INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z17_14443/03_2024/7z17_14443_neut_trim.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7z17_14443_neut_trim.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : I9X
Sorry: 
    Atoms in the input are supposed to be bound
     
    P08(I9X) - C05(I9X) = 2.34

    Fix the input file and retry

    EXITING