Starting phenix.real_space_refine
on Fri Jul  3 12:52:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wh5_37529/07_2026/8wh5_37529.map"
  }
  resolution = 3.58
  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: 5
    Type Number    sf(0)   Gaussians
     P     266      5.49       5
     S      29      5.16       5
     C    8448      2.51       5
     N    2701      2.21       5
     O    3219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14663
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 766
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "B"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 617
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 662
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    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: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 695
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "F"
      Number of atoms: 706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 706
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    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: 2710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2710
          Classifications: {'DNA': 133}
          Link IDs: {'rna3p': 132}
    Chain: "J"
      Number of atoms: 2743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2743
          Classifications: {'DNA': 133}
          Link IDs: {'rna3p': 132}
    Chain: "K"
      Number of atoms: 3604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3604
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 16, 'TRANS': 428}
          Chain breaks: 1
  Time building chain proxies: 2.50, per 1000 atoms: 0.17
  Number of scatterers: 14663
  At special positions: 0
  Unit cell: (135.09, 135.945, 117.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P     266     15.00
     O    3219      8.00
     N    2701      7.00
     C    8448      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 459.6 milliseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      64.7% alpha, 4.1% beta
      103 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.524A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.911A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.803A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.793A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.567A  pdb=" N   GLY B  28 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.054A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 46 through 75
      removed outlier: 4.082A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.625A  pdb=" N   ILE C  84 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 98
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 108
      removed outlier: 3.521A  pdb=" N   MET D  84 " --> pdb=" O   SER D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.604A  pdb=" N   ILE D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 149
      removed outlier: 3.823A  pdb=" N   SER D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 55
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 87 through 114
      removed outlier: 3.680A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.711A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 40
    Processing helix  chain 'F' and resid 50 through 75
      removed outlier: 4.243A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.636A  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 75
      removed outlier: 4.423A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG G  72 " --> pdb=" O   GLY G  68 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASP G  73 " --> pdb=" O   ASN G  69 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.512A  pdb=" N   ILE G  84 " --> pdb=" O   VAL G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 98
    Processing helix  chain 'H' and resid 62 through 74
      removed outlier: 3.701A  pdb=" N   LYS H  68 " --> pdb=" O   ILE H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 109
      removed outlier: 4.328A  pdb=" N   SER H  89 " --> pdb=" O   GLY H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 115 through 126
    Processing helix  chain 'H' and resid 129 through 148
      removed outlier: 3.927A  pdb=" N   LYS H 133 " --> pdb=" O   GLY H 129 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 207 through 220
    Processing helix  chain 'K' and resid 233 through 245
      removed outlier: 3.789A  pdb=" N   PHE K 240 " --> pdb=" O   GLN K 236 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU K 241 " --> pdb=" O   THR K 237 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 249
      removed outlier: 4.175A  pdb=" N   LEU K 249 " --> pdb=" O   GLY K 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 246 through 249'
    Processing helix  chain 'K' and resid 258 through 269
    Processing helix  chain 'K' and resid 285 through 294
      removed outlier: 4.216A  pdb=" N   ARG K 292 " --> pdb=" O   ARG K 288 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG K 293 " --> pdb=" O   ASP K 289 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 310 through 317
    Processing helix  chain 'K' and resid 317 through 323
      removed outlier: 4.067A  pdb=" N   ILE K 321 " --> pdb=" O   ASP K 317 " (cutoff:3.500A)
