Modrefiner

Dear Sir/Mam,
I have some query related to modrefiner tools. when I refine protein modal by using
modrefiner and its pdb submit to other bioinformatics tools like prosa
web or other docking server its always showed wrong pdb. I have attached pdb file of protein which was refined by modrefiner. Can you explain
me what is the problem behind it and give me suggestion if I follow any
wrong path for modal refinement.