Starting phenix.real_space_refine
on Wed Feb 14 00:41:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvi_14178/02_2024/7qvi_14178_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 544 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P      32      5.49       5
     Mg     16      5.21       5
     S     240      5.16       5
     C   35760      2.51       5
     N   10040      2.21       5
     O   10512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   11": "NH1" <-> "NH2"
    Residue "A ARG   72": "NH1" <-> "NH2"
    Residue "A ARG   79": "NH1" <-> "NH2"
    Residue "A TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  113": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  147": "NH1" <-> "NH2"
    Residue "A TYR  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  221": "NH1" <-> "NH2"
    Residue "A GLU  241": "OE1" <-> "OE2"
    Residue "A PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  267": "NH1" <-> "NH2"
    Residue "A ARG  268": "NH1" <-> "NH2"
    Residue "A ARG  269": "NH1" <-> "NH2"
    Residue "A GLU  272": "OE1" <-> "OE2"
    Residue "A ARG  325": "NH1" <-> "NH2"
    Residue "A PHE  349": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  397": "NH1" <-> "NH2"
    Residue "A ARG  400": "NH1" <-> "NH2"
    Residue "A GLU  432": "OE1" <-> "OE2"
    Residue "A GLU  433": "OE1" <-> "OE2"
    Residue "A ARG  442": "NH1" <-> "NH2"
    Residue "A GLU  446": "OE1" <-> "OE2"
    Residue "B TYR    6": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   72": "NH1" <-> "NH2"
    Residue "B TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   79": "NH1" <-> "NH2"
    Residue "B TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  147": "NH1" <-> "NH2"
    Residue "B GLU  177": "OE1" <-> "OE2"
    Residue "B ARG  221": "NH1" <-> "NH2"
    Residue "B PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  267": "NH1" <-> "NH2"
    Residue "B ARG  268": "NH1" <-> "NH2"
    Residue "B ARG  269": "NH1" <-> "NH2"
    Residue "B ARG  325": "NH1" <-> "NH2"
    Residue "B ARG  397": "NH1" <-> "NH2"
    Residue "B ARG  400": "NH1" <-> "NH2"
    Residue "B GLU  433": "OE1" <-> "OE2"
    Residue "B ARG  436": "NH1" <-> "NH2"
    Residue "B ARG  442": "NH1" <-> "NH2"
    Residue "C GLU   61": "OE1" <-> "OE2"
    Residue "C GLU   71": "OE1" <-> "OE2"
    Residue "C ARG   72": "NH1" <-> "NH2"
    Residue "C ARG   79": "NH1" <-> "NH2"
    Residue "C TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  147": "NH1" <-> "NH2"
    Residue "C ARG  221": "NH1" <-> "NH2"
    Residue "C ARG  267": "NH1" <-> "NH2"
    Residue "C ARG  268": "NH1" <-> "NH2"
    Residue "C ARG  269": "NH1" <-> "NH2"
    Residue "C ARG  325": "NH1" <-> "NH2"
    Residue "C ARG  397": "NH1" <-> "NH2"
    Residue "C ARG  400": "NH1" <-> "NH2"
    Residue "C ARG  442": "NH1" <-> "NH2"
    Residue "D ARG    3": "NH1" <-> "NH2"
    Residue "D GLU    7": "OE1" <-> "OE2"
    Residue "D GLU   53": "OE1" <-> "OE2"
    Residue "D GLU   71": "OE1" <-> "OE2"
    Residue "D ARG   72": "NH1" <-> "NH2"
    Residue "D ARG   79": "NH1" <-> "NH2"
    Residue "D GLU   81": "OE1" <-> "OE2"
    Residue "D PHE  113": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  147": "NH1" <-> "NH2"
    Residue "D TYR  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  206": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  221": "NH1" <-> "NH2"
    Residue "D GLU  241": "OE1" <-> "OE2"
    Residue "D ARG  267": "NH1" <-> "NH2"
    Residue "D ARG  268": "NH1" <-> "NH2"
    Residue "D ARG  269": "NH1" <-> "NH2"
    Residue "D GLU  271": "OE1" <-> "OE2"
    Residue "D ARG  325": "NH1" <-> "NH2"
    Residue "D GLU  327": "OE1" <-> "OE2"
    Residue "D ASP  338": "OD1" <-> "OD2"
    Residue "D PHE  361": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  397": "NH1" <-> "NH2"
    Residue "D ARG  400": "NH1" <-> "NH2"
    Residue "D GLU  426": "OE1" <-> "OE2"
    Residue "D GLU  429": "OE1" <-> "OE2"
    Residue "D ARG  442": "NH1" <-> "NH2"
    Residue "D GLU  446": "OE1" <-> "OE2"
    Residue "E GLU   61": "OE1" <-> "OE2"
    Residue "E ARG   72": "NH1" <-> "NH2"
    Residue "E TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG   79": "NH1" <-> "NH2"
    Residue "E ARG  147": "NH1" <-> "NH2"
    Residue "E TYR  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  221": "NH1" <-> "NH2"
    Residue "E GLU  245": "OE1" <-> "OE2"
    Residue "E TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  267": "NH1" <-> "NH2"
    Residue "E ARG  268": "NH1" <-> "NH2"
    Residue "E ARG  269": "NH1" <-> "NH2"
    Residue "E GLU  271": "OE1" <-> "OE2"
    Residue "E PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  322": "OE1" <-> "OE2"
    Residue "E ASP  324": "OD1" <-> "OD2"
    Residue "E ARG  325": "NH1" <-> "NH2"
    Residue "E GLU  327": "OE1" <-> "OE2"
    Residue "E PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  397": "NH1" <-> "NH2"
    Residue "E ARG  400": "NH1" <-> "NH2"
    Residue "E GLU  411": "OE1" <-> "OE2"
    Residue "E GLU  440": "OE1" <-> "OE2"
    Residue "E ARG  442": "NH1" <-> "NH2"
    Residue "F GLU   44": "OE1" <-> "OE2"
    Residue "F ARG   72": "NH1" <-> "NH2"
    Residue "F TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   79": "NH1" <-> "NH2"
    Residue "F GLU  144": "OE1" <-> "OE2"
    Residue "F ARG  147": "NH1" <-> "NH2"
    Residue "F ARG  221": "NH1" <-> "NH2"
    Residue "F ARG  267": "NH1" <-> "NH2"
    Residue "F ARG  268": "NH1" <-> "NH2"
    Residue "F ARG  269": "NH1" <-> "NH2"
    Residue "F ARG  325": "NH1" <-> "NH2"
    Residue "F PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  397": "NH1" <-> "NH2"
    Residue "F ARG  400": "NH1" <-> "NH2"
    Residue "F GLU  419": "OE1" <-> "OE2"
    Residue "F ARG  436": "NH1" <-> "NH2"
    Residue "F ARG  442": "NH1" <-> "NH2"
    Residue "F GLU  446": "OE1" <-> "OE2"
    Residue "G ARG   14": "NH1" <-> "NH2"
    Residue "G ASP   26": "OD1" <-> "OD2"
    Residue "G GLU   53": "OE1" <-> "OE2"
    Residue "G ARG   72": "NH1" <-> "NH2"
    Residue "G ARG   79": "NH1" <-> "NH2"
    Residue "G GLU   96": "OE1" <-> "OE2"
    Residue "G ARG  147": "NH1" <-> "NH2"
    Residue "G ARG  201": "NH1" <-> "NH2"
    Residue "G GLU  209": "OE1" <-> "OE2"
    Residue "G ARG  221": "NH1" <-> "NH2"
    Residue "G GLU  234": "OE1" <-> "OE2"
    Residue "G GLU  241": "OE1" <-> "OE2"
    Residue "G PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  267": "NH1" <-> "NH2"
    Residue "G ARG  268": "NH1" <-> "NH2"
    Residue "G ARG  269": "NH1" <-> "NH2"
    Residue "G ARG  325": "NH1" <-> "NH2"
    Residue "G ASP  333": "OD1" <-> "OD2"
    Residue "G GLU  337": "OE1" <-> "OE2"
    Residue "G PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  397": "NH1" <-> "NH2"
    Residue "G ARG  400": "NH1" <-> "NH2"
    Residue "G GLU  429": "OE1" <-> "OE2"
    Residue "G ARG  436": "NH1" <-> "NH2"
    Residue "G ARG  442": "NH1" <-> "NH2"
    Residue "H ARG   11": "NH1" <-> "NH2"
    Residue "H GLU   15": "OE1" <-> "OE2"
    Residue "H GLU   61": "OE1" <-> "OE2"
    Residue "H ARG   72": "NH1" <-> "NH2"
    Residue "H ARG   79": "NH1" <-> "NH2"
    Residue "H ARG  147": "NH1" <-> "NH2"
    Residue "H ARG  180": "NH1" <-> "NH2"
    Residue "H GLU  209": "OE1" <-> "OE2"
    Residue "H GLU  220": "OE1" <-> "OE2"
    Residue "H ARG  221": "NH1" <-> "NH2"
    Residue "H GLU  234": "OE1" <-> "OE2"
    Residue "H ARG  267": "NH1" <-> "NH2"
    Residue "H ARG  268": "NH1" <-> "NH2"
    Residue "H ARG  269": "NH1" <-> "NH2"
    Residue "H ARG  325": "NH1" <-> "NH2"
    Residue "H GLU  327": "OE1" <-> "OE2"
    Residue "H PHE  350": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  353": "OD1" <-> "OD2"
    Residue "H ARG  397": "NH1" <-> "NH2"
    Residue "H ARG  400": "NH1" <-> "NH2"
    Residue "H ARG  428": "NH1" <-> "NH2"
    Residue "H ARG  442": "NH1" <-> "NH2"
    Residue "I ARG   11": "NH1" <-> "NH2"
    Residue "I GLU   15": "OE1" <-> "OE2"
    Residue "I GLU   61": "OE1" <-> "OE2"
    Residue "I GLU   71": "OE1" <-> "OE2"
    Residue "I ARG   72": "NH1" <-> "NH2"
    Residue "I ARG   79": "NH1" <-> "NH2"
    Residue "I GLU   96": "OE1" <-> "OE2"
    Residue "I ARG  147": "NH1" <-> "NH2"
    Residue "I ARG  173": "NH1" <-> "NH2"
    Residue "I GLU  215": "OE1" <-> "OE2"
    Residue "I ARG  221": "NH1" <-> "NH2"
    Residue "I TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  267": "NH1" <-> "NH2"
    Residue "I ARG  268": "NH1" <-> "NH2"
    Residue "I ARG  269": "NH1" <-> "NH2"
    Residue "I GLU  272": "OE1" <-> "OE2"
    Residue "I ARG  325": "NH1" <-> "NH2"
    Residue "I ASP  338": "OD1" <-> "OD2"
    Residue "I ARG  397": "NH1" <-> "NH2"
    Residue "I ARG  400": "NH1" <-> "NH2"
    Residue "I GLU  429": "OE1" <-> "OE2"
    Residue "I ARG  436": "NH1" <-> "NH2"
    Residue "I ARG  442": "NH1" <-> "NH2"
    Residue "J GLU   15": "OE1" <-> "OE2"
    Residue "J PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J GLU   61": "OE1" <-> "OE2"
    Residue "J GLU   71": "OE1" <-> "OE2"
    Residue "J ARG   72": "NH1" <-> "NH2"
    Residue "J ARG   79": "NH1" <-> "NH2"
    Residue "J TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG  147": "NH1" <-> "NH2"
    Residue "J TYR  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J GLU  215": "OE1" <-> "OE2"
    Residue "J ARG  221": "NH1" <-> "NH2"
    Residue "J ARG  267": "NH1" <-> "NH2"
    Residue "J ARG  268": "NH1" <-> "NH2"
    Residue "J ARG  269": "NH1" <-> "NH2"
    Residue "J GLU  271": "OE1" <-> "OE2"
    Residue "J ASP  288": "OD1" <-> "OD2"
    Residue "J ASP  324": "OD1" <-> "OD2"
    Residue "J ARG  325": "NH1" <-> "NH2"
    Residue "J PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG  397": "NH1" <-> "NH2"
    Residue "J ARG  400": "NH1" <-> "NH2"
    Residue "J GLU  411": "OE1" <-> "OE2"
    Residue "J ARG  436": "NH1" <-> "NH2"
    Residue "J ARG  442": "NH1" <-> "NH2"
    Residue "K GLU    7": "OE1" <-> "OE2"
    Residue "K ASP   69": "OD1" <-> "OD2"
    Residue "K ARG   72": "NH1" <-> "NH2"
    Residue "K ARG   79": "NH1" <-> "NH2"
    Residue "K ARG  147": "NH1" <-> "NH2"
    Residue "K GLU  217": "OE1" <-> "OE2"
    Residue "K ARG  221": "NH1" <-> "NH2"
    Residue "K GLU  241": "OE1" <-> "OE2"
    Residue "K GLU  245": "OE1" <-> "OE2"
    Residue "K ARG  267": "NH1" <-> "NH2"
    Residue "K ARG  268": "NH1" <-> "NH2"
    Residue "K ARG  269": "NH1" <-> "NH2"
    Residue "K GLU  271": "OE1" <-> "OE2"
    Residue "K ARG  325": "NH1" <-> "NH2"
    Residue "K ARG  397": "NH1" <-> "NH2"
    Residue "K ARG  400": "NH1" <-> "NH2"
    Residue "K GLU  419": "OE1" <-> "OE2"
    Residue "K ARG  436": "NH1" <-> "NH2"
    Residue "K ARG  442": "NH1" <-> "NH2"
    Residue "L GLU    7": "OE1" <-> "OE2"
    Residue "L GLU   61": "OE1" <-> "OE2"
    Residue "L ARG   72": "NH1" <-> "NH2"
    Residue "L ARG   79": "NH1" <-> "NH2"
    Residue "L GLU  144": "OE1" <-> "OE2"
    Residue "L ARG  147": "NH1" <-> "NH2"
    Residue "L ASP  189": "OD1" <-> "OD2"
    Residue "L GLU  209": "OE1" <-> "OE2"
    Residue "L ARG  221": "NH1" <-> "NH2"
    Residue "L ARG  267": "NH1" <-> "NH2"
    Residue "L ARG  268": "NH1" <-> "NH2"
    Residue "L ARG  269": "NH1" <-> "NH2"
    Residue "L PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ARG  325": "NH1" <-> "NH2"
    Residue "L ARG  397": "NH1" <-> "NH2"
    Residue "L ARG  400": "NH1" <-> "NH2"
    Residue "L GLU  411": "OE1" <-> "OE2"
    Residue "L GLU  419": "OE1" <-> "OE2"
    Residue "L ARG  436": "NH1" <-> "NH2"
    Residue "L ARG  442": "NH1" <-> "NH2"
    Residue "M ARG   14": "NH1" <-> "NH2"
    Residue "M GLU   15": "OE1" <-> "OE2"
    Residue "M ARG   72": "NH1" <-> "NH2"
    Residue "M ARG   79": "NH1" <-> "NH2"
    Residue "M TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU   96": "OE1" <-> "OE2"
    Residue "M ASP  146": "OD1" <-> "OD2"
    Residue "M ARG  147": "NH1" <-> "NH2"
    Residue "M GLU  215": "OE1" <-> "OE2"
    Residue "M GLU  220": "OE1" <-> "OE2"
    Residue "M ARG  221": "NH1" <-> "NH2"
    Residue "M ARG  267": "NH1" <-> "NH2"
    Residue "M ARG  268": "NH1" <-> "NH2"
    Residue "M ARG  269": "NH1" <-> "NH2"
    Residue "M GLU  272": "OE1" <-> "OE2"
    Residue "M ARG  325": "NH1" <-> "NH2"
    Residue "M GLU  327": "OE1" <-> "OE2"
    Residue "M PHE  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG  397": "NH1" <-> "NH2"
    Residue "M ARG  400": "NH1" <-> "NH2"
    Residue "M ARG  436": "NH1" <-> "NH2"
    Residue "M ARG  442": "NH1" <-> "NH2"
    Residue "N ARG   72": "NH1" <-> "NH2"
    Residue "N ARG   79": "NH1" <-> "NH2"
    Residue "N ASP   83": "OD1" <-> "OD2"
    Residue "N PHE  113": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG  147": "NH1" <-> "NH2"
    Residue "N ARG  221": "NH1" <-> "NH2"
    Residue "N GLU  234": "OE1" <-> "OE2"
    Residue "N PHE  260": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG  267": "NH1" <-> "NH2"
    Residue "N ARG  268": "NH1" <-> "NH2"
    Residue "N ARG  269": "NH1" <-> "NH2"
    Residue "N GLU  272": "OE1" <-> "OE2"
    Residue "N ARG  397": "NH1" <-> "NH2"
    Residue "N ARG  400": "NH1" <-> "NH2"
    Residue "N ARG  436": "NH1" <-> "NH2"
    Residue "N ARG  442": "NH1" <-> "NH2"
    Residue "O ASP   21": "OD1" <-> "OD2"
    Residue "O ARG   72": "NH1" <-> "NH2"
    Residue "O ARG   79": "NH1" <-> "NH2"
    Residue "O ARG  147": "NH1" <-> "NH2"
    Residue "O GLU  170": "OE1" <-> "OE2"
    Residue "O GLU  177": "OE1" <-> "OE2"
    Residue "O ARG  201": "NH1" <-> "NH2"
    Residue "O ARG  221": "NH1" <-> "NH2"
    Residue "O GLU  241": "OE1" <-> "OE2"
    Residue "O ARG  267": "NH1" <-> "NH2"
    Residue "O ARG  268": "NH1" <-> "NH2"
    Residue "O ARG  269": "NH1" <-> "NH2"
    Residue "O PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O GLU  322": "OE1" <-> "OE2"
    Residue "O ARG  325": "NH1" <-> "NH2"
    Residue "O GLU  327": "OE1" <-> "OE2"
    Residue "O ARG  397": "NH1" <-> "NH2"
    Residue "O ARG  400": "NH1" <-> "NH2"
    Residue "O GLU  411": "OE1" <-> "OE2"
    Residue "O ARG  436": "NH1" <-> "NH2"
    Residue "O ARG  442": "NH1" <-> "NH2"
    Residue "P GLU   61": "OE1" <-> "OE2"
    Residue "P ARG   72": "NH1" <-> "NH2"
    Residue "P ARG   79": "NH1" <-> "NH2"
    Residue "P ARG  147": "NH1" <-> "NH2"
    Residue "P ARG  180": "NH1" <-> "NH2"
    Residue "P ASP  202": "OD1" <-> "OD2"
    Residue "P GLU  217": "OE1" <-> "OE2"
    Residue "P GLU  220": "OE1" <-> "OE2"
    Residue "P ARG  221": "NH1" <-> "NH2"
    Residue "P ARG  267": "NH1" <-> "NH2"
    Residue "P ARG  268": "NH1" <-> "NH2"
    Residue "P ARG  269": "NH1" <-> "NH2"
    Residue "P PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ARG  325": "NH1" <-> "NH2"
    Residue "P GLU  327": "OE1" <-> "OE2"
    Residue "P ASP  333": "OD1" <-> "OD2"
    Residue "P ARG  397": "NH1" <-> "NH2"
    Residue "P ARG  400": "NH1" <-> "NH2"
    Residue "P ARG  436": "NH1" <-> "NH2"
    Residue "P ARG  442": "NH1" <-> "NH2"
  Time to flip residues: 0.14s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 56600
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "G"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "J"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "K"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "M"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "O"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3528
          Classifications: {'peptide': 447}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "P"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3503
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "I"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "J"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "K"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "L"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "M"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "N"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "O"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "P"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {' MG': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 21.43, per 1000 atoms: 0.38
  Number of scatterers: 56600
  At special positions: 0
  Unit cell: (134.757, 135.594, 209.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     240     16.00
     P      32     15.00
     Mg     16     11.99
     O   10512      8.00
     N   10040      7.00
     C   35760      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 16.27
  Conformation dependent library (CDL) restraints added in 7.9 seconds
  

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  12880

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      342 helices and 48 sheets defined
      44.0% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 11.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 15
      No H-bonds generated for 'chain 'A' and resid 13 through 15'
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 63 through 65
      No H-bonds generated for 'chain 'A' and resid 63 through 65'
    Processing helix  chain 'A' and resid 70 through 73
      No H-bonds generated for 'chain 'A' and resid 70 through 73'
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 99 through 105
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 4.185A  pdb=" N   THR A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 168 through 180
    Processing helix  chain 'A' and resid 200 through 216
      removed outlier: 3.802A  pdb=" N   LEU A 205 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 245
    Processing helix  chain 'A' and resid 261 through 272
