You must close all udp and tcp ports on ur vps or dedi server
and just open the nesseccary ports for ur server like tcp port 80 for website and 15779 for gateway and 15884 for agent and port of downloadserver if u will make updates
this could help ur server and will close smc exploit, then u need to download bee guardian to block any flood packets , about gateway and agent u will find some guides about how to fix those exploits in them .