Starting phenix.real_space_refine (version: 1.21rc1)
on Sat Apr 22 09:56:05 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvv_4443/04_2023/6rvv_4443.pdb"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
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=   0.003 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Au    120     10.57       5
     S     264      5.16       5
     C   69432      2.51       5
     N   18216      2.21       5
     O   22176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "AA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "BK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "CK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "DK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "ED PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "EK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "FK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "GK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "HK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "ID PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "II PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "IK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "JK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "KK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "LK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "ME PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "MK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "ND PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "NK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "OK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "PK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "QK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "RK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "SK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "TK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "UK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "VK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "WK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XA PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XB PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XC PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XD PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XE PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XF PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XG PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XH PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XI PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XJ PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "XK PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.29s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 110208
  Number of models: 1
  Model: ""
    Number of chains: 384
    Chain: "AA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "AK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "BK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "CK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "DK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "ED"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "EK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "FK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "GK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HB"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HC"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HD"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HE"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HF"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HG"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HH"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HI"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HJ"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "HK"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 417
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "IA"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Number of conformers: 1
      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Number of conformers: 1
      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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    Chain: "KH"
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Number of conformers: 1
      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
          Chain breaks: 1
    Chain: "LA"
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      Number of conformers: 1
      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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    Chain: "LD"
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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    Chain: "MA"
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      Conformer: ""
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          Classifications: {'peptide': 55}
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    Chain: "MB"
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
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    Chain: "MF"
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      Conformer: ""
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          Classifications: {'peptide': 55}
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      Conformer: ""
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    Chain: "MH"
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      Conformer: ""
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    Chain: "MI"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "OB"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "OK"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "PD"
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      Conformer: ""
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    Chain: "PE"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "QC"
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      Conformer: ""
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    Chain: "QD"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "RB"
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      Conformer: ""
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    Chain: "RC"
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      Conformer: ""
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    Chain: "RD"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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    Chain: "SA"
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Conformer: ""
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      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "FF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "FG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "FH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "FI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "FJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GD"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "GJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HD"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "HJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "II"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "IJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "JA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "JB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "JG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "JH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "KC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "KD"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "KE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "KF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "LJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "MA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "MB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "NC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "ND"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "NE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "NF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "OJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "PA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "PB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "PC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "PD"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "QG"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "QH"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "RC"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "RD"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "RE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "RF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "SE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "SF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "TE"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "TF"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "TI"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "TJ"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "WA"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}
    Chain: "WB"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AU': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    139  SG  CYSAA  35     150.313 108.639  20.247  1.00 77.92           S
  ATOM  45175  SG  CYSJJ  35     150.872 113.443  20.317  1.00 81.29           S
  ATOM    556  SG  CYSAB  35     169.151 102.965  28.630  1.00 65.12           S
  ATOM  44758  SG  CYSJI  35     169.881 107.646  28.510  1.00 75.48           S
  ATOM    973  SG  CYSAC  35     180.472  88.238  39.715  1.00 62.61           S
  ATOM  57268  SG  CYSMF  35     184.345  90.057  41.707  1.00 63.41           S
  ATOM   1390  SG  CYSAD  35     180.399  69.253  49.850  1.00 60.51           S
  ATOM  56851  SG  CYSME  35     184.182  71.214  51.877  1.00 61.78           S
  ATOM   1807  SG  CYSAE  35     169.027  51.877  55.904  1.00 59.54           S
  ATOM  38086  SG  CYSID  35     171.023  49.798  59.717  1.00 65.48           S
  ATOM   2224  SG  CYSAF  35     150.092  41.765  55.895  1.00 64.17           S
  ATOM  37669  SG  CYSIC  35     152.013  39.658  59.582  1.00 66.55           S
  ATOM   2641  SG  CYSAG  35     129.268  42.081  49.834  1.00 76.01           S
  ATOM  48928  SG  CYSKH  35     126.594  39.499  52.539  1.00 77.42           S
  ATOM   3058  SG  CYSAH  35     113.534  52.561  39.303  1.00 75.28           S
  ATOM  48511  SG  CYSKG  35     110.960  49.675  42.019  1.00 73.40           S
  ATOM   3475  SG  CYSAI  35     107.679  70.285  28.337  1.00 75.77           S
  ATOM  87709  SG  CYSTB  35     103.108  71.045  28.627  1.00 65.85           S
  ATOM   3892  SG  CYSAJ  35     113.444  89.241  20.136  1.00 81.20           S
  ATOM  87292  SG  CYSTA  35     108.707  89.908  20.245  1.00 78.71           S
  ATOM   4726  SG  CYSBA  35     219.804 131.298  89.898  1.00 74.99           S
  ATOM  58936  SG  CYSMJ  35     219.853 126.690  89.164  1.00 74.27           S
  ATOM   5143  SG  CYSBB  35     211.405 137.006  71.110  1.00 67.52           S
  ATOM  58519  SG  CYSMI  35     211.749 132.474  70.275  1.00 73.68           S
  ATOM   5560  SG  CYSBC  35     200.493 151.903  59.666  1.00 65.57           S
  ATOM  43507  SG  CYSJF  35     198.401 150.017  55.854  1.00 62.75           S
  ATOM   5977  SG  CYSBD  35     190.319 171.008  59.716  1.00 66.11           S
  ATOM  43090  SG  CYSJE  35     188.360 168.986  55.923  1.00 58.87           S
  ATOM   6394  SG  CYSBE  35     184.196 188.403  71.218  1.00 62.19           S
  ATOM  19738  SG  CYSED  35     180.590 190.287  69.240  1.00 67.51           S
  ATOM   6811  SG  CYSBF  35     184.383 198.509  90.113  1.00 58.26           S
  ATOM  19321  SG  CYSEC  35     180.515 200.420  88.212  1.00 66.11           S
  ATOM   7228  SG  CYSBG  35     190.448 198.117 110.896  1.00 62.67           S
  ATOM  12232  SG  CYSCH  35     187.596 200.686 113.558  1.00 64.70           S
  ATOM   7645  SG  CYSBH  35     200.825 187.623 126.629  1.00 64.25           S
  ATOM  11815  SG  CYSCG  35     198.074 190.319 129.310  1.00 64.00           S
  ATOM   8062  SG  CYSBI  35     211.815 169.973 132.443  1.00 72.76           S
  ATOM  51013  SG  CYSLB  35     211.464 169.104 137.063  1.00 66.34           S
  ATOM   8479  SG  CYSBJ  35     219.790 150.938 126.658  1.00 79.63           S
  ATOM  50596  SG  CYSLA  35     219.728 150.318 131.481  1.00 77.05           S
  ATOM   9313  SG  CYSCA  35     131.438 219.866 150.330  1.00 75.35           S
  ATOM  77284  SG  CYSQJ  35     126.854 219.752 151.003  1.00 74.08           S
  ATOM   9730  SG  CYSCB  35     137.171 211.527 169.250  1.00 66.81           S
  ATOM  76867  SG  CYSQI  35     132.483 211.706 169.932  1.00 73.32           S
  ATOM  10147  SG  CYSCC  35     151.944 200.484 180.501  1.00 66.29           S
  ATOM  A02F6  SG  CYSWF  35     150.078 198.410 184.267  1.00 64.02           S
  ATOM  10564  SG  CYSCD  35     170.892 190.267 180.390  1.00 65.38           S
  ATOM  A023L  SG  CYSWE  35     169.103 188.390 184.326  1.00 60.03           S
  ATOM  10981  SG  CYSCE  35     188.277 184.153 168.987  1.00 63.16           S
  ATOM  51847  SG  CYSLD  35     190.300 180.550 170.961  1.00 68.20           S
  ATOM  11398  SG  CYSCF  35     198.520 184.345 150.072  1.00 58.15           S
  ATOM  51430  SG  CYSLC  35     200.466 180.546 152.022  1.00 66.71           S
  ATOM  12649  SG  CYSCI  35     169.994 211.789 107.651  1.00 73.16           S
  ATOM  18904  SG  CYSEB  35     169.161 211.555 103.050  1.00 66.59           S
  ATOM  13066  SG  CYSCJ  35     151.027 219.842 113.478  1.00 81.16           S
  ATOM  18487  SG  CYSEA  35     150.361 219.876 108.680  1.00 77.95           S
  ATOM  13900  SG  CYSDA  35      20.354 150.323 108.706  1.00 78.04           S
  ATOM  63523  SG  CYSNJ  35      20.175 150.964 113.459  1.00 79.44           S
  ATOM  14317  SG  CYSDB  35      28.609 169.164 102.975  1.00 65.51           S
  ATOM  63106  SG  CYSNI  35      28.262 169.907 107.661  1.00 73.07           S
  ATOM  14734  SG  CYSDC  35      39.722 180.504  88.130  1.00 67.41           S
  ATOM  29746  SG  CYSGF  35      41.741 184.292  90.048  1.00 58.96           S
