Starting phenix.real_space_refine
on Fri Jul  3 13:24:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bg9_12174/07_2026/7bg9_12174.map"
  }
  resolution = 3.8
  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=   0.003
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     262      5.49       5
     S      37      5.16       5
     C    8028      2.51       5
     N    2586      2.21       5
     O    3320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  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: 14233
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 913, 7333
          Classifications: {'peptide': 913}
          Link IDs: {'PTRANS': 51, 'TRANS': 861}
          Chain breaks: 4
    Chain: "N"
      Number of atoms: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 127
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "M"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "L"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 643
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "B"
      Number of atoms: 5431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 5431
          Classifications: {'RNA': 256}
          Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 10, 'rna3p_pur': 103, 'rna3p_pyr': 130}
          Link IDs: {'rna2p': 23, 'rna3p': 232}
          Chain breaks: 3
  Time building chain proxies: 3.32, per 1000 atoms: 0.23
  Number of scatterers: 14233
  At special positions: 0
  Unit cell: (134.31, 139.86, 135.42, 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      37     16.00
     P     262     15.00
     O    3320      8.00
     N    2586      7.00
     C    8028      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 467.4 milliseconds
  

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      54.7% alpha, 6.5% beta
      70 base pairs and 128 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 3.727A  pdb=" N   ARG A  15 " --> pdb=" O   ARG A  11 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   SER A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A  21 " --> pdb=" O   HIS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 4.297A  pdb=" N   VAL A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 100
      removed outlier: 4.322A  pdb=" N   PHE A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 100'
    Processing helix  chain 'A' and resid 133 through 145
      removed outlier: 3.543A  pdb=" N   LEU A 141 " --> pdb=" O   TRP A 137 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.113A  pdb=" N   ALA A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 179
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 3.630A  pdb=" N   LYS A 329 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
      removed outlier: 3.523A  pdb=" N   LEU A 347 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 366
      removed outlier: 4.184A  pdb=" N   ARG A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 4.044A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 3.593A  pdb=" N   VAL A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 470
      removed outlier: 4.117A  pdb=" N   GLY A 463 " --> pdb=" O   TRP A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 4.012A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLY A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 474 through 479'
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 4.259A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 558
      removed outlier: 3.599A  pdb=" N   ILE A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 542 " --> pdb=" O   GLU A 538 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TRP A 547 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A 556 " --> pdb=" O   TYR A 552 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 595
      removed outlier: 3.574A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 595 " --> pdb=" O   GLN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 610
      removed outlier: 3.839A  pdb=" N   GLN A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 3.509A  pdb=" N   VAL A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ARG A 669 " --> pdb=" O   LEU A 665 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A 670 " --> pdb=" O   ASN A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 683 through 697
      removed outlier: 3.587A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
      removed outlier: 4.204A  pdb=" N   LEU A 725 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 731 " --> pdb=" O   GLU A 727 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE A 732 " --> pdb=" O   VAL A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 781
    Processing helix  chain 'A' and resid 782 through 784
      No H-bonds generated for 'chain 'A' and resid 782 through 784'
    Processing helix  chain 'A' and resid 801 through 815
      removed outlier: 3.706A  pdb=" N   PHE A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 854
      removed outlier: 3.541A  pdb=" N   CYS A 842 " --> pdb=" O   SER A 838 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR A 846 " --> pdb=" O   CYS A 842 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN A 851 " --> pdb=" O   GLY A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 889
      removed outlier: 3.843A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A 881 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 882 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.854A  pdb=" N   SER A 957 " --> pdb=" O   SER A 953 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 958 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 953 through 958'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.810A  pdb=" N   ARG A 972 " --> pdb=" O   ARG A 968 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU A 980 " --> pdb=" O   GLY A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.725A  pdb=" N   LEU A 987 " --> pdb=" O   HIS A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1017
      removed outlier: 4.017A  pdb=" N   THR A 999 " --> pdb=" O   GLN A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1027
      removed outlier: 3.531A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1024 through 1027'
    Processing helix  chain 'A' and resid 1028 through 1052
      removed outlier: 4.230A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A1033 " --> pdb=" O   PRO A1029 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASP A1038 " --> pdb=" O   ARG A1034 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A1042 " --> pdb=" O   ASP A1038 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A1049 " --> pdb=" O   SER A1045 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1083
      removed outlier: 4.412A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   HIS A1075 " --> pdb=" O   GLN A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1090
      removed outlier: 3.903A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1106
      removed outlier: 3.901A  pdb=" N   ALA A1099 " --> pdb=" O   SER A1095 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.510A  pdb=" N   THR A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA A1114 " --> pdb=" O   THR A1110 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A1118 " --> pdb=" O   ALA A1114 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 38 through 50
      removed outlier: 3.801A  pdb=" N   TYR M  43 " --> pdb=" O   SER M  39 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 4.108A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL M  67 " --> pdb=" O   MET M  63 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASN M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE M  74 " --> pdb=" O   ILE M  70 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 4.193A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL M  99 " --> pdb=" O   ILE M  95 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU M 101 " --> pdb=" O   THR M  97 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 124
      removed outlier: 3.550A  pdb=" N   LYS M 109 " --> pdb=" O   GLY M 105 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS M 121 " --> pdb=" O   LYS M 117 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 35
      removed outlier: 3.517A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 74
      removed outlier: 4.561A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL L  55 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU L  56 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR L  58 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU L  64 " --> pdb=" O   THR L  60 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA L  67 " --> pdb=" O   ILE L  63 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASP L  73 " --> pdb=" O   ASN L  69 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASN L  74 " --> pdb=" O   ALA L  70 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 91
      removed outlier: 3.810A  pdb=" N   ALA L  87 " --> pdb=" O   HIS L  83 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG L  89 " --> pdb=" O   GLN L  85 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 98
      removed outlier: 3.596A  pdb=" N   LEU L  97 " --> pdb=" O   GLU L  93 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 4.151A  pdb=" N   LEU A  24 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 600
    Processing sheet with id=AA4, first strand: chain 'A' and resid 619 through 625
    Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 866
      removed outlier: 3.722A  pdb=" N   LEU A 866 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 905 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 761
      removed outlier: 3.598A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 930
    Processing sheet with id=AA8, first strand: chain 'M' and resid 89 through 90
      removed outlier: 3.757A  pdb=" N   ILE M  90 " --> pdb=" O   ARG L  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    339 hydrogen bonds defined for protein.