      removed outlier: 3.584A  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: 3.873A  pdb=" N   HIS K 351 " --> pdb=" O   ARG K 347 " (cutoff:3.500A)
      removed outlier: 4.230A  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: 3.652A  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 474
      removed outlier: 3.534A  pdb=" N   GLU K 474 " --> pdb=" O   ALA K 470 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 488 through 499
    Processing helix  chain 'K' and resid 500 through 508
    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: 3.563A  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 604 through 608
      removed outlier: 3.520A  pdb=" N   ILE K 607 " --> pdb=" O   GLY K 604 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN K 608 " --> pdb=" O   LEU K 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 604 through 608'
    Processing helix  chain 'K' and resid 623 through 635
      removed outlier: 4.322A  pdb=" N   ASP K 627 " --> pdb=" O   ASN K 623 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS K 634 " --> pdb=" O   ALA K 630 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 653 through 674
      removed outlier: 3.654A  pdb=" N   VAL K 672 " --> pdb=" O   LEU K 668 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.379A  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 'B' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.401A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA5, first strand: chain 'F' and resid 97 through 98
      removed outlier: 3.696A  pdb=" N   TYR F  98 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.507A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'K' and resid 278 through 280
      removed outlier: 6.673A  pdb=" N   TYR K 253 " --> pdb=" O   VAL K 307 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   THR K 309 " --> pdb=" O   TYR K 253 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL K 255 " --> pdb=" O   THR K 309 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU K 254 " --> pdb=" O   VAL K 331 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 444 through 450
      removed outlier: 3.587A  pdb=" N   MET K 448 " --> pdb=" O   ARG K 647 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER K 649 " --> pdb=" O   MET K 448 " (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: 6.904A  pdb=" N   LEU K 617 " --> pdb=" O   LEU K 648 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   THR K 650 " --> pdb=" O   LEU K 617 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   LEU K 544 " --> pdb=" O   ILE K 616 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 568 through 570
      removed outlier: 6.350A  pdb=" N   CYS K 568 " --> pdb=" O   LEU K 597 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    500 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      269 hydrogen bonds
      530 hydrogen bond angles
      0 basepair planarities
      103 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1730
        1.28 -     1.42: 4899
        1.42 -     1.55: 8153
        1.55 -     1.69: 643
        1.69 -     1.82: 48
  Bond restraints: 15473
  Sorted by residual:
  bond pdb=" C   SER K 653 "
       pdb=" O   SER K 653 "
    ideal  model  delta    sigma   weight residual
    1.235  1.315 -0.080 1.02e-02 9.61e+03 6.15e+01
  bond pdb=" C   VAL H 136 "
       pdb=" O   VAL H 136 "
    ideal  model  delta    sigma   weight residual
    1.237  1.148  0.089 1.14e-02 7.69e+03 6.11e+01
  bond pdb=" C   PRO K 258 "
       pdb=" O   PRO K 258 "
    ideal  model  delta    sigma   weight residual
    1.235  1.150  0.085 1.30e-02 5.92e+03 4.30e+01
  bond pdb=" C   ILE K 491 "
       pdb=" O   ILE K 491 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.051 9.80e-03 1.04e+04 2.76e+01
  bond pdb=" CA  SER K 653 "
       pdb=" C   SER K 653 "
    ideal  model  delta    sigma   weight residual
    1.524  1.588 -0.064 1.25e-02 6.40e+03 2.59e+01
  ... (remaining 15468 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 21338
        3.47 -     6.94: 647
        6.94 -    10.42: 33
       10.42 -    13.89: 0
       13.89 -    17.36: 2
  Bond angle restraints: 22020
  Sorted by residual:
  angle pdb=" N   LYS H 104 "
        pdb=" CA  LYS H 104 "
        pdb=" C   LYS H 104 "
      ideal   model   delta    sigma   weight residual
     111.28  103.00    8.28 1.09e+00 8.42e-01 5.77e+01
  angle pdb=" N   GLU K 518 "
        pdb=" CA  GLU K 518 "
        pdb=" C   GLU K 518 "
      ideal   model   delta    sigma   weight residual
     114.56  104.94    9.62 1.27e+00 6.20e-01 5.74e+01
  angle pdb=" O3'  DC I 107 "
        pdb=" C3'  DC I 107 "
        pdb=" C2'  DC I 107 "
      ideal   model   delta    sigma   weight residual
     109.40  126.76  -17.36 2.50e+00 1.60e-01 4.82e+01
  angle pdb=" N   ARG D 107 "
        pdb=" CA  ARG D 107 "
        pdb=" C   ARG D 107 "
      ideal   model   delta    sigma   weight residual
     110.97  103.50    7.47 1.09e+00 8.42e-01 4.69e+01
  angle pdb=" O3'  DG J 112 "
        pdb=" C3'  DG J 112 "
        pdb=" C2'  DG J 112 "
      ideal   model   delta    sigma   weight residual
     109.40  126.00  -16.60 2.50e+00 1.60e-01 4.41e+01