  ATOM  15151  SG  CYSDD  35      49.883 180.441  69.324  1.00 66.08           S
  ATOM  29329  SG  CYSGE  35      51.733 184.202  71.118  1.00 62.46           S
  ATOM  15568  SG  CYSDE  35      55.858 168.985  51.823  1.00 61.01           S
  ATOM  97717  SG  CYSVD  35      59.733 170.908  49.820  1.00 59.56           S
  ATOM  15985  SG  CYSDF  35      55.786 150.088  41.602  1.00 64.64           S
  ATOM  97300  SG  CYSVC  35      59.612 151.898  39.705  1.00 64.00           S
  ATOM  16402  SG  CYSDG  35      49.633 129.211  41.950  1.00 73.15           S
  ATOM  90211  SG  CYSTH  35      52.455 126.612  39.238  1.00 74.36           S
  ATOM  16819  SG  CYSDH  35      39.542 113.588  52.530  1.00 76.47           S
  ATOM  89794  SG  CYSTG  35      41.944 110.889  49.678  1.00 76.02           S
  ATOM  17236  SG  CYSDI  35      28.411 107.727  70.159  1.00 73.25           S
  ATOM  92296  SG  CYSUB  35      28.567 103.008  70.738  1.00 68.89           S
  ATOM  17653  SG  CYSDJ  35      20.197 113.430  89.184  1.00 74.12           S
  ATOM  91879  SG  CYSUA  35      20.324 108.734  89.867  1.00 74.80           S
  ATOM  20155  SG  CYSEE  35     169.008 184.148  52.011  1.00 61.01           S
  ATOM  42673  SG  CYSJD  35     171.015 180.382  49.764  1.00 60.26           S
  ATOM  20572  SG  CYSEF  35     150.036 184.417  41.654  1.00 63.36           S
  ATOM  42256  SG  CYSJC  35     151.972 180.524  39.771  1.00 63.15           S
  ATOM  20989  SG  CYSEG  35     129.229 190.474  41.962  1.00 73.93           S
  ATOM  99385  SG  CYSVH  35     126.609 187.666  39.434  1.00 76.47           S
  ATOM  21406  SG  CYSEH  35     113.471 200.689  52.510  1.00 76.11           S
  ATOM  98968  SG  CYSVG  35     110.906 198.140  49.670  1.00 75.67           S
  ATOM  21823  SG  CYSEI  35     107.734 211.803  70.174  1.00 73.11           S
  ATOM  28078  SG  CYSGB  35     103.024 211.598  70.874  1.00 67.86           S
  ATOM  22240  SG  CYSEJ  35     113.461 219.969  89.190  1.00 74.08           S
  ATOM  27661  SG  CYSGA  35     108.748 219.892  89.859  1.00 74.81           S
  ATOM  23074  SG  CYSFA  35      20.358  89.817 131.429  1.00 78.57           S
  ATOM  95632  SG  CYSUJ  35      20.217  89.151 126.664  1.00 79.05           S
  ATOM  23491  SG  CYSFB  35      28.569  70.977 137.148  1.00 66.90           S
  ATOM  95215  SG  CYSUI  35      28.259  70.055 132.491  1.00 72.40           S
  ATOM  23908  SG  CYSFC  35      39.644  59.618 152.014  1.00 67.44           S
  ATOM  34333  SG  CYSHF  35      41.718  55.857 149.992  1.00 59.93           S
  ATOM  24325  SG  CYSFD  35      49.876  59.611 170.790  1.00 68.31           S
  ATOM  33916  SG  CYSHE  35      51.740  55.933 168.992  1.00 63.31           S
  ATOM  24742  SG  CYSFE  35      55.911  71.159 188.222  1.00 61.96           S
  ATOM  65608  SG  CYSOD  35      59.633  69.161 190.351  1.00 61.28           S
  ATOM  25159  SG  CYSFF  35      55.881  90.056 198.464  1.00 63.68           S
  ATOM  65191  SG  CYSOC  35      59.587  88.134 200.439  1.00 65.64           S
  ATOM  25576  SG  CYSFG  35      49.784 110.899 198.183  1.00 73.21           S
  ATOM  71863  SG  CYSPH  35      52.448 113.460 200.950  1.00 73.85           S
  ATOM  25993  SG  CYSFH  35      39.447 126.623 187.635  1.00 76.51           S
  ATOM  71446  SG  CYSPG  35      41.971 129.249 190.457  1.00 75.83           S
  ATOM  26410  SG  CYSFI  35      28.481 132.465 169.980  1.00 73.99           S
  ATOM  60187  SG  CYSNB  35      28.471 137.246 169.336  1.00 67.91           S
  ATOM  26827  SG  CYSFJ  35      20.248 126.654 150.939  1.00 73.98           S
  ATOM  59770  SG  CYSNA  35      20.309 131.379 150.307  1.00 75.55           S
  ATOM  28495  SG  CYSGC  35      88.217 200.471  59.636  1.00 66.22           S
  ATOM  98551  SG  CYSVF  35      90.090 198.505  55.845  1.00 62.95           S
  ATOM  28912  SG  CYSGD  35      69.166 190.338  59.624  1.00 65.10           S
  ATOM  98134  SG  CYSVE  35      71.122 188.287  55.891  1.00 58.23           S
  ATOM  30163  SG  CYSGG  35      42.024 190.474 110.948  1.00 63.26           S
  ATOM  62689  SG  CYSNH  35      39.405 187.610 113.558  1.00 66.05           S
  ATOM  30580  SG  CYSGH  35      52.605 200.769 126.493  1.00 63.97           S
  ATOM  62272  SG  CYSNG  35      49.850 198.015 129.242  1.00 64.37           S
  ATOM  30997  SG  CYSGI  35      70.174 211.867 132.514  1.00 72.42           S
  ATOM  73948  SG  CYSQB  35      71.063 211.528 137.124  1.00 66.28           S
  ATOM  31414  SG  CYSGJ  35      89.208 219.833 126.645  1.00 78.31           S
  ATOM  73531  SG  CYSQA  35      89.788 219.715 131.527  1.00 76.61           S
  ATOM  32248  SG  CYSHA  35     108.739  20.292 150.264  1.00 75.53           S
  ATOM  86458  SG  CYSSJ  35     113.504  20.259 150.901  1.00 74.18           S
  ATOM  32665  SG  CYSHB  35     102.965  28.494 169.284  1.00 68.24           S
  ATOM  86041  SG  CYSSI  35     107.692  28.468 169.897  1.00 73.28           S
  ATOM  33082  SG  CYSHC  35      88.241  39.634 180.503  1.00 65.40           S
  ATOM  66442  SG  CYSOF  35      90.045  41.594 184.329  1.00 63.86           S
  ATOM  33499  SG  CYSHD  35      69.237  49.813 180.499  1.00 64.86           S
  ATOM  66025  SG  CYSOE  35      71.122  51.796 184.250  1.00 58.33           S
  ATOM  34750  SG  CYSHG  35      41.976  49.606 129.205  1.00 63.45           S
  ATOM  94798  SG  CYSUH  35      39.372  52.473 126.595  1.00 64.58           S
  ATOM  35167  SG  CYSHH  35      52.489  39.231 113.577  1.00 64.36           S
  ATOM  94381  SG  CYSUG  35      49.706  42.040 110.914  1.00 62.60           S
  ATOM  35584  SG  CYSHI  35      70.170  28.231 107.653  1.00 72.50           S
  ATOM  46426  SG  CYSKB  35      71.060  28.590 103.032  1.00 66.25           S
  ATOM  36001  SG  CYSHJ  35      89.191  20.295 113.532  1.00 79.18           S
  ATOM  46009  SG  CYSKA  35      89.847  20.347 108.667  1.00 77.51           S
  ATOM  36835  SG  CYSIA  35     131.368  20.329  89.844  1.00 74.02           S
  ATOM  49762  SG  CYSKJ  35     126.784  20.264  89.169  1.00 74.53           S
  ATOM  37252  SG  CYSIB  35     137.126  28.627  70.898  1.00 65.93           S
  ATOM  49345  SG  CYSKI  35     132.462  28.396  70.213  1.00 72.78           S
  ATOM  38503  SG  CYSIE  35     188.336  55.943  71.185  1.00 63.51           S
  ATOM  56434  SG  CYSMD  35     190.216  59.624  69.241  1.00 67.39           S
  ATOM  38920  SG  CYSIF  35     198.529  55.714  90.096  1.00 59.26           S
  ATOM  56017  SG  CYSMC  35     200.375  59.657  88.171  1.00 65.95           S
  ATOM  39337  SG  CYSIG  35     198.062  49.802 110.801  1.00 63.77           S
  ATOM  81037  SG  CYSRH  35     200.804  52.519 113.451  1.00 65.71           S
  ATOM  39754  SG  CYSIH  35     187.525  39.395 126.566  1.00 64.83           S
  ATOM  80620  SG  CYSRG  35     190.397  42.042 129.187  1.00 64.84           S
  ATOM  40171  SG  CYSII  35     169.973  28.402 132.480  1.00 74.11           S
  ATOM  83122  SG  CYSSB  35     169.161  28.660 137.110  1.00 67.14           S
  ATOM  40588  SG  CYSIJ  35     150.985  20.486 126.719  1.00 79.22           S
  ATOM  82705  SG  CYSSA  35     150.376  20.217 131.448  1.00 79.21           S
  ATOM  41422  SG  CYSJA  35     131.481 150.392  20.198  1.00 77.01           S
  ATOM  A0063  SG  CYSVJ  35     126.768 150.950  20.197  1.00 81.09           S
  ATOM  41839  SG  CYSJB  35     137.172 169.227  28.675  1.00 65.06           S
  ATOM  99802  SG  CYSVI  35     132.442 169.914  28.475  1.00 75.30           S
  ATOM  43924  SG  CYSJG  35     198.112 129.235  49.841  1.00 74.50           S
  ATOM  58102  SG  CYSMH  35     200.721 126.606  52.632  1.00 73.90           S
  ATOM  44341  SG  CYSJH  35     187.626 113.520  39.465  1.00 74.47           S
  ATOM  57685  SG  CYSMG  35     190.519 110.933  42.067  1.00 73.23           S
  ATOM  46843  SG  CYSKC  35      59.627  39.746  88.162  1.00 65.75           S
  ATOM  93964  SG  CYSUF  35      55.797  41.658  90.046  1.00 58.34           S
  ATOM  47260  SG  CYSKD  35      59.589  49.805  69.139  1.00 66.55           S
  ATOM  93547  SG  CYSUE  35      55.962  51.784  71.054  1.00 62.83           S
  ATOM  47677  SG  CYSKE  35      71.126  55.861  51.769  1.00 61.33           S
  ATOM  88543  SG  CYSTD  35      69.153  59.685  49.731  1.00 59.07           S
  ATOM  48094  SG  CYSKF  35      90.043  55.853  41.713  1.00 63.99           S
  ATOM  88126  SG  CYSTC  35      88.258  59.646  39.681  1.00 63.56           S
  ATOM  52264  SG  CYSLE  35     184.217 168.934 188.265  1.00 62.16           S
  ATOM  A01S0  SG  CYSWD  35     180.411 170.892 190.258  1.00 60.37           S
  ATOM  52681  SG  CYSLF  35     184.345 150.030 198.419  1.00 63.63           S
  ATOM  A01GF  SG  CYSWC  35     180.661 152.002 200.490  1.00 64.17           S
  ATOM  53098  SG  CYSLG  35     190.488 129.196 198.065  1.00 73.39           S
  ATOM  A06LR  SG  CYSXH  35     187.594 126.635 200.724  1.00 74.79           S
  ATOM  53515  SG  CYSLH  35     200.636 113.518 187.469  1.00 76.99           S
  ATOM  A06A6  SG  CYSXG  35     198.026 110.823 190.236  1.00 77.37           S
  ATOM  53932  SG  CYSLI  35     211.726 107.679 169.909  1.00 73.51           S
  ATOM  78535  SG  CYSRB  35     211.564 103.144 169.084  1.00 68.20           S
  ATOM  54349  SG  CYSLJ  35     220.046 113.367 150.924  1.00 73.08           S
  ATOM  78118  SG  CYSRA  35     219.768 108.720 150.172  1.00 74.11           S
  ATOM  55183  SG  CYSMA  35     219.784  89.797 108.621  1.00 78.14           S
  ATOM  81871  SG  CYSRJ  35     219.848  89.118 113.460  1.00 79.69           S
  ATOM  55600  SG  CYSMB  35     211.561  70.924 102.972  1.00 66.27           S
  ATOM  81454  SG  CYSRI  35     211.924  70.090 107.645  1.00 72.77           S
  ATOM  60604  SG  CYSNC  35      39.683 151.903 180.504  1.00 67.08           S
  ATOM  71029  SG  CYSPF  35      41.675 150.097 184.314  1.00 63.98           S
  ATOM  61021  SG  CYSND  35      49.884 170.864 180.447  1.00 65.60           S
  ATOM  70612  SG  CYSPE  35      51.826 169.140 184.155  1.00 60.72           S
  ATOM  61438  SG  CYSNE  35      56.004 188.352 169.005  1.00 63.53           S
  ATOM  74782  SG  CYSQD  35      59.616 190.380 170.975  1.00 69.23           S
  ATOM  61855  SG  CYSNF  35      55.832 198.437 150.023  1.00 58.90           S
  ATOM  74365  SG  CYSQC  35      59.645 200.392 152.002  1.00 67.05           S
  ATOM  64357  SG  CYSOA  35      89.841 108.694 219.946  1.00 78.43           S
  ATOM  72697  SG  CYSPJ  35      89.238 113.396 219.926  1.00 81.58           S
  ATOM  64774  SG  CYSOB  35      71.021 103.001 211.527  1.00 65.50           S
  ATOM  72280  SG  CYSPI  35      70.208 107.730 211.860  1.00 74.67           S
  ATOM  66859  SG  CYSOG  35     110.890  41.977 190.415  1.00 74.98           S
  ATOM  85624  SG  CYSSH  35     113.478  39.449 187.628  1.00 75.44           S
  ATOM  67276  SG  CYSOH  35     126.613  52.460 200.751  1.00 73.70           S
  ATOM  85207  SG  CYSSG  35     129.223  49.660 198.115  1.00 73.41           S
  ATOM  67693  SG  CYSOI  35     132.465  70.169 211.668  1.00 76.09           S
  ATOM  A04O9  SG  CYSXB  35     137.187  70.930 211.440  1.00 64.54           S
  ATOM  68110  SG  CYSOJ  35     126.804  89.141 219.830  1.00 81.33           S
  ATOM  A04CO  SG  CYSXA  35     131.480  89.779 219.865  1.00 77.41           S
  ATOM  68944  SG  CYSPA  35     108.716 150.225 219.854  1.00 79.34           S
  ATOM  A03PI  SG  CYSWJ  35     113.440 150.980 219.947  1.00 81.50           S
  ATOM  69361  SG  CYSPB  35     103.101 169.180 211.482  1.00 67.01           S
  ATOM  A03DX  SG  CYSWI  35     107.715 169.936 211.785  1.00 75.64           S
  ATOM  69778  SG  CYSPC  35      88.253 180.601 200.479  1.00 64.33           S
  ATOM  75616  SG  CYSQF  35      90.136 184.316 198.509  1.00 63.58           S
  ATOM  70195  SG  CYSPD  35      69.362 180.507 190.216  1.00 60.56           S
  ATOM  75199  SG  CYSQE  35      71.130 184.304 188.356  1.00 64.16           S
  ATOM  76033  SG  CYSQG  35     110.894 190.532 198.149  1.00 72.11           S
  ATOM  A032C  SG  CYSWH  35     113.510 187.605 200.753  1.00 75.32           S
  ATOM  76450  SG  CYSQH  35     126.644 200.628 187.604  1.00 76.54           S
  ATOM  A02QR  SG  CYSWG  35     129.274 198.160 190.449  1.00 76.20           S
  ATOM  78952  SG  CYSRC  35     200.438  88.281 180.434  1.00 65.86           S
  ATOM  A05YL  SG  CYSXF  35     198.340  90.061 184.159  1.00 64.82           S
  ATOM  79369  SG  CYSRD  35     190.302  69.231 180.400  1.00 66.23           S
  ATOM  A05N0  SG  CYSXE  35     188.482  71.016 184.281  1.00 59.22           S
  ATOM  79786  SG  CYSRE  35     184.220  51.725 168.974  1.00 62.15           S
  ATOM  83956  SG  CYSSD  35     180.536  49.792 170.889  1.00 66.91           S
  ATOM  80203  SG  CYSRF  35     184.342  41.601 150.066  1.00 59.22           S
  ATOM  83539  SG  CYSSC  35     180.480  39.726 151.926  1.00 67.92           S
  ATOM  84373  SG  CYSSE  35     168.949  55.956 188.170  1.00 61.58           S
  ATOM  A05BF  SG  CYSXD  35     171.004  59.689 190.301  1.00 59.75           S
  ATOM  84790  SG  CYSSF  35     150.121  55.814 198.476  1.00 63.39           S
  ATOM  A04ZU  SG  CYSXC  35     151.926  59.715 200.333  1.00 63.63           S
  ATOM  88960  SG  CYSTE  35      51.782  71.014  55.766  1.00 59.12           S
  ATOM  93130  SG  CYSUD  35      49.789  69.177  59.617  1.00 64.38           S
  ATOM  89377  SG  CYSTF  35      41.589  90.022  55.721  1.00 62.71           S
  ATOM  92713  SG  CYSUC  35      39.658  88.170  59.586  1.00 67.09           S
  ATOM  90628  SG  CYSTI  35      70.302 132.494  28.386  1.00 75.06           S
  ATOM  96883  SG  CYSVB  35      70.944 137.073  28.644  1.00 65.96           S
  ATOM  91045  SG  CYSTJ  35      89.222 126.786  20.178  1.00 82.08           S
  ATOM  96466  SG  CYSVA  35      89.801 131.444  20.108  1.00 77.02           S
  ATOM  A00T9  SG  CYSWA  35     150.406 131.529 219.956  1.00 79.56           S
  ATOM  A078X  SG  CYSXJ  35     150.944 126.780 219.768  1.00 80.78           S
  ATOM  A014U  SG  CYSWB  35     169.116 137.054 211.334  1.00 65.71           S
  ATOM  A06XC  SG  CYSXI  35     169.877 132.495 211.580  1.00 76.57           S

