  0.046   0.231   3185
  Planarity :  0.005   0.049   2576
  Dihedral  : 28.002 177.010   4914
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.04 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.21), residues: 1622
  helix:  1.29 (0.17), residues: 949
  sheet: -1.96 (0.43), residues: 134
  loop : -1.85 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG K 430 
 TYR   0.016   0.002   TYR B  88 
 PHE   0.015   0.002   PHE K 240 
 TRP   0.017   0.002   TRP L 212 
 HIS   0.006   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.19 (20028)
  covalent geometry    : angle       0.70951 /  0.39 (28253)
  hydrogen bonds       : bond        0.06080 /  4.36 (  914)
  hydrogen bonds       : angle       3.76973 /  2.69 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9688 (ttpt) cc_final: 0.9428 (ttpp)
REVERT: A   59 GLU cc_start: 0.7757 (pp20) cc_final: 0.7363 (pp20)
REVERT: A   68 GLN cc_start: 0.8702 (tt0) cc_final: 0.8448 (mt0)
REVERT: C   62 GLU cc_start: 0.7680 (tp30) cc_final: 0.7247 (tp30)
REVERT: C   65 GLU cc_start: 0.8487 (pt0) cc_final: 0.7760 (pt0)
REVERT: C   96 LYS cc_start: 0.8717 (mppt) cc_final: 0.8108 (mmtp)
REVERT: D   72 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: D   84 MET cc_start: 0.8916 (tpp) cc_final: 0.8673 (tpp)
REVERT: E  120 MET cc_start: 0.8775 (mpp) cc_final: 0.8552 (mtp)
REVERT: K  241 LEU cc_start: 0.6919 (mm) cc_final: 0.6637 (pp)
REVERT: K  338 LEU cc_start: 0.8685 (mp) cc_final: 0.8463 (tt)
REVERT: K  432 MET cc_start: 0.5078 (mpp) cc_final: 0.4707 (ptp)
REVERT: K  469 GLU cc_start: 0.7563 (pt0) cc_final: 0.7007 (tp30)
REVERT: K  577 ASP cc_start: 0.7939 (t0) cc_final: 0.7549 (p0)
REVERT: K  661 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8363 (ttp80)
REVERT: L  206 GLN cc_start: 0.8230 (mt0) cc_final: 0.7774 (tm-30)
REVERT: L  229 MET cc_start: 0.7417 (ptp) cc_final: 0.7197 (ptp)
REVERT: L  268 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7877 (tm-30)
REVERT: L  315 MET cc_start: 0.8598 (ttt) cc_final: 0.8380 (ttm)
REVERT: L  446 ILE cc_start: 0.7604 (mp) cc_final: 0.7077 (tp)
REVERT: L  448 MET cc_start: 0.7998 (mpp) cc_final: 0.7558 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1441
  time to fit residues: 52.0864
Evaluate side-chains
  179 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 161 optimal weight:    0.9990
   chunk 83 optimal weight:   50.0000
   chunk 174 optimal weight:   10.0000
   chunk 159 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 73 optimal weight:   30.0000
   chunk 105 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9990
   chunk 92 optimal weight:   20.0000
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
F  27 GLN
F  93 GLN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.100941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.070102 restraints weight = 70916.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.071338 restraints weight = 44671.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.071527 restraints weight = 27206.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.071742 restraints weight = 27373.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071767 restraints weight = 24165.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.6812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20028  Z= 0.141
  Angle     :  0.671  12.010  28253  Z= 0.367
  Chirality :  0.044   0.275   3185
  Planarity :  0.004   0.045   2576
  Dihedral  : 27.917 176.595   4914
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.55 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.22), residues: 1622
  helix:  1.57 (0.17), residues: 931
  sheet: -1.83 (0.41), residues: 150
  loop : -1.73 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 527 
 TYR   0.023   0.002   TYR B  88 
 PHE   0.013   0.001   PHE K 240 
 TRP   0.023   0.002   TRP K 373 
 HIS   0.004   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.14 (20028)
  covalent geometry    : angle       0.67119 /  0.37 (28253)