  ... (remaining 22015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.56: 7380
       35.56 -    71.12: 1198
       71.12 -   106.68: 26
      106.68 -   142.25: 5
      142.25 -   177.81: 5
  Dihedral angle restraints: 8614
    sinusoidal: 5274
      harmonic: 3340
  Sorted by residual:
  dihedral pdb=" CA  VAL B  81 "
           pdb=" C   VAL B  81 "
           pdb=" N   THR B  82 "
           pdb=" CA  THR B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.34  -22.66     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" C4'  DC I 110 "
           pdb=" C3'  DC I 110 "
           pdb=" O3'  DC I 110 "
           pdb=" P    DC I 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.81 -177.81     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I   3 "
           pdb=" C3'  DC I   3 "
           pdb=" O3'  DC I   3 "
           pdb=" P    DG I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   29.39 -169.39     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 8611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.177: 2446
       0.177 -    0.355: 51
       0.355 -    0.532: 0
       0.532 -    0.710: 0
       0.710 -    0.887: 2
  Chirality restraints: 2499
  Sorted by residual:
  chirality pdb=" C3'  DG J 112 "
            pdb=" C4'  DG J 112 "
            pdb=" O3'  DG J 112 "
            pdb=" C2'  DG J 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -1.84   -0.89 2.00e-01 2.50e+01 1.97e+01
  chirality pdb=" C3'  DC I 107 "
            pdb=" C4'  DC I 107 "
            pdb=" O3'  DC I 107 "
            pdb=" C2'  DC I 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -1.96   -0.77 2.00e-01 2.50e+01 1.50e+01
  chirality pdb=" CA  LEU K 372 "
            pdb=" N   LEU K 372 "
            pdb=" C   LEU K 372 "
            pdb=" CB  LEU K 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 2496 not shown)

  Planarity restraints: 1858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H 148 "    0.024 2.00e-02 2.50e+03   4.70e-02 2.21e+01
        pdb=" C   SER H 148 "   -0.081 2.00e-02 2.50e+03
        pdb=" O   SER H 148 "    0.030 2.00e-02 2.50e+03
        pdb=" N   SER H 149 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU K 376 "    0.021 2.00e-02 2.50e+03   4.38e-02 1.92e+01
        pdb=" C   LEU K 376 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LEU K 376 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN K 377 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  85 "    0.021 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   GLN A  85 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   GLN A  85 "    0.025 2.00e-02 2.50e+03
        pdb=" N   SER A  86 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1855 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2326
        2.76 -     3.29: 14097
        3.29 -     3.83: 25940
        3.83 -     4.36: 32559
        4.36 -     4.90: 45781
  Nonbonded interactions: 120703
  Sorted by model distance:
  nonbonded pdb=" O   SER K 620 "
            pdb=" OD1 ASP K 621 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD2 ASP K 621 "
            pdb=" OD1 ASP K 627 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASN K 368 "
            pdb=" N   SER K 370 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   LYS K 294 "
            pdb=" NZ  LYS K 294 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" O   GLU G  92 "
            pdb=" OG  SER G  95 "
     model   vdw
     2.351 3.040
  ... (remaining 120698 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 50 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 100)
  selection = (chain 'F' and resid 25 through 100)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 21 through 108)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 61 through 149)
}

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:             1.710
  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:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.830
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.089  15473  Z= 0.922
  Angle     :  1.365  17.360  22020  Z= 1.021
  Chirality :  0.075   0.887   2499
  Planarity :  0.008   0.047   1858
  Dihedral  : 25.452 177.808   6458
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  7.39 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.30 %
    Favored  : 92.78 %
  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: -3.46 (0.21), residues: 1136
  helix: -1.56 (0.17), residues: 691
  sheet: -3.21 (0.55), residues: 55
  loop : -3.36 (0.26), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 431 
 TYR   0.041   0.003   TYR K 329 
 PHE   0.028   0.003   PHE D  67 
 TRP   0.015   0.002   TRP K 482 
 HIS   0.015   0.002   HIS H  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01225 /  0.92 (15473)
  covalent geometry    : angle       1.36456 /  1.02 (22020)
  hydrogen bonds       : bond        0.22449 / 14.88 (  769)
  hydrogen bonds       : angle       9.65229 /  6.95 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 328
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.8930 (pt) cc_final: 0.8556 (mt)
REVERT: A   73 GLU cc_start: 0.8019 (tt0) cc_final: 0.7759 (tt0)
REVERT: B   25 ASN cc_start: 0.5358 (m110) cc_final: 0.4649 (m-40)