    972 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      182 hydrogen bonds
      350 hydrogen bond angles
      0 basepair planarities
      70 basepair parallelities
      128 stacking parallelities
  Total time for adding SS restraints: 3.55

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1592
        1.29 -     1.43: 5038
        1.43 -     1.56: 7769
        1.56 -     1.70: 613
        1.70 -     1.84: 51
  Bond restraints: 15063
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" C   VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.524  1.622 -0.097 1.05e-02 9.07e+03 8.57e+01
  bond pdb=" C   VAL A 529 "
       pdb=" N   PRO A 530 "
    ideal  model  delta    sigma   weight residual
    1.328  1.441 -0.113 1.25e-02 6.40e+03 8.22e+01
  bond pdb=" C   PHE A 560 "
       pdb=" O   PHE A 560 "
    ideal  model  delta    sigma   weight residual
    1.235  1.148  0.088 1.02e-02 9.61e+03 7.37e+01
  bond pdb=" C   GLN A1023 "
       pdb=" O   GLN A1023 "
    ideal  model  delta    sigma   weight residual
    1.235  1.327 -0.092 1.14e-02 7.69e+03 6.49e+01
  bond pdb=" CA  ILE A1004 "
       pdb=" C   ILE A1004 "
    ideal  model  delta    sigma   weight residual
    1.524  1.439  0.085 1.22e-02 6.72e+03 4.84e+01
  ... (remaining 15058 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.29: 20383
        3.29 -     6.59: 1134
        6.59 -     9.88: 98
        9.88 -    13.18: 22
       13.18 -    16.47: 5
  Bond angle restraints: 21642
  Sorted by residual:
  angle pdb=" N   LYS A 410 "
        pdb=" CA  LYS A 410 "
        pdb=" C   LYS A 410 "
      ideal   model   delta    sigma   weight residual
     112.68   99.30   13.38 1.33e+00 5.65e-01 1.01e+02
  angle pdb=" N   ASP A 337 "
        pdb=" CA  ASP A 337 "
        pdb=" C   ASP A 337 "
      ideal   model   delta    sigma   weight residual
     111.02  123.23  -12.21 1.22e+00 6.72e-01 1.00e+02
  angle pdb=" N   PHE A 561 "
        pdb=" CA  PHE A 561 "
        pdb=" C   PHE A 561 "
      ideal   model   delta    sigma   weight residual
     108.76  125.23  -16.47 1.69e+00 3.50e-01 9.50e+01
  angle pdb=" C   VAL A 529 "
        pdb=" N   PRO A 530 "
        pdb=" CA  PRO A 530 "
      ideal   model   delta    sigma   weight residual
     120.85  110.36   10.49 1.08e+00 8.57e-01 9.44e+01
  angle pdb=" N   LYS A 338 "
        pdb=" CA  LYS A 338 "
        pdb=" C   LYS A 338 "
      ideal   model   delta    sigma   weight residual
     111.71  122.61  -10.90 1.15e+00 7.56e-01 8.99e+01
  ... (remaining 21637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.65: 8712
       35.65 -    71.29: 690
       71.29 -   106.94: 111
      106.94 -   142.59: 6
      142.59 -   178.24: 7
  Dihedral angle restraints: 9526
    sinusoidal: 6373
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" C5'   A B 176 "
           pdb=" C4'   A B 176 "
           pdb=" C3'   A B 176 "
           pdb=" O3'   A B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   73.18   73.82     1      8.00e+00 1.56e-02 1.08e+02
  dihedral pdb=" O4'   U B 316 "
           pdb=" C1'   U B 316 "
           pdb=" N1    U B 316 "
           pdb=" C2    U B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.07 -176.07     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" C4'   U B 307 "
           pdb=" C3'   U B 307 "
           pdb=" C2'   U B 307 "
           pdb=" C1'   U B 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   23.52  -58.52     1      8.00e+00 1.56e-02 7.17e+01
  ... (remaining 9523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.156: 2266
       0.156 -    0.313: 359
       0.313 -    0.469: 28
       0.469 -    0.625: 2
       0.625 -    0.782: 3
  Chirality restraints: 2658
  Sorted by residual:
  chirality pdb=" C3'   U B 312 "
            pdb=" C4'   U B 312 "
            pdb=" O3'   U B 312 "
            pdb=" C2'   U B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.70   -0.78 2.00e-01 2.50e+01 1.53e+01
  chirality pdb=" C3'   G B 300 "
            pdb=" C4'   G B 300 "
            pdb=" O3'   G B 300 "
            pdb=" C2'   G B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.07   -0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" C3'   A B 176 "
            pdb=" C4'   A B 176 "
            pdb=" O3'   A B 176 "
            pdb=" C2'   A B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.11   -0.63 2.00e-01 2.50e+01 9.94e+00
  ... (remaining 2655 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA N  15 "    0.077 2.00e-02 2.50e+03   3.25e-02 2.90e+01
        pdb=" N9   DA N  15 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8   DA N  15 "   -0.015 2.00e-02 2.50e+03
        pdb=" N7   DA N  15 "   -0.018 2.00e-02 2.50e+03
        pdb=" C5   DA N  15 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6   DA N  15 "    0.028 2.00e-02 2.50e+03
        pdb=" N6   DA N  15 "    0.039 2.00e-02 2.50e+03
        pdb=" N1   DA N  15 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2   DA N  15 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DA N  15 "   -0.017 2.00e-02 2.50e+03
        pdb=" C4   DA N  15 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 177 "   -0.073 2.00e-02 2.50e+03   3.57e-02 2.86e+01
        pdb=" N1    U B 177 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U B 177 "    0.023 2.00e-02 2.50e+03
        pdb=" O2    U B 177 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    U B 177 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    U B 177 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U B 177 "   -0.051 2.00e-02 2.50e+03
