INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qel_4537/05_2022/6qel_4537_trim.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6qel_4537_trim.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : ADP
  Using monomer library entry ADP as template

  Attempting to download Chemical Components file for 08T
  Running eLBOW on 08T.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  O2'(11) xyz:(-5.578, -1.043, -0.685) and
      Atom  C2'(10) xyz:(-3.671,  0.646,  2.595) should be unknown, not    4.15
    Bond between
      Atom  C3'( 8) xyz:(-3.662,  0.192, -1.419) and
      Atom  C2'(10) xyz:(-3.671,  0.646,  2.595) should be unknown, not    4.04
    Bond between
      Atom  C4'( 6) xyz:(-1.970, -1.378, -0.983) and
      Atom  O4'( 7) xyz:(-3.704,  1.988,  1.826) should be unknown, not    4.71
    Bond between
      Atom  C4 (25) xyz:( 0.248,  0.497,  1.646) and
      Atom  N9 (31) xyz:(-3.564,  0.690,  4.342) should be unknown, not    4.67
    Bond between
      Atom  N9 (31) xyz:(-3.564,  0.690,  4.342) and
      Atom  C8 (30) xyz:(-0.545,  1.550, -0.084) should be unknown, not    5.43
    Bond between
      Atom  C6 (27) xyz:(-0.756, -1.330,  0.530) and
      Atom  N6 (28) xyz:(-7.288,  3.540, -1.008) should be unknown, not    8.29
    Bond between
      Atom  C3'( 8) xyz:(-3.662,  0.192, -1.419) and
      Atom  H4 (35) xyz:(-2.127, -3.512, -0.755) should be unknown, not    4.06
    Bond between
      Atom  C2'(10) xyz:(-3.671,  0.646,  2.595) and
      Atom  H6 (37) xyz:(-3.819, -1.942, -1.191) should be unknown, not    4.59
    Bond between
      Atom  C2 (17) xyz:( 1.570, -1.146,  0.633) and
      Atom  H10(41) xyz:(-8.058,  0.644,  2.252) should be unknown, not    9.93


08T  O3'     C3'    single        3.048 0.020     3.048
1.398717
Sorry: Bond length too long : 3.05