      removed outlier: 3.511A  pdb=" N   GLU A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 326 through 336
    Processing helix  chain 'A' and resid 344 through 346
      No H-bonds generated for 'chain 'A' and resid 344 through 346'
    Processing helix  chain 'A' and resid 370 through 380
      Proline residue:  A 374  - end of helix
      removed outlier: 3.834A  pdb=" N   PHE A 380 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 393
      No H-bonds generated for 'chain 'A' and resid 390 through 393'
    Processing helix  chain 'A' and resid 399 through 418
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 6.151A  pdb=" N   ARG A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   GLU A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 447
    Processing helix  chain 'B' and resid 13 through 15
      No H-bonds generated for 'chain 'B' and resid 13 through 15'
    Processing helix  chain 'B' and resid 43 through 53
      removed outlier: 3.639A  pdb=" N   ALA B  48 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 66
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 99 through 106
      removed outlier: 3.674A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 133
      removed outlier: 4.214A  pdb=" N   THR B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 148
    Processing helix  chain 'B' and resid 168 through 181
    Processing helix  chain 'B' and resid 200 through 218
      removed outlier: 3.926A  pdb=" N   LEU B 205 " --> pdb=" O   ARG B 201 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET B 208 " --> pdb=" O   PHE B 204 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 245
    Processing helix  chain 'B' and resid 260 through 272
    Processing helix  chain 'B' and resid 284 through 288
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 325 through 336
    Processing helix  chain 'B' and resid 344 through 346
      No H-bonds generated for 'chain 'B' and resid 344 through 346'
    Processing helix  chain 'B' and resid 370 through 380
      Proline residue:  B 374  - end of helix
      removed outlier: 3.817A  pdb=" N   VAL B 377 " --> pdb=" O   PRO B 374 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE B 379 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 380 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 393
      No H-bonds generated for 'chain 'B' and resid 390 through 393'
    Processing helix  chain 'B' and resid 399 through 418
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 6.811A  pdb=" N   ARG B 428 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   GLU B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 445
    Processing helix  chain 'C' and resid 13 through 17
      removed outlier: 3.661A  pdb=" N   THR C  16 " --> pdb=" O   TYR C  13 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   TYR C  17 " --> pdb=" O   ARG C  14 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 13 through 17'
    Processing helix  chain 'C' and resid 43 through 53
    Processing helix  chain 'C' and resid 63 through 67
    Processing helix  chain 'C' and resid 70 through 73
      No H-bonds generated for 'chain 'C' and resid 70 through 73'
    Processing helix  chain 'C' and resid 91 through 93
      No H-bonds generated for 'chain 'C' and resid 91 through 93'
    Processing helix  chain 'C' and resid 99 through 104
    Processing helix  chain 'C' and resid 128 through 133
      removed outlier: 4.138A  pdb=" N   THR C 133 " --> pdb=" O   ALA C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 148
    Processing helix  chain 'C' and resid 168 through 181
    Processing helix  chain 'C' and resid 200 through 218
      removed outlier: 3.819A  pdb=" N   LEU C 205 " --> pdb=" O   ARG C 201 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET C 208 " --> pdb=" O   PHE C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 260 through 272
    Processing helix  chain 'C' and resid 284 through 287
      No H-bonds generated for 'chain 'C' and resid 284 through 287'
    Processing helix  chain 'C' and resid 297 through 307
    Processing helix  chain 'C' and resid 325 through 336
    Processing helix  chain 'C' and resid 344 through 346
      No H-bonds generated for 'chain 'C' and resid 344 through 346'
    Processing helix  chain 'C' and resid 370 through 380
      Proline residue:  C 374  - end of helix
      removed outlier: 3.757A  pdb=" N   VAL C 377 " --> pdb=" O   PRO C 374 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE C 380 " --> pdb=" O   VAL C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 393
      No H-bonds generated for 'chain 'C' and resid 390 through 393'
    Processing helix  chain 'C' and resid 399 through 418
    Processing helix  chain 'C' and resid 423 through 435
      removed outlier: 6.048A  pdb=" N   ARG C 428 " --> pdb=" O   LEU C 424 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   GLU C 429 " --> pdb=" O   ALA C 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 447
    Processing helix  chain 'D' and resid 13 through 17
      removed outlier: 3.628A  pdb=" N   THR D  16 " --> pdb=" O   TYR D  13 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   TYR D  17 " --> pdb=" O   ARG D  14 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 13 through 17'
    Processing helix  chain 'D' and resid 43 through 53
      removed outlier: 4.240A  pdb=" N   ALA D  48 " --> pdb=" O   GLU D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 67
    Processing helix  chain 'D' and resid 70 through 73
      No H-bonds generated for 'chain 'D' and resid 70 through 73'
    Processing helix  chain 'D' and resid 91 through 93
      No H-bonds generated for 'chain 'D' and resid 91 through 93'
    Processing helix  chain 'D' and resid 99 through 106
      removed outlier: 3.638A  pdb=" N   ILE D 106 " --> pdb=" O   ILE D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 112
      No H-bonds generated for 'chain 'D' and resid 110 through 112'
    Processing helix  chain 'D' and resid 128 through 133
      removed outlier: 4.521A  pdb=" N   THR D 133 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 148
      removed outlier: 3.710A  pdb=" N   GLU D 144 " --> pdb=" O   GLY D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 181
    Processing helix  chain 'D' and resid 200 through 218
      removed outlier: 4.099A  pdb=" N   LEU D 205 " --> pdb=" O   ARG D 201 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR D 206 " --> pdb=" O   ASP D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 245
    Processing helix  chain 'D' and resid 260 through 272
      removed outlier: 3.624A  pdb=" N   ARG D 269 " --> pdb=" O   SER D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 286
      No H-bonds generated for 'chain 'D' and resid 284 through 286'
    Processing helix  chain 'D' and resid 297 through 307
    Processing helix  chain 'D' and resid 325 through 336
    Processing helix  chain 'D' and resid 344 through 346
      No H-bonds generated for 'chain 'D' and resid 344 through 346'
    Processing helix  chain 'D' and resid 370 through 380
      Proline residue:  D 374  - end of helix
      removed outlier: 3.714A  pdb=" N   VAL D 377 " --> pdb=" O   PRO D 374 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE D 379 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE D 380 " --> pdb=" O   VAL D 377 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 390 through 393
      No H-bonds generated for 'chain 'D' and resid 390 through 393'
    Processing helix  chain 'D' and resid 399 through 419
    Processing helix  chain 'D' and resid 423 through 435
      removed outlier: 6.796A  pdb=" N   ARG D 428 " --> pdb=" O   LEU D 424 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLU D 429 " --> pdb=" O   ALA D 425 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 439 through 447
      removed outlier: 3.605A  pdb=" N   GLU D 443 " --> pdb=" O   PRO D 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 17
      removed outlier: 3.749A  pdb=" N   TYR E  17 " --> pdb=" O   ARG E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 53
      removed outlier: 4.539A  pdb=" N   ALA E  48 " --> pdb=" O   GLU E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 67
    Processing helix  chain 'E' and resid 70 through 73
      No H-bonds generated for 'chain 'E' and resid 70 through 73'
    Processing helix  chain 'E' and resid 91 through 93
      No H-bonds generated for 'chain 'E' and resid 91 through 93'
    Processing helix  chain 'E' and resid 99 through 105
    Processing helix  chain 'E' and resid 110 through 112
      No H-bonds generated for 'chain 'E' and resid 110 through 112'
    Processing helix  chain 'E' and resid 128 through 133
      removed outlier: 4.450A  pdb=" N   THR E 133 " --> pdb=" O   ALA E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 140 through 148
    Processing helix  chain 'E' and resid 168 through 181
    Processing helix  chain 'E' and resid 200 through 217
      removed outlier: 3.847A  pdb=" N   LEU E 205 " --> pdb=" O   ARG E 201 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU E 209 " --> pdb=" O   LEU E 205 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA E 216 " --> pdb=" O   ARG E 212 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU E 217 " --> pdb=" O   LYS E 213 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 245
    Processing helix  chain 'E' and resid 260 through 272
      removed outlier: 3.616A  pdb=" N   ARG E 269 " --> pdb=" O   SER E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 287
      No H-bonds generated for 'chain 'E' and resid 284 through 287'
    Processing helix  chain 'E' and resid 297 through 307
    Processing helix  chain 'E' and resid 325 through 336
      removed outlier: 3.666A  pdb=" N   LEU E 329 " --> pdb=" O   ARG E 325 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 344 through 346
      No H-bonds generated for 'chain 'E' and resid 344 through 346'
    Processing helix  chain 'E' and resid 370 through 380
      Proline residue:  E 374  - end of helix
      removed outlier: 3.860A  pdb=" N   VAL E 377 " --> pdb=" O   PRO E 374 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   SER E 378 " --> pdb=" O   ASP E 375 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE E 380 " --> pdb=" O   VAL E 377 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 390 through 393
      No H-bonds generated for 'chain 'E' and resid 390 through 393'
    Processing helix  chain 'E' and resid 398 through 419
      removed outlier: 4.095A  pdb=" N   GLU E 419 " --> pdb=" O   GLN E 415 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 423 through 435
      removed outlier: 5.690A  pdb=" N   ARG E 428 " --> pdb=" O   LEU E 424 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   GLU E 429 " --> pdb=" O   ALA E 425 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 439 through 447
    Processing helix  chain 'F' and resid 14 through 17
      No H-bonds generated for 'chain 'F' and resid 14 through 17'
    Processing helix  chain 'F' and resid 43 through 53
    Processing helix  chain 'F' and resid 63 through 67
      removed outlier: 3.658A  pdb=" N   LEU F  66 " --> pdb=" O   TRP F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 70 through 72
      No H-bonds generated for 'chain 'F' and resid 70 through 72'
    Processing helix  chain 'F' and resid 91 through 93
      No H-bonds generated for 'chain 'F' and resid 91 through 93'
    Processing helix  chain 'F' and resid 99 through 106
    Processing helix  chain 'F' and resid 110 through 112
      No H-bonds generated for 'chain 'F' and resid 110 through 112'
    Processing helix  chain 'F' and resid 128 through 133
      removed outlier: 4.915A  pdb=" N   THR F 133 " --> pdb=" O   ALA F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 141 through 148
    Processing helix  chain 'F' and resid 168 through 181
    Processing helix  chain 'F' and resid 200 through 218
      removed outlier: 4.000A  pdb=" N   LEU F 205 " --> pdb=" O   ARG F 201 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA F 216 " --> pdb=" O   ARG F 212 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU F 217 " --> pdb=" O   LYS F 213 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 246
    Processing helix  chain 'F' and resid 255 through 258
      No H-bonds generated for 'chain 'F' and resid 255 through 258'
    Processing helix  chain 'F' and resid 260 through 272
    Processing helix  chain 'F' and resid 284 through 288
    Processing helix  chain 'F' and resid 297 through 307
    Processing helix  chain 'F' and resid 325 through 336
    Processing helix  chain 'F' and resid 344 through 346
      No H-bonds generated for 'chain 'F' and resid 344 through 346'
    Processing helix  chain 'F' and resid 370 through 380
      Proline residue:  F 374  - end of helix
      removed outlier: 3.824A  pdb=" N   VAL F 377 " --> pdb=" O   PRO F 374 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE F 380 " --> pdb=" O   VAL F 377 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 393
      removed outlier: 3.656A  pdb=" N   HIS F 393 " --> pdb=" O   GLY F 389 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 389 through 393'
    Processing helix  chain 'F' and resid 399 through 417
    Processing helix  chain 'F' and resid 423 through 437
      removed outlier: 6.914A  pdb=" N   ARG F 428 " --> pdb=" O   LEU F 424 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLU F 429 " --> pdb=" O   ALA F 425 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   TRP F 437 " --> pdb=" O   GLU F 433 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 439 through 447
    Processing helix  chain 'G' and resid 13 through 17
      removed outlier: 3.586A  pdb=" N   THR G  16 " --> pdb=" O   TYR G  13 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TYR G  17 " --> pdb=" O   ARG G  14 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 13 through 17'
    Processing helix  chain 'G' and resid 43 through 53
    Processing helix  chain 'G' and resid 63 through 67
      removed outlier: 3.677A  pdb=" N   LEU G  66 " --> pdb=" O   TRP G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 70 through 72
      No H-bonds generated for 'chain 'G' and resid 70 through 72'
    Processing helix  chain 'G' and resid 91 through 93
      No H-bonds generated for 'chain 'G' and resid 91 through 93'
    Processing helix  chain 'G' and resid 99 through 105
    Processing helix  chain 'G' and resid 109 through 112
    Processing helix  chain 'G' and resid 128 through 133
      removed outlier: 4.318A  pdb=" N   THR G 133 " --> pdb=" O   ALA G 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 140 through 148
      removed outlier: 3.780A  pdb=" N   GLU G 144 " --> pdb=" O   GLY G 140 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 168 through 181
    Processing helix  chain 'G' and resid 200 through 218
      removed outlier: 3.549A  pdb=" N   LEU G 205 " --> pdb=" O   ARG G 201 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 233 through 245
    Processing helix  chain 'G' and resid 260 through 273
    Processing helix  chain 'G' and resid 284 through 288
    Processing helix  chain 'G' and resid 297 through 307
    Processing helix  chain 'G' and resid 326 through 336
    Processing helix  chain 'G' and resid 344 through 346
      No H-bonds generated for 'chain 'G' and resid 344 through 346'
    Processing helix  chain 'G' and resid 370 through 379
      Proline residue:  G 374  - end of helix
      removed outlier: 3.855A  pdb=" N   VAL G 377 " --> pdb=" O   PRO G 374 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 390 through 393
      No H-bonds generated for 'chain 'G' and resid 390 through 393'
    Processing helix  chain 'G' and resid 399 through 419
      removed outlier: 3.589A  pdb=" N   GLU G 419 " --> pdb=" O   GLN G 415 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 423 through 435
      removed outlier: 6.418A  pdb=" N   ARG G 428 " --> pdb=" O   LEU G 424 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   GLU G 429 " --> pdb=" O   ALA G 425 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 439 through 445
    Processing helix  chain 'H' and resid 13 through 15
      No H-bonds generated for 'chain 'H' and resid 13 through 15'
    Processing helix  chain 'H' and resid 43 through 53
    Processing helix  chain 'H' and resid 63 through 67
      removed outlier: 3.574A  pdb=" N   LEU H  66 " --> pdb=" O   TRP H  63 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 70 through 73
      No H-bonds generated for 'chain 'H' and resid 70 through 73'
    Processing helix  chain 'H' and resid 91 through 93
      No H-bonds generated for 'chain 'H' and resid 91 through 93'
    Processing helix  chain 'H' and resid 99 through 105
    Processing helix  chain 'H' and resid 128 through 133
      removed outlier: 4.863A  pdb=" N   THR H 133 " --> pdb=" O   ALA H 129 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 141 through 148
      removed outlier: 3.705A  pdb=" N   ASP H 146 " --> pdb=" O   GLN H 142 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 168 through 181
      removed outlier: 3.502A  pdb=" N   ARG H 173 " --> pdb=" O   LYS H 169 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 200 through 218
      removed outlier: 4.007A  pdb=" N   LEU H 205 " --> pdb=" O   ARG H 201 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 233 through 245
    Processing helix  chain 'H' and resid 261 through 272
