INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhz_9124/12_2022/6mhz_9124.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6mhz_9124.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for AOV
  Running eLBOW on AOV.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  C4'(11) xyz:(-3.086, -2.369, -2.468) and
      Atom  O4'(12) xyz:(-4.508,  2.035,  1.820) should be unknown, not    6.31
    Bond between
      Atom  C3'(13) xyz:(-4.470, -0.534, -2.964) and
      Atom  C2'(15) xyz:(-4.475,  0.693,  2.589) should be unknown, not    5.69
    Bond between
      Atom  C2'(15) xyz:(-4.475,  0.693,  2.589) and
      Atom  O2'(16) xyz:(-6.386, -1.787, -2.261) should be unknown, not    5.77
    Bond between
      Atom  N9 (18) xyz:(-4.368,  0.737,  4.336) and
      Atom  C8 (19) xyz:( 1.922,  1.017,  0.978) should be unknown, not    7.14
    Bond between
      Atom  N9 (18) xyz:(-4.368,  0.737,  4.336) and
      Atom  C4 (27) xyz:(-0.023,  0.267,  1.620) should be unknown, not    5.14
    Bond between
      Atom  C6 (22) xyz:(-0.327, -1.177, -0.241) and
      Atom  N6 (23) xyz:(-7.155,  4.178, -1.121) should be unknown, not    8.72
    Bond between
      Atom  C3'(13) xyz:(-4.470, -0.534, -2.964) and
      Atom  H3'(38) xyz:(-3.243, -3.633, -0.734) should be unknown, not    4.01
    Bond between
      Atom  C2'(15) xyz:(-4.475,  0.693,  2.589) and
      Atom  H2'(41) xyz:(-4.627, -1.798, -1.230) should be unknown, not    4.56
    Bond between
      Atom  C8 (19) xyz:( 1.922,  1.017,  0.978) and
      Atom  H8 (43) xyz:(-3.079,  0.985, -1.433) should be unknown, not    5.55
    Bond between
      Atom  C2 (25) xyz:(-2.140,  0.018,  0.625) and
      Atom  H2 (46) xyz:(-8.578,  1.410,  2.028) should be unknown, not    6.73


AOV   PB      O1B   double        1.479 0.020     1.479
AOV   PB      O2B   single        1.610 0.020     1.610
AOV   PB      O3B   single        1.610 0.020     1.610
AOV   PB      O3A   single        1.610 0.020     1.610
AOV   O3B     VG    single        1.840 0.020     1.840
AOV   PA      O1A   double        1.480 0.020     1.480
AOV   PA      O2A   single        1.610 0.020     1.610
AOV   PA      O3A   single        1.609 0.020     1.609
AOV   PA     O5'    single        1.610 0.020     1.610
AOV  O5'     C5'    single        2.018 0.020     2.018
AOV  C5'     C4'    single        3.023 0.020     3.023
1.527126
Sorry: Bond length too long : 3.02