        pdb=" C5    U B 177 "    0.018 2.00e-02 2.50e+03
        pdb=" C6    U B 177 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 547 "    0.043 2.00e-02 2.50e+03   3.25e-02 2.64e+01
        pdb=" CG  TRP A 547 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 547 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 547 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 547 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 547 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 547 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 547 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 547 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 547 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 18
        2.38 -     3.01: 6647
        3.01 -     3.64: 21617
        3.64 -     4.27: 32552
        4.27 -     4.90: 47474
  Nonbonded interactions: 108308
  Sorted by model distance:
  nonbonded pdb=" CB  PRO A  23 "
            pdb=" CZ3 TRP A  60 "
     model   vdw
     1.745 3.740
  nonbonded pdb=" ND1 HIS A1022 "
            pdb=" O2'   U B 312 "
     model   vdw
     1.946 3.120
  nonbonded pdb=" CG  PRO A  23 "
            pdb=" CZ3 TRP A  60 "
     model   vdw
     2.132 3.740
  nonbonded pdb=" CE2 TRP A 510 "
            pdb=" NE2 HIS A1022 "
     model   vdw
     2.209 2.672
  nonbonded pdb=" C   VAL A 529 "
            pdb=" N6    A B 318 "
     model   vdw
     2.238 3.350
  ... (remaining 108303 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.920
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
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      :  0.013   0.143  15064  Z= 0.893
  Angle     :  1.643  16.474  21642  Z= 1.049
  Chirality :  0.110   0.782   2658
  Planarity :  0.009   0.101   1784
  Dihedral  : 22.530 178.236   7486
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  1.59 %
    Allowed  : 11.95 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.39 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.05 (0.20), residues: 1071
  helix: -3.42 (0.15), residues: 461
  sheet: -3.45 (0.47), residues: 66
  loop : -3.29 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.002   ARG A1011 
 TYR   0.050   0.008   TYR A 325 
 PHE   0.067   0.009   PHE A 575 
 TRP   0.067   0.009   TRP A 547 
 HIS   0.023   0.004   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01345 /  0.89 (15063)
  covalent geometry    : angle       1.64270 /  1.05 (21642)
  hydrogen bonds       : bond        0.29173 / 19.27 (  521)
  hydrogen bonds       : angle       9.52310 /  6.69 ( 1322)
  Misc. bond           : bond        0.08793 /  4.63 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 184
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8887 (tp30) cc_final: 0.8649 (tm-30)
REVERT: A   60 TRP cc_start: 0.5856 (p90) cc_final: 0.5106 (p-90)
REVERT: A   91 ARG cc_start: 0.4298 (tpt170) cc_final: 0.3908 (mmm-85)
REVERT: A  152 LEU cc_start: 0.8796 (mp) cc_final: 0.8445 (tt)
REVERT: A  345 PHE cc_start: 0.8013 (t80) cc_final: 0.7797 (t80)
REVERT: A  347 LEU cc_start: 0.9199 (mp) cc_final: 0.8922 (tt)
REVERT: A  450 GLN cc_start: 0.8956 (mm110) cc_final: 0.8437 (tp40)
REVERT: A  491 THR cc_start: 0.8828 (m) cc_final: 0.8528 (m)
REVERT: A  502 LYS cc_start: 0.8544 (mttp) cc_final: 0.8329 (ptmm)
REVERT: A  553 VAL cc_start: 0.8552 (t) cc_final: 0.8334 (p)
REVERT: A  559 SER cc_start: 0.8315 (t) cc_final: 0.7863 (t)
REVERT: A  560 PHE cc_start: 0.8958 (m-80) cc_final: 0.8711 (m-10)
REVERT: A  607 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8602 (mpt180)
REVERT: A  608 GLN cc_start: 0.9012 (mp10) cc_final: 0.8445 (pp30)
REVERT: A  610 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8629 (mtt180)
REVERT: A  766 LEU cc_start: 0.8398 (mm) cc_final: 0.7832 (tt)
REVERT: A  770 GLN cc_start: 0.9170 (mt0) cc_final: 0.8476 (mm110)
REVERT: A  813 MET cc_start: 0.9261 (ptm) cc_final: 0.9031 (ppp)
REVERT: A  854 PHE cc_start: 0.7242 (m-80) cc_final: 0.6997 (m-10)
REVERT: A  893 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9328 (tm-30)
REVERT: A  899 ASN cc_start: 0.9187 (m-40) cc_final: 0.8828 (p0)
REVERT: A  922 MET cc_start: 0.7376 (ptp) cc_final: 0.6949 (mpp)
REVERT: A  941 GLU cc_start: 0.8450 (tt0) cc_final: 0.7884 (tm-30)
REVERT: M   41 TYR cc_start: 0.9139 (m-80) cc_final: 0.8698 (m-10)
REVERT: M   44 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8191 (mttp)
REVERT: M   55 ILE cc_start: 0.8213 (tp) cc_final: 0.7881 (tt)
REVERT: M   63 MET cc_start: 0.9586 (ptt) cc_final: 0.9067 (mmt)
REVERT: M   73 ARG cc_start: 0.9100 (mmt-90) cc_final: 0.8690 (mtp180)
REVERT: M  122 TYR cc_start: 0.8569 (t80) cc_final: 0.7785 (t80)
REVERT: L   18 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6946 (mtm-85)
REVERT: L   40 TYR cc_start: 0.7600 (m-80) cc_final: 0.7323 (m-80)
REVERT: L   62 GLU cc_start: 0.8939 (tp30) cc_final: 0.8653 (tt0)
REVERT: L   69 ASN cc_start: 0.8027 (m-40) cc_final: 0.7779 (m110)
REVERT: L   72 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7946 (mtp-110)
REVERT: L   75 LYS cc_start: 0.7682 (tppt) cc_final: 0.7368 (ttpp)
REVERT: L   91 ASP cc_start: 0.8345 (t70) cc_final: 0.7936 (t70)
  outliers start: 7
  outliers final: 1
  residues processed: 190
  average time/residue: 0.1689
  time to fit residues: 42.8199
Evaluate side-chains
  125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
A  40 GLN
A 169 GLN
