INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfz_30668/01_2024/7dfz_30668_neut_trim.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7dfz_30668_neut_trim.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : H56
Sorry: 
    Atoms in the input are supposed to be bound
     
    N1(H56) - C1(H56) = 1.76

    Fix the input file and retry

    EXITING