REVERT: D   81 SER cc_start: 0.8822 (t) cc_final: 0.8573 (p)
REVERT: E   97 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7158 (mt-10)
REVERT: E  123 ASP cc_start: 0.8469 (m-30) cc_final: 0.8235 (m-30)
REVERT: G   74 ASN cc_start: 0.8122 (t0) cc_final: 0.7855 (t0)
REVERT: K  373 TRP cc_start: 0.5573 (t60) cc_final: 0.5303 (t-100)
REVERT: K  432 MET cc_start: 0.8212 (mmm) cc_final: 0.7497 (ttm)
REVERT: K  615 CYS cc_start: 0.7641 (m) cc_final: 0.7156 (m)
REVERT: K  631 MET cc_start: 0.9284 (mtp) cc_final: 0.9074 (mtp)
  outliers start: 9
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1514
  time to fit residues: 67.2119
Evaluate side-chains
  171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   40.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   50.0000
   chunk 55 optimal weight:    1.9990
   overall best weight:    3.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
D  72 GLN
E  85 GLN
G  90 ASN
G 105 ASN
G 111 ASN
** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 629 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.095078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.068104 restraints weight = 51953.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.070372 restraints weight = 27348.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.070718 restraints weight = 16206.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.071008 restraints weight = 15053.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.071012 restraints weight = 14230.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  15473  Z= 0.246
  Angle     :  0.874  14.259  22020  Z= 0.485
  Chirality :  0.054   0.304   2499
  Planarity :  0.006   0.043   1858
  Dihedral  : 29.680 171.691   4149
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.28 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.75 %
    Favored  : 81.10 %
  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: -1.08 (0.24), residues: 1136
  helix:  0.58 (0.19), residues: 702
  sheet: -2.58 (0.60), residues: 57
  loop : -2.95 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  92 
 TYR   0.018   0.002   TYR K 663 
 PHE   0.014   0.002   PHE A  67 
 TRP   0.013   0.002   TRP K 212 
 HIS   0.008   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00503 /  0.25 (15473)
  covalent geometry    : angle       0.87394 /  0.48 (22020)
  hydrogen bonds       : bond        0.08858 /  5.96 (  769)
  hydrogen bonds       : angle       4.40324 /  3.15 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 180
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.7832 (t0) cc_final: 0.7605 (t0)
REVERT: E  105 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: G   74 ASN cc_start: 0.8128 (t0) cc_final: 0.7738 (t0)
REVERT: G   93 GLU cc_start: 0.8460 (mp0) cc_final: 0.7988 (mt-10)
REVERT: H  101 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7782 (mm-30)
REVERT: K  315 MET cc_start: 0.8383 (tmm) cc_final: 0.8130 (tmm)
  outliers start: 31
  outliers final: 17
  residues processed: 202
  average time/residue: 0.1205
  time to fit residues: 35.9999
Evaluate side-chains
  167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain G residue  111 ASN
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  668 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 111 optimal weight:    7.9990
   chunk 84 optimal weight:   20.0000
   chunk 116 optimal weight:   20.0000
   chunk 83 optimal weight:   20.0000
   chunk 130 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    4.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
C  90 ASN
E  93 GLN
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 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 = 0.3783 r_free = 0.3783 target = 0.092083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.063948 restraints weight = 49800.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.065980 restraints weight = 26439.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.066254 restraints weight = 16158.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.066619 restraints weight = 15202.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.066583 restraints weight = 14069.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  15473  Z= 0.242
  Angle     :  0.753  13.352  22020  Z= 0.431
  Chirality :  0.048   0.349   2499
  Planarity :  0.005   0.055   1858
  Dihedral  : 29.577 166.343   4149
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.07 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 16.46 %
    Favored  : 79.17 %
  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: -0.13 (0.25), residues: 1136
  helix:  1.36 (0.20), residues: 701
  sheet: -1.94 (0.63), residues: 57
  loop : -2.68 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 117 
 TYR   0.017   0.002   TYR D 108 
 PHE   0.021   0.002   PHE K 240 
 TRP   0.013   0.002   TRP K 373 
 HIS   0.009   0.002   HIS G 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00508 /  0.24 (15473)
  covalent geometry    : angle       0.75300 /  0.43 (22020)
  hydrogen bonds       : bond        0.08129 /  5.47 (  769)
  hydrogen bonds       : angle       4.07001 /  2.90 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 158