      removed outlier: 3.510A  pdb=" N   ARG H 269 " --> pdb=" O   SER H 265 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 284 through 287
      No H-bonds generated for 'chain 'H' and resid 284 through 287'
    Processing helix  chain 'H' and resid 297 through 307
    Processing helix  chain 'H' and resid 325 through 336
    Processing helix  chain 'H' and resid 370 through 380
      Proline residue:  H 374  - end of helix
      removed outlier: 3.764A  pdb=" N   VAL H 377 " --> pdb=" O   PRO H 374 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE H 380 " --> pdb=" O   VAL H 377 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 389 through 393
      removed outlier: 3.957A  pdb=" N   HIS H 393 " --> pdb=" O   GLY H 389 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 389 through 393'
    Processing helix  chain 'H' and resid 398 through 419
      removed outlier: 3.862A  pdb=" N   GLU H 419 " --> pdb=" O   GLN H 415 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 423 through 437
      removed outlier: 6.627A  pdb=" N   ARG H 428 " --> pdb=" O   LEU H 424 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   GLU H 429 " --> pdb=" O   ALA H 425 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP H 437 " --> pdb=" O   GLU H 433 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 439 through 448
      removed outlier: 3.846A  pdb=" N   GLU H 443 " --> pdb=" O   PRO H 439 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA H 444 " --> pdb=" O   GLU H 440 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU H 447 " --> pdb=" O   GLU H 443 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TRP H 448 " --> pdb=" O   ALA H 444 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 13 through 17
    Processing helix  chain 'I' and resid 43 through 53
    Processing helix  chain 'I' and resid 63 through 67
      removed outlier: 3.521A  pdb=" N   LEU I  66 " --> pdb=" O   TRP I  63 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 70 through 73
      No H-bonds generated for 'chain 'I' and resid 70 through 73'
    Processing helix  chain 'I' and resid 91 through 93
      No H-bonds generated for 'chain 'I' and resid 91 through 93'
    Processing helix  chain 'I' and resid 99 through 105
    Processing helix  chain 'I' and resid 110 through 112
      No H-bonds generated for 'chain 'I' and resid 110 through 112'
    Processing helix  chain 'I' and resid 128 through 133
      removed outlier: 4.404A  pdb=" N   THR I 133 " --> pdb=" O   ALA I 129 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 140 through 148
      removed outlier: 3.592A  pdb=" N   GLU I 144 " --> pdb=" O   GLY I 140 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 168 through 180
    Processing helix  chain 'I' and resid 200 through 218
      removed outlier: 3.730A  pdb=" N   LEU I 205 " --> pdb=" O   ARG I 201 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU I 217 " --> pdb=" O   LYS I 213 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 233 through 245
      removed outlier: 3.512A  pdb=" N   PHE I 242 " --> pdb=" O   LYS I 238 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 255 through 258
      No H-bonds generated for 'chain 'I' and resid 255 through 258'
    Processing helix  chain 'I' and resid 260 through 272
    Processing helix  chain 'I' and resid 297 through 307
    Processing helix  chain 'I' and resid 325 through 336
    Processing helix  chain 'I' and resid 370 through 380
      Proline residue:  I 374  - end of helix
      removed outlier: 3.602A  pdb=" N   VAL I 377 " --> pdb=" O   PRO I 374 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   PHE I 380 " --> pdb=" O   VAL I 377 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 390 through 393
      No H-bonds generated for 'chain 'I' and resid 390 through 393'
    Processing helix  chain 'I' and resid 399 through 419
    Processing helix  chain 'I' and resid 427 through 435
    Processing helix  chain 'I' and resid 439 through 447
    Processing helix  chain 'J' and resid 13 through 15
      No H-bonds generated for 'chain 'J' and resid 13 through 15'
    Processing helix  chain 'J' and resid 43 through 55
      removed outlier: 3.555A  pdb=" N   SER J  55 " --> pdb=" O   ALA J  51 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 63 through 67
      removed outlier: 3.718A  pdb=" N   LEU J  66 " --> pdb=" O   TRP J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 70 through 73
      No H-bonds generated for 'chain 'J' and resid 70 through 73'
    Processing helix  chain 'J' and resid 91 through 93
      No H-bonds generated for 'chain 'J' and resid 91 through 93'
    Processing helix  chain 'J' and resid 99 through 105
    Processing helix  chain 'J' and resid 110 through 112
      No H-bonds generated for 'chain 'J' and resid 110 through 112'
    Processing helix  chain 'J' and resid 128 through 133
      removed outlier: 4.581A  pdb=" N   THR J 133 " --> pdb=" O   ALA J 129 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 141 through 148
      removed outlier: 3.511A  pdb=" N   ASP J 146 " --> pdb=" O   GLN J 142 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 168 through 181
    Processing helix  chain 'J' and resid 200 through 218
    Processing helix  chain 'J' and resid 233 through 245
      removed outlier: 3.734A  pdb=" N   LYS J 238 " --> pdb=" O   GLU J 234 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 260 through 272
    Processing helix  chain 'J' and resid 284 through 287
      No H-bonds generated for 'chain 'J' and resid 284 through 287'
    Processing helix  chain 'J' and resid 297 through 307
    Processing helix  chain 'J' and resid 325 through 336
    Processing helix  chain 'J' and resid 370 through 380
      Proline residue:  J 374  - end of helix
      removed outlier: 3.813A  pdb=" N   VAL J 377 " --> pdb=" O   PRO J 374 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE J 380 " --> pdb=" O   VAL J 377 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 390 through 393
      No H-bonds generated for 'chain 'J' and resid 390 through 393'
    Processing helix  chain 'J' and resid 399 through 418
    Processing helix  chain 'J' and resid 427 through 437
      removed outlier: 3.880A  pdb=" N   TRP J 437 " --> pdb=" O   GLU J 433 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 439 through 447
    Processing helix  chain 'K' and resid 13 through 15
      No H-bonds generated for 'chain 'K' and resid 13 through 15'
    Processing helix  chain 'K' and resid 43 through 53
    Processing helix  chain 'K' and resid 63 through 67
      removed outlier: 3.629A  pdb=" N   LEU K  66 " --> pdb=" O   TRP K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 70 through 72
      No H-bonds generated for 'chain 'K' and resid 70 through 72'
    Processing helix  chain 'K' and resid 91 through 93
      No H-bonds generated for 'chain 'K' and resid 91 through 93'
    Processing helix  chain 'K' and resid 99 through 105
    Processing helix  chain 'K' and resid 109 through 112
      removed outlier: 3.567A  pdb=" N   GLY K 112 " --> pdb=" O   ASN K 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 109 through 112'
    Processing helix  chain 'K' and resid 128 through 131
      No H-bonds generated for 'chain 'K' and resid 128 through 131'
    Processing helix  chain 'K' and resid 142 through 148
    Processing helix  chain 'K' and resid 168 through 181
    Processing helix  chain 'K' and resid 200 through 218
    Processing helix  chain 'K' and resid 233 through 245
    Processing helix  chain 'K' and resid 260 through 272
    Processing helix  chain 'K' and resid 284 through 288
    Processing helix  chain 'K' and resid 297 through 307
      removed outlier: 3.610A  pdb=" N   LYS K 302 " --> pdb=" O   ARG K 298 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 325 through 336
    Processing helix  chain 'K' and resid 344 through 346
      No H-bonds generated for 'chain 'K' and resid 344 through 346'
    Processing helix  chain 'K' and resid 370 through 380
      Proline residue:  K 374  - end of helix
      removed outlier: 3.835A  pdb=" N   VAL K 377 " --> pdb=" O   PRO K 374 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE K 380 " --> pdb=" O   VAL K 377 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 390 through 393
      No H-bonds generated for 'chain 'K' and resid 390 through 393'
    Processing helix  chain 'K' and resid 398 through 419
    Processing helix  chain 'K' and resid 423 through 435
      removed outlier: 5.766A  pdb=" N   ARG K 428 " --> pdb=" O   LEU K 424 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   GLU K 429 " --> pdb=" O   ALA K 425 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 439 through 447
    Processing helix  chain 'L' and resid 13 through 15
      No H-bonds generated for 'chain 'L' and resid 13 through 15'
    Processing helix  chain 'L' and resid 43 through 52
    Processing helix  chain 'L' and resid 63 through 67
      removed outlier: 3.690A  pdb=" N   LEU L  66 " --> pdb=" O   TRP L  63 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 70 through 72
      No H-bonds generated for 'chain 'L' and resid 70 through 72'
    Processing helix  chain 'L' and resid 91 through 93
      No H-bonds generated for 'chain 'L' and resid 91 through 93'
    Processing helix  chain 'L' and resid 99 through 104
    Processing helix  chain 'L' and resid 110 through 112
      No H-bonds generated for 'chain 'L' and resid 110 through 112'
    Processing helix  chain 'L' and resid 128 through 133
      removed outlier: 4.644A  pdb=" N   THR L 133 " --> pdb=" O   ALA L 129 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 140 through 148
    Processing helix  chain 'L' and resid 168 through 181
    Processing helix  chain 'L' and resid 200 through 218
      removed outlier: 3.732A  pdb=" N   LEU L 205 " --> pdb=" O   ARG L 201 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET L 208 " --> pdb=" O   PHE L 204 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLU L 209 " --> pdb=" O   LEU L 205 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA L 210 " --> pdb=" O   TYR L 206 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 233 through 246
    Processing helix  chain 'L' and resid 261 through 273
    Processing helix  chain 'L' and resid 284 through 286
      No H-bonds generated for 'chain 'L' and resid 284 through 286'
    Processing helix  chain 'L' and resid 297 through 307
    Processing helix  chain 'L' and resid 325 through 334
    Processing helix  chain 'L' and resid 344 through 346
      No H-bonds generated for 'chain 'L' and resid 344 through 346'
    Processing helix  chain 'L' and resid 370 through 380
      Proline residue:  L 374  - end of helix
      removed outlier: 3.805A  pdb=" N   VAL L 377 " --> pdb=" O   PRO L 374 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   PHE L 380 " --> pdb=" O   VAL L 377 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 390 through 393
      No H-bonds generated for 'chain 'L' and resid 390 through 393'
    Processing helix  chain 'L' and resid 399 through 419
      removed outlier: 3.743A  pdb=" N   GLU L 419 " --> pdb=" O   GLN L 415 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 423 through 437
      removed outlier: 6.902A  pdb=" N   ARG L 428 " --> pdb=" O   LEU L 424 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   GLU L 429 " --> pdb=" O   ALA L 425 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   TRP L 437 " --> pdb=" O   GLU L 433 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 439 through 447
    Processing helix  chain 'M' and resid 13 through 17
      removed outlier: 4.067A  pdb=" N   TYR M  17 " --> pdb=" O   ARG M  14 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 43 through 53
    Processing helix  chain 'M' and resid 63 through 67
      removed outlier: 3.625A  pdb=" N   LEU M  66 " --> pdb=" O   TRP M  63 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 70 through 73
      No H-bonds generated for 'chain 'M' and resid 70 through 73'
    Processing helix  chain 'M' and resid 91 through 93
      No H-bonds generated for 'chain 'M' and resid 91 through 93'
    Processing helix  chain 'M' and resid 99 through 105
    Processing helix  chain 'M' and resid 128 through 133
      removed outlier: 4.307A  pdb=" N   THR M 133 " --> pdb=" O   ALA M 129 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 140 through 148
    Processing helix  chain 'M' and resid 168 through 181
    Processing helix  chain 'M' and resid 200 through 218
      removed outlier: 4.044A  pdb=" N   LEU M 205 " --> pdb=" O   ARG M 201 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 233 through 245
    Processing helix  chain 'M' and resid 260 through 273
    Processing helix  chain 'M' and resid 285 through 288
      No H-bonds generated for 'chain 'M' and resid 285 through 288'
    Processing helix  chain 'M' and resid 297 through 307
    Processing helix  chain 'M' and resid 325 through 336
    Processing helix  chain 'M' and resid 344 through 346
      No H-bonds generated for 'chain 'M' and resid 344 through 346'
    Processing helix  chain 'M' and resid 370 through 380
      removed outlier: 3.634A  pdb=" N   VAL M 373 " --> pdb=" O   VAL M 370 " (cutoff:3.500A)
      Proline residue:  M 374  - end of helix
      removed outlier: 3.809A  pdb=" N   VAL M 377 " --> pdb=" O   PRO M 374 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   PHE M 380 " --> pdb=" O   VAL M 377 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 390 through 393
      No H-bonds generated for 'chain 'M' and resid 390 through 393'
    Processing helix  chain 'M' and resid 398 through 418
    Processing helix  chain 'M' and resid 423 through 434
      removed outlier: 5.856A  pdb=" N   ARG M 428 " --> pdb=" O   LEU M 424 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   GLU M 429 " --> pdb=" O   ALA M 425 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 439 through 447
      removed outlier: 4.002A  pdb=" N   GLU M 446 " --> pdb=" O   ARG M 442 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU M 447 " --> pdb=" O   GLU M 443 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 15
      No H-bonds generated for 'chain 'N' and resid 13 through 15'
    Processing helix  chain 'N' and resid 43 through 53
    Processing helix  chain 'N' and resid 63 through 67
      removed outlier: 3.561A  pdb=" N   LEU N  66 " --> pdb=" O   TRP N  63 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 70 through 72
      No H-bonds generated for 'chain 'N' and resid 70 through 72'
    Processing helix  chain 'N' and resid 91 through 93
      No H-bonds generated for 'chain 'N' and resid 91 through 93'
    Processing helix  chain 'N' and resid 99 through 105
    Processing helix  chain 'N' and resid 128 through 133
      removed outlier: 4.821A  pdb=" N   THR N 133 " --> pdb=" O   ALA N 129 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 140 through 148
    Processing helix  chain 'N' and resid 168 through 181
    Processing helix  chain 'N' and resid 200 through 218
      removed outlier: 3.873A  pdb=" N   LEU N 205 " --> pdb=" O   ARG N 201 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 233 through 246
    Processing helix  chain 'N' and resid 255 through 258
      No H-bonds generated for 'chain 'N' and resid 255 through 258'
    Processing helix  chain 'N' and resid 260 through 273
      removed outlier: 3.594A  pdb=" N   ARG N 269 " --> pdb=" O   SER N 265 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 284 through 287
      No H-bonds generated for 'chain 'N' and resid 284 through 287'
    Processing helix  chain 'N' and resid 297 through 307
    Processing helix  chain 'N' and resid 325 through 336
    Processing helix  chain 'N' and resid 370 through 372
      No H-bonds generated for 'chain 'N' and resid 370 through 372'
    Processing helix  chain 'N' and resid 374 through 380
      removed outlier: 4.548A  pdb=" N   ILE N 379 " --> pdb=" O   ASP N 375 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 390 through 393
      No H-bonds generated for 'chain 'N' and resid 390 through 393'
    Processing helix  chain 'N' and resid 399 through 418
    Processing helix  chain 'N' and resid 423 through 435
      removed outlier: 6.244A  pdb=" N   ARG N 428 " --> pdb=" O   LEU N 424 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   GLU N 429 " --> pdb=" O   ALA N 425 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 439 through 447
    Processing helix  chain 'O' and resid 13 through 17
      removed outlier: 3.893A  pdb=" N   TYR O  17 " --> pdb=" O   ARG O  14 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 43 through 53
    Processing helix  chain 'O' and resid 63 through 66
    Processing helix  chain 'O' and resid 70 through 73
      No H-bonds generated for 'chain 'O' and resid 70 through 73'
    Processing helix  chain 'O' and resid 91 through 93
      No H-bonds generated for 'chain 'O' and resid 91 through 93'
    Processing helix  chain 'O' and resid 99 through 112
      removed outlier: 3.989A  pdb=" N   VAL O 107 " --> pdb=" O   MET O 103 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLY O 108 " --> pdb=" O   SER O 104 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ASN O 109 " --> pdb=" O   SER O 105 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL O 110 " --> pdb=" O   ILE O 106 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   PHE O 111 " --> pdb=" O   VAL O 107 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLY O 112 " --> pdb=" O   GLY O 108 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 128 through 131