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 GLN
A 546 HIS
A 571 ASN
A 748 GLN
A 990 GLN
A 995 GLN
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1024 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.111864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.076163 restraints weight = 48556.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.076942 restraints weight = 28761.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.077139 restraints weight = 21422.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.077523 restraints weight = 19867.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.077472 restraints weight = 18909.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15064  Z= 0.203
  Angle     :  0.800   9.733  21642  Z= 0.446
  Chirality :  0.045   0.315   2658
  Planarity :  0.007   0.075   1784
  Dihedral  : 23.672 179.845   5380
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.26 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.03 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.51 (0.23), residues: 1071
  helix: -1.76 (0.20), residues: 513
  sheet: -2.65 (0.48), residues: 72
  loop : -2.88 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 577 
 TYR   0.022   0.002   TYR A 552 
 PHE   0.024   0.003   PHE A 708 
 TRP   0.032   0.003   TRP A  60 
 HIS   0.024   0.002   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.20 (15063)
  covalent geometry    : angle       0.80037 /  0.45 (21642)
  hydrogen bonds       : bond        0.08642 /  5.73 (  521)
  hydrogen bonds       : angle       5.28533 /  3.81 ( 1322)
  Misc. bond           : bond        0.00189 /  0.10 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 LEU cc_start: 0.8743 (mp) cc_final: 0.8369 (tt)
REVERT: A  347 LEU cc_start: 0.8882 (mp) cc_final: 0.8438 (tt)
REVERT: A  762 HIS cc_start: 0.7125 (t-90) cc_final: 0.6769 (t-90)
REVERT: A  770 GLN cc_start: 0.8919 (mt0) cc_final: 0.8093 (mm110)
REVERT: A  772 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6033 (m-80)
REVERT: A  774 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6312 (mmm160)
REVERT: M   69 ASP cc_start: 0.8337 (t0) cc_final: 0.8089 (t0)
REVERT: M  122 TYR cc_start: 0.8109 (t80) cc_final: 0.7838 (t80)
REVERT: L   18 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6955 (mtm-85)
REVERT: L   75 LYS cc_start: 0.7741 (tppt) cc_final: 0.7497 (tttp)
REVERT: L   96 LYS cc_start: 0.8706 (tppt) cc_final: 0.8379 (mppt)
  outliers start: 24
  outliers final: 9
  residues processed: 141
  average time/residue: 0.1542
  time to fit residues: 30.0795
Evaluate side-chains
  107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  747 VAL
Chi-restraints excluded: chain A residue  772 TYR
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 124 optimal weight:   50.0000
   chunk 111 optimal weight:   50.0000
   chunk 32 optimal weight:    0.8980
   chunk 115 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 97 optimal weight:    9.9990
   overall best weight:    3.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1022 HIS ** 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 = 0.4024 r_free = 0.4024 target = 0.110845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.073425 restraints weight = 49437.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.075221 restraints weight = 27549.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.076326 restraints weight = 20030.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076821 restraints weight = 16834.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.077259 restraints weight = 15496.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  15064  Z= 0.201
  Angle     :  0.709   8.523  21642  Z= 0.393
  Chirality :  0.042   0.327   2658
  Planarity :  0.006   0.070   1784
  Dihedral  : 23.546 179.192   5380
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.63 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.24), residues: 1071
  helix: -0.94 (0.21), residues: 523
  sheet: -2.04 (0.55), residues: 73
  loop : -2.71 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 610 
 TYR   0.019   0.002   TYR A  18 
 PHE   0.023   0.002   PHE A 708 
 TRP   0.028   0.002   TRP A  60 
 HIS   0.020   0.002   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.20 (15063)
  covalent geometry    : angle       0.70928 /  0.39 (21642)
  hydrogen bonds       : bond        0.07659 /  5.09 (  521)
  hydrogen bonds       : angle       4.83849 /  3.46 ( 1322)
  Misc. bond           : bond        0.00209 /  0.11 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 LEU cc_start: 0.8760 (mp) cc_final: 0.8395 (tt)
REVERT: A  347 LEU cc_start: 0.8881 (mp) cc_final: 0.8503 (tt)
REVERT: A  685 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7835 (m-30)
REVERT: A  770 GLN cc_start: 0.8815 (mt0) cc_final: 0.8055 (mm110)
REVERT: A  772 TYR cc_start: 0.7149 (t80) cc_final: 0.6076 (m-80)
REVERT: A  774 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6435 (mmm160)
REVERT: A  829 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.6893 (tm-30)
REVERT: M   63 MET cc_start: 0.9260 (ptt) cc_final: 0.8831 (mmt)
REVERT: M   69 ASP cc_start: 0.8211 (t0) cc_final: 0.7906 (t0)
REVERT: M   72 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8937 (mm-30)
REVERT: M   73 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7821 (mtm180)
REVERT: M  122 TYR cc_start: 0.8375 (t80) cc_final: 0.7715 (t80)
REVERT: L   18 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6924 (mtm-85)
