INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foa_29343/03_2024/8foa_29343.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 8foa_29343.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

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

  There is a tetra-coordinated nitrogen in your input.  You may need to add
  charge to the nitrogen thus:

ATOM  19767    NPOV A 805      81.133  95.464  68.527  1.00 46.56           N+1


  Build ligand and use monomer library to name atoms : Y01
Sorry: 
    Atoms in the input are supposed to be bound
     
    CAZ(Y01) - CAV(Y01) = 1.91

    Fix the input file and retry

    EXITING