Using LinuxGSM to deply the server

15:15 [Info] [SmoothRestart] Server will restart in 1 minutes!
15:15 [Warning] Calling 'OnServerCommand' on 'Logger v2.2.1' took 761ms [GARBAGE COLLECT]
15:15 [Warning] Calling 'OnItemCraft' on 'Logger v2.2.1' took 765ms [GARBAGE COLLECT]
15:15 [Info] [Better Chat] ?AxialAtom: ffs
15:15 [Warning] Calling 'OnItemCraftFinished' on 'Logger v2.2.1' took average 2298ms
15:16 [Info] [Better Chat] VAFLIUS :0: scamer
15:16 [Info] [Better Chat] NaruHUN: restart?
15:17 [Info] [Better Chat] ?AxialAtom: who scammed??
15:17 [Info] [Better Chat] VAFLIUS :0: c6
15:17 [Info] [Better Chat] deb?lku_1337: he fusking shoot me
15:17 [Info] [Better Chat] VAFLIUS :0: lul
15:17 [Info] [Better Chat] ?AxialAtom: if u man dare to ****** shoot me
15:17 [Info] [Better Chat] ^TuttimannTuttiLibeNaFidan*: 1 min is over admin!

Is it not shutting down or just not starting again?

Plugins cannot start the server, only shut it down. Per the notes on the documentation for Smooth Restarter, you'd need something external to actually start the server after it being shut down.

It does not even shut it down. Instead a weird lag in server occurs where people get teleportad back few sec when running

Does the normal 'quit' command work? If not, then the issue isn't with this plugin.