REVERT: L   40 TYR cc_start: 0.6825 (m-80) cc_final: 0.6480 (m-80)
REVERT: L   75 LYS cc_start: 0.7746 (tppt) cc_final: 0.7525 (tttp)
  outliers start: 31
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1257
  time to fit residues: 21.8952
Evaluate side-chains
  106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  685 ASP
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  820 ILE
Chi-restraints excluded: chain A residue  829 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  893 GLU
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 46 optimal weight:    0.5980
   chunk 97 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0050
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.4798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
A 736 GLN
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.112165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.079943 restraints weight = 49366.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.079761 restraints weight = 34536.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.080376 restraints weight = 27548.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.080418 restraints weight = 23778.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.080538 restraints weight = 22927.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15064  Z= 0.142
  Angle     :  0.625   7.908  21642  Z= 0.346
  Chirality :  0.038   0.273   2658
  Planarity :  0.006   0.085   1784
  Dihedral  : 23.419 179.338   5378
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.45 %
    Favored  : 79.55 %
  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: -2.10 (0.25), residues: 1071
  helix: -0.34 (0.22), residues: 522
  sheet: -1.85 (0.56), residues: 75
  loop : -2.55 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 607 
 TYR   0.017   0.002   TYR A  18 
 PHE   0.021   0.002   PHE M  71 
 TRP   0.021   0.002   TRP A  60 
 HIS   0.015   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 (15063)
  covalent geometry    : angle       0.62463 /  0.35 (21642)
  hydrogen bonds       : bond        0.05843 /  3.88 (  521)
  hydrogen bonds       : angle       4.33440 /  3.14 ( 1322)
  Misc. bond           : bond        0.00083 /  0.04 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8714 (mp) cc_final: 0.8429 (tt)
REVERT: A  770 GLN cc_start: 0.8515 (mt0) cc_final: 0.7867 (mm110)
REVERT: A  772 TYR cc_start: 0.6785 (t80) cc_final: 0.6205 (m-80)
REVERT: M   73 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7707 (mtm180)
REVERT: M  122 TYR cc_start: 0.7932 (t80) cc_final: 0.7634 (t80)
REVERT: L   75 LYS cc_start: 0.7850 (tppt) cc_final: 0.7644 (tttp)
REVERT: L   96 LYS cc_start: 0.8616 (tppt) cc_final: 0.8260 (mmtt)
  outliers start: 28
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1254
  time to fit residues: 21.6541
Evaluate side-chains
  97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 114 optimal weight:   30.0000
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0770
   chunk 95 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    1.6146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.112445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075412 restraints weight = 49504.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.077299 restraints weight = 26919.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.078463 restraints weight = 19238.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.079020 restraints weight = 16087.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.079428 restraints weight = 14776.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15064  Z= 0.133
  Angle     :  0.597   9.932  21642  Z= 0.330
  Chirality :  0.038   0.271   2658
  Planarity :  0.005   0.062   1784
  Dihedral  : 23.388 179.832   5378
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.27 %
    Favored  : 77.41 %
  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: -1.78 (0.25), residues: 1071
  helix: -0.01 (0.23), residues: 526
  sheet: -1.65 (0.60), residues: 75
  loop : -2.52 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M  93 
 TYR   0.022   0.002   TYR A  18 
 PHE   0.025   0.002   PHE M  66 
 TRP   0.020   0.002   TRP A  60 
 HIS   0.012   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 (15063)
  covalent geometry    : angle       0.59717 /  0.33 (21642)
  hydrogen bonds       : bond        0.05567 /  3.69 (  521)
  hydrogen bonds       : angle       4.16935 /  3.03 ( 1322)
  Misc. bond           : bond        0.00147 /  0.08 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6378 (t70)
REVERT: A  347 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8532 (tt)
REVERT: A  722 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7472 (mm110)
REVERT: A  762 HIS cc_start: 0.7424 (t-90) cc_final: 0.7211 (t-90)
REVERT: A  770 GLN cc_start: 0.8648 (mt0) cc_final: 0.7868 (mm110)
REVERT: A  772 TYR cc_start: 0.7249 (t80) cc_final: 0.6139 (m-80)
REVERT: A  774 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6789 (mmm160)
REVERT: A  894 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: M   62 ILE cc_start: 0.8741 (tp) cc_final: 0.8296 (tt)
REVERT: M   64 ASN cc_start: 0.8276 (m110) cc_final: 0.8043 (m110)
REVERT: M   66 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6886 (t80)
REVERT: M  122 TYR cc_start: 0.8151 (t80) cc_final: 0.7600 (t80)
REVERT: L   75 LYS cc_start: 0.7772 (tppt) cc_final: 0.7566 (tttp)
  outliers start: 31
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1175
