INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kyb_23074/12_2021/7kyb_23074.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7kyb_23074.eff

  Preparation for phenix.refine

    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  10701    NPOV A1601     129.458 158.757 132.124  1.00 58.83           N+1


  Build ligand and use chemical components : ALF

   Residue has metal at the centre of a coordination sphere. Using input
   geometry to generate restraints. Hydrogens may not be added.
   

  Mapped the ligand (ALF) to the monomer library restraints
  

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

  OUTPUT
  
    Writing model to 7kyb_23074.updated.pdb
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/build/../modules/elbow/elbow/command_line/ready_set.py", line 1104, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/build/../modules/elbow/elbow/command_line/ready_set.py", line 911, in run
    f.close()
IOError: [Errno 28] No space left on device