      No H-bonds generated for 'chain 'O' and resid 128 through 131'
    Processing helix  chain 'O' and resid 140 through 148
    Processing helix  chain 'O' and resid 168 through 181
    Processing helix  chain 'O' and resid 200 through 218
      removed outlier: 3.677A  pdb=" N   LEU O 205 " --> pdb=" O   ARG O 201 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET O 208 " --> pdb=" O   PHE O 204 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU O 217 " --> pdb=" O   LYS O 213 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 233 through 245
    Processing helix  chain 'O' and resid 261 through 272
    Processing helix  chain 'O' and resid 297 through 307
    Processing helix  chain 'O' and resid 325 through 336
      removed outlier: 3.511A  pdb=" N   LEU O 329 " --> pdb=" O   ARG O 325 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 370 through 380
      Proline residue:  O 374  - end of helix
      removed outlier: 3.788A  pdb=" N   VAL O 377 " --> pdb=" O   PRO O 374 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE O 380 " --> pdb=" O   VAL O 377 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 390 through 393
      No H-bonds generated for 'chain 'O' and resid 390 through 393'
    Processing helix  chain 'O' and resid 398 through 419
    Processing helix  chain 'O' and resid 423 through 435
      removed outlier: 6.187A  pdb=" N   ARG O 428 " --> pdb=" O   LEU O 424 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLU O 429 " --> pdb=" O   ALA O 425 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 439 through 447
      removed outlier: 3.641A  pdb=" N   GLU O 443 " --> pdb=" O   PRO O 439 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 13 through 17
      removed outlier: 3.868A  pdb=" N   TYR P  17 " --> pdb=" O   ARG P  14 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 43 through 53
    Processing helix  chain 'P' and resid 63 through 67
      removed outlier: 3.649A  pdb=" N   LEU P  66 " --> pdb=" O   TRP P  63 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 70 through 73
      No H-bonds generated for 'chain 'P' and resid 70 through 73'
    Processing helix  chain 'P' and resid 91 through 93
      No H-bonds generated for 'chain 'P' and resid 91 through 93'
    Processing helix  chain 'P' and resid 99 through 105
    Processing helix  chain 'P' and resid 110 through 112
      No H-bonds generated for 'chain 'P' and resid 110 through 112'
    Processing helix  chain 'P' and resid 128 through 133
      removed outlier: 4.820A  pdb=" N   THR P 133 " --> pdb=" O   ALA P 129 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 140 through 148
    Processing helix  chain 'P' and resid 168 through 181
    Processing helix  chain 'P' and resid 200 through 218
    Processing helix  chain 'P' and resid 233 through 246
      removed outlier: 3.543A  pdb=" N   PHE P 242 " --> pdb=" O   LYS P 238 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 260 through 272
    Processing helix  chain 'P' and resid 284 through 288
    Processing helix  chain 'P' and resid 297 through 307
    Processing helix  chain 'P' and resid 325 through 336
      removed outlier: 3.632A  pdb=" N   LEU P 329 " --> pdb=" O   ARG P 325 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 344 through 346
      No H-bonds generated for 'chain 'P' and resid 344 through 346'
    Processing helix  chain 'P' and resid 370 through 380
      Proline residue:  P 374  - end of helix
      removed outlier: 3.863A  pdb=" N   VAL P 377 " --> pdb=" O   PRO P 374 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE P 380 " --> pdb=" O   VAL P 377 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 390 through 393
      No H-bonds generated for 'chain 'P' and resid 390 through 393'
    Processing helix  chain 'P' and resid 399 through 419
    Processing helix  chain 'P' and resid 423 through 437
      removed outlier: 5.791A  pdb=" N   ARG P 428 " --> pdb=" O   LEU P 424 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   GLU P 429 " --> pdb=" O   ALA P 425 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TRP P 437 " --> pdb=" O   GLU P 433 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 439 through 447
    Processing sheet with id=  A, first strand: chain 'A' and resid 118 through 125
      removed outlier: 6.802A  pdb=" N   ALA A  32 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   MET A 124 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU A  30 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A  84 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG A  79 " --> pdb=" O   TYR A  86 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA A  88 " --> pdb=" O   CYS A  77 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   CYS A  77 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 155 through 157
      removed outlier: 8.021A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 362 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA A 364 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 250 through 254
      removed outlier: 6.115A  pdb=" N   MET A 276 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   VAL A 253 " --> pdb=" O   MET A 276 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   HIS A 278 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'B' and resid 118 through 125
      removed outlier: 6.862A  pdb=" N   ALA B  32 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   MET B 124 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LEU B  30 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG B  79 " --> pdb=" O   TYR B  86 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ALA B  88 " --> pdb=" O   CYS B  77 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   CYS B  77 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 250 through 254
      removed outlier: 6.373A  pdb=" N   MET B 276 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   VAL B 253 " --> pdb=" O   MET B 276 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   HIS B 278 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  E
    Processing sheet with id=  F, first strand: chain 'B' and resid 311 through 313
      removed outlier: 6.257A  pdb=" N   PHE B 361 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 118 through 125
      removed outlier: 3.537A  pdb=" N   ALA C 118 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA C  32 " --> pdb=" O   GLU C 122 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   MET C 124 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU C  30 " --> pdb=" O   MET C 124 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ARG C  79 " --> pdb=" O   TYR C  86 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ALA C  88 " --> pdb=" O   CYS C  77 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   CYS C  77 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 155 through 157
      removed outlier: 8.100A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 362 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA C 364 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 250 through 254
      removed outlier: 6.260A  pdb=" N   MET C 276 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   VAL C 253 " --> pdb=" O   MET C 276 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   HIS C 278 " --> pdb=" O   VAL C 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  I
    Processing sheet with id=  J, first strand: chain 'D' and resid 118 through 125
      removed outlier: 6.754A  pdb=" N   ALA D  32 " --> pdb=" O   GLU D 122 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   MET D 124 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LEU D  30 " --> pdb=" O   MET D 124 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG D  79 " --> pdb=" O   TYR D  86 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ALA D  88 " --> pdb=" O   CYS D  77 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   CYS D  77 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'D' and resid 155 through 157
      removed outlier: 7.989A  pdb=" N   LEU D 387 " --> pdb=" O   PRO D 362 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ALA D 364 " --> pdb=" O   LEU D 387 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'D' and resid 250 through 254
      removed outlier: 6.130A  pdb=" N   MET D 276 " --> pdb=" O   ILE D 251 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   VAL D 253 " --> pdb=" O   MET D 276 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   HIS D 278 " --> pdb=" O   VAL D 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  L
    Processing sheet with id=  M, first strand: chain 'E' and resid 118 through 125
      removed outlier: 6.760A  pdb=" N   ALA E  32 " --> pdb=" O   GLU E 122 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   MET E 124 " --> pdb=" O   LEU E  30 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU E  30 " --> pdb=" O   MET E 124 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ARG E  79 " --> pdb=" O   TYR E  86 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ALA E  88 " --> pdb=" O   CYS E  77 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   CYS E  77 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'E' and resid 155 through 157
      removed outlier: 8.001A  pdb=" N   LEU E 387 " --> pdb=" O   PRO E 362 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA E 364 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'E' and resid 250 through 254
      removed outlier: 6.230A  pdb=" N   MET E 276 " --> pdb=" O   ILE E 251 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   VAL E 253 " --> pdb=" O   MET E 276 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   HIS E 278 " --> pdb=" O   VAL E 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  O
    Processing sheet with id=  P, first strand: chain 'F' and resid 118 through 125
      removed outlier: 6.736A  pdb=" N   ALA F  32 " --> pdb=" O   GLU F 122 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   MET F 124 " --> pdb=" O   LEU F  30 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LEU F  30 " --> pdb=" O   MET F 124 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG F  79 " --> pdb=" O   TYR F  86 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ALA F  88 " --> pdb=" O   CYS F  77 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   CYS F  77 " --> pdb=" O   ALA F  88 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'F' and resid 155 through 157
      removed outlier: 8.013A  pdb=" N   LEU F 387 " --> pdb=" O   PRO F 362 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA F 364 " --> pdb=" O   LEU F 387 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'F' and resid 250 through 254
      removed outlier: 6.533A  pdb=" N   MET F 276 " --> pdb=" O   ILE F 251 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   VAL F 253 " --> pdb=" O   MET F 276 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   HIS F 278 " --> pdb=" O   VAL F 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  R
    Processing sheet with id=  S, first strand: chain 'G' and resid 118 through 125
      removed outlier: 6.797A  pdb=" N   ALA G  32 " --> pdb=" O   GLU G 122 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   MET G 124 " --> pdb=" O   LEU G  30 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU G  30 " --> pdb=" O   MET G 124 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG G  79 " --> pdb=" O   TYR G  86 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA G  88 " --> pdb=" O   CYS G  77 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   CYS G  77 " --> pdb=" O   ALA G  88 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'G' and resid 155 through 157
      removed outlier: 7.962A  pdb=" N   LEU G 387 " --> pdb=" O   PRO G 362 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ALA G 364 " --> pdb=" O   LEU G 387 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'G' and resid 250 through 254
      removed outlier: 6.187A  pdb=" N   MET G 276 " --> pdb=" O   ILE G 251 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   VAL G 253 " --> pdb=" O   MET G 276 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   HIS G 278 " --> pdb=" O   VAL G 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  U
    Processing sheet with id=  V, first strand: chain 'H' and resid 118 through 125
      removed outlier: 6.973A  pdb=" N   ALA H  32 " --> pdb=" O   GLU H 122 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   MET H 124 " --> pdb=" O   LEU H  30 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU H  30 " --> pdb=" O   MET H 124 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG H  79 " --> pdb=" O   TYR H  86 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ALA H  88 " --> pdb=" O   CYS H  77 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   CYS H  77 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'H' and resid 155 through 157
      removed outlier: 7.848A  pdb=" N   LEU H 387 " --> pdb=" O   PRO H 362 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ALA H 364 " --> pdb=" O   LEU H 387 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'H' and resid 250 through 254
      removed outlier: 6.111A  pdb=" N   MET H 276 " --> pdb=" O   ILE H 251 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   VAL H 253 " --> pdb=" O   MET H 276 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   HIS H 278 " --> pdb=" O   VAL H 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  X
    Processing sheet with id=  Y, first strand: chain 'I' and resid 118 through 125
      removed outlier: 6.803A  pdb=" N   ALA I  32 " --> pdb=" O   GLU I 122 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   MET I 124 " --> pdb=" O   LEU I  30 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU I  30 " --> pdb=" O   MET I 124 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ARG I  79 " --> pdb=" O   TYR I  86 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ALA I  88 " --> pdb=" O   CYS I  77 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   CYS I  77 " --> pdb=" O   ALA I  88 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'I' and resid 155 through 157
      removed outlier: 7.996A  pdb=" N   LEU I 387 " --> pdb=" O   PRO I 362 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ALA I 364 " --> pdb=" O   LEU I 387 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'I' and resid 250 through 254
      removed outlier: 6.438A  pdb=" N   MET I 276 " --> pdb=" O   ILE I 251 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   VAL I 253 " --> pdb=" O   MET I 276 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   HIS I 278 " --> pdb=" O   VAL I 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AA
    Processing sheet with id= AB, first strand: chain 'J' and resid 118 through 125
      removed outlier: 6.853A  pdb=" N   ALA J  32 " --> pdb=" O   GLU J 122 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   MET J 124 " --> pdb=" O   LEU J  30 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU J  30 " --> pdb=" O   MET J 124 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG J  79 " --> pdb=" O   TYR J  86 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ALA J  88 " --> pdb=" O   CYS J  77 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   CYS J  77 " --> pdb=" O   ALA J  88 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'J' and resid 155 through 157
      removed outlier: 7.906A  pdb=" N   LEU J 387 " --> pdb=" O   PRO J 362 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA J 364 " --> pdb=" O   LEU J 387 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'J' and resid 250 through 254
      removed outlier: 6.659A  pdb=" N   MET J 276 " --> pdb=" O   ILE J 251 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   VAL J 253 " --> pdb=" O   MET J 276 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   HIS J 278 " --> pdb=" O   VAL J 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AD
    Processing sheet with id= AE, first strand: chain 'K' and resid 118 through 125
      removed outlier: 6.878A  pdb=" N   ALA K  32 " --> pdb=" O   GLU K 122 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   MET K 124 " --> pdb=" O   LEU K  30 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU K  30 " --> pdb=" O   MET K 124 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ALA K  88 " --> pdb=" O   CYS K  77 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   CYS K  77 " --> pdb=" O   ALA K  88 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'K' and resid 155 through 157
      removed outlier: 7.790A  pdb=" N   LEU K 387 " --> pdb=" O   PRO K 362 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ALA K 364 " --> pdb=" O   LEU K 387 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'K' and resid 250 through 254
      removed outlier: 6.126A  pdb=" N   MET K 276 " --> pdb=" O   ILE K 251 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL K 253 " --> pdb=" O   MET K 276 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   HIS K 278 " --> pdb=" O   VAL K 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AG
    Processing sheet with id= AH, first strand: chain 'L' and resid 118 through 125
      removed outlier: 6.680A  pdb=" N   ALA L  32 " --> pdb=" O   GLU L 122 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   MET L 124 " --> pdb=" O   LEU L  30 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU L  30 " --> pdb=" O   MET L 124 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG L  79 " --> pdb=" O   TYR L  86 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA L  88 " --> pdb=" O   CYS L  77 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   CYS L  77 " --> pdb=" O   ALA L  88 " (cutoff:3.500A)