  time to fit residues: 20.4875
Evaluate side-chains
  110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  894 TYR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   66 PHE
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0470
   chunk 41 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 116 optimal weight:   10.0000
   chunk 118 optimal weight:   40.0000
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 121 optimal weight:   20.0000
   overall best weight:    2.3484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
A 534 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 HIS
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.112053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.075010 restraints weight = 49543.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.076887 restraints weight = 27001.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.078036 restraints weight = 19335.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.078658 restraints weight = 16196.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.078907 restraints weight = 14787.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15064  Z= 0.153
  Angle     :  0.610   8.303  21642  Z= 0.337
  Chirality :  0.038   0.272   2658
  Planarity :  0.005   0.062   1784
  Dihedral  : 23.405 179.870   5378
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.66 %
    Favored  : 75.91 %
  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: -1.67 (0.25), residues: 1071
  helix:  0.08 (0.23), residues: 527
  sheet: -1.48 (0.62), residues: 75
  loop : -2.48 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M  93 
 TYR   0.021   0.002   TYR A  18 
 PHE   0.017   0.002   PHE A 708 
 TRP   0.018   0.001   TRP A  60 
 HIS   0.015   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 (15063)
  covalent geometry    : angle       0.61000 /  0.34 (21642)
  hydrogen bonds       : bond        0.05619 /  3.72 (  521)
  hydrogen bonds       : angle       4.17769 /  3.02 ( 1322)
  Misc. bond           : bond        0.00123 /  0.06 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8570 (tt)
REVERT: A  722 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7517 (mm110)
REVERT: A  762 HIS cc_start: 0.7523 (t-90) cc_final: 0.7289 (t-90)
REVERT: A  770 GLN cc_start: 0.8590 (mt0) cc_final: 0.8218 (tp-100)
REVERT: A  772 TYR cc_start: 0.7298 (t80) cc_final: 0.6279 (m-80)
REVERT: A  774 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6909 (mmm160)
REVERT: A  776 PHE cc_start: 0.8450 (t80) cc_final: 0.8250 (t80)
REVERT: A  894 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6718 (t80)
REVERT: M   62 ILE cc_start: 0.8677 (tp) cc_final: 0.8359 (tt)
REVERT: M   69 ASP cc_start: 0.8250 (t0) cc_final: 0.7953 (t0)
REVERT: M   73 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7467 (mtm180)
REVERT: M   96 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7749 (mp10)
REVERT: M  122 TYR cc_start: 0.8143 (t80) cc_final: 0.7594 (t80)
REVERT: L   96 LYS cc_start: 0.8689 (tppt) cc_final: 0.8221 (mmtt)
  outliers start: 32
  outliers final: 17
  residues processed: 114
  average time/residue: 0.1300
  time to fit residues: 21.5176
Evaluate side-chains
  107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  894 TYR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   77 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 128 optimal weight:   50.0000
   chunk 107 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 109 optimal weight:   40.0000
   chunk 19 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 HIS
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.111604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.074669 restraints weight = 48921.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076529 restraints weight = 27139.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.077610 restraints weight = 19506.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.078206 restraints weight = 16423.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.078501 restraints weight = 15020.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15064  Z= 0.160
  Angle     :  0.615   9.781  21642  Z= 0.339
  Chirality :  0.038   0.271   2658
  Planarity :  0.005   0.062   1784
  Dihedral  : 23.451 179.351   5378
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.99 %
    Favored  : 75.48 %
  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: -1.50 (0.26), residues: 1071
  helix:  0.20 (0.23), residues: 529
  sheet: -1.27 (0.63), residues: 75
  loop : -2.39 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M  93 
 TYR   0.021   0.002   TYR A  18 
 PHE   0.027   0.002   PHE A 345 
 TRP   0.019   0.002   TRP A  60 
 HIS   0.012   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 (15063)
  covalent geometry    : angle       0.61529 /  0.34 (21642)
  hydrogen bonds       : bond        0.05724 /  3.77 (  521)
  hydrogen bonds       : angle       4.19059 /  3.02 ( 1322)
  Misc. bond           : bond        0.00051 /  0.03 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8473 (tt)
REVERT: A  631 ARG cc_start: 0.8467 (ttp-170) cc_final: 0.8205 (ptp-110)
REVERT: A  722 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7492 (mm110)
REVERT: A  762 HIS cc_start: 0.7508 (t-90) cc_final: 0.7274 (t-90)
REVERT: A  770 GLN cc_start: 0.8565 (mt0) cc_final: 0.8209 (tp-100)
REVERT: A  772 TYR cc_start: 0.7280 (t80) cc_final: 0.6504 (m-80)
REVERT: A  774 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7442 (ptt-90)
