INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud3_20731/03_2024/6ud3_20731.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6ud3_20731.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : RI5
Sorry: 
    Atoms in the input are supposed to be bound
     
    C07(RI5) - C08(RI5) = 1.88

    Fix the input file and retry

    EXITING