    Processing sheet with id= AI, first strand: chain 'L' and resid 250 through 254
      removed outlier: 6.178A  pdb=" N   MET L 276 " --> pdb=" O   ILE L 251 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   VAL L 253 " --> pdb=" O   MET L 276 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   HIS L 278 " --> pdb=" O   VAL L 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AI
    Processing sheet with id= AJ, first strand: chain 'L' and resid 311 through 313
      removed outlier: 6.532A  pdb=" N   PHE L 361 " --> pdb=" O   VAL L 312 " (cutoff:3.500A)
    Processing sheet with id= AK, first strand: chain 'M' and resid 118 through 125
      removed outlier: 3.503A  pdb=" N   ALA M 118 " --> pdb=" O   THR M  36 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ALA M  32 " --> pdb=" O   GLU M 122 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   MET M 124 " --> pdb=" O   LEU M  30 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU M  30 " --> pdb=" O   MET M 124 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG M  79 " --> pdb=" O   TYR M  86 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ALA M  88 " --> pdb=" O   CYS M  77 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   CYS M  77 " --> pdb=" O   ALA M  88 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'M' and resid 155 through 157
      removed outlier: 7.817A  pdb=" N   LEU M 387 " --> pdb=" O   PRO M 362 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ALA M 364 " --> pdb=" O   LEU M 387 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'M' and resid 250 through 254
      removed outlier: 6.054A  pdb=" N   MET M 276 " --> pdb=" O   ILE M 251 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   VAL M 253 " --> pdb=" O   MET M 276 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   HIS M 278 " --> pdb=" O   VAL M 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AM
    Processing sheet with id= AN, first strand: chain 'N' and resid 118 through 125
      removed outlier: 6.705A  pdb=" N   ALA N  32 " --> pdb=" O   GLU N 122 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   MET N 124 " --> pdb=" O   LEU N  30 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LEU N  30 " --> pdb=" O   MET N 124 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ARG N  79 " --> pdb=" O   TYR N  86 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ALA N  88 " --> pdb=" O   CYS N  77 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   CYS N  77 " --> pdb=" O   ALA N  88 " (cutoff:3.500A)
    Processing sheet with id= AO, first strand: chain 'N' and resid 155 through 157
      removed outlier: 7.893A  pdb=" N   LEU N 387 " --> pdb=" O   PRO N 362 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ALA N 364 " --> pdb=" O   LEU N 387 " (cutoff:3.500A)
    Processing sheet with id= AP, first strand: chain 'N' and resid 250 through 254
      removed outlier: 6.463A  pdb=" N   MET N 276 " --> pdb=" O   ILE N 251 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   VAL N 253 " --> pdb=" O   MET N 276 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   HIS N 278 " --> pdb=" O   VAL N 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AP
    Processing sheet with id= AQ, first strand: chain 'O' and resid 79 through 81
      removed outlier: 3.834A  pdb=" N   ARG O  79 " --> pdb=" O   TYR O  86 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASP O 123 " --> pdb=" O   ALA O  32 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ARG O  34 " --> pdb=" O   LEU O 121 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LEU O 121 " --> pdb=" O   ARG O  34 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   THR O  36 " --> pdb=" O   LEU O 119 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU O 119 " --> pdb=" O   THR O  36 " (cutoff:3.500A)
    Processing sheet with id= AR, first strand: chain 'O' and resid 155 through 157
      removed outlier: 7.985A  pdb=" N   LEU O 387 " --> pdb=" O   PRO O 362 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ALA O 364 " --> pdb=" O   LEU O 387 " (cutoff:3.500A)
    Processing sheet with id= AS, first strand: chain 'O' and resid 250 through 254
      removed outlier: 6.281A  pdb=" N   MET O 276 " --> pdb=" O   ILE O 251 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL O 253 " --> pdb=" O   MET O 276 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   HIS O 278 " --> pdb=" O   VAL O 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AS
    Processing sheet with id= AT, first strand: chain 'P' and resid 118 through 125
      removed outlier: 6.780A  pdb=" N   ALA P  32 " --> pdb=" O   GLU P 122 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   MET P 124 " --> pdb=" O   LEU P  30 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU P  30 " --> pdb=" O   MET P 124 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG P  79 " --> pdb=" O   TYR P  86 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA P  88 " --> pdb=" O   CYS P  77 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   CYS P  77 " --> pdb=" O   ALA P  88 " (cutoff:3.500A)
    Processing sheet with id= AU, first strand: chain 'P' and resid 155 through 157
      removed outlier: 7.940A  pdb=" N   LEU P 387 " --> pdb=" O   PRO P 362 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ALA P 364 " --> pdb=" O   LEU P 387 " (cutoff:3.500A)
    Processing sheet with id= AV, first strand: chain 'P' and resid 250 through 254
      removed outlier: 6.155A  pdb=" N   MET P 276 " --> pdb=" O   ILE P 251 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   VAL P 253 " --> pdb=" O   MET P 276 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   HIS P 278 " --> pdb=" O   VAL P 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AV

    1913 hydrogen bonds defined for protein.
    5412 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 17.03

  Time building geometry restraints manager: 17.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 17629
        1.33 -     1.45: 9284
        1.45 -     1.57: 30614
        1.57 -     1.69: 1
        1.69 -     1.81: 432
  Bond restraints: 57960
  Sorted by residual:
  bond pdb=" O5  CAP F 501 "
       pdb=" P2  CAP F 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.758 -0.148 2.00e-02 2.50e+03 5.46e+01
  bond pdb=" O5  CAP L 501 "
       pdb=" P2  CAP L 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.757 -0.147 2.00e-02 2.50e+03 5.37e+01
  bond pdb=" O5  CAP D 501 "
       pdb=" P2  CAP D 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.756 -0.146 2.00e-02 2.50e+03 5.33e+01
  bond pdb=" O5  CAP H 501 "
       pdb=" P2  CAP H 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.756 -0.146 2.00e-02 2.50e+03 5.30e+01
  bond pdb=" O5  CAP B 501 "
       pdb=" P2  CAP B 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.755 -0.145 2.00e-02 2.50e+03 5.27e+01
  ... (remaining 57955 not shown)

  Histogram of bond angle deviations from ideal:
       96.64 -   104.14: 965
      104.14 -   111.63: 25553
      111.63 -   119.13: 20636
      119.13 -   126.62: 30327
      126.62 -   134.12: 1119
  Bond angle restraints: 78600
  Sorted by residual:
  angle pdb=" CA  PRO H 439 "
        pdb=" N   PRO H 439 "
        pdb=" CD  PRO H 439 "
      ideal   model   delta    sigma   weight residual
     112.00  104.66    7.34 1.40e+00 5.10e-01 2.75e+01
  angle pdb=" O5  CAP E 501 "
        pdb=" P2  CAP E 501 "
        pdb=" O6P CAP E 501 "
      ideal   model   delta    sigma   weight residual
     109.50   96.64   12.86 3.00e+00 1.11e-01 1.84e+01
  angle pdb=" CA  THR M  56 "
        pdb=" C   THR M  56 "
        pdb=" N   GLY M  57 "
      ideal   model   delta    sigma   weight residual
     116.84  123.55   -6.71 1.71e+00 3.42e-01 1.54e+01
  angle pdb=" O5  CAP I 501 "
        pdb=" P2  CAP I 501 "
        pdb=" O6P CAP I 501 "
      ideal   model   delta    sigma   weight residual
     109.50   97.98   11.52 3.00e+00 1.11e-01 1.47e+01
  angle pdb=" O1  CAP I 501 "
        pdb=" P1  CAP I 501 "
        pdb=" O3P CAP I 501 "
      ideal   model   delta    sigma   weight residual
     109.50   98.09   11.41 3.00e+00 1.11e-01 1.45e+01
  ... (remaining 78595 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.43: 33461
       34.43 -    68.86: 630
       68.86 -   103.30: 48
      103.30 -   137.73: 13
      137.73 -   172.16: 16
  Dihedral angle restraints: 34168
    sinusoidal: 13920
      harmonic: 20248
  Sorted by residual:
  dihedral pdb=" C3  CAP P 501 "
           pdb=" C   CAP P 501 "
           pdb=" C2  CAP P 501 "
           pdb=" O6  CAP P 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      81.86 -105.98 -172.16     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C3  CAP J 501 "
           pdb=" C   CAP J 501 "
           pdb=" C2  CAP J 501 "
           pdb=" O6  CAP J 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      81.86 -106.99 -171.15     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C3  CAP D 501 "
           pdb=" C   CAP D 501 "
           pdb=" C2  CAP D 501 "
           pdb=" O6  CAP D 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      81.86 -107.51 -170.62     1      2.00e+01 2.50e-03 4.77e+01
  ... (remaining 34165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 5781
       0.039 -    0.078: 1903
       0.078 -    0.116: 499
       0.116 -    0.155: 61
       0.155 -    0.194: 4
  Chirality restraints: 8248
  Sorted by residual:
  chirality pdb=" CG  LEU B 304 "
            pdb=" CB  LEU B 304 "
            pdb=" CD1 LEU B 304 "
            pdb=" CD2 LEU B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.39e-01
  chirality pdb=" CA  PRO H 439 "
            pdb=" N   PRO H 439 "
            pdb=" C   PRO H 439 "
            pdb=" CB  PRO H 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.91e-01
  chirality pdb=" CB  ILE M 379 "
            pdb=" CA  ILE M 379 "
            pdb=" CG1 ILE M 379 "
            pdb=" CG2 ILE M 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.33e-01
  ... (remaining 8245 not shown)

  Planarity restraints: 10328
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS H 438 "    0.074 5.00e-02 4.00e+02   1.07e-01 1.84e+01
        pdb=" N   PRO H 439 "   -0.185 5.00e-02 4.00e+02
        pdb=" CA  PRO H 439 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO H 439 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS I 438 "    0.032 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO I 439 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO I 439 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO I 439 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS O 358 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO O 359 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO O 359 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO O 359 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 10325 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 612
        2.55 -     3.14: 43658
        3.14 -     3.72: 92262
        3.72 -     4.31: 138616
        4.31 -     4.90: 230501
  Nonbonded interactions: 505649
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP O 189 "
            pdb="MG    MG O 502 "
     model   vdw
     1.960 2.170
  nonbonded pdb=" OD1 ASP M 189 "
            pdb="MG    MG M 502 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O3  CAP O 501 "
            pdb="MG    MG O 502 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" OD1 ASP P 189 "
            pdb="MG    MG P 502 "
     model   vdw
     1.991 2.170
  nonbonded pdb=" OE1 GLU C 190 "
            pdb="MG    MG C 502 "
     model   vdw
     1.993 2.170
  ... (remaining 505644 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'C'
  selection = (chain 'D' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'E'
  selection = (chain 'F' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'G'
  selection = (chain 'H' and (resid 6 through 449 or resid 501 through 502))
  selection = (chain 'I' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'J'
  selection = (chain 'K' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'L'
  selection = (chain 'M' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'N'
  selection = (chain 'O' and (resid 6 through 449 or resid 501 through 502))
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.250
  Construct map_model_manager:             0.050
  Extract box with map and model:          14.670
  Check model and map are aligned:         0.620
  Set scattering table:                    0.400
  Process input model:                     114.790
  Find NCS groups from input model:        3.280
  Set up NCS constraints:                  0.200
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  151.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
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      :  0.005   0.148  57960  Z= 0.323
  Angle     :  0.730  12.860  78600  Z= 0.373
  Chirality :  0.040   0.194   8248
  Planarity :  0.004   0.107  10328
  Dihedral  : 14.799 172.159  21288
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.10), residues: 7048
  helix: -0.90 (0.09), residues: 3032
  sheet: -0.60 (0.16), residues: 920
  loop : -0.66 (0.11), residues: 3096

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 437 
 HIS   0.006   0.001   HIS F 284 
 PHE   0.019   0.002   PHE E 287 
 TYR   0.018   0.001   TYR A 250 
 ARG   0.024   0.000   ARG N 268 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  700 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 700
  time to evaluate  : 4.799 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ASN cc_start: 0.8815 (t0) cc_final: 0.8614 (t0)
REVERT: B  190 GLU cc_start: 0.8226 (pm20) cc_final: 0.7512 (pm20)
REVERT: B  220 GLU cc_start: 0.8098 (mp0) cc_final: 0.7866 (mp0)
REVERT: B  437 TRP cc_start: 0.7052 (p-90) cc_final: 0.6411 (m100)
REVERT: C   61 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7001 (tp30)
REVERT: C  124 MET cc_start: 0.7569 (ttp) cc_final: 0.7335 (ttp)
REVERT: C  433 GLU cc_start: 0.7526 (mp0) cc_final: 0.7292 (mp0)
REVERT: E  149 ASN cc_start: 0.8915 (t0) cc_final: 0.8596 (t0)
REVERT: E  159 THR cc_start: 0.8963 (m) cc_final: 0.8725 (m)
REVERT: E  415 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7526 (tp-100)
REVERT: F  144 GLU cc_start: 0.7317 (tt0) cc_final: 0.7073 (tt0)
REVERT: F  159 THR cc_start: 0.8162 (m) cc_final: 0.7943 (m)
REVERT: F  290 GLN cc_start: 0.8406 (mm110) cc_final: 0.8140 (mp10)
REVERT: G  415 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: G  419 GLU cc_start: 0.7730 (pt0) cc_final: 0.7486 (pt0)
REVERT: H  306 MET cc_start: 0.8618 (mtp) cc_final: 0.8305 (mtp)
REVERT: I   11 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7675 (mmp80)
REVERT: I  415 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7892 (tm-30)
REVERT: J  149 ASN cc_start: 0.8927 (t0) cc_final: 0.8683 (t0)
REVERT: L  316 THR cc_start: 0.8308 (p) cc_final: 0.8100 (p)
REVERT: L  337 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7789 (tt0)
REVERT: L  436 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7588 (ttp80)
REVERT: M  428 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7205 (mmt-90)
REVERT: N  337 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: P  375 ASP cc_start: 0.7908 (m-30) cc_final: 0.7645 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 700
  average time/residue: 1.5666
  time to fit residues: 1360.3789
Evaluate side-chains
  473 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 473
  time to evaluate  : 4.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 594 optimal weight:    0.7980
   chunk 533 optimal weight:    6.9990
   chunk 296 optimal weight:    2.9990
   chunk 182 optimal weight:   10.0000
   chunk 359 optimal weight:   10.0000
   chunk 285 optimal weight:    5.9990
   chunk 551 optimal weight:    0.8980
   chunk 213 optimal weight:    5.9990
   chunk 335 optimal weight:    0.9990
   chunk 410 optimal weight:    5.9990
   chunk 639 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 149 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
G 149 ASN
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 191 ASN
J 109 ASN
J 117 GLN
J 142 GLN
K 142 GLN
** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 193 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  57960  Z= 0.235
  Angle     :  0.542   9.387  78600  Z= 0.277
  Chirality :  0.041   0.173   8248
  Planarity :  0.004   0.048  10328
  Dihedral  :  9.157 175.557   8208
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.07 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.10), residues: 7048
  helix:  0.01 (0.09), residues: 3008
  sheet: -0.45 (0.17), residues: 840
  loop : -0.62 (0.11), residues: 3200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 437 
 HIS   0.004   0.001   HIS A 311 
 PHE   0.014   0.002   PHE J 297 
 TYR   0.015   0.001   TYR A 250 
 ARG   0.008   0.000   ARG I 428 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  593 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 521
  time to evaluate  : 4.725 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7116 (m-80)
REVERT: A  234 GLU cc_start: 0.7444 (mp0) cc_final: 0.7240 (mp0)
REVERT: B  220 GLU cc_start: 0.8188 (mp0) cc_final: 0.7887 (mp0)
REVERT: B  346 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7218 (mtt180)
