INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8b_24892/01_2022/7s8b_24892.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7s8b_24892.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  19780    NPOV A 807     110.984  74.432  67.282  1.00  9.14           N+1


  Build ligand and use monomer library to name atoms : Y01
  Using monomer library entry Y01 as template

  group index 6
change? False

ChiralClass
	Atom  HBD(59) xyz:( 0.394, -0.838, -1.088)     
	Atom  CBD(18) xyz:(-0.672, -0.274, -1.633)    S ring index: 1
	Atom  CAK(19) xyz:(-0.174, -0.043, -3.246)      ring index: 1
	Atom  CBF(17) xyz:(-0.640,  1.411, -0.772)    S ring index: 1
	Atom  CBG(12) xyz:(-1.587, -0.799, -1.485)    S ring index: 1

	not correct chiralisation
	Difficulties in the ring structures may lead to problems later

  Attempting to download Chemical Components file for PCW
  Running eLBOW on PCW.cif

MoleculeClass :  C:44  N: 1  O: 8  P: 1 (CHEMICAL COMPONENTS format)
	138 atoms
	137 bonds
	262 angles
	363 dihedrals
	0 rings (groups, rings, atoms) 0 0
	1 chirals : R 

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

  Build ligand and use user provided restraints : PCW

  Attempting to download Chemical Components file for R2R
  Running eLBOW on R2R.cif
Sorry: 
  eLBOW not suitable for metal clusters unless the --final_geometry option
  is used.