What version of Linux are you using ?
3gb of ram isn't much but it should be okay as long as your not running too many other processes, I prefer at least 3.0ghz cores to run my servers on, but with 16 cores that should also be okay. Everything else seems normal. You say these FPS drops happen even without metmod and amxx ?
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{FJ}Justice STEAM_0:0:633975 If anyone needs any help with their server, Just add me to steam friends and I'll help you out.