REVERT: B  437 TRP cc_start: 0.7077 (p-90) cc_final: 0.6433 (m100)
REVERT: C   61 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6965 (tp30)
REVERT: C  102 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8505 (tp)
REVERT: C  424 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7940 (mm)
REVERT: C  436 ARG cc_start: 0.8278 (mtm110) cc_final: 0.8037 (mtp85)
REVERT: D  146 ASP cc_start: 0.7778 (m-30) cc_final: 0.7522 (m-30)
REVERT: D  205 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: E  109 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7941 (m-40)
REVERT: E  159 THR cc_start: 0.9002 (m) cc_final: 0.8756 (m)
REVERT: E  252 MET cc_start: 0.8480 (ttt) cc_final: 0.8212 (ttt)
REVERT: E  346 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8141 (mtm180)
REVERT: E  415 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7346 (tp-100)
REVERT: F  159 THR cc_start: 0.8143 (m) cc_final: 0.7923 (m)
REVERT: F  276 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7897 (ttm)
REVERT: F  290 GLN cc_start: 0.8454 (mm110) cc_final: 0.8115 (mp10)
REVERT: G  415 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: G  419 GLU cc_start: 0.7757 (pt0) cc_final: 0.7462 (pt0)
REVERT: H  306 MET cc_start: 0.8593 (mtp) cc_final: 0.8252 (mtp)
REVERT: H  375 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7499 (t0)
REVERT: H  440 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7879 (tp30)
REVERT: I   11 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7660 (mmp80)
REVERT: J  149 ASN cc_start: 0.8947 (t0) cc_final: 0.8669 (t0)
REVERT: J  346 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7774 (mtp180)
REVERT: K  142 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7506 (mp-120)
REVERT: K  241 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7113 (mt-10)
REVERT: K  269 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7036 (tpt-90)
REVERT: L  316 THR cc_start: 0.8129 (p) cc_final: 0.7917 (p)
REVERT: L  337 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7729 (tt0)
REVERT: N  163 LYS cc_start: 0.8317 (tttm) cc_final: 0.8050 (tttt)
REVERT: N  268 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7574 (ttp80)
REVERT: N  432 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7448 (mm-30)
REVERT: O  102 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: P   43 MET cc_start: 0.7955 (tpp) cc_final: 0.7371 (tpp)
REVERT: P  205 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8422 (mt)
  outliers start: 72
  outliers final: 18
  residues processed: 563
  average time/residue: 1.5042
  time to fit residues: 1062.5411
Evaluate side-chains
  503 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 471
  time to evaluate  : 4.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  346 ARG
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain E residue  109 ASN
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain F residue  276 MET
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  424 LEU
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain H residue  440 GLU
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain L residue  241 GLU
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  288 ASP
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue  338 ASP
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain O residue  205 LEU
Chi-restraints excluded: chain P residue  205 LEU
Chi-restraints excluded: chain P residue  343 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 355 optimal weight:    3.9990
   chunk 198 optimal weight:    3.9990
   chunk 532 optimal weight:   10.0000
   chunk 435 optimal weight:    0.0870
   chunk 176 optimal weight:   20.0000
   chunk 640 optimal weight:    0.0670
   chunk 691 optimal weight:    8.9990
   chunk 570 optimal weight:    6.9990
   chunk 635 optimal weight:    0.9980
   chunk 218 optimal weight:    1.9990
   chunk 513 optimal weight:    2.9990
   overall best weight:    1.2300

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
B 101 ASN
** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
** H   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 ASN
** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 191 ASN
J 109 ASN
J 117 GLN
J 142 GLN
** J 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 193 ASN
K 290 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 117 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  57960  Z= 0.181
  Angle     :  0.489   6.983  78600  Z= 0.248
  Chirality :  0.040   0.157   8248
  Planarity :  0.004   0.039  10328
  Dihedral  :  8.506 179.608   8208
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.45 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.10), residues: 7048
  helix:  0.59 (0.10), residues: 2960
  sheet: -0.15 (0.18), residues: 840
  loop : -0.56 (0.11), residues: 3248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 437 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.014   0.001   PHE J 113 
 TYR   0.015   0.001   TYR K 250 
 ARG   0.009   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  625 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 95
    poor density    : 530
  time to evaluate  : 4.752 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7089 (m-80)
REVERT: B  102 ILE cc_start: 0.9228 (tt) cc_final: 0.8993 (pt)
REVERT: B  220 GLU cc_start: 0.8200 (mp0) cc_final: 0.7972 (mp0)
REVERT: B  437 TRP cc_start: 0.7162 (p-90) cc_final: 0.6459 (m100)
REVERT: C   61 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6882 (tp30)
REVERT: C  433 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7536 (mp0)
REVERT: C  436 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8057 (mtp85)
REVERT: D  146 ASP cc_start: 0.7790 (m-30) cc_final: 0.7544 (m-30)
REVERT: E  109 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7957 (m-40)
REVERT: E  159 THR cc_start: 0.8958 (m) cc_final: 0.8681 (m)
REVERT: E  252 MET cc_start: 0.8473 (ttt) cc_final: 0.8213 (ttt)
REVERT: E  415 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7199 (tp-100)
REVERT: F  159 THR cc_start: 0.8144 (m) cc_final: 0.7913 (m)
REVERT: F  290 GLN cc_start: 0.8436 (mm110) cc_final: 0.8170 (mp10)
REVERT: F  361 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7818 (m-80)
REVERT: G  415 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: H  109 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (t160)
REVERT: H  306 MET cc_start: 0.8678 (mtp) cc_final: 0.8356 (mtp)
REVERT: H  375 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7519 (t0)
REVERT: H  440 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7902 (tp30)
REVERT: I   11 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7678 (mmp80)
REVERT: I  283 MET cc_start: 0.8898 (ttt) cc_final: 0.8694 (ttt)
REVERT: J   10 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8724 (p)
REVERT: J  149 ASN cc_start: 0.8977 (t0) cc_final: 0.8662 (t0)
REVERT: J  346 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7830 (mtp180)
REVERT: K  142 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7442 (mp-120)
REVERT: K  241 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7142 (mt-10)
REVERT: K  269 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7059 (tpt-90)
REVERT: M  212 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7621 (ptp-170)
REVERT: N  163 LYS cc_start: 0.8290 (tttm) cc_final: 0.8057 (tttt)
REVERT: O  445 MET cc_start: 0.8237 (mtm) cc_final: 0.7671 (mtm)
REVERT: P   43 MET cc_start: 0.7993 (tpp) cc_final: 0.7511 (tpp)
REVERT: P  205 LEU cc_start: 0.8801 (tp) cc_final: 0.8468 (mt)
REVERT: P  245 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (mt-10)
REVERT: P  343 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8188 (m-30)
REVERT: P  432 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7514 (mt-10)
  outliers start: 95
  outliers final: 22
  residues processed: 586
  average time/residue: 1.4659
  time to fit residues: 1082.8984
Evaluate side-chains
  503 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 468
  time to evaluate  : 4.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  433 GLU
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  109 ASN
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  424 LEU
Chi-restraints excluded: chain H residue  109 ASN
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain H residue  440 GLU
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue  358 LYS
Chi-restraints excluded: chain I residue  447 LEU
Chi-restraints excluded: chain J residue   10 VAL
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  245 GLU
Chi-restraints excluded: chain P residue  245 GLU
Chi-restraints excluded: chain P residue  343 ASP
Chi-restraints excluded: chain P residue  375 ASP
Chi-restraints excluded: chain P residue  432 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 632 optimal weight:    7.9990
   chunk 481 optimal weight:    4.9990
   chunk 332 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 305 optimal weight:    0.0030
   chunk 430 optimal weight:    8.9990
   chunk 642 optimal weight:    4.9990
   chunk 680 optimal weight:    4.9990
   chunk 335 optimal weight:    9.9990
   chunk 609 optimal weight:    2.9990
   chunk 183 optimal weight:    6.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
A 406 ASN
** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   5 GLN
H   5 GLN
H 109 ASN
I 101 ASN
I 191 ASN
I 193 ASN
J 109 ASN
J 142 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
** O 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 415 GLN
P 117 GLN
P 406 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  57960  Z= 0.385
  Angle     :  0.570   8.423  78600  Z= 0.287
  Chirality :  0.043   0.181   8248
  Planarity :  0.004   0.040  10328
  Dihedral  :  8.495 177.985   8208
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.24 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.10), residues: 7048
  helix:  0.63 (0.10), residues: 2912
  sheet: -0.09 (0.18), residues: 824
  loop : -0.59 (0.11), residues: 3312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K 200 
 HIS   0.006   0.001   HIS F 311 
 PHE   0.018   0.002   PHE J 113 
 TYR   0.015   0.001   TYR L 250 
 ARG   0.011   0.000   ARG E 436 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  612 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 129
    poor density    : 483
  time to evaluate  : 4.888 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7198 (m-80)
REVERT: A  234 GLU cc_start: 0.7587 (mp0) cc_final: 0.7239 (mp0)
REVERT: B   61 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7393 (mp0)
REVERT: B  102 ILE cc_start: 0.9165 (tt) cc_final: 0.8892 (pt)
REVERT: B  220 GLU cc_start: 0.8259 (mp0) cc_final: 0.7969 (mp0)
REVERT: B  346 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7289 (mtt180)
REVERT: B  437 TRP cc_start: 0.7135 (p-90) cc_final: 0.6455 (m100)
REVERT: C   61 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6875 (tp30)
REVERT: C  433 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7529 (mp0)
REVERT: C  436 ARG cc_start: 0.8314 (mtm110) cc_final: 0.8022 (mtp85)
REVERT: D  117 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8104 (mt0)
REVERT: D  146 ASP cc_start: 0.7819 (m-30) cc_final: 0.7513 (m-30)
REVERT: E  159 THR cc_start: 0.9094 (m) cc_final: 0.8801 (m)
REVERT: E  252 MET cc_start: 0.8749 (ttt) cc_final: 0.8513 (ttt)
REVERT: E  346 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8151 (mtm180)
REVERT: E  415 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7203 (tp-100)
REVERT: E  436 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.7015 (ptm160)
REVERT: F  159 THR cc_start: 0.8211 (m) cc_final: 0.7982 (m)
REVERT: F  290 GLN cc_start: 0.8518 (mm110) cc_final: 0.8050 (mp10)
REVERT: F  361 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7820 (m-80)
REVERT: G  322 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8001 (tp30)
REVERT: G  415 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: H  283 MET cc_start: 0.8691 (ttm) cc_final: 0.8179 (ttm)
REVERT: H  375 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7533 (t0)
REVERT: H  440 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7982 (tp30)
REVERT: I   11 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7697 (mmp80)
REVERT: I  250 TYR cc_start: 0.7984 (m-80) cc_final: 0.7653 (m-80)
REVERT: I  337 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7471 (mp0)
REVERT: I  436 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7979 (mtp180)
REVERT: J  149 ASN cc_start: 0.9083 (t0) cc_final: 0.8775 (t0)
REVERT: J  212 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7561 (mtp180)
REVERT: J  276 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.7944 (mpp)
REVERT: J  346 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7950 (mtp180)
REVERT: K  142 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7488 (mp-120)
REVERT: K  241 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7215 (mt-10)
REVERT: K  269 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7286 (tpt-90)
REVERT: M  212 ARG cc_start: 0.7863 (ptp-170) cc_final: 0.7650 (ptp-170)
REVERT: N  163 LYS cc_start: 0.8476 (tttm) cc_final: 0.8240 (tttt)
REVERT: O  307 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8694 (p)
REVERT: O  445 MET cc_start: 0.8297 (mtm) cc_final: 0.8047 (mtm)
REVERT: P   21 ASP cc_start: 0.8241 (t0) cc_final: 0.8018 (t0)
REVERT: P  109 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8093 (t0)
REVERT: P  205 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8458 (mt)
REVERT: P  245 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7505 (mt-10)
  outliers start: 129
  outliers final: 41
  residues processed: 570
  average time/residue: 1.5029
  time to fit residues: 1073.8236
Evaluate side-chains
  519 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 459
  time to evaluate  : 4.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  346 ARG
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  433 GLU
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  117 GLN
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  424 LEU
Chi-restraints excluded: chain H residue  126 ILE
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  233 THR
Chi-restraints excluded: chain H residue  245 GLU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain H residue  440 GLU
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain I residue  358 LYS
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   10 VAL
Chi-restraints excluded: chain J residue   29 LEU
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  265 SER
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain L residue  307 VAL
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  245 GLU
Chi-restraints excluded: chain M residue  288 ASP
Chi-restraints excluded: chain O residue  304 LEU
Chi-restraints excluded: chain O residue  307 VAL
Chi-restraints excluded: chain P residue   60 THR
Chi-restraints excluded: chain P residue  109 ASN
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  205 LEU
Chi-restraints excluded: chain P residue  245 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 566 optimal weight:    7.9990
   chunk 386 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 506 optimal weight:    4.9990
   chunk 280 optimal weight:    0.8980
   chunk 580 optimal weight:    3.9990
   chunk 470 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 347 optimal weight:    9.9990
   chunk 610 optimal weight:    5.9990
   chunk 171 optimal weight:   10.0000
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
H 406 ASN
I 191 ASN
J 109 ASN
J 142 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 117 GLN
P 406 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  57960  Z= 0.269
  Angle     :  0.521   8.812  78600  Z= 0.263
  Chirality :  0.041   0.182   8248
  Planarity :  0.004   0.036  10328
  Dihedral  :  8.286 177.595   8208
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.12 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.10), residues: 7048
  helix:  0.73 (0.10), residues: 2920
  sheet: -0.01 (0.18), residues: 824
  loop : -0.57 (0.11), residues: 3304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K 200 
 HIS   0.005   0.001   HIS F 311 
 PHE   0.014   0.002   PHE N 113 
 TYR   0.015   0.001   TYR K 250 
 ARG   0.009   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  614 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 133
    poor density    : 481
  time to evaluate  : 4.845 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7204 (m-80)
REVERT: B   61 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7322 (mp0)
REVERT: B  102 ILE cc_start: 0.9173 (tt) cc_final: 0.8890 (pt)
REVERT: B  437 TRP cc_start: 0.7163 (p-90) cc_final: 0.6430 (m100)
REVERT: B  445 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7090 (mmm)
REVERT: C   61 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6820 (tp30)
REVERT: C  433 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: C  436 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8069 (mtp85)
REVERT: D  146 ASP cc_start: 0.7830 (m-30) cc_final: 0.7572 (m-30)
REVERT: E  159 THR cc_start: 0.9079 (m) cc_final: 0.8760 (m)
REVERT: E  252 MET cc_start: 0.8641 (ttt) cc_final: 0.8397 (ttt)
REVERT: E  415 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7204 (tp-100)
REVERT: F  159 THR cc_start: 0.8211 (m) cc_final: 0.7978 (m)
REVERT: F  290 GLN cc_start: 0.8476 (mm110) cc_final: 0.8016 (mp10)
REVERT: F  361 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7782 (m-80)
