INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xnl_6741/12_2022/5xnl_6741.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 5xnl_6741.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

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

  Build ligand and use chemical components : OEX
Sorry: 
    Atoms in the input are supposed to be bound
     
    MN4(OEX) - O5(OEX) = 3.31

    Fix the input file and retry

    EXITING