  Time building chain proxies: 40.65, per 1000 atoms: 0.37
  Number of scatterers: 110208
  At special positions: 0
  Unit cell: (241.86, 241.86, 241.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Au    120     78.96
     S     264     16.00
     O   22176      8.00
     N   18216      7.00
     C   69432      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: 28.77
  Conformation dependent library (CDL) restraints added in 11.6 seconds
  

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  26400

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 264 sheets defined
      0.0% alpha, 45.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 7.73
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'AA' and resid 66 through 70
    Processing sheet with id=AA2, first strand: chain 'AA' and resid 34 through 36
    Processing sheet with id=AA3, first strand: chain 'AB' and resid 66 through 70
    Processing sheet with id=AA4, first strand: chain 'AC' and resid 66 through 70
    Processing sheet with id=AA5, first strand: chain 'AD' and resid 66 through 70
    Processing sheet with id=AA6, first strand: chain 'AE' and resid 66 through 70
    Processing sheet with id=AA7, first strand: chain 'AF' and resid 66 through 70
    Processing sheet with id=AA8, first strand: chain 'AG' and resid 66 through 70
    Processing sheet with id=AA9, first strand: chain 'AH' and resid 66 through 70
    Processing sheet with id=AB1, first strand: chain 'AI' and resid 66 through 70
    Processing sheet with id=AB2, first strand: chain 'AJ' and resid 66 through 70
    Processing sheet with id=AB3, first strand: chain 'BA' and resid 66 through 70
    Processing sheet with id=AB4, first strand: chain 'BA' and resid 34 through 36
    Processing sheet with id=AB5, first strand: chain 'BB' and resid 66 through 70
    Processing sheet with id=AB6, first strand: chain 'BC' and resid 66 through 70
    Processing sheet with id=AB7, first strand: chain 'BD' and resid 66 through 70
    Processing sheet with id=AB8, first strand: chain 'BE' and resid 66 through 70
    Processing sheet with id=AB9, first strand: chain 'BF' and resid 66 through 70
    Processing sheet with id=AC1, first strand: chain 'BG' and resid 66 through 70
    Processing sheet with id=AC2, first strand: chain 'BH' and resid 66 through 70
    Processing sheet with id=AC3, first strand: chain 'BI' and resid 66 through 70
    Processing sheet with id=AC4, first strand: chain 'BJ' and resid 66 through 70
    Processing sheet with id=AC5, first strand: chain 'CA' and resid 66 through 70
    Processing sheet with id=AC6, first strand: chain 'CA' and resid 34 through 36
    Processing sheet with id=AC7, first strand: chain 'CB' and resid 66 through 70
    Processing sheet with id=AC8, first strand: chain 'CC' and resid 66 through 70
    Processing sheet with id=AC9, first strand: chain 'CD' and resid 66 through 70
    Processing sheet with id=AD1, first strand: chain 'CE' and resid 66 through 70
    Processing sheet with id=AD2, first strand: chain 'CF' and resid 66 through 70
    Processing sheet with id=AD3, first strand: chain 'CG' and resid 66 through 70
    Processing sheet with id=AD4, first strand: chain 'CH' and resid 66 through 70
    Processing sheet with id=AD5, first strand: chain 'CI' and resid 66 through 70
    Processing sheet with id=AD6, first strand: chain 'CJ' and resid 66 through 70
    Processing sheet with id=AD7, first strand: chain 'DA' and resid 66 through 70
    Processing sheet with id=AD8, first strand: chain 'DA' and resid 34 through 36
    Processing sheet with id=AD9, first strand: chain 'DB' and resid 66 through 70
    Processing sheet with id=AE1, first strand: chain 'DC' and resid 66 through 70
    Processing sheet with id=AE2, first strand: chain 'DD' and resid 66 through 70
    Processing sheet with id=AE3, first strand: chain 'DE' and resid 66 through 70
    Processing sheet with id=AE4, first strand: chain 'DF' and resid 66 through 70
    Processing sheet with id=AE5, first strand: chain 'DG' and resid 66 through 70
    Processing sheet with id=AE6, first strand: chain 'DH' and resid 66 through 70
    Processing sheet with id=AE7, first strand: chain 'DI' and resid 66 through 70
    Processing sheet with id=AE8, first strand: chain 'DJ' and resid 66 through 70
    Processing sheet with id=AE9, first strand: chain 'EA' and resid 66 through 70
    Processing sheet with id=AF1, first strand: chain 'EA' and resid 34 through 36
    Processing sheet with id=AF2, first strand: chain 'EB' and resid 66 through 70
    Processing sheet with id=AF3, first strand: chain 'EC' and resid 66 through 70
    Processing sheet with id=AF4, first strand: chain 'ED' and resid 66 through 70
    Processing sheet with id=AF5, first strand: chain 'EE' and resid 66 through 70
    Processing sheet with id=AF6, first strand: chain 'EF' and resid 66 through 70
    Processing sheet with id=AF7, first strand: chain 'EG' and resid 66 through 70
    Processing sheet with id=AF8, first strand: chain 'EH' and resid 66 through 70
    Processing sheet with id=AF9, first strand: chain 'EI' and resid 66 through 70
    Processing sheet with id=AG1, first strand: chain 'EJ' and resid 66 through 70
    Processing sheet with id=AG2, first strand: chain 'FA' and resid 66 through 70
    Processing sheet with id=AG3, first strand: chain 'FA' and resid 34 through 36
    Processing sheet with id=AG4, first strand: chain 'FB' and resid 66 through 70
    Processing sheet with id=AG5, first strand: chain 'FC' and resid 66 through 70
    Processing sheet with id=AG6, first strand: chain 'FD' and resid 66 through 70
    Processing sheet with id=AG7, first strand: chain 'FE' and resid 66 through 70
    Processing sheet with id=AG8, first strand: chain 'FF' and resid 66 through 70
    Processing sheet with id=AG9, first strand: chain 'FG' and resid 66 through 70
    Processing sheet with id=AH1, first strand: chain 'FH' and resid 66 through 70
    Processing sheet with id=AH2, first strand: chain 'FI' and resid 66 through 70
    Processing sheet with id=AH3, first strand: chain 'FJ' and resid 66 through 70
    Processing sheet with id=AH4, first strand: chain 'GA' and resid 66 through 70
    Processing sheet with id=AH5, first strand: chain 'GA' and resid 34 through 36
    Processing sheet with id=AH6, first strand: chain 'GB' and resid 66 through 70
    Processing sheet with id=AH7, first strand: chain 'GC' and resid 66 through 70
    Processing sheet with id=AH8, first strand: chain 'GD' and resid 66 through 70
    Processing sheet with id=AH9, first strand: chain 'GE' and resid 66 through 70
    Processing sheet with id=AI1, first strand: chain 'GF' and resid 66 through 70
    Processing sheet with id=AI2, first strand: chain 'GG' and resid 66 through 70
    Processing sheet with id=AI3, first strand: chain 'GH' and resid 66 through 70
    Processing sheet with id=AI4, first strand: chain 'GI' and resid 66 through 70
    Processing sheet with id=AI5, first strand: chain 'GJ' and resid 66 through 70
    Processing sheet with id=AI6, first strand: chain 'HA' and resid 66 through 70
    Processing sheet with id=AI7, first strand: chain 'HA' and resid 34 through 36
    Processing sheet with id=AI8, first strand: chain 'HB' and resid 66 through 70
    Processing sheet with id=AI9, first strand: chain 'HC' and resid 66 through 70
    Processing sheet with id=AJ1, first strand: chain 'HD' and resid 66 through 70
    Processing sheet with id=AJ2, first strand: chain 'HE' and resid 66 through 70
    Processing sheet with id=AJ3, first strand: chain 'HF' and resid 66 through 70
    Processing sheet with id=AJ4, first strand: chain 'HG' and resid 66 through 70
    Processing sheet with id=AJ5, first strand: chain 'HH' and resid 66 through 70
    Processing sheet with id=AJ6, first strand: chain 'HI' and resid 66 through 70
    Processing sheet with id=AJ7, first strand: chain 'HJ' and resid 66 through 70
    Processing sheet with id=AJ8, first strand: chain 'IA' and resid 66 through 70
    Processing sheet with id=AJ9, first strand: chain 'IA' and resid 34 through 36
    Processing sheet with id=AK1, first strand: chain 'IB' and resid 66 through 70
    Processing sheet with id=AK2, first strand: chain 'IC' and resid 66 through 70
    Processing sheet with id=AK3, first strand: chain 'ID' and resid 66 through 70
    Processing sheet with id=AK4, first strand: chain 'IE' and resid 66 through 70
    Processing sheet with id=AK5, first strand: chain 'IF' and resid 66 through 70
    Processing sheet with id=AK6, first strand: chain 'IG' and resid 66 through 70
    Processing sheet with id=AK7, first strand: chain 'IH' and resid 66 through 70
    Processing sheet with id=AK8, first strand: chain 'II' and resid 66 through 70
    Processing sheet with id=AK9, first strand: chain 'IJ' and resid 66 through 70
    Processing sheet with id=AL1, first strand: chain 'JA' and resid 66 through 70
    Processing sheet with id=AL2, first strand: chain 'JA' and resid 34 through 36
    Processing sheet with id=AL3, first strand: chain 'JB' and resid 66 through 70
    Processing sheet with id=AL4, first strand: chain 'JC' and resid 66 through 70
    Processing sheet with id=AL5, first strand: chain 'JD' and resid 66 through 70
    Processing sheet with id=AL6, first strand: chain 'JE' and resid 66 through 70
    Processing sheet with id=AL7, first strand: chain 'JF' and resid 66 through 70
    Processing sheet with id=AL8, first strand: chain 'JG' and resid 66 through 70
    Processing sheet with id=AL9, first strand: chain 'JH' and resid 66 through 70
    Processing sheet with id=AM1, first strand: chain 'JI' and resid 66 through 70
    Processing sheet with id=AM2, first strand: chain 'JJ' and resid 66 through 70
    Processing sheet with id=AM3, first strand: chain 'KA' and resid 66 through 70
    Processing sheet with id=AM4, first strand: chain 'KA' and resid 34 through 36
    Processing sheet with id=AM5, first strand: chain 'KB' and resid 66 through 70
    Processing sheet with id=AM6, first strand: chain 'KC' and resid 66 through 70
    Processing sheet with id=AM7, first strand: chain 'KD' and resid 66 through 70
    Processing sheet with id=AM8, first strand: chain 'KE' and resid 66 through 70
    Processing sheet with id=AM9, first strand: chain 'KF' and resid 66 through 70
    Processing sheet with id=AN1, first strand: chain 'KG' and resid 66 through 70
    Processing sheet with id=AN2, first strand: chain 'KH' and resid 66 through 70
    Processing sheet with id=AN3, first strand: chain 'KI' and resid 66 through 70
    Processing sheet with id=AN4, first strand: chain 'KJ' and resid 66 through 70
    Processing sheet with id=AN5, first strand: chain 'LA' and resid 66 through 70
    Processing sheet with id=AN6, first strand: chain 'LA' and resid 34 through 36
    Processing sheet with id=AN7, first strand: chain 'LB' and resid 66 through 70
    Processing sheet with id=AN8, first strand: chain 'LC' and resid 66 through 70
    Processing sheet with id=AN9, first strand: chain 'LD' and resid 66 through 70
    Processing sheet with id=AO1, first strand: chain 'LE' and resid 66 through 70
    Processing sheet with id=AO2, first strand: chain 'LF' and resid 66 through 70