REVERT: G  322 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7976 (tp30)
REVERT: G  415 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: H  440 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7976 (tp30)
REVERT: I   11 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7744 (mmp80)
REVERT: I  436 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8041 (mtp180)
REVERT: J  149 ASN cc_start: 0.9078 (t0) cc_final: 0.8765 (t0)
REVERT: J  212 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7581 (mtp180)
REVERT: J  276 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7875 (mpp)
REVERT: J  346 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7938 (mtp180)
REVERT: K  142 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7506 (mp-120)
REVERT: K  269 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7281 (tpt-90)
REVERT: M  322 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6898 (tt0)
REVERT: N  163 LYS cc_start: 0.8418 (tttm) cc_final: 0.8200 (tttt)
REVERT: O  324 ASP cc_start: 0.7839 (t0) cc_final: 0.7457 (t0)
REVERT: O  445 MET cc_start: 0.8267 (mtm) cc_final: 0.7871 (mtm)
REVERT: P    7 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6911 (mt-10)
REVERT: P   21 ASP cc_start: 0.8256 (t0) cc_final: 0.8041 (t0)
REVERT: P  205 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8481 (mt)
REVERT: P  245 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7504 (mt-10)
REVERT: P  343 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (m-30)
  outliers start: 133
  outliers final: 50
  residues processed: 569
  average time/residue: 1.4892
  time to fit residues: 1063.2215
Evaluate side-chains
  531 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 464
  time to evaluate  : 4.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain C residue  433 GLU
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  103 MET
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  436 ARG
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  288 ASP
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  424 LEU
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  245 GLU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  440 GLU
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain I residue  358 LYS
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   10 VAL
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  232 SER
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain K residue  375 ASP
Chi-restraints excluded: chain K residue  411 GLU
Chi-restraints excluded: chain L residue  307 VAL
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain M residue  379 ILE
Chi-restraints excluded: chain N residue  213 LYS
Chi-restraints excluded: chain O residue  208 MET
Chi-restraints excluded: chain P residue    7 GLU
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue   60 THR
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  205 LEU
Chi-restraints excluded: chain P residue  245 GLU
Chi-restraints excluded: chain P residue  343 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 228 optimal weight:    8.9990
   chunk 612 optimal weight:    3.9990
   chunk 134 optimal weight:    0.6980
   chunk 399 optimal weight:    0.3980
   chunk 167 optimal weight:    1.9990
   chunk 681 optimal weight:    0.7980
   chunk 565 optimal weight:    2.9990
   chunk 315 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 225 optimal weight:    6.9990
   chunk 357 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
A 406 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 109 ASN
G 101 ASN
** I 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 191 ASN
J 109 ASN
J 117 GLN
J 142 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 109 ASN
P 117 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  57960  Z= 0.175
  Angle     :  0.479   6.949  78600  Z= 0.243
  Chirality :  0.039   0.154   8248
  Planarity :  0.004   0.052  10328
  Dihedral  :  7.920 178.133   8208
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.91 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.10), residues: 7048
  helix:  0.95 (0.10), residues: 2960
  sheet:  0.15 (0.18), residues: 824
  loop : -0.55 (0.11), residues: 3264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 303 
 HIS   0.004   0.001   HIS K 311 
 PHE   0.014   0.001   PHE G 361 
 TYR   0.014   0.001   TYR K 250 
 ARG   0.011   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  647 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 121
    poor density    : 526
  time to evaluate  : 4.857 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7124 (m-80)
REVERT: B   61 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7360 (mt-10)
REVERT: B  102 ILE cc_start: 0.9129 (tt) cc_final: 0.8844 (pt)
REVERT: B  437 TRP cc_start: 0.7201 (p-90) cc_final: 0.6413 (m100)
REVERT: B  445 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7090 (mmm)
REVERT: C   61 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6803 (tp30)
REVERT: C  436 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8031 (mtp85)
REVERT: D  146 ASP cc_start: 0.7813 (m-30) cc_final: 0.7607 (m-30)
REVERT: E  159 THR cc_start: 0.8995 (m) cc_final: 0.8655 (m)
REVERT: E  252 MET cc_start: 0.8477 (ttt) cc_final: 0.8237 (ttt)
REVERT: E  346 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8274 (mtm180)
REVERT: E  415 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7189 (tp-100)
REVERT: F  159 THR cc_start: 0.8212 (m) cc_final: 0.7972 (m)
REVERT: F  290 GLN cc_start: 0.8411 (mm110) cc_final: 0.8013 (mp10)
REVERT: F  361 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7707 (m-80)
REVERT: G  322 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7971 (tp30)
REVERT: G  415 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: H  246 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8557 (mm)
REVERT: H  375 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7558 (t0)
REVERT: H  440 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7957 (tp30)
REVERT: I   11 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7672 (mmp80)
REVERT: I  436 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7948 (mtp180)
REVERT: J   10 VAL cc_start: 0.9035 (t) cc_final: 0.8756 (p)
REVERT: J  106 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9052 (mp)
REVERT: J  149 ASN cc_start: 0.9069 (t0) cc_final: 0.8759 (t0)
REVERT: J  212 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7509 (mtp180)
REVERT: J  276 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7855 (mpp)
REVERT: J  322 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6732 (tt0)
REVERT: J  346 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7881 (mtp180)
REVERT: K  142 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7425 (mp-120)
REVERT: K  241 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7253 (mt-10)
REVERT: K  269 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7286 (tpt-90)
REVERT: K  445 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8012 (mtm)
REVERT: L  268 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7452 (ttp-170)
REVERT: L  283 MET cc_start: 0.9116 (ttp) cc_final: 0.8376 (ttt)
REVERT: L  346 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8091 (mtp85)
REVERT: L  428 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7409 (ttm110)
REVERT: M  322 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6917 (tt0)
REVERT: O  445 MET cc_start: 0.8235 (mtm) cc_final: 0.7823 (mtm)
REVERT: P   21 ASP cc_start: 0.8228 (t0) cc_final: 0.8007 (t0)
REVERT: P  205 LEU cc_start: 0.8786 (tp) cc_final: 0.8477 (mt)
REVERT: P  343 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8460 (m-30)
  outliers start: 121
  outliers final: 47
  residues processed: 609
  average time/residue: 1.4588
  time to fit residues: 1121.5616
Evaluate side-chains
  538 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 471
  time to evaluate  : 4.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  314 THR
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain E residue  436 ARG
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  424 LEU
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  246 LEU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain H residue  440 GLU
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  358 LYS
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue  106 ILE
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  232 SER
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  322 GLU
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain K residue   29 LEU
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain K residue  445 MET
Chi-restraints excluded: chain L residue  288 ASP
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain L residue  346 ARG
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  245 GLU
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue  314 THR
Chi-restraints excluded: chain O residue  423 ILE
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue  109 ASN
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  307 VAL
Chi-restraints excluded: chain P residue  343 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 656 optimal weight:    0.9990
   chunk 76 optimal weight:    9.9990
   chunk 388 optimal weight:    1.9990
   chunk 497 optimal weight:    4.9990
   chunk 385 optimal weight:    2.9990
   chunk 573 optimal weight:    8.9990
   chunk 380 optimal weight:    0.5980
   chunk 678 optimal weight:    8.9990
   chunk 424 optimal weight:    3.9990
   chunk 413 optimal weight:    0.7980
   chunk 313 optimal weight:    9.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
A 406 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 101 ASN
E 109 ASN
G 101 ASN
** I 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 191 ASN
J 109 ASN
J 117 GLN
J 142 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 109 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  57960  Z= 0.201
  Angle     :  0.490   6.601  78600  Z= 0.248
  Chirality :  0.040   0.148   8248
  Planarity :  0.004   0.052  10328
  Dihedral  :  7.728 176.742   8208
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.90 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.10), residues: 7048
  helix:  1.04 (0.10), residues: 2960
  sheet:  0.23 (0.18), residues: 824
  loop : -0.52 (0.11), residues: 3264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP F 303 
 HIS   0.005   0.001   HIS F 278 
 PHE   0.016   0.001   PHE P 111 
 TYR   0.014   0.001   TYR K 250 
 ARG   0.010   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  600 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 113
    poor density    : 487
  time to evaluate  : 4.846 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7130 (m-80)
REVERT: A  234 GLU cc_start: 0.7564 (mp0) cc_final: 0.7273 (mp0)
REVERT: B  437 TRP cc_start: 0.7200 (p-90) cc_final: 0.6406 (m100)
REVERT: B  445 MET cc_start: 0.7505 (mtm) cc_final: 0.7082 (mmm)
REVERT: C   61 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6802 (tp30)
REVERT: C  436 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8054 (mtp85)
REVERT: E  109 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7349 (m110)
REVERT: E  159 THR cc_start: 0.8992 (m) cc_final: 0.8646 (m)
REVERT: E  252 MET cc_start: 0.8519 (ttt) cc_final: 0.8281 (ttt)
REVERT: E  346 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8262 (mtm180)
REVERT: E  415 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7157 (tp-100)
REVERT: F  159 THR cc_start: 0.8225 (m) cc_final: 0.7982 (m)
REVERT: F  290 GLN cc_start: 0.8419 (mm110) cc_final: 0.8023 (mp10)
REVERT: F  361 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7627 (m-80)
REVERT: G  322 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7980 (tp30)
REVERT: G  415 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: H  375 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7548 (t0)
REVERT: I   11 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7664 (mmp80)
REVERT: I  436 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (mtp180)
REVERT: J   10 VAL cc_start: 0.9032 (t) cc_final: 0.8745 (p)
REVERT: J   69 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7911 (t70)
REVERT: J  106 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9077 (mp)
REVERT: J  149 ASN cc_start: 0.9076 (t0) cc_final: 0.8758 (t0)
REVERT: J  212 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7511 (mtp180)
REVERT: J  276 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7843 (mpp)
REVERT: J  322 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6731 (tt0)
REVERT: J  346 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7937 (mtp180)
REVERT: K  142 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7428 (mp-120)
REVERT: K  269 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7270 (tpt-90)
REVERT: K  445 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8111 (mtm)
REVERT: L  268 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7440 (ttp-170)
REVERT: L  283 MET cc_start: 0.9183 (ttp) cc_final: 0.8430 (ttt)
REVERT: L  337 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7187 (mt-10)
REVERT: L  428 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7430 (ttm110)
REVERT: M  322 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6928 (tt0)
REVERT: O  421 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7769 (mtp180)
REVERT: O  445 MET cc_start: 0.8257 (mtm) cc_final: 0.7881 (mtm)
REVERT: P  205 LEU cc_start: 0.8791 (tp) cc_final: 0.8481 (mt)
  outliers start: 113
  outliers final: 52
  residues processed: 564
  average time/residue: 1.4760
  time to fit residues: 1049.2855
Evaluate side-chains
  527 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 458
  time to evaluate  : 4.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  109 ASN
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  314 THR
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain E residue  436 ARG
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain H residue  189 ASP
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  124 MET
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   29 LEU
Chi-restraints excluded: chain J residue   69 ASP
Chi-restraints excluded: chain J residue  106 ILE
Chi-restraints excluded: chain J residue  193 ASN
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  232 SER
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  322 GLU
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue   29 LEU
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain K residue  411 GLU
Chi-restraints excluded: chain K residue  445 MET
Chi-restraints excluded: chain L residue  185 THR
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  337 GLU
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain O residue  423 ILE
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue  110 VAL
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  307 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 419 optimal weight:    1.9990
   chunk 270 optimal weight:    9.9990
   chunk 405 optimal weight:    2.9990
   chunk 204 optimal weight:    0.0030
   chunk 133 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   chunk 431 optimal weight:    0.7980
   chunk 462 optimal weight:    5.9990
   chunk 335 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 533 optimal weight:    6.9990
   overall best weight:    1.9596

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 117 GLN
I 191 ASN
J 109 ASN
J 117 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  57960  Z= 0.237
  Angle     :  0.504   7.090  78600  Z= 0.253
  Chirality :  0.040   0.160   8248
  Planarity :  0.004   0.051  10328
  Dihedral  :  7.625 174.729   8208
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.59 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.10), residues: 7048
  helix:  1.09 (0.10), residues: 2920
  sheet:  0.26 (0.18), residues: 824
  loop : -0.46 (0.11), residues: 3304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 303 
 HIS   0.005   0.001   HIS A 311 
 PHE   0.018   0.001   PHE E 111 
 TYR   0.030   0.001   TYR E  22 
 ARG   0.013   0.000   ARG H 428 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  576 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 104
    poor density    : 472
  time to evaluate  : 4.763 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: A  234 GLU cc_start: 0.7577 (mp0) cc_final: 0.7305 (mp0)
REVERT: B   61 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6693 (mt-10)
REVERT: B  102 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8813 (pt)
REVERT: B  437 TRP cc_start: 0.7207 (p-90) cc_final: 0.6424 (m100)
REVERT: B  445 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7079 (mmm)
REVERT: C   61 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6810 (tp30)
REVERT: C  248 SER cc_start: 0.8535 (t) cc_final: 0.8224 (m)
REVERT: E  159 THR cc_start: 0.9021 (m) cc_final: 0.8690 (m)
REVERT: E  252 MET cc_start: 0.8540 (ttt) cc_final: 0.8293 (ttt)
REVERT: E  346 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8278 (mtm180)
REVERT: E  415 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7151 (tp-100)
REVERT: F  159 THR cc_start: 0.8246 (m) cc_final: 0.8003 (m)
REVERT: F  290 GLN cc_start: 0.8427 (mm110) cc_final: 0.8019 (mp10)
REVERT: F  361 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7615 (m-80)
REVERT: G  322 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (tp30)
REVERT: G  415 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: H  375 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7529 (t0)