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8135 (t0) cc_final: 0.7482 (t0)
REVERT: D  101 GLU cc_start: 0.8161 (tp30) cc_final: 0.7765 (tp30)
REVERT: E  105 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7903 (tm-30)
REVERT: G   74 ASN cc_start: 0.8198 (t0) cc_final: 0.7760 (t0)
REVERT: G   93 GLU cc_start: 0.8493 (mp0) cc_final: 0.7969 (mt-10)
REVERT: G  111 ASN cc_start: 0.7690 (p0) cc_final: 0.7401 (p0)
REVERT: H  101 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: K  346 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8433 (mt)
  outliers start: 43
  outliers final: 23
  residues processed: 190
  average time/residue: 0.1230
  time to fit residues: 34.4766
Evaluate side-chains
  166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  107 ARG
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   84 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue  143 VAL
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  346 LEU
Chi-restraints excluded: chain K residue  464 VAL
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  556 MET
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  668 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    0.0030
   chunk 116 optimal weight:    0.0040
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 57 optimal weight:    0.3980
   chunk 121 optimal weight:    0.0040
   chunk 22 optimal weight:    9.9990
   chunk 69 optimal weight:   30.0000
   overall best weight:    0.2414

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
** F  75 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 = 0.3831 r_free = 0.3831 target = 0.094597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.067210 restraints weight = 49805.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.069123 restraints weight = 25998.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.069464 restraints weight = 16104.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.069715 restraints weight = 15245.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.069763 restraints weight = 13976.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  15473  Z= 0.153
  Angle     :  0.656  10.070  22020  Z= 0.385
  Chirality :  0.044   0.292   2499
  Planarity :  0.004   0.049   1858
  Dihedral  : 29.266 168.219   4149
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.70 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.58 (0.26), residues: 1136
  helix:  1.92 (0.20), residues: 704
  sheet: -1.35 (0.64), residues: 57
  loop : -2.49 (0.28), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  82 
 TYR   0.023   0.002   TYR K 513 
 PHE   0.017   0.001   PHE G  34 
 TRP   0.015   0.002   TRP K 265 
 HIS   0.005   0.001   HIS D 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.15 (15473)
  covalent geometry    : angle       0.65584 /  0.39 (22020)
  hydrogen bonds       : bond        0.06626 /  4.45 (  769)
  hydrogen bonds       : angle       3.56090 /  2.57 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8085 (t0) cc_final: 0.7607 (t0)
REVERT: D  101 GLU cc_start: 0.8135 (tp30) cc_final: 0.7753 (tp30)
REVERT: G   74 ASN cc_start: 0.8192 (t0) cc_final: 0.7728 (t0)
REVERT: G   93 GLU cc_start: 0.8390 (mp0) cc_final: 0.7963 (mt-10)
REVERT: H  101 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7615 (mm-30)
REVERT: K  432 MET cc_start: 0.7309 (mmp) cc_final: 0.6362 (tpt)
  outliers start: 24
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1161
  time to fit residues: 28.1685
Evaluate side-chains
  148 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:   40.0000
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 93 optimal weight:   20.0000
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
D 134 HIS
F  75 HIS
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.093453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.066042 restraints weight = 50748.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.067995 restraints weight = 26263.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.068265 restraints weight = 16471.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.068555 restraints weight = 15503.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.068619 restraints weight = 14216.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15473  Z= 0.148
  Angle     :  0.626   8.788  22020  Z= 0.368
  Chirality :  0.042   0.263   2499
  Planarity :  0.004   0.046   1858
  Dihedral  : 29.213 171.407   4149
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.58 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.51 %
    Favored  : 77.64 %
  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:  0.89 (0.26), residues: 1136
  helix:  2.13 (0.20), residues: 704
  sheet: -0.90 (0.67), residues: 57
  loop : -2.35 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K 601 
 TYR   0.022   0.001   TYR K 513 
 PHE   0.013   0.001   PHE K 240 
 TRP   0.012   0.001   TRP K 482 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.15 (15473)
  covalent geometry    : angle       0.62601 /  0.37 (22020)
  hydrogen bonds       : bond        0.06355 /  4.29 (  769)
  hydrogen bonds       : angle       3.46298 /  2.50 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8101 (t0) cc_final: 0.7680 (t0)
