Server lag with plenty of CPU / RAM available

I'm hosting this server for me and my friends, and I have this problem that it keeps skipping ticks, even when no one is online and nothing laggy is happening in the Spawn chunks. I have tried debugging and I keep getting the message root.level.worlds, root.save, root, root.levels and root.jobs is taking too long. My CPU and RAM usage is nowhere near 100% when it's happening.

Debug will be attached further down.

(I have researched before making this post and no solution has been found)