    Processing sheet with id=AO3, first strand: chain 'LG' and resid 66 through 70
    Processing sheet with id=AO4, first strand: chain 'LH' and resid 66 through 70
    Processing sheet with id=AO5, first strand: chain 'LI' and resid 66 through 70
    Processing sheet with id=AO6, first strand: chain 'LJ' and resid 66 through 70
    Processing sheet with id=AO7, first strand: chain 'MA' and resid 66 through 70
    Processing sheet with id=AO8, first strand: chain 'MA' and resid 34 through 36
    Processing sheet with id=AO9, first strand: chain 'MB' and resid 66 through 70
    Processing sheet with id=AP1, first strand: chain 'MC' and resid 66 through 70
    Processing sheet with id=AP2, first strand: chain 'MD' and resid 66 through 70
    Processing sheet with id=AP3, first strand: chain 'ME' and resid 66 through 70
    Processing sheet with id=AP4, first strand: chain 'MF' and resid 66 through 70
    Processing sheet with id=AP5, first strand: chain 'MG' and resid 66 through 70
    Processing sheet with id=AP6, first strand: chain 'MH' and resid 66 through 70
    Processing sheet with id=AP7, first strand: chain 'MI' and resid 66 through 70
    Processing sheet with id=AP8, first strand: chain 'MJ' and resid 66 through 70
    Processing sheet with id=AP9, first strand: chain 'NA' and resid 66 through 70
    Processing sheet with id=AQ1, first strand: chain 'NA' and resid 34 through 36
    Processing sheet with id=AQ2, first strand: chain 'NB' and resid 66 through 70
    Processing sheet with id=AQ3, first strand: chain 'NC' and resid 66 through 70
    Processing sheet with id=AQ4, first strand: chain 'ND' and resid 66 through 70
    Processing sheet with id=AQ5, first strand: chain 'NE' and resid 66 through 70
    Processing sheet with id=AQ6, first strand: chain 'NF' and resid 66 through 70
    Processing sheet with id=AQ7, first strand: chain 'NG' and resid 66 through 70
    Processing sheet with id=AQ8, first strand: chain 'NH' and resid 66 through 70
    Processing sheet with id=AQ9, first strand: chain 'NI' and resid 66 through 70
    Processing sheet with id=AR1, first strand: chain 'NJ' and resid 66 through 70
    Processing sheet with id=AR2, first strand: chain 'OA' and resid 66 through 70
    Processing sheet with id=AR3, first strand: chain 'OA' and resid 34 through 36
    Processing sheet with id=AR4, first strand: chain 'OB' and resid 66 through 70
    Processing sheet with id=AR5, first strand: chain 'OC' and resid 66 through 70
    Processing sheet with id=AR6, first strand: chain 'OD' and resid 66 through 70
    Processing sheet with id=AR7, first strand: chain 'OE' and resid 66 through 70
    Processing sheet with id=AR8, first strand: chain 'OF' and resid 66 through 70
    Processing sheet with id=AR9, first strand: chain 'OG' and resid 66 through 70
    Processing sheet with id=AS1, first strand: chain 'OH' and resid 66 through 70
    Processing sheet with id=AS2, first strand: chain 'OI' and resid 66 through 70
    Processing sheet with id=AS3, first strand: chain 'OJ' and resid 66 through 70
    Processing sheet with id=AS4, first strand: chain 'PA' and resid 66 through 70
    Processing sheet with id=AS5, first strand: chain 'PA' and resid 34 through 36
    Processing sheet with id=AS6, first strand: chain 'PB' and resid 66 through 70
    Processing sheet with id=AS7, first strand: chain 'PC' and resid 66 through 70
    Processing sheet with id=AS8, first strand: chain 'PD' and resid 66 through 70
    Processing sheet with id=AS9, first strand: chain 'PE' and resid 66 through 70
    Processing sheet with id=AT1, first strand: chain 'PF' and resid 66 through 70
    Processing sheet with id=AT2, first strand: chain 'PG' and resid 66 through 70
    Processing sheet with id=AT3, first strand: chain 'PH' and resid 66 through 70
    Processing sheet with id=AT4, first strand: chain 'PI' and resid 66 through 70
    Processing sheet with id=AT5, first strand: chain 'PJ' and resid 66 through 70
    Processing sheet with id=AT6, first strand: chain 'QA' and resid 66 through 70
    Processing sheet with id=AT7, first strand: chain 'QA' and resid 34 through 36
    Processing sheet with id=AT8, first strand: chain 'QB' and resid 66 through 70
    Processing sheet with id=AT9, first strand: chain 'QC' and resid 66 through 70
    Processing sheet with id=AU1, first strand: chain 'QD' and resid 66 through 70
    Processing sheet with id=AU2, first strand: chain 'QE' and resid 66 through 70
    Processing sheet with id=AU3, first strand: chain 'QF' and resid 66 through 70
    Processing sheet with id=AU4, first strand: chain 'QG' and resid 66 through 70
    Processing sheet with id=AU5, first strand: chain 'QH' and resid 66 through 70
    Processing sheet with id=AU6, first strand: chain 'QI' and resid 66 through 70
    Processing sheet with id=AU7, first strand: chain 'QJ' and resid 66 through 70
    Processing sheet with id=AU8, first strand: chain 'RA' and resid 66 through 70
    Processing sheet with id=AU9, first strand: chain 'RA' and resid 34 through 36
    Processing sheet with id=AV1, first strand: chain 'RB' and resid 66 through 70
    Processing sheet with id=AV2, first strand: chain 'RC' and resid 66 through 70
    Processing sheet with id=AV3, first strand: chain 'RD' and resid 66 through 70
    Processing sheet with id=AV4, first strand: chain 'RE' and resid 66 through 70
    Processing sheet with id=AV5, first strand: chain 'RF' and resid 66 through 70
    Processing sheet with id=AV6, first strand: chain 'RG' and resid 66 through 70
    Processing sheet with id=AV7, first strand: chain 'RH' and resid 66 through 70
    Processing sheet with id=AV8, first strand: chain 'RI' and resid 66 through 70
    Processing sheet with id=AV9, first strand: chain 'RJ' and resid 66 through 70
    Processing sheet with id=AW1, first strand: chain 'SA' and resid 66 through 70
    Processing sheet with id=AW2, first strand: chain 'SA' and resid 34 through 36
    Processing sheet with id=AW3, first strand: chain 'SB' and resid 66 through 70
    Processing sheet with id=AW4, first strand: chain 'SC' and resid 66 through 70
    Processing sheet with id=AW5, first strand: chain 'SD' and resid 66 through 70
    Processing sheet with id=AW6, first strand: chain 'SE' and resid 66 through 70
    Processing sheet with id=AW7, first strand: chain 'SF' and resid 66 through 70
    Processing sheet with id=AW8, first strand: chain 'SG' and resid 66 through 70
    Processing sheet with id=AW9, first strand: chain 'SH' and resid 66 through 70
    Processing sheet with id=AX1, first strand: chain 'SI' and resid 66 through 70
    Processing sheet with id=AX2, first strand: chain 'SJ' and resid 66 through 70
    Processing sheet with id=AX3, first strand: chain 'TA' and resid 66 through 70
    Processing sheet with id=AX4, first strand: chain 'TA' and resid 34 through 36
    Processing sheet with id=AX5, first strand: chain 'TB' and resid 66 through 70
    Processing sheet with id=AX6, first strand: chain 'TC' and resid 66 through 70
    Processing sheet with id=AX7, first strand: chain 'TD' and resid 66 through 70
    Processing sheet with id=AX8, first strand: chain 'TE' and resid 66 through 70
    Processing sheet with id=AX9, first strand: chain 'TF' and resid 66 through 70
    Processing sheet with id=AY1, first strand: chain 'TG' and resid 66 through 70
    Processing sheet with id=AY2, first strand: chain 'TH' and resid 66 through 70
    Processing sheet with id=AY3, first strand: chain 'TI' and resid 66 through 70
    Processing sheet with id=AY4, first strand: chain 'TJ' and resid 66 through 70
    Processing sheet with id=AY5, first strand: chain 'UA' and resid 66 through 70
    Processing sheet with id=AY6, first strand: chain 'UA' and resid 34 through 36
    Processing sheet with id=AY7, first strand: chain 'UB' and resid 66 through 70
    Processing sheet with id=AY8, first strand: chain 'UC' and resid 66 through 70
    Processing sheet with id=AY9, first strand: chain 'UD' and resid 66 through 70
    Processing sheet with id=AZ1, first strand: chain 'UE' and resid 66 through 70
    Processing sheet with id=AZ2, first strand: chain 'UF' and resid 66 through 70
    Processing sheet with id=AZ3, first strand: chain 'UG' and resid 66 through 70
    Processing sheet with id=AZ4, first strand: chain 'UH' and resid 66 through 70
    Processing sheet with id=AZ5, first strand: chain 'UI' and resid 66 through 70
    Processing sheet with id=AZ6, first strand: chain 'UJ' and resid 66 through 70
    Processing sheet with id=AZ7, first strand: chain 'VA' and resid 66 through 70
    Processing sheet with id=AZ8, first strand: chain 'VA' and resid 34 through 36
    Processing sheet with id=AZ9, first strand: chain 'VB' and resid 66 through 70
    Processing sheet with id=BA1, first strand: chain 'VC' and resid 66 through 70
    Processing sheet with id=BA2, first strand: chain 'VD' and resid 66 through 70
    Processing sheet with id=BA3, first strand: chain 'VE' and resid 66 through 70
    Processing sheet with id=BA4, first strand: chain 'VF' and resid 66 through 70
    Processing sheet with id=BA5, first strand: chain 'VG' and resid 66 through 70
    Processing sheet with id=BA6, first strand: chain 'VH' and resid 66 through 70
    Processing sheet with id=BA7, first strand: chain 'VI' and resid 66 through 70
    Processing sheet with id=BA8, first strand: chain 'VJ' and resid 66 through 70
    Processing sheet with id=BA9, first strand: chain 'WA' and resid 66 through 70
    Processing sheet with id=BB1, first strand: chain 'WA' and resid 34 through 36
    Processing sheet with id=BB2, first strand: chain 'WB' and resid 66 through 70
    Processing sheet with id=BB3, first strand: chain 'WC' and resid 66 through 70
    Processing sheet with id=BB4, first strand: chain 'WD' and resid 66 through 70
    Processing sheet with id=BB5, first strand: chain 'WE' and resid 66 through 70
    Processing sheet with id=BB6, first strand: chain 'WF' and resid 66 through 70
    Processing sheet with id=BB7, first strand: chain 'WG' and resid 66 through 70
    Processing sheet with id=BB8, first strand: chain 'WH' and resid 66 through 70
    Processing sheet with id=BB9, first strand: chain 'WI' and resid 66 through 70
    Processing sheet with id=BC1, first strand: chain 'WJ' and resid 66 through 70
    Processing sheet with id=BC2, first strand: chain 'XA' and resid 66 through 70
    Processing sheet with id=BC3, first strand: chain 'XA' and resid 34 through 36
    Processing sheet with id=BC4, first strand: chain 'XB' and resid 66 through 70
    Processing sheet with id=BC5, first strand: chain 'XC' and resid 66 through 70
    Processing sheet with id=BC6, first strand: chain 'XD' and resid 66 through 70
    Processing sheet with id=BC7, first strand: chain 'XE' and resid 66 through 70
    Processing sheet with id=BC8, first strand: chain 'XF' and resid 66 through 70
    Processing sheet with id=BC9, first strand: chain 'XG' and resid 66 through 70
    Processing sheet with id=BD1, first strand: chain 'XH' and resid 66 through 70
    Processing sheet with id=BD2, first strand: chain 'XI' and resid 66 through 70
    Processing sheet with id=BD3, first strand: chain 'XJ' and resid 66 through 70

