INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddq_27338/03_2024/8ddq_27338.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 8ddq_27338.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  More than 20 percent of the atoms are missing for 3PH
  as compared to the Monomer Library

  More than 20 percent of the atoms are missing for 3PH
  as compared to the Chemical Components

  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