INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5i_30582/12_2022/7d5i_30582.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7d5i_30582.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for HDD
  Running eLBOW on HDD.cif

   Residue has metal at the centre of a coordination sphere. Using input
   geometry to generate restraints. Hydrogens may not be added.
   

 Suspicious bonds
    Bond between
      Atom  CHA( 2) xyz:( 5.855,  3.113,  3.323) and
      Atom  C4D(37) xyz:( 1.359, -1.471, -0.844) should be unknown, not    7.65
    Bond between
      Atom  CHA( 2) xyz:( 5.855,  3.113,  3.323) and
      Atom  HHA(45) xyz:( 3.410,  0.274, -0.520) should be unknown, not    5.37
    Bond between
      Atom  CHB( 3) xyz:( 1.396,  2.120,  4.173) and
      Atom  HHB(46) xyz:(-1.364,  4.302, -1.572) should be unknown, not    6.74
    Bond between
      Atom  CHC( 4) xyz:( 0.704,  6.119,  6.151) and
      Atom  HHC(47) xyz:(-4.955,  0.292,  1.471) should be unknown, not    9.37
    Bond between
      Atom  CHD( 5) xyz:( 5.314,  7.239,  5.517) and
      Atom  C1D(34) xyz:( 0.810, -1.889, -2.295) should be unknown, not   12.83
    Bond between
      Atom  CHD( 5) xyz:( 5.314,  7.239,  5.517) and
      Atom  HHD(48) xyz:(-0.839, -4.283, -0.213) should be unknown, not   14.26
    Bond between
      Atom  C2B(19) xyz:( 0.224,  2.733,  6.314) and
      Atom  CMB(22) xyz:(-4.162,  4.027, -2.303) should be unknown, not    9.75
    Bond between
      Atom  C3B(20) xyz:( 0.072,  3.937,  6.931) and
      Atom  CAB(23) xyz:(-6.043,  2.016, -0.718) should be unknown, not    9.98
    Bond between
      Atom  C2C(27) xyz:( 1.814,  8.280,  4.986) and
      Atom  CMC(30) xyz:(-4.530, -2.019,  3.086) should be unknown, not   12.24
    Bond between
      Atom  C3C(28) xyz:( 3.130,  8.580,  4.757) and
      Atom  CAC(31) xyz:(-2.464, -4.328,  2.280) should be unknown, not   14.28
    Bond between
      Atom  ND (33) xyz:( 5.075,  4.398,  5.795) and
      Atom  C1D(34) xyz:( 0.810, -1.889, -2.295) should be unknown, not   11.10
    Bond between
      Atom  ND (33) xyz:( 5.075,  4.398,  5.795) and
      Atom  C4D(37) xyz:( 1.359, -1.471, -0.844) should be unknown, not    9.61
    Bond between
      Atom  CAD(39) xyz:( 1.359, -2.720,  1.318) and
      Atom  CBD(40) xyz:(-0.494,  1.522,  0.000) should be unknown, not    4.81
    Bond between
      Atom  CAD(39) xyz:( 1.359, -2.720,  1.318) and
      Atom HAD1(72) xyz:( 3.072, -2.478, -3.248) should be unknown, not    4.88
    Bond between
      Atom  CAD(39) xyz:( 1.359, -2.720,  1.318) and
      Atom HAD2(73) xyz:( 3.361, -0.833, -2.609) should be unknown, not    4.79
    Bond between
      Atom  CBD(40) xyz:(-0.494,  1.522,  0.000) and
      Atom HBD1(74) xyz:( 5.156, -3.129, -2.514) should be unknown, not    7.74
    Bond between
      Atom  CBD(40) xyz:(-0.494,  1.522,  0.000) and
      Atom HBD2(75) xyz:( 5.447, -1.483, -1.891) should be unknown, not    6.92
    Bond between
      Atom  CGD(41) xyz:( 0.800,  2.462,  0.000) and
      Atom  O1D(42) xyz:( 3.269, -2.719, -0.123) should be unknown, not    5.74
    Bond between
      Atom  CGD(41) xyz:( 0.800,  2.462,  0.000) and
      Atom  O2D(43) xyz:( 5.436, -3.266,  0.245) should be unknown, not    7.37


HDD  FE       NA    single        1.921 0.020     1.921
HDD  FE       NB    single        1.929 0.020     1.929
HDD  FE       NC    single        1.930 0.020     1.930
HDD  FE       ND    single        1.914 0.020     1.914
HDD   CHA     C1A   single        1.867 0.020     1.867
HDD   CHA     C4D   double        7.655 0.020     7.655
1.527126
Sorry: Bond length too long : 7.65