    6336 hydrogen bonds defined for protein.
    15048 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: 83.80

  Time building geometry restraints manager: 31.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 36696
        1.34 -     1.46: 22432
        1.46 -     1.57: 51488
        1.57 -     1.69: 0
        1.69 -     1.80: 264
  Bond restraints: 110880
  Sorted by residual:
  bond pdb=" CB  ILEOG  43 "
       pdb=" CG2 ILEOG  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.09e+00
  bond pdb=" CB  ILEQE  43 "
       pdb=" CG2 ILEQE  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.09e+00
  bond pdb=" CB  ILEAG  43 "
       pdb=" CG2 ILEAG  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.08e+00
  bond pdb=" CB  ILEUA  43 "
       pdb=" CG2 ILEUA  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.08e+00
  bond pdb=" CB  ILEIJ  43 "
       pdb=" CG2 ILEIJ  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.07e+00
  ... (remaining 110875 not shown)

  Histogram of bond angle deviations from ideal:
      106.06 -   111.12: 51774
      111.12 -   116.18: 27189
      116.18 -   121.24: 37003
      121.24 -   126.30: 32402
      126.30 -   131.36: 528
  Bond angle restraints: 148896
  Sorted by residual:
  angle pdb=" NE  ARGOA  56 "
        pdb=" CZ  ARGOA  56 "
        pdb=" NH1 ARGOA  56 "
      ideal   model   delta    sigma   weight residual
     121.50  119.70    1.80 1.00e+00 1.00e+00 3.25e+00
  angle pdb=" NE  ARGPD  56 "
        pdb=" CZ  ARGPD  56 "
        pdb=" NH1 ARGPD  56 "
      ideal   model   delta    sigma   weight residual
     121.50  119.71    1.79 1.00e+00 1.00e+00 3.21e+00
  angle pdb=" N   HISVF  49 "
        pdb=" CA  HISVF  49 "
        pdb=" C   HISVF  49 "
      ideal   model   delta    sigma   weight residual
     111.14  113.07   -1.93 1.08e+00 8.57e-01 3.21e+00
  angle pdb=" NE  ARGOK  56 "
        pdb=" CZ  ARGOK  56 "
        pdb=" NH1 ARGOK  56 "
      ideal   model   delta    sigma   weight residual
     121.50  119.72    1.78 1.00e+00 1.00e+00 3.19e+00
  angle pdb=" N   HISRF  49 "
        pdb=" CA  HISRF  49 "
        pdb=" C   HISRF  49 "
      ideal   model   delta    sigma   weight residual
     111.14  113.06   -1.92 1.08e+00 8.57e-01 3.17e+00
  ... (remaining 148891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.80: 50054
        8.80 -    17.60: 9346
       17.60 -    26.40: 3730
       26.40 -    35.20: 2078
       35.20 -    44.00: 792
  Dihedral angle restraints: 66000
    sinusoidal: 25344
      harmonic: 40656
  Sorted by residual:
  dihedral pdb=" CA  ILEMG  43 "
           pdb=" CB  ILEMG  43 "
           pdb=" CG1 ILEMG  43 "
           pdb=" CD1 ILEMG  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.14  -43.14     3      1.50e+01 4.44e-03 7.75e+00
  dihedral pdb=" CA  ILEIE  43 "
           pdb=" CB  ILEIE  43 "
           pdb=" CG1 ILEIE  43 "
           pdb=" CD1 ILEIE  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.12  -43.12     3      1.50e+01 4.44e-03 7.75e+00
  dihedral pdb=" CA  ILEKD  43 "
           pdb=" CB  ILEKD  43 "
           pdb=" CG1 ILEKD  43 "
           pdb=" CD1 ILEKD  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.12  -43.12     3      1.50e+01 4.44e-03 7.75e+00
  ... (remaining 65997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 10020
       0.025 -    0.051: 3671
       0.051 -    0.076: 1537
       0.076 -    0.101: 1532
       0.101 -    0.127: 1456
  Chirality restraints: 18216
  Sorted by residual:
  chirality pdb=" CA  ILEXK  68 "
            pdb=" N   ILEXK  68 "
            pdb=" C   ILEXK  68 "
            pdb=" CB  ILEXK  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  ILEEH  68 "
            pdb=" N   ILEEH  68 "
            pdb=" C   ILEEH  68 "
            pdb=" CB  ILEEH  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  ILEWK  68 "
            pdb=" N   ILEWK  68 "
            pdb=" C   ILEWK  68 "
            pdb=" CB  ILEWK  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  ... (remaining 18213 not shown)