  hydrogen bonds       : bond        0.05524 /  4.04 (  914)
  hydrogen bonds       : angle       3.57673 /  2.56 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9671 (ttpt) cc_final: 0.9404 (ttpp)
REVERT: A   59 GLU cc_start: 0.7841 (pp20) cc_final: 0.7361 (pp20)
REVERT: A   64 LYS cc_start: 0.8883 (mptt) cc_final: 0.8493 (mmtp)
REVERT: C   62 GLU cc_start: 0.7546 (tp30) cc_final: 0.7261 (tp30)
REVERT: C   65 GLU cc_start: 0.8380 (pt0) cc_final: 0.7783 (pt0)
REVERT: C   96 LYS cc_start: 0.8357 (mppt) cc_final: 0.7813 (mmtp)
REVERT: D   72 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: D   84 MET cc_start: 0.8826 (tpp) cc_final: 0.8606 (tpp)
REVERT: E  120 MET cc_start: 0.8757 (mpp) cc_final: 0.8384 (mtp)
REVERT: F   50 ILE cc_start: 0.9369 (mm) cc_final: 0.9162 (mm)
REVERT: G   92 GLU cc_start: 0.7652 (pm20) cc_final: 0.7438 (tp30)
REVERT: H  110 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7771 (mmmt)
REVERT: K  241 LEU cc_start: 0.6869 (mm) cc_final: 0.6627 (pp)
REVERT: K  363 THR cc_start: 0.8018 (m) cc_final: 0.7630 (m)
REVERT: K  373 TRP cc_start: 0.6898 (t60) cc_final: 0.6667 (t60)
REVERT: K  469 GLU cc_start: 0.7484 (pt0) cc_final: 0.6960 (tp30)
REVERT: K  577 ASP cc_start: 0.7845 (t0) cc_final: 0.7512 (p0)
REVERT: L  206 GLN cc_start: 0.8177 (mt0) cc_final: 0.7723 (tm-30)
REVERT: L  229 MET cc_start: 0.7399 (ptp) cc_final: 0.7173 (ptp)
REVERT: L  268 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: L  296 MET cc_start: 0.7631 (ptt) cc_final: 0.7126 (mpp)
REVERT: L  315 MET cc_start: 0.8482 (ttt) cc_final: 0.8273 (ttm)
REVERT: L  432 MET cc_start: 0.6516 (mmm) cc_final: 0.6265 (tpp)
REVERT: L  446 ILE cc_start: 0.7579 (mp) cc_final: 0.7003 (tp)
REVERT: L  448 MET cc_start: 0.8121 (mpp) cc_final: 0.7732 (mpp)
REVERT: L  614 THR cc_start: 0.8188 (p) cc_final: 0.7695 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.1413
  time to fit residues: 54.9575
Evaluate side-chains
  185 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 171 optimal weight:    0.9980
   chunk 157 optimal weight:    0.7980
   chunk 140 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 81 optimal weight:   40.0000
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 177 optimal weight:   10.0000
   chunk 135 optimal weight:   20.0000
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
D  74 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.100757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.069456 restraints weight = 71408.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.070998 restraints weight = 42763.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.071469 restraints weight = 26714.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071645 restraints weight = 23961.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071638 restraints weight = 22263.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.6952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  20028  Z= 0.141
  Angle     :  0.672  11.584  28253  Z= 0.366
  Chirality :  0.044   0.298   3185
  Planarity :  0.004   0.046   2576
  Dihedral  : 27.893 176.839   4914
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.61 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.37 (0.22), residues: 1622
  helix:  1.58 (0.17), residues: 946
  sheet: -1.94 (0.41), residues: 138
  loop : -1.59 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 527 
 TYR   0.019   0.002   TYR D  65 
 PHE   0.014   0.001   PHE K 546 
 TRP   0.017   0.002   TRP K 373 
 HIS   0.005   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.14 (20028)
  covalent geometry    : angle       0.67151 /  0.37 (28253)
  hydrogen bonds       : bond        0.05494 /  4.03 (  914)
  hydrogen bonds       : angle       3.52496 /  2.52 ( 2423)

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

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

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3244 Ramachandran restraints generated.