REVERT: I   11 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7671 (mmp80)
REVERT: I  337 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7147 (mp0)
REVERT: I  436 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7932 (mtp180)
REVERT: J  106 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9096 (mp)
REVERT: J  212 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7500 (mtp180)
REVERT: J  276 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7846 (mpp)
REVERT: J  322 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6767 (tt0)
REVERT: J  346 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7954 (mtp180)
REVERT: K  142 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7416 (mp-120)
REVERT: K  241 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7249 (mt-10)
REVERT: K  269 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7281 (tpt-90)
REVERT: K  445 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8135 (mtm)
REVERT: L  268 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7441 (ttp-170)
REVERT: L  337 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7203 (mt-10)
REVERT: L  346 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8078 (mtp85)
REVERT: M  322 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6952 (tt0)
REVERT: O  421 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7760 (mtp180)
REVERT: O  429 GLU cc_start: 0.7624 (mp0) cc_final: 0.7196 (mp0)
REVERT: O  445 MET cc_start: 0.8266 (mtm) cc_final: 0.7883 (mtm)
REVERT: P  205 LEU cc_start: 0.8811 (tp) cc_final: 0.8491 (mt)
  outliers start: 104
  outliers final: 58
  residues processed: 544
  average time/residue: 1.4927
  time to fit residues: 1021.8533
Evaluate side-chains
  526 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 449
  time to evaluate  : 4.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  254 ASP
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  314 THR
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  245 GLU
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain H residue  126 ILE
Chi-restraints excluded: chain H residue  189 ASP
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  124 MET
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   29 LEU
Chi-restraints excluded: chain J residue  106 ILE
Chi-restraints excluded: chain J residue  193 ASN
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  232 SER
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  322 GLU
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue   29 LEU
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain K residue  445 MET
Chi-restraints excluded: chain L residue  185 THR
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  337 GLU
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain L residue  346 ARG
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain M residue  379 ILE
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue  314 THR
Chi-restraints excluded: chain O residue  423 ILE
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue  117 GLN
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  307 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 617 optimal weight:    7.9990
   chunk 650 optimal weight:    6.9990
   chunk 593 optimal weight:    0.8980
   chunk 632 optimal weight:    6.9990
   chunk 649 optimal weight:    0.9990
   chunk 380 optimal weight:    0.2980
   chunk 275 optimal weight:    2.9990
   chunk 496 optimal weight:    5.9990
   chunk 194 optimal weight:    7.9990
   chunk 571 optimal weight:    2.9990
   chunk 598 optimal weight:    5.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 227 ASN
I 191 ASN
J 109 ASN
J 117 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  57960  Z= 0.212
  Angle     :  0.498   9.152  78600  Z= 0.251
  Chirality :  0.040   0.146   8248
  Planarity :  0.004   0.055  10328
  Dihedral  :  7.513 175.125   8208
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.98 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.10), residues: 7048
  helix:  1.08 (0.10), residues: 2960
  sheet:  0.37 (0.17), residues: 904
  loop : -0.50 (0.11), residues: 3184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F 303 
 HIS   0.005   0.001   HIS A 311 
 PHE   0.014   0.001   PHE G 361 
 TYR   0.032   0.001   TYR E  22 
 ARG   0.013   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 99
    poor density    : 462
  time to evaluate  : 4.923 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7200 (m-80)
REVERT: A  234 GLU cc_start: 0.7578 (mp0) cc_final: 0.7272 (mp0)
REVERT: B  102 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8803 (pt)
REVERT: B  437 TRP cc_start: 0.7201 (p-90) cc_final: 0.6391 (m100)
REVERT: B  445 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7178 (mmm)
REVERT: C   61 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6811 (tp30)
REVERT: C  436 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8101 (mtp85)
REVERT: E  159 THR cc_start: 0.9004 (m) cc_final: 0.8665 (m)
REVERT: E  252 MET cc_start: 0.8498 (ttt) cc_final: 0.8260 (ttt)
REVERT: E  346 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8177 (mtm180)
REVERT: E  415 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7120 (tp-100)
REVERT: F  159 THR cc_start: 0.8249 (m) cc_final: 0.8005 (m)
REVERT: F  290 GLN cc_start: 0.8409 (mm110) cc_final: 0.8009 (mp10)
REVERT: F  361 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7676 (m-80)
REVERT: G  322 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7976 (tp30)
REVERT: G  415 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: H  375 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7518 (t0)
REVERT: I   11 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7676 (mmp80)
REVERT: I  337 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7108 (mp0)
REVERT: I  436 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7914 (mtp180)
REVERT: J   10 VAL cc_start: 0.9032 (t) cc_final: 0.8743 (p)
REVERT: J  106 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9095 (mp)
REVERT: J  212 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7500 (mtp180)
REVERT: J  276 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7837 (mpp)
REVERT: J  322 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6774 (tt0)
REVERT: J  346 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7935 (mtp180)
REVERT: K  142 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7423 (mp-120)
REVERT: K  269 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7288 (tpt-90)
REVERT: K  445 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8133 (mtm)
REVERT: L  268 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7443 (ttp-170)
REVERT: L  346 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8076 (mtp85)
REVERT: L  436 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7623 (ttp80)
REVERT: M  322 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6961 (tt0)
REVERT: O  421 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7768 (mtp180)
REVERT: O  429 GLU cc_start: 0.7631 (mp0) cc_final: 0.7214 (mp0)
REVERT: O  445 MET cc_start: 0.8258 (mtm) cc_final: 0.7884 (mtm)
REVERT: P   29 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7866 (mp)
REVERT: P  205 LEU cc_start: 0.8804 (tp) cc_final: 0.8494 (mt)
  outliers start: 99
  outliers final: 55
  residues processed: 532
  average time/residue: 1.5166
  time to fit residues: 1011.5031
Evaluate side-chains
  518 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 445
  time to evaluate  : 4.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain B residue  445 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  238 LYS
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  232 SER
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  254 ASP
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  314 THR
Chi-restraints excluded: chain E residue  346 ARG
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  245 GLU
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain H residue  126 ILE
Chi-restraints excluded: chain H residue  202 ASP
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  304 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  124 MET
Chi-restraints excluded: chain I residue  358 LYS
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   29 LEU
Chi-restraints excluded: chain J residue  106 ILE
Chi-restraints excluded: chain J residue  193 ASN
Chi-restraints excluded: chain J residue  212 ARG
Chi-restraints excluded: chain J residue  232 SER
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  322 GLU
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain J residue  351 ASP
Chi-restraints excluded: chain K residue   29 LEU
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain K residue  411 GLU
Chi-restraints excluded: chain K residue  445 MET
Chi-restraints excluded: chain L residue  185 THR
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  338 ASP
Chi-restraints excluded: chain L residue  346 ARG
Chi-restraints excluded: chain M residue   29 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue  314 THR
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue   29 LEU
Chi-restraints excluded: chain P residue  173 ARG
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  279 CYS
Chi-restraints excluded: chain P residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 630 optimal weight:    0.8980
   chunk 415 optimal weight:    0.9980
   chunk 668 optimal weight:    0.8980
   chunk 408 optimal weight:    0.9980
   chunk 317 optimal weight:    1.9990
   chunk 464 optimal weight:    5.9990
   chunk 701 optimal weight:    0.0020
   chunk 645 optimal weight:    8.9990
   chunk 558 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 431 optimal weight:    3.9990
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
A 149 ASN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 191 ASN
I 278 HIS
J 109 ASN
J 117 GLN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  57960  Z= 0.148
  Angle     :  0.474  11.193  78600  Z= 0.238
  Chirality :  0.039   0.161   8248
  Planarity :  0.003   0.054  10328
  Dihedral  :  7.210 173.551   8208
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 16.49 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.10), residues: 7048
  helix:  1.27 (0.10), residues: 2952
  sheet:  0.52 (0.17), residues: 904
  loop : -0.45 (0.11), residues: 3192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 371 
 HIS   0.004   0.001   HIS A 311 
 PHE   0.012   0.001   PHE G 361 
 TYR   0.029   0.001   TYR E  22 
 ARG   0.015   0.000   ARG I 442 

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

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

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14096 Ramachandran restraints generated.
    7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  593 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 515
  time to evaluate  : 4.875 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7133 (m-80)
REVERT: A  234 GLU cc_start: 0.7574 (mp0) cc_final: 0.7264 (mp0)
REVERT: B  102 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8804 (pt)
REVERT: B  205 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (mt)
REVERT: B  437 TRP cc_start: 0.7194 (p-90) cc_final: 0.6354 (m100)
REVERT: B  445 MET cc_start: 0.7401 (mtm) cc_final: 0.7145 (mmm)
REVERT: C   61 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6836 (tp30)
REVERT: C  436 ARG cc_start: 0.8420 (mtm110) cc_final: 0.8046 (mtp85)
REVERT: D  208 MET cc_start: 0.8527 (mmm) cc_final: 0.8192 (mmm)
REVERT: E  149 ASN cc_start: 0.8929 (t0) cc_final: 0.8440 (t0)
REVERT: E  159 THR cc_start: 0.8957 (m) cc_final: 0.8587 (m)
REVERT: E  415 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7056 (tp-100)
REVERT: F  159 THR cc_start: 0.8242 (m) cc_final: 0.7995 (m)
REVERT: F  290 GLN cc_start: 0.8390 (mm110) cc_final: 0.8039 (mp10)
REVERT: F  361 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7645 (m-80)
REVERT: G  322 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7907 (tp30)
REVERT: G  415 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: H  375 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7513 (t0)
REVERT: I   11 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7684 (mmp80)
REVERT: I   29 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8506 (tp)
REVERT: I  337 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7169 (mp0)
REVERT: I  436 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7871 (mtp180)
REVERT: J   10 VAL cc_start: 0.8935 (t) cc_final: 0.8636 (p)
REVERT: J   69 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7892 (t70)
REVERT: J  149 ASN cc_start: 0.9080 (t0) cc_final: 0.8776 (t0)
REVERT: J  276 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7796 (mpp)
REVERT: J  322 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6667 (tt0)
REVERT: J  346 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7866 (mtp180)
REVERT: K  269 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7218 (tpt-90)
REVERT: L  142 GLN cc_start: 0.7859 (mp-120) cc_final: 0.7657 (mp10)
REVERT: L  268 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7401 (ttp-170)
REVERT: L  346 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8073 (mtp85)
REVERT: L  411 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7228 (tp30)
REVERT: L  436 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7503 (tmm160)
REVERT: M  322 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6999 (tt0)
REVERT: O  429 GLU cc_start: 0.7624 (mp0) cc_final: 0.7255 (mp0)
REVERT: O  445 MET cc_start: 0.8226 (mtm) cc_final: 0.7897 (mtm)
REVERT: P   69 ASP cc_start: 0.7626 (p0) cc_final: 0.7361 (p0)
REVERT: P  205 LEU cc_start: 0.8783 (tp) cc_final: 0.8487 (mt)
  outliers start: 78
  outliers final: 34
  residues processed: 571
  average time/residue: 1.4545
  time to fit residues: 1051.5285
Evaluate side-chains
  520 residues out of total 5664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 471
  time to evaluate  : 4.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 TYR
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  358 LYS
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  358 LYS
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain D residue   16 THR
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  269 ARG
Chi-restraints excluded: chain E residue  314 THR
Chi-restraints excluded: chain F residue   21 ASP
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue  361 PHE
Chi-restraints excluded: chain F residue  379 ILE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain H residue  126 ILE
Chi-restraints excluded: chain H residue  205 LEU
Chi-restraints excluded: chain H residue  370 VAL
Chi-restraints excluded: chain H residue  375 ASP
Chi-restraints excluded: chain I residue   16 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue  436 ARG
Chi-restraints excluded: chain J residue   29 LEU
Chi-restraints excluded: chain J residue   69 ASP
Chi-restraints excluded: chain J residue  245 GLU
Chi-restraints excluded: chain J residue  276 MET
Chi-restraints excluded: chain J residue  322 GLU
Chi-restraints excluded: chain J residue  346 ARG
Chi-restraints excluded: chain K residue   29 LEU
Chi-restraints excluded: chain K residue  269 ARG
Chi-restraints excluded: chain K residue  361 PHE
Chi-restraints excluded: chain L residue  159 THR
Chi-restraints excluded: chain L residue  317 VAL
Chi-restraints excluded: chain L residue  346 ARG
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  322 GLU
Chi-restraints excluded: chain M residue  353 ASP
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue  314 THR
Chi-restraints excluded: chain P residue   16 THR
Chi-restraints excluded: chain P residue  185 THR
Chi-restraints excluded: chain P residue  279 CYS
Chi-restraints excluded: chain P residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 704
   random chunks:
   chunk 342 optimal weight:    6.9990
   chunk 443 optimal weight:    0.9980
   chunk 594 optimal weight:    0.0010
   chunk 171 optimal weight:   10.0000
   chunk 514 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 155 optimal weight:    3.9990
   chunk 559 optimal weight:    3.9990
   chunk 234 optimal weight:    7.9990
   chunk 574 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  65 ASN
D  65 ASN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 117 GLN
I 191 ASN
J 109 ASN
J 117 GLN
J 406 ASN
** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 117 GLN
O 415 GLN
P 406 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.108859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.092962 restraints weight = 80410.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.94
r_work: 0.2960 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  57960  Z= 0.309
  Angle     :  0.540  10.859  78600  Z= 0.271
  Chirality :  0.042   0.206   8248
  Planarity :  0.004   0.055  10328
  Dihedral  :  7.270 175.811   8208
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.16 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.10), residues: 7048
  helix:  1.14 (0.10), residues: 2912
  sheet:  0.24 (0.18), residues: 872
  loop : -0.38 (0.11), residues: 3264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 371 
 HIS   0.007   0.001   HIS A 311 
 PHE   0.017   0.002   PHE G 361 
 TYR   0.029   0.001   TYR E  22 
 ARG   0.014   0.000   ARG I 442 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15976.23 seconds
wall clock time: 279 minutes 32.89 seconds (16772.89 seconds total)