  Planarity restraints: 18744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHESB   7 "    0.005 2.00e-02 2.50e+03   5.36e-03 5.04e-01
        pdb=" CG  PHESB   7 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHESB   7 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHESB   7 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHESB   7 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHESB   7 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHESB   7 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHEXH   7 "    0.006 2.00e-02 2.50e+03   5.29e-03 4.89e-01
        pdb=" CG  PHEXH   7 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHEXH   7 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHEXH   7 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHEXH   7 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHEXH   7 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHEXH   7 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHEWK   7 "   -0.005 2.00e-02 2.50e+03   5.24e-03 4.81e-01
        pdb=" CG  PHEWK   7 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHEWK   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHEWK   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHEWK   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHEWK   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHEWK   7 "    0.000 2.00e-02 2.50e+03
  ... (remaining 18741 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 19687
        2.78 -     3.31: 79662
        3.31 -     3.84: 170366
        3.84 -     4.37: 196382
        4.37 -     4.90: 361500
  Nonbonded interactions: 827597
  Sorted by model distance:
  nonbonded pdb=" SG  CYSHE  35 "
            pdb="AU    AUFD 101 "
     model   vdw
     2.245 2.980
  nonbonded pdb=" SG  CYSFD  35 "
            pdb="AU    AUFD 101 "
     model   vdw
     2.254 2.980
  nonbonded pdb=" SG  CYSED  35 "
            pdb="AU    AUBE 101 "
     model   vdw
     2.260 2.980
  nonbonded pdb=" SG  CYSPE  35 "
            pdb="AU    AUND 101 "
     model   vdw
     2.263 2.980
  nonbonded pdb=" SG  CYSBE  35 "
            pdb="AU    AUBE 101 "
     model   vdw
     2.264 2.980
  ... (remaining 827592 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 'AA' and resid 6 through 71)
  selection = (chain 'AB' and resid 6 through 71)
  selection = (chain 'AC' and resid 6 through 71)
  selection = (chain 'AD' and resid 6 through 71)
  selection = (chain 'AE' and resid 6 through 71)
  selection = (chain 'AF' and resid 6 through 71)
  selection = (chain 'AG' and resid 6 through 71)
  selection = (chain 'AH' and resid 6 through 71)
  selection = (chain 'AI' and resid 6 through 71)
  selection = (chain 'AJ' and resid 6 through 71)
  selection = chain 'AK'
  selection = (chain 'BA' and resid 6 through 71)
  selection = (chain 'BB' and resid 6 through 71)
  selection = (chain 'BC' and resid 6 through 71)
  selection = (chain 'BD' and resid 6 through 71)
  selection = (chain 'BE' and resid 6 through 71)
  selection = (chain 'BF' and resid 6 through 71)
  selection = (chain 'BG' and resid 6 through 71)
  selection = (chain 'BH' and resid 6 through 71)
  selection = (chain 'BI' and resid 6 through 71)
  selection = (chain 'BJ' and resid 6 through 71)
  selection = chain 'BK'
  selection = (chain 'CA' and resid 6 through 71)
  selection = (chain 'CB' and resid 6 through 71)
  selection = (chain 'CC' and resid 6 through 71)
  selection = (chain 'CD' and resid 6 through 71)
  selection = (chain 'CE' and resid 6 through 71)
  selection = (chain 'CF' and resid 6 through 71)
  selection = chain 'CG'
  selection = chain 'CH'
  selection = (chain 'CI' and resid 6 through 71)
  selection = (chain 'CJ' and resid 6 through 71)
  selection = chain 'CK'
  selection = (chain 'DA' and resid 6 through 71)
  selection = (chain 'DB' and resid 6 through 71)
  selection = (chain 'DC' and resid 6 through 71)
  selection = (chain 'DD' and resid 6 through 71)
  selection = (chain 'DE' and resid 6 through 71)
  selection = (chain 'DF' and resid 6 through 71)
  selection = (chain 'DG' and resid 6 through 71)
  selection = (chain 'DH' and resid 6 through 71)
  selection = (chain 'DI' and resid 6 through 71)
  selection = (chain 'DJ' and resid 6 through 71)
  selection = chain 'DK'
  selection = chain 'EA'
  selection = chain 'EB'
  selection = chain 'EC'
  selection = chain 'ED'
  selection = (chain 'EE' and resid 6 through 71)
  selection = (chain 'EF' and resid 6 through 71)
  selection = (chain 'EG' and resid 6 through 71)
  selection = (chain 'EH' and resid 6 through 71)
  selection = (chain 'EI' and resid 6 through 71)
  selection = (chain 'EJ' and resid 6 through 71)
  selection = chain 'EK'
  selection = (chain 'FA' and resid 6 through 71)
  selection = (chain 'FB' and resid 6 through 71)
  selection = (chain 'FC' and resid 6 through 71)
  selection = (chain 'FD' and resid 6 through 71)
  selection = (chain 'FE' and resid 6 through 71)
  selection = (chain 'FF' and resid 6 through 71)
  selection = (chain 'FG' and resid 6 through 71)
  selection = (chain 'FH' and resid 6 through 71)
  selection = (chain 'FI' and resid 6 through 71)
  selection = (chain 'FJ' and resid 6 through 71)
  selection = chain 'FK'
  selection = chain 'GA'
  selection = chain 'GB'
  selection = (chain 'GC' and resid 6 through 71)
  selection = (chain 'GD' and resid 6 through 71)
  selection = chain 'GE'
  selection = chain 'GF'
  selection = (chain 'GG' and resid 6 through 71)
  selection = (chain 'GH' and resid 6 through 71)
  selection = (chain 'GI' and resid 6 through 71)
  selection = (chain 'GJ' and resid 6 through 71)
  selection = chain 'GK'
  selection = (chain 'HA' and resid 6 through 71)
  selection = (chain 'HB' and resid 6 through 71)
  selection = (chain 'HC' and resid 6 through 71)
  selection = (chain 'HD' and resid 6 through 71)
  selection = chain 'HE'
  selection = chain 'HF'
  selection = (chain 'HG' and resid 6 through 71)
  selection = (chain 'HH' and resid 6 through 71)
  selection = (chain 'HI' and resid 6 through 71)
  selection = (chain 'HJ' and resid 6 through 71)
  selection = chain 'HK'
  selection = (chain 'IA' and resid 6 through 71)
  selection = (chain 'IB' and resid 6 through 71)
  selection = chain 'IC'
  selection = chain 'ID'
  selection = (chain 'IE' and resid 6 through 71)
  selection = (chain 'IF' and resid 6 through 71)
  selection = (chain 'IG' and resid 6 through 71)
  selection = (chain 'IH' and resid 6 through 71)
  selection = (chain 'II' and resid 6 through 71)
  selection = (chain 'IJ' and resid 6 through 71)
  selection = chain 'IK'
  selection = (chain 'JA' and resid 6 through 71)
  selection = (chain 'JB' and resid 6 through 71)
  selection = chain 'JC'
  selection = chain 'JD'
  selection = chain 'JE'
  selection = chain 'JF'
  selection = (chain 'JG' and resid 6 through 71)
  selection = (chain 'JH' and resid 6 through 71)
  selection = chain 'JI'
  selection = chain 'JJ'
  selection = chain 'JK'
  selection = chain 'KA'
  selection = chain 'KB'
  selection = (chain 'KC' and resid 6 through 71)
  selection = (chain 'KD' and resid 6 through 71)
  selection = (chain 'KE' and resid 6 through 71)
  selection = (chain 'KF' and resid 6 through 71)
  selection = chain 'KG'
  selection = chain 'KH'
  selection = chain 'KI'
  selection = chain 'KJ'
  selection = chain 'KK'
  selection = chain 'LA'
  selection = chain 'LB'
  selection = chain 'LC'
  selection = chain 'LD'
  selection = (chain 'LE' and resid 6 through 71)
  selection = (chain 'LF' and resid 6 through 71)
  selection = (chain 'LG' and resid 6 through 71)
  selection = (chain 'LH' and resid 6 through 71)
  selection = (chain 'LI' and resid 6 through 71)
  selection = (chain 'LJ' and resid 6 through 71)
  selection = chain 'LK'
  selection = (chain 'MA' and resid 6 through 71)
  selection = (chain 'MB' and resid 6 through 71)
  selection = chain 'MC'
  selection = chain 'MD'
  selection = chain 'ME'
  selection = chain 'MF'
  selection = chain 'MG'
  selection = chain 'MH'
  selection = chain 'MI'
  selection = chain 'MJ'
  selection = chain 'MK'
  selection = chain 'NA'
  selection = chain 'NB'
  selection = (chain 'NC' and resid 6 through 71)
  selection = (chain 'ND' and resid 6 through 71)
  selection = (chain 'NE' and resid 6 through 71)
  selection = (chain 'NF' and resid 6 through 71)
  selection = chain 'NG'
  selection = chain 'NH'
  selection = chain 'NI'
  selection = chain 'NJ'
  selection = chain 'NK'
  selection = (chain 'OA' and resid 6 through 71)
  selection = (chain 'OB' and resid 6 through 71)
  selection = chain 'OC'
  selection = chain 'OD'
  selection = chain 'OE'
  selection = chain 'OF'
  selection = (chain 'OG' and resid 6 through 71)
  selection = (chain 'OH' and resid 6 through 71)
  selection = (chain 'OI' and resid 6 through 71)
  selection = (chain 'OJ' and resid 6 through 71)
  selection = chain 'OK'
  selection = (chain 'PA' and resid 6 through 71)
  selection = (chain 'PB' and resid 6 through 71)
  selection = (chain 'PC' and resid 6 through 71)
  selection = (chain 'PD' and resid 6 through 71)
  selection = chain 'PE'
  selection = chain 'PF'
  selection = chain 'PG'
  selection = chain 'PH'
  selection = chain 'PI'
  selection = chain 'PJ'
  selection = chain 'PK'
  selection = chain 'QA'
  selection = chain 'QB'
  selection = chain 'QC'
  selection = chain 'QD'
  selection = chain 'QE'
  selection = chain 'QF'
  selection = (chain 'QG' and resid 6 through 71)
  selection = (chain 'QH' and resid 6 through 71)
  selection = chain 'QI'
  selection = chain 'QJ'
  selection = chain 'QK'
  selection = chain 'RA'
  selection = chain 'RB'
  selection = (chain 'RC' and resid 6 through 71)
  selection = (chain 'RD' and resid 6 through 71)
  selection = (chain 'RE' and resid 6 through 71)
  selection = (chain 'RF' and resid 6 through 71)
  selection = chain 'RG'
  selection = chain 'RH'
  selection = chain 'RI'
  selection = chain 'RJ'
  selection = chain 'RK'
  selection = chain 'SA'
  selection = chain 'SB'
  selection = chain 'SC'
  selection = chain 'SD'
  selection = (chain 'SE' and resid 6 through 71)
  selection = (chain 'SF' and resid 6 through 71)
  selection = chain 'SG'
  selection = chain 'SH'
  selection = chain 'SI'
  selection = chain 'SJ'
  selection = chain 'SK'
  selection = chain 'TA'
  selection = chain 'TB'
  selection = chain 'TC'
  selection = chain 'TD'
  selection = (chain 'TE' and resid 6 through 71)
  selection = (chain 'TF' and resid 6 through 71)
  selection = chain 'TG'
  selection = chain 'TH'
  selection = (chain 'TI' and resid 6 through 71)
  selection = (chain 'TJ' and resid 6 through 71)
  selection = chain 'TK'
  selection = chain 'UA'
  selection = chain 'UB'
  selection = chain 'UC'
  selection = chain 'UD'
  selection = chain 'UE'
  selection = chain 'UF'
  selection = chain 'UG'
  selection = chain 'UH'
  selection = chain 'UI'
  selection = chain 'UJ'
  selection = chain 'UK'
  selection = chain 'VA'
  selection = chain 'VB'
  selection = chain 'VC'
  selection = chain 'VD'
  selection = chain 'VE'
  selection = chain 'VF'
  selection = chain 'VG'
  selection = chain 'VH'
  selection = chain 'VI'
  selection = chain 'VJ'
  selection = chain 'VK'
  selection = (chain 'WA' and resid 6 through 71)
  selection = (chain 'WB' and resid 6 through 71)
  selection = chain 'WC'
  selection = chain 'WD'
  selection = chain 'WE'
  selection = chain 'WF'
  selection = chain 'WG'
  selection = chain 'WH'
  selection = chain 'WI'
  selection = chain 'WJ'
  selection = chain 'WK'
  selection = chain 'XA'
  selection = chain 'XB'
  selection = chain 'XC'
  selection = chain 'XD'
  selection = chain 'XE'
  selection = chain 'XF'
  selection = chain 'XG'
  selection = chain 'XH'
  selection = chain 'XI'
  selection = chain 'XJ'
  selection = chain 'XK'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.100
  Extract box with map and model:          10.640
  Check model and map are aligned:         1.230
  Set scattering table:                    0.760
  Process input model:                     245.400
  Find NCS groups from input model:        8.470
  Set up NCS constraints:                  4.630
  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:             0.020
  Load rotamer database and sin/cos tables:2.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  273.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
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      :  0.006   0.034 110880  Z= 0.426
  Angle     :  0.603   2.878 148896  Z= 0.375
  Chirality :  0.049   0.127  18216
  Planarity :  0.002   0.006  18744
  Dihedral  : 13.268  43.999  39600
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.44 (0.06), residues: 13464
  helix:  None (None), residues: 0
  sheet: -1.25 (0.05), residues: 8712
  loop : -2.05 (0.06), residues: 4752

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5407 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 5407
  time to evaluate  : 10.004
Fit side-chains
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 5407
  average time/residue: 0.9564
  time to fit residues: 8890.4840
Evaluate side-chains
  3309 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 3309
  time to evaluate  : 10.168
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 13.2176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 1114 optimal weight:    6.9990
   chunk 1000 optimal weight:    3.9990
   chunk 555 optimal weight:    9.9990
   chunk 341 optimal weight:    9.9990
   chunk 674 optimal weight:    0.4980
   chunk 534 optimal weight:    6.9990
   chunk 1034 optimal weight:    9.9990
   chunk 400 optimal weight:   10.0000
   chunk 629 optimal weight:   10.0000
   chunk 770 optimal weight:   10.0000
   chunk 1198 optimal weight:    4.9990
   overall best weight:    4.6988