    1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9668 (ttpt) cc_final: 0.9407 (ttpp)
REVERT: A   59 GLU cc_start: 0.7713 (pp20) cc_final: 0.7312 (pp20)
REVERT: A   64 LYS cc_start: 0.8858 (mptt) cc_final: 0.8591 (mmtp)
REVERT: B   88 TYR cc_start: 0.8750 (m-10) cc_final: 0.7614 (m-10)
REVERT: C   62 GLU cc_start: 0.7589 (tp30) cc_final: 0.7130 (tp30)
REVERT: C   65 GLU cc_start: 0.8398 (pt0) cc_final: 0.7760 (pt0)
REVERT: D   72 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: D  108 TYR cc_start: 0.7624 (t80) cc_final: 0.7233 (t80)
REVERT: E  120 MET cc_start: 0.8740 (mpp) cc_final: 0.8349 (mtp)
REVERT: F   50 ILE cc_start: 0.9350 (mm) cc_final: 0.9138 (mm)
REVERT: F   66 ILE cc_start: 0.9348 (mm) cc_final: 0.9122 (mm)
REVERT: G   42 GLU cc_start: 0.8473 (pp20) cc_final: 0.7723 (pp20)
REVERT: G   92 GLU cc_start: 0.7617 (pm20) cc_final: 0.7413 (tp30)
REVERT: K  241 LEU cc_start: 0.6865 (mm) cc_final: 0.6640 (pp)
REVERT: K  363 THR cc_start: 0.7918 (m) cc_final: 0.7532 (m)
REVERT: K  469 GLU cc_start: 0.7521 (pt0) cc_final: 0.6909 (tp30)
REVERT: K  577 ASP cc_start: 0.7895 (t0) cc_final: 0.7526 (p0)
REVERT: L  206 GLN cc_start: 0.8142 (mt0) cc_final: 0.7711 (tm-30)
REVERT: L  268 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: L  296 MET cc_start: 0.7781 (ptt) cc_final: 0.6839 (mpp)
REVERT: L  315 MET cc_start: 0.8466 (ttt) cc_final: 0.8259 (ttm)
REVERT: L  432 MET cc_start: 0.6517 (mmm) cc_final: 0.6267 (tpp)
REVERT: L  446 ILE cc_start: 0.7616 (mp) cc_final: 0.7037 (tp)
REVERT: L  448 MET cc_start: 0.8058 (mpp) cc_final: 0.7670 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1440
  time to fit residues: 52.9022
Evaluate side-chains
  180 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 122 optimal weight:    8.9990
   chunk 85 optimal weight:   50.0000
   chunk 71 optimal weight:   30.0000
   chunk 170 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 90 optimal weight:   30.0000
   chunk 120 optimal weight:   20.0000
   chunk 121 optimal weight:    5.9990
   overall best weight:    3.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  74 HIS
F  27 GLN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.099012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.067749 restraints weight = 71447.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.068578 restraints weight = 44235.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.069215 restraints weight = 28225.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.069445 restraints weight = 23128.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.069373 restraints weight = 22759.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.7200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  20028  Z= 0.188
  Angle     :  0.715  12.113  28253  Z= 0.386
  Chirality :  0.046   0.312   3185
  Planarity :  0.005   0.047   2576
  Dihedral  : 27.937 176.002   4914
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.23 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.21), residues: 1622
  helix:  1.42 (0.17), residues: 941
  sheet: -1.34 (0.52), residues: 92
  loop : -1.71 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L 527 
 TYR   0.023   0.002   TYR K 559 
 PHE   0.021   0.002   PHE K 384 
 TRP   0.022   0.002   TRP K 265 
 HIS   0.008   0.001   HIS K 499 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.19 (20028)
  covalent geometry    : angle       0.71508 /  0.39 (28253)
  hydrogen bonds       : bond        0.06155 /  4.44 (  914)
  hydrogen bonds       : angle       3.79285 /  2.73 ( 2423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3070.24 seconds
wall clock time: 53 minutes 44.41 seconds (3224.41 seconds total)