REVERT: A  894 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6572 (t80)
REVERT: M   62 ILE cc_start: 0.8639 (tp) cc_final: 0.8356 (tt)
REVERT: M  122 TYR cc_start: 0.8154 (t80) cc_final: 0.7557 (t80)
REVERT: L   85 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8042 (pt0)
  outliers start: 33
  outliers final: 25
  residues processed: 109
  average time/residue: 0.1179
  time to fit residues: 18.5186
Evaluate side-chains
  114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  894 TYR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   77 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 118 optimal weight:   40.0000
   chunk 22 optimal weight:    5.9990
   chunk 120 optimal weight:   50.0000
   chunk 76 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0070
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.6004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
A 608 GLN
A 925 HIS
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.112359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.077311 restraints weight = 50001.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.078224 restraints weight = 29215.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.078702 restraints weight = 19787.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.078998 restraints weight = 18736.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.078858 restraints weight = 17139.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15064  Z= 0.129
  Angle     :  0.587   8.168  21642  Z= 0.324
  Chirality :  0.037   0.250   2658
  Planarity :  0.005   0.062   1784
  Dihedral  : 23.451 178.744   5378
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.16 %
    Favored  : 75.37 %
  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: -1.35 (0.26), residues: 1071
  helix:  0.31 (0.23), residues: 529
  sheet: -1.08 (0.64), residues: 74
  loop : -2.34 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 390 
 TYR   0.021   0.002   TYR A  18 
 PHE   0.023   0.002   PHE A 345 
 TRP   0.015   0.001   TRP A  60 
 HIS   0.011   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.13 (15063)
  covalent geometry    : angle       0.58704 /  0.32 (21642)
  hydrogen bonds       : bond        0.05061 /  3.33 (  521)
  hydrogen bonds       : angle       4.08742 /  2.96 ( 1322)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8441 (tt)
REVERT: A  516 ASP cc_start: 0.6802 (m-30) cc_final: 0.6435 (p0)
REVERT: A  631 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8180 (ptp-110)
REVERT: A  722 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7238 (mm110)
REVERT: A  762 HIS cc_start: 0.7475 (t-90) cc_final: 0.7230 (t-90)
REVERT: A  770 GLN cc_start: 0.8648 (mt0) cc_final: 0.8187 (tp-100)
REVERT: A  772 TYR cc_start: 0.7382 (t80) cc_final: 0.6412 (m-80)
REVERT: A  774 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6898 (ptt-90)
REVERT: M   96 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7732 (mp10)
REVERT: M  122 TYR cc_start: 0.8112 (t80) cc_final: 0.7559 (t80)
REVERT: L   85 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8011 (pt0)
REVERT: L   96 LYS cc_start: 0.8354 (tppt) cc_final: 0.8050 (tppt)
  outliers start: 23
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1131
  time to fit residues: 17.2538
Evaluate side-chains
  105 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 TYR
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   77 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 99 optimal weight:    0.5980
   chunk 90 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:   30.0000
   chunk 106 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0470
   chunk 0 optimal weight:   10.0000
   chunk 117 optimal weight:   20.0000
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.6480

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1022 HIS ** 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 = 0.4063 r_free = 0.4063 target = 0.113024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.076699 restraints weight = 49610.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.078643 restraints weight = 26499.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.079815 restraints weight = 18688.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.080432 restraints weight = 15492.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.080808 restraints weight = 14105.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  15064  Z= 0.114
  Angle     :  0.579   8.053  21642  Z= 0.318
  Chirality :  0.036   0.237   2658
  Planarity :  0.005   0.061   1784
  Dihedral  : 23.431 178.946   5378
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.48 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.26), residues: 1071
  helix:  0.44 (0.23), residues: 526
  sheet: -1.08 (0.63), residues: 74
  loop : -2.28 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 390 
 TYR   0.020   0.002   TYR A  18 
 PHE   0.025   0.001   PHE A 345 
 TRP   0.014   0.001   TRP A  60 
 HIS   0.010   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 (15063)
  covalent geometry    : angle       0.57895 /  0.32 (21642)
  hydrogen bonds       : bond        0.04704 /  3.09 (  521)
  hydrogen bonds       : angle       3.98626 /  2.89 ( 1322)
  Misc. bond           : bond        0.00045 /  0.02 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 ASP cc_start: 0.6994 (m-30) cc_final: 0.6475 (p0)
REVERT: A  631 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.8187 (ptp-110)