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

Flipped N/Q/H residues before XYZ refinement:
AK  62 GLN
BC  62 GLN
BE  62 GLN
BI  62 GLN
CI  62 GLN
CK  45 GLN
CK  62 GLN
DC  49 HIS
DG  49 HIS
DI  49 HIS
DI  62 GLN
DK  62 GLN
EE  62 GLN
EG  49 HIS
EI  49 HIS
EK  62 GLN
FC  49 HIS
FC  62 GLN
FI  49 HIS
FI  62 GLN
FK  49 HIS
FK  62 GLN
GD  45 GLN
GG  49 HIS
GI  62 GLN
HG  49 HIS
HI  62 GLN
HK  49 HIS
HK  62 GLN
IE  62 GLN
II  62 GLN
JI  49 HIS
JK  62 GLN
KC  62 GLN
KE  62 GLN
KI  62 GLN
KK  62 GLN
LC  49 HIS
LC  62 GLN
LD  45 GLN
LI  49 HIS
LI  62 GLN
LK  62 GLN
MC  62 GLN
MD  45 GLN
MI  62 GLN
MK  62 GLN
NI  62 GLN
NK  49 HIS
NK  62 GLN
OD  45 GLN
OG  49 HIS
OI  49 HIS
OI  62 GLN
PA  62 GLN
PE  62 GLN
PI  62 GLN
PK  62 GLN
QF  62 GLN
QI  62 GLN
QK  62 GLN
RE  62 GLN
RI  62 GLN
RK  45 GLN
RK  49 HIS
RK  62 GLN
SI  49 HIS
SI  62 GLN
SK  49 HIS
SK  62 GLN
TA  62 GLN
TG  49 HIS
TI  62 GLN
UD  45 GLN
UI  62 GLN
VA  62 GLN
VI  49 HIS
VI  62 GLN
VK  62 GLN
WK  45 GLN
WK  62 GLN
XE  62 GLN
XI  49 HIS
XI  62 GLN
XK  62 GLN

Total number of N/Q/H flips: 85

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.052 110880  Z= 0.358
  Angle     :  0.566   6.437 148896  Z= 0.313
  Chirality :  0.053   0.233  18216
  Planarity :  0.003   0.043  18744
  Dihedral  :  4.411  17.215  14520
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Rotamer Outliers :  4.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.87 (0.05), residues: 8712
  loop : -0.99 (0.08), residues: 4752

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  4290 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 551
    poor density    : 3739
  time to evaluate  : 10.115
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 551
  outliers final: 434
  residues processed: 3999
  average time/residue: 0.9520
  time to fit residues: 6717.6809
Evaluate side-chains
  3639 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 434
    poor density    : 3205
  time to evaluate  : 9.128 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 434
  outliers final: 1
  residues processed: 434
  average time/residue: 0.7890
  time to fit residues: 669.1106
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 666 optimal weight:    9.9990
   chunk 372 optimal weight:    6.9990
   chunk 997 optimal weight:    7.9990
   chunk 816 optimal weight:    8.9990
   chunk 330 optimal weight:   10.0000
   chunk 1200 optimal weight:    8.9990
   chunk 1297 optimal weight:    5.9990
   chunk 1069 optimal weight:    6.9990
   chunk 1190 optimal weight:    6.9990
   chunk 409 optimal weight:    2.9990
   chunk 963 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
AD  45 GLN
AE  62 GLN
BF  49 HIS
BK  62 GLN
CE  62 GLN
CF  49 HIS
CI  49 HIS
DD  45 GLN
DE  62 GLN
EF  49 HIS
FD  45 GLN
GE  62 GLN
GI  49 HIS
GK  62 GLN
HD  45 GLN
HE  62 GLN
HF  49 HIS
HI  49 HIS
** HK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
IF  49 HIS
IK  62 GLN
JE  62 GLN
JF  49 HIS
KC  62 GLN
KF  49 HIS
KF  62 GLN
** KK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
LE  62 GLN
MC  62 GLN
ME  62 GLN
ND  45 GLN
NE  62 GLN
NI  49 HIS
OA  62 GLN
OE  62 GLN
OK  62 GLN
PA  62 GLN
PD  62 GLN
PE  62 GLN
PF  49 HIS
RF  49 HIS
RI  49 HIS
SE  62 GLN
SF  62 GLN
TA  62 GLN
TF  49 HIS
TK  62 GLN
UE  62 GLN
UK  62 GLN
VA  62 GLN
VD  45 GLN
VE  62 GLN
WE  62 GLN
WF  49 HIS
WI  49 HIS

Total number of N/Q/H flips: 53

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.049 110880  Z= 0.376
  Angle     :  0.569   5.809 148896  Z= 0.313
  Chirality :  0.053   0.224  18216
  Planarity :  0.002   0.028  18744
  Dihedral  :  4.439  19.465  14520
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer Outliers :  2.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.38 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.65 (0.05), residues: 8712
  loop : -1.17 (0.07), residues: 4752

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3751 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 308
    poor density    : 3443
  time to evaluate  : 10.126
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 308
  outliers final: 218
  residues processed: 3589
  average time/residue: 0.8742
  time to fit residues: 5551.9373
Evaluate side-chains
  3377 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 218
    poor density    : 3159
  time to evaluate  : 10.166
Switching outliers to nearest non-outliers
  outliers start: 218
  outliers final: 0
  residues processed: 218
  average time/residue: 0.7463
  time to fit residues: 319.7169
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 1186 optimal weight:    0.9980
   chunk 902 optimal weight:    5.9990
   chunk 623 optimal weight:    9.9990
   chunk 132 optimal weight:    0.6980
   chunk 573 optimal weight:    0.0970
   chunk 806 optimal weight:    8.9990
   chunk 1205 optimal weight:    4.9990
   chunk 1275 optimal weight:    8.9990
   chunk 629 optimal weight:    2.9990
   chunk 1142 optimal weight:    0.9990
   chunk 343 optimal weight:    8.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
AA  62 GLN
AD  62 GLN
AF  49 HIS
AH  62 GLN
BA  62 GLN
BC  62 GLN
BF  49 HIS
BH  62 GLN
BI  49 HIS
CA  62 GLN
CF  49 HIS
CH  62 GLN
DF  49 HIS
EA  62 GLN
EF  49 HIS
FC  49 HIS
FF  49 HIS
GA  62 GLN
GF  49 HIS
GI  49 HIS
HA  62 GLN
HF  49 HIS
HG  62 GLN
HI  49 HIS
** HK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
IF  49 HIS
IH  62 GLN
JA  62 GLN
JD  45 GLN
JF  49 HIS
KA  62 GLN
KF  49 HIS
KI  49 HIS
LA  62 GLN
LC  49 HIS
LD  62 GLN
MA  62 GLN
MF  49 HIS
NA  62 GLN
NF  49 HIS
NH  62 GLN
NI  49 HIS
OF  49 HIS
PA  62 GLN
PE  62 GLN
PF  49 HIS
QE  62 GLN
QI  49 HIS
RF  49 HIS
RI  49 HIS
SD  45 GLN
SF  49 HIS
SF  62 GLN
TA  62 GLN
TD  62 GLN
TE  62 GLN
TF  49 HIS
TH  62 GLN
UA  62 GLN
UF  49 HIS
UH  62 GLN
UI  49 HIS
VA  62 GLN
VF  49 HIS
WD  45 GLN
WD  62 GLN
WF  49 HIS
XD  45 GLN
XF  49 HIS
XH  62 GLN

Total number of N/Q/H flips: 69

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029 110880  Z= 0.155
  Angle     :  0.492   5.110 148896  Z= 0.271
  Chirality :  0.051   0.197  18216
  Planarity :  0.002   0.021  18744
  Dihedral  :  3.775  16.510  14520
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Rotamer Outliers :  2.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.50 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet:  0.10 (0.06), residues: 8184
  loop : -0.91 (0.07), residues: 5280

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3801 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 279
    poor density    : 3522
  time to evaluate  : 10.206
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 279
  outliers final: 195
  residues processed: 3608
  average time/residue: 0.8888
  time to fit residues: 5663.1569
Evaluate side-chains
  3452 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 195
    poor density    : 3257
  time to evaluate  : 10.035
Switching outliers to nearest non-outliers
  outliers start: 195
  outliers final: 0
  residues processed: 195
  average time/residue: 0.7451
  time to fit residues: 291.0205
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 1062 optimal weight:    0.9990
   chunk 724 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0270
   chunk 950 optimal weight:   10.0000
   chunk 526 optimal weight:   10.0000
   chunk 1088 optimal weight:    8.9990
   chunk 881 optimal weight:    0.0170
   chunk 1 optimal weight:    9.9990
   chunk 651 optimal weight:    9.9990
   chunk 1145 optimal weight:   10.0000
   chunk 321 optimal weight:    9.9990
   overall best weight:    4.0082

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

Flipped N/Q/H residues before XYZ refinement:
AA  62 GLN
AF  49 HIS
AH  62 GLN
AI  49 HIS
BA  62 GLN
BH  62 GLN
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CA  62 GLN
CE  62 GLN
CH  62 GLN
DF  49 HIS
EA  62 GLN
EF  49 HIS
FC  62 GLN
FF  49 HIS
GF  49 HIS
GI  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HF  49 HIS
HG  62 GLN
HI  49 HIS
** HK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
IH  62 GLN
II  49 HIS
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JF  49 HIS
KA  62 GLN
KF  49 HIS
KK  62 GLN
LA  62 GLN
MA  62 GLN
MF  49 HIS
MI  49 HIS
NA  62 GLN
NF  49 HIS
NH  62 GLN
NI  49 HIS
OK  62 GLN
PA  62 GLN
PE  62 GLN
PF  49 HIS
RF  49 HIS
RI  49 HIS
SF  49 HIS
TA  62 GLN
TF  49 HIS
TH  62 GLN
TI  49 HIS
TK  62 GLN
UA  62 GLN
UF  49 HIS
UH  62 GLN
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
VA  62 GLN
VF  49 HIS
WF  49 HIS
XF  49 HIS
XH  62 GLN

Total number of N/Q/H flips: 54

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.043 110880  Z= 0.314
  Angle     :  0.537   5.222 148896  Z= 0.295
  Chirality :  0.051   0.172  18216
  Planarity :  0.002   0.031  18744
  Dihedral  :  4.203  17.008  14520
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer Outliers :  3.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.69 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.05 (0.06), residues: 8448
  loop : -1.02 (0.07), residues: 5016

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3713 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 435
    poor density    : 3278
  time to evaluate  : 10.187
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 435
  outliers final: 284
  residues processed: 3458
  average time/residue: 0.8770
  time to fit residues: 5397.5915
Evaluate side-chains
  3409 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 284
    poor density    : 3125
  time to evaluate  : 10.070
Switching outliers to nearest non-outliers
  outliers start: 284
  outliers final: 0
  residues processed: 284
  average time/residue: 0.7648
  time to fit residues: 425.5095
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 429 optimal weight:   10.0000
   chunk 1149 optimal weight:    9.9990
   chunk 252 optimal weight:   10.0000
   chunk 749 optimal weight:    0.5980
   chunk 314 optimal weight:    3.9990
   chunk 1277 optimal weight:   10.0000
   chunk 1060 optimal weight:    8.9990
   chunk 591 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 422 optimal weight:    6.9990
   chunk 670 optimal weight:   10.0000
   overall best weight:    5.5188

