INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddr_27339/03_2024/8ddr_27339.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 8ddr_27339.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : 3PH
  Using monomer library entry 3PH as template

  Build ligand and use monomer library to name atoms : 9Z9
Sorry: 
    Atoms in the input are supposed to be bound
     
    C74(9Z9) - C75(9Z9) = 1.90

    Fix the input file and retry

    EXITING