REVERT: D  101 GLU cc_start: 0.8102 (tp30) cc_final: 0.7767 (tp30)
REVERT: G   36 LYS cc_start: 0.8964 (tppt) cc_final: 0.8755 (tptt)
REVERT: G   74 ASN cc_start: 0.8140 (t0) cc_final: 0.7669 (t0)
REVERT: G   85 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: H  101 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7598 (mm-30)
REVERT: K  432 MET cc_start: 0.7420 (mmp) cc_final: 0.6406 (tpp)
REVERT: K  582 GLN cc_start: 0.8679 (mt0) cc_final: 0.8178 (tt0)
  outliers start: 28
  outliers final: 19
  residues processed: 164
  average time/residue: 0.1073
  time to fit residues: 26.5052
Evaluate side-chains
  162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   94 LEU
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  668 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 123 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.091981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064289 restraints weight = 49072.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.065824 restraints weight = 26037.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.066539 restraints weight = 16093.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.066759 restraints weight = 14825.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.066795 restraints weight = 13810.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15473  Z= 0.159
  Angle     :  0.630   9.520  22020  Z= 0.368
  Chirality :  0.043   0.253   2499
  Planarity :  0.004   0.045   1858
  Dihedral  : 29.252 173.737   4149
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.87 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.92 %
    Favored  : 76.93 %
  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:  1.03 (0.26), residues: 1136
  helix:  2.20 (0.20), residues: 703
  sheet: -0.52 (0.69), residues: 57
  loop : -2.23 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 580 
 TYR   0.016   0.002   TYR K 663 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.020   0.002   TRP K 217 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.16 (15473)
  covalent geometry    : angle       0.62984 /  0.37 (22020)
  hydrogen bonds       : bond        0.06427 /  4.34 (  769)
  hydrogen bonds       : angle       3.40366 /  2.42 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8199 (t0) cc_final: 0.7791 (t0)
REVERT: D  101 GLU cc_start: 0.8124 (tp30) cc_final: 0.7801 (tp30)
REVERT: G   74 ASN cc_start: 0.8084 (t0) cc_final: 0.7591 (t0)
REVERT: G   85 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: G   93 GLU cc_start: 0.8409 (mp0) cc_final: 0.7774 (mt-10)
REVERT: H  101 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7638 (mm-30)
REVERT: K  582 GLN cc_start: 0.8712 (mt0) cc_final: 0.8207 (tt0)
  outliers start: 31
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1224
  time to fit residues: 30.3552
Evaluate side-chains
  158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   94 LEU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Chi-restraints excluded: chain K residue  666 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 116 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 84 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 69 optimal weight:   30.0000
   chunk 111 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    2.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 341 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.090513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.062489 restraints weight = 49148.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.064323 restraints weight = 25977.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.064752 restraints weight = 15866.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.065017 restraints weight = 15395.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.065052 restraints weight = 14043.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.5484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  15473  Z= 0.176
  Angle     :  0.632   7.996  22020  Z= 0.369
  Chirality :  0.042   0.246   2499
  Planarity :  0.004   0.046   1858
  Dihedral  : 29.249 175.649   4149
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.40 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.53 %
    Favored  : 76.42 %
  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:  1.11 (0.26), residues: 1136
  helix:  2.21 (0.20), residues: 710
  sheet: -0.08 (0.73), residues: 57
  loop : -2.26 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 117 
 TYR   0.041   0.002   TYR D 108 
 PHE   0.010   0.001   PHE D  67 
 TRP   0.030   0.002   TRP K 217 
 HIS   0.006   0.001   HIS G 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.18 (15473)
  covalent geometry    : angle       0.63240 /  0.37 (22020)
  hydrogen bonds       : bond        0.06561 /  4.42 (  769)
  hydrogen bonds       : angle       3.40970 /  2.44 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.8102 (mp0) cc_final: 0.7736 (mp0)
REVERT: C  105 ASN cc_start: 0.8276 (t0) cc_final: 0.7954 (t0)
REVERT: D  101 GLU cc_start: 0.8148 (tp30) cc_final: 0.7843 (tp30)
REVERT: G   74 ASN cc_start: 0.8250 (t0) cc_final: 0.7762 (t0)
REVERT: G   85 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8383 (tm-30)
