11 TPS with 50 player online

Drop your render distance.

I keep mine at 5

Used to be able to get away with 8-10 on 1.8.

 

Have you tried reducing the activation ranges of your entities in the spigot.yml?

 

Perhaps you have a process load on the processor. Try to kill the process that load your CPU most (/htop and enter /kill PID more loading process)

 

I guess one of the things we all forgot to ask is what are the specs for your server?

 

You can lower the load if you pregenerate chunks with plugin like WorldBorder. It will take some time, but you will see way less lag. I usually pregenerate my main world and leave nether and end as they are, because players do not wander alot there.

 

Does Spigot still sleep 10ms between chunk saves or was that patched?

 

Do you have world edit? Then you should get FastAsyncWorldEdit. I recommend it.

 

They are running both.

You installed it but did you set it to generate all the chunks inside the border?

 

That's a fairly poor CPU;

http://www.cpubenchmark.net/[email protected]+2.13GHz&id=2086

I would expect this is the cause.

 

I run a 20 slot server on Intel dn2800mt (low end passive cooled processor). Pregenerating chunks helps alot and i do not get complains about lags unless someone makes something stupid with redstone or spawners.

As @Foulwerp says WorldBorder has a command to fill the world inside border. So read how to do it, set a reasonable size border and fill it. Keep in mind filling is CPU intensive task and can take alot time(and disk space!). On my server filling 7000 block radius border takes 5+ hours and in that time game is very very laggy. I usually fill worlds when server is empty - there is command to pause and resume the operation.