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

Flipped N/Q/H residues before XYZ refinement:
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BF  49 HIS
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CF  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
DF  49 HIS
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
FC  49 HIS
FF  49 HIS
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GA  62 GLN
GF  49 HIS
GI  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HA  62 GLN
HI  49 HIS
HK  62 GLN
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JA  62 GLN
JC  49 HIS
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KC  49 HIS
LC  49 HIS
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MI  49 HIS
NI  49 HIS
OA  62 GLN
OC  49 HIS
OK  62 GLN
** PK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
QG  49 HIS
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RF  49 HIS
RI  49 HIS
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SE  62 GLN
TD  62 GLN
TI  49 HIS
UF  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
VD  49 HIS
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** WK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
XK  62 GLN

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.048 110880  Z= 0.413
  Angle     :  0.594   6.105 148896  Z= 0.324
  Chirality :  0.052   0.211  18216
  Planarity :  0.003   0.040  18744
  Dihedral  :  4.524  19.160  14520
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer Outliers :  3.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.74 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet:  0.00 (0.06), residues: 8184
  loop : -1.18 (0.07), residues: 5280

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3738 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 441
    poor density    : 3297
  time to evaluate  : 10.133
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 441
  outliers final: 287
  residues processed: 3522
  average time/residue: 0.8678
  time to fit residues: 5451.4531
Evaluate side-chains
  3414 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 287
    poor density    : 3127
  time to evaluate  : 10.287
Switching outliers to nearest non-outliers
  outliers start: 287
  outliers final: 0
  residues processed: 287
  average time/residue: 0.7633
  time to fit residues: 431.2443
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 1231 optimal weight:    0.9990
   chunk 143 optimal weight:    4.9990
   chunk 727 optimal weight:   10.0000
   chunk 932 optimal weight:    1.9990
   chunk 722 optimal weight:    6.9990
   chunk 1075 optimal weight:    6.9990
   chunk 713 optimal weight:    8.9990
   chunk 1272 optimal weight:    8.9990
   chunk 796 optimal weight:    4.9990
   chunk 775 optimal weight:    2.9990
   chunk 587 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
AF  49 HIS
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BF  49 HIS
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CE  62 GLN
CF  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
DF  49 HIS
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
EF  49 HIS
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
FF  49 HIS
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GF  49 HIS
GI  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HF  49 HIS
HI  49 HIS
IF  49 HIS
IK  18 ASN
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JF  49 HIS
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KF  49 HIS
KG  49 HIS
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MI  49 HIS
NI  49 HIS
PE  62 GLN
PF  49 HIS
PI  49 HIS
** PK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RD  45 GLN
RF  49 HIS
RI  49 HIS
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SF  49 HIS
TF  49 HIS
TI  49 HIS
UF  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
WF  49 HIS
WK  62 GLN
XD  62 GLN
XF  49 HIS

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035 110880  Z= 0.270
  Angle     :  0.548   5.882 148896  Z= 0.299
  Chirality :  0.051   0.186  18216
  Planarity :  0.002   0.035  18744
  Dihedral  :  4.179  17.633  14520
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer Outliers :  1.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.64 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet:  0.09 (0.06), residues: 8184
  loop : -1.16 (0.07), residues: 5280

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3541 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 237
    poor density    : 3304
  time to evaluate  : 10.075
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 237
  outliers final: 145
  residues processed: 3409
  average time/residue: 0.8718
  time to fit residues: 5280.3417
Evaluate side-chains
  3274 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 145
    poor density    : 3129
  time to evaluate  : 10.117
Switching outliers to nearest non-outliers
  outliers start: 145
  outliers final: 0
  residues processed: 145
  average time/residue: 0.7141
  time to fit residues: 209.0813
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 787 optimal weight:    0.9980
   chunk 508 optimal weight:    2.9990
   chunk 759 optimal weight:    7.9990
   chunk 383 optimal weight:    8.9990
   chunk 249 optimal weight:    4.9990
   chunk 246 optimal weight:    5.9990
   chunk 808 optimal weight:    9.9990
   chunk 866 optimal weight:   10.0000
   chunk 629 optimal weight:    9.9990
   chunk 118 optimal weight:    1.9990
   chunk 1000 optimal weight:   10.0000
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
AF  49 HIS
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CF  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
DF  49 HIS
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
EF  49 HIS
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GF  49 HIS
GI  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HF  49 HIS
HI  49 HIS
IF  49 HIS
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JF  49 HIS
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KF  49 HIS
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MA  62 GLN
MI  49 HIS
** MK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
NA  49 HIS
ND  62 GLN
NI  49 HIS
OK  62 GLN
PF  49 HIS
PI  49 HIS
** PK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
QG  49 HIS
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RF  49 HIS
RI  49 HIS
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SF  49 HIS
TD  62 GLN
TF  49 HIS
TI  49 HIS
UF  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
WF  49 HIS
XF  49 HIS

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.5775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043 110880  Z= 0.286
  Angle     :  0.561   6.710 148896  Z= 0.306
  Chirality :  0.051   0.241  18216
  Planarity :  0.002   0.045  18744
  Dihedral  :  4.190  18.537  14520
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Rotamer Outliers :  1.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.74 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.06 (0.06), residues: 8448
  loop : -1.10 (0.07), residues: 5016

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3443 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 240
    poor density    : 3203
  time to evaluate  : 12.264
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 240
  outliers final: 147
  residues processed: 3300
  average time/residue: 0.9319
  time to fit residues: 5469.0062
Evaluate side-chains
  3262 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 147
    poor density    : 3115
  time to evaluate  : 10.100
Switching outliers to nearest non-outliers
  outliers start: 147
  outliers final: 0
  residues processed: 147
  average time/residue: 0.7973
  time to fit residues: 235.4632
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 1157 optimal weight:   10.0000
   chunk 1218 optimal weight:    3.9990
   chunk 1112 optimal weight:   10.0000
   chunk 1185 optimal weight:    0.8980
   chunk 713 optimal weight:    9.9990
   chunk 516 optimal weight:    0.4980
   chunk 930 optimal weight:    5.9990
   chunk 363 optimal weight:    0.9980
   chunk 1071 optimal weight:    8.9990
   chunk 1121 optimal weight:    9.9990
   chunk 1181 optimal weight:    0.0050
   overall best weight:    1.2796

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

Flipped N/Q/H residues before XYZ refinement:
AF  62 GLN
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BA  62 GLN
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CF  62 GLN
CI  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
FA  62 GLN
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GI  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HI  49 HIS
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JH  62 GLN
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KA  62 GLN
KG  49 HIS
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MA  62 GLN
MI  49 HIS
** MK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
NA  49 HIS
NI  49 HIS
PF  62 GLN
PI  49 HIS
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RA  62 GLN
RF  62 GLN
RI  49 HIS
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SE  62 GLN
SG  49 HIS
TI  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
XD  62 GLN
XF  49 HIS
XF  62 GLN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.5820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038 110880  Z= 0.182
  Angle     :  0.543   7.103 148896  Z= 0.296
  Chirality :  0.051   0.251  18216
  Planarity :  0.002   0.066  18744
  Dihedral  :  3.854  17.784  14520
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Rotamer Outliers :  0.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet:  0.30 (0.06), residues: 8184
  loop : -1.04 (0.07), residues: 5280

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3469 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 117
    poor density    : 3352
  time to evaluate  : 10.145
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 117
  outliers final: 63
  residues processed: 3394
  average time/residue: 0.9075
  time to fit residues: 5495.8507
Evaluate side-chains
  3229 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 3166
  time to evaluate  : 10.236
Switching outliers to nearest non-outliers
  outliers start: 63
  outliers final: 0
  residues processed: 63
  average time/residue: 0.8141
  time to fit residues: 110.3283
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 778 optimal weight:    9.9990
   chunk 1253 optimal weight:    6.9990
   chunk 765 optimal weight:    6.9990
   chunk 594 optimal weight:    2.9990
   chunk 871 optimal weight:    9.9990
   chunk 1315 optimal weight:    5.9990
   chunk 1210 optimal weight:   10.0000
   chunk 1047 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 808 optimal weight:    9.9990
   chunk 642 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BA  62 GLN
BD  49 HIS
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CI  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
ED  18 ASN
EI  49 HIS
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
FG  49 HIS
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GI  49 HIS
GK  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HD  18 ASN
HI  49 HIS
IG  62 GLN
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JH  62 GLN
JI  49 HIS
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KA  62 GLN
LD  62 GLN
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MD  18 ASN
MI  49 HIS
** MK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
NA  49 HIS
NI  49 HIS
** NK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
OD  18 ASN
PI  49 HIS
** PK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
QG  49 HIS
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RA  62 GLN
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SA  49 HIS
SF  62 GLN
** SK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
TD  62 GLN
TI  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
VI  49 HIS
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
XD  62 GLN
XF  49 HIS
XF  62 GLN

Total number of N/Q/H flips: 33

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.5930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.057 110880  Z= 0.495
  Angle     :  0.672   7.183 148896  Z= 0.362
  Chirality :  0.054   0.219  18216
  Planarity :  0.003   0.057  18744
  Dihedral  :  4.666  20.095  14520
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.86 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.15 (0.06), residues: 8448
  loop : -1.16 (0.07), residues: 5016

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

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

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  26928 Ramachandran restraints generated.
    13464 Oldfield, 0 Emsley, 13464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3270 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 190
    poor density    : 3080
  time to evaluate  : 10.361
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 190
  outliers final: 123
  residues processed: 3161
  average time/residue: 0.8709
  time to fit residues: 4929.3931
Evaluate side-chains
  3156 residues out of total 12144 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 123
    poor density    : 3033
  time to evaluate  : 10.169
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 123
  outliers final: 2
  residues processed: 123
  average time/residue: 0.7418
  time to fit residues: 187.1199
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1320
   random chunks:
   chunk 831 optimal weight:    7.9990
   chunk 1115 optimal weight:    2.9990
   chunk 320 optimal weight:    2.9990
   chunk 965 optimal weight:    3.9990
   chunk 154 optimal weight:    5.9990
   chunk 291 optimal weight:    8.9990
   chunk 1048 optimal weight:    5.9990
   chunk 438 optimal weight:    9.9990
   chunk 1077 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   chunk 193 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
AI  49 HIS
** AK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BD  49 HIS
** BK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
CI  49 HIS
** CK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** DK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
EA  49 HIS
EI  49 HIS
** EK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** FK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
GI  49 HIS
GK  49 HIS
** GK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
HI  49 HIS
** IK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
JH  62 GLN
JI  49 HIS
** JK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
KI  49 HIS
LD  62 GLN
LI  49 HIS
** LK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
MG  49 HIS
MI  49 HIS
** MK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
NA  49 HIS
NI  49 HIS
** NK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
PI  49 HIS
** PK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** QK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
RI  49 HIS
** RK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
SA  49 HIS
SG  49 HIS
SI  49 HIS
** SK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
TI  49 HIS
UA  49 HIS
UI  49 HIS
** UK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
VI  49 HIS
** VK  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
WG  49 HIS
WI  49 HIS
XD  62 GLN
XE  62 GLN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.116330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.091789 restraints weight = 51327.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.092414 restraints weight = 45690.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.092921 restraints weight = 41713.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.5952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.040 110880  Z= 0.305
  Angle     :  0.607   7.584 148896  Z= 0.330
  Chirality :  0.052   0.234  18216
  Planarity :  0.003   0.052  18744
  Dihedral  :  4.308  20.148  14520
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer Outliers :  1.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.79 (0.07), residues: 13464
  helix:  None (None), residues: 0
  sheet: -0.11 (0.06), residues: 8448
  loop : -1.11 (0.07), residues: 5016

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Job complete
usr+sys time: 67275.34 seconds
wall clock time: 1153 minutes 38.63 seconds (69218.63 seconds total)