REVERT: G   93 GLU cc_start: 0.8457 (mp0) cc_final: 0.7868 (mt-10)
REVERT: H  101 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7687 (mm-30)
REVERT: K  582 GLN cc_start: 0.8755 (mt0) cc_final: 0.8246 (tt0)
  outliers start: 30
  outliers final: 23
  residues processed: 165
  average time/residue: 0.1198
  time to fit residues: 29.8992
Evaluate side-chains
  161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   94 LEU
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  325 TYR
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:   40.0000
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0670
   chunk 21 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.4126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G 111 ASN
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 295 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.090373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062446 restraints weight = 49815.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.064032 restraints weight = 26026.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.064619 restraints weight = 16364.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.064698 restraints weight = 15415.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.064771 restraints weight = 14330.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15473  Z= 0.163
  Angle     :  0.622   8.057  22020  Z= 0.362
  Chirality :  0.042   0.236   2499
  Planarity :  0.004   0.042   1858
  Dihedral  : 29.264 175.854   4149
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.87 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.34 %
    Favored  : 75.81 %
  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:  1.14 (0.26), residues: 1136
  helix:  2.21 (0.20), residues: 709
  sheet:  0.08 (0.74), residues: 57
  loop : -2.19 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 633 
 TYR   0.016   0.002   TYR K 663 
 PHE   0.007   0.001   PHE B  61 
 TRP   0.024   0.002   TRP K 217 
 HIS   0.004   0.001   HIS K 670 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (15473)
  covalent geometry    : angle       0.62221 /  0.36 (22020)
  hydrogen bonds       : bond        0.06327 /  4.25 (  769)
  hydrogen bonds       : angle       3.33827 /  2.38 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8321 (t0) cc_final: 0.8022 (t0)
REVERT: D  101 GLU cc_start: 0.8150 (tp30) cc_final: 0.7835 (tp30)
REVERT: G   74 ASN cc_start: 0.8228 (t0) cc_final: 0.7755 (t0)
REVERT: G   85 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8345 (tm-30)
REVERT: G   93 GLU cc_start: 0.8457 (mp0) cc_final: 0.7835 (mt-10)
REVERT: H  101 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7669 (mm-30)
REVERT: H  118 GLU cc_start: 0.7899 (mp0) cc_final: 0.7544 (mp0)
REVERT: K  582 GLN cc_start: 0.8786 (mt0) cc_final: 0.8248 (tt0)
  outliers start: 28
  outliers final: 23
  residues processed: 164
  average time/residue: 0.1169
  time to fit residues: 28.9988
Evaluate side-chains
  164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain G residue  111 ASN
Chi-restraints excluded: chain K residue  224 ILE
Chi-restraints excluded: chain K residue  317 ASP
Chi-restraints excluded: chain K residue  325 TYR
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:   40.0000
   chunk 82 optimal weight:   30.0000
   chunk 22 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 107 optimal weight:   20.0000
   chunk 104 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 134 HIS
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.088245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.060223 restraints weight = 49728.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061735 restraints weight = 25893.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.062021 restraints weight = 17138.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.062439 restraints weight = 15777.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.062446 restraints weight = 14563.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.5893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  15473  Z= 0.257
  Angle     :  0.706   8.894  22020  Z= 0.400
  Chirality :  0.045   0.336   2499
  Planarity :  0.005   0.041   1858
  Dihedral  : 29.382 175.706   4149
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.02 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.53 %
    Favored  : 76.52 %
  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:  0.87 (0.26), residues: 1136
  helix:  2.00 (0.20), residues: 709
  sheet:  0.15 (0.76), residues: 57
  loop : -2.32 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  30 
 TYR   0.020   0.002   TYR K 513 
 PHE   0.014   0.002   PHE E  67 
 TRP   0.024   0.002   TRP K 217 
 HIS   0.028   0.002   HIS G 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.26 (15473)
  covalent geometry    : angle       0.70612 /  0.40 (22020)
  hydrogen bonds       : bond        0.07299 /  4.93 (  769)
  hydrogen bonds       : angle       3.60166 /  2.55 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8362 (t0) cc_final: 0.8066 (t0)
REVERT: D  101 GLU cc_start: 0.8217 (tp30) cc_final: 0.7882 (tp30)
REVERT: G   36 LYS cc_start: 0.9021 (tptt) cc_final: 0.8773 (tptt)