REVERT: A  722 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6847 (mm110)
REVERT: A  770 GLN cc_start: 0.8543 (mt0) cc_final: 0.8086 (tp-100)
REVERT: A  772 TYR cc_start: 0.7334 (t80) cc_final: 0.6379 (m-80)
REVERT: A  774 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6966 (ptt-90)
REVERT: A  813 MET cc_start: 0.7914 (ppp) cc_final: 0.7638 (ppp)
REVERT: M   96 GLN cc_start: 0.8074 (mt0) cc_final: 0.7760 (mp10)
REVERT: M  122 TYR cc_start: 0.8124 (t80) cc_final: 0.7533 (t80)
REVERT: L   85 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7992 (pt0)
REVERT: L   96 LYS cc_start: 0.8358 (tppt) cc_final: 0.8045 (tppt)
  outliers start: 21
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1210
  time to fit residues: 18.5453
Evaluate side-chains
  106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   77 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 126 optimal weight:   20.0000
   chunk 115 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 92 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.112319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.077422 restraints weight = 50329.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.078576 restraints weight = 29640.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.078575 restraints weight = 20151.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.078902 restraints weight = 19800.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.078701 restraints weight = 17205.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15064  Z= 0.141
  Angle     :  0.594  10.938  21642  Z= 0.326
  Chirality :  0.037   0.250   2658
  Planarity :  0.005   0.060   1784
  Dihedral  : 23.442 179.432   5378
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.48 %
    Favored  : 75.05 %
  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: -1.19 (0.26), residues: 1071
  helix:  0.49 (0.23), residues: 531
  sheet: -1.09 (0.63), residues: 74
  loop : -2.32 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 390 
 TYR   0.018   0.002   TYR A  18 
 PHE   0.024   0.002   PHE A 345 
 TRP   0.015   0.001   TRP A  60 
 HIS   0.011   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (15063)
  covalent geometry    : angle       0.59436 /  0.33 (21642)
  hydrogen bonds       : bond        0.05226 /  3.42 (  521)
  hydrogen bonds       : angle       4.09174 /  2.96 ( 1322)
  Misc. bond           : bond        0.00034 /  0.02 (    1)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  631 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8259 (ptp-110)
REVERT: A  722 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6918 (mm110)
REVERT: A  770 GLN cc_start: 0.8663 (mt0) cc_final: 0.8149 (tp-100)
REVERT: A  772 TYR cc_start: 0.7426 (t80) cc_final: 0.6458 (m-80)
REVERT: A  774 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6992 (ptt-90)
REVERT: M   96 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7535 (mp10)
REVERT: M  122 TYR cc_start: 0.8085 (t80) cc_final: 0.7489 (t80)
REVERT: L   85 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7957 (pt0)
REVERT: L   96 LYS cc_start: 0.8376 (tppt) cc_final: 0.8067 (tppt)
  outliers start: 23
  outliers final: 18
  residues processed: 103
  average time/residue: 0.1231
  time to fit residues: 18.4858
Evaluate side-chains
  107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain A residue  774 ARG
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue   96 GLN
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   77 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 114 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 119 optimal weight:   30.0000
   chunk 93 optimal weight:    0.0570
   chunk 109 optimal weight:   40.0000
   chunk 58 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.8104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 HIS
A 169 GLN
A 608 GLN
** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  96 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.112546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078489 restraints weight = 50271.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.078779 restraints weight = 30898.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.078682 restraints weight = 22275.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.079151 restraints weight = 22037.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.079032 restraints weight = 18660.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15064  Z= 0.132
  Angle     :  0.589  10.772  21642  Z= 0.323
  Chirality :  0.037   0.242   2658
  Planarity :  0.005   0.060   1784
  Dihedral  : 23.453 178.917   5378
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 22.81 %
    Favored  : 75.05 %
  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: 1071
  helix:  0.58 (0.23), residues: 525
  sheet: -1.27 (0.62), residues: 76
  loop : -2.28 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 390 
 TYR   0.020   0.002   TYR A  18 
 PHE   0.024   0.002   PHE A 345 
 TRP   0.015   0.001   TRP A  60 
 HIS   0.011   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 (15063)
  covalent geometry    : angle       0.58887 /  0.32 (21642)
  hydrogen bonds       : bond        0.05024 /  3.30 (  521)
  hydrogen bonds       : angle       4.06301 /  2.96 ( 1322)
  Misc. bond           : bond        0.00028 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.00 seconds
wall clock time: 45 minutes 40.30 seconds (2740.30 seconds total)