REVERT: G   85 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: H  101 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7615 (mm-30)
REVERT: K  582 GLN cc_start: 0.8833 (mt0) cc_final: 0.8315 (tt0)
  outliers start: 29
  outliers final: 24
  residues processed: 157
  average time/residue: 0.1181
  time to fit residues: 27.8219
Evaluate side-chains
  157 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue   79 ILE
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain K residue  224 ILE
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Chi-restraints excluded: chain K residue  615 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 84 optimal weight:   20.0000
   chunk 78 optimal weight:   50.0000
   chunk 116 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.089450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061464 restraints weight = 48821.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.062977 restraints weight = 26596.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063410 restraints weight = 16645.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.063667 restraints weight = 15289.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.063749 restraints weight = 14353.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.6015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15473  Z= 0.165
  Angle     :  0.637   9.434  22020  Z= 0.368
  Chirality :  0.042   0.250   2499
  Planarity :  0.004   0.041   1858
  Dihedral  : 29.276 176.515   4149
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.05 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.83 %
    Favored  : 76.83 %
  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:  1.02 (0.26), residues: 1136
  helix:  2.13 (0.20), residues: 709
  sheet: -0.04 (0.72), residues: 62
  loop : -2.29 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  30 
 TYR   0.031   0.002   TYR K 663 
 PHE   0.011   0.001   PHE B 100 
 TRP   0.025   0.002   TRP K 217 
 HIS   0.003   0.001   HIS K 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.16 (15473)
  covalent geometry    : angle       0.63723 /  0.37 (22020)
  hydrogen bonds       : bond        0.06471 /  4.35 (  769)
  hydrogen bonds       : angle       3.37958 /  2.41 ( 2006)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: C  105 ASN cc_start: 0.8280 (t0) cc_final: 0.8052 (t0)
REVERT: D  101 GLU cc_start: 0.8185 (tp30) cc_final: 0.7873 (tp30)
REVERT: G   36 LYS cc_start: 0.8966 (tptt) cc_final: 0.8713 (mmtt)
REVERT: G   85 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: G   93 GLU cc_start: 0.8384 (mp0) cc_final: 0.7818 (mt-10)
REVERT: H  101 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: H  118 GLU cc_start: 0.7959 (mp0) cc_final: 0.7613 (mp0)
REVERT: K  582 GLN cc_start: 0.8792 (mt0) cc_final: 0.8257 (tt0)
  outliers start: 23
  outliers final: 21
  residues processed: 153
  average time/residue: 0.1226
  time to fit residues: 28.4436
Evaluate side-chains
  152 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 ASP
Chi-restraints excluded: chain K residue  224 ILE
Chi-restraints excluded: chain K residue  336 HIS
Chi-restraints excluded: chain K residue  472 LEU
Chi-restraints excluded: chain K residue  487 ASN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain K residue  570 ILE
Chi-restraints excluded: chain K residue  609 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 130 optimal weight:    8.9990
   chunk 78 optimal weight:   50.0000
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   chunk 128 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G 111 ASN
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.089813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061882 restraints weight = 48807.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063554 restraints weight = 25676.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.063865 restraints weight = 16611.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.064163 restraints weight = 15322.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.064275 restraints weight = 14311.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.6225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15473  Z= 0.160
  Angle     :  0.620   9.439  22020  Z= 0.361
  Chirality :  0.041   0.245   2499
  Planarity :  0.004   0.042   1858
  Dihedral  : 29.233 177.565   4149
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.40 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.34 %
    Favored  : 76.32 %
  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:  1.20 (0.26), residues: 1136
  helix:  2.24 (0.20), residues: 708
  sheet:  0.10 (0.72), residues: 62
  loop : -2.14 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  30 
 TYR   0.032   0.002   TYR K 663 
 PHE   0.010   0.001   PHE D  67 
 TRP   0.025   0.002   TRP K 217 
 HIS   0.003   0.001   HIS K 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.16 (15473)
  covalent geometry    : angle       0.62035 /  0.36 (22020)
  hydrogen bonds       : bond        0.06137 /  4.12 (  769)
  hydrogen bonds       : angle       3.28515 /  2.36 ( 2006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2376.16 seconds
wall clock time: 41 minutes 48.58 seconds (2508.58 seconds total)