Read timed-out errors are like a server crash in that players cannot join the server any longer, but it is still running, as plugins will still perform their functions, etc. As a result, the server may still appear online, but users cannot connect to it. This error typically appears near the end of the server log/console, before all players are disconnected: "Read Timed Out".
In most cases, this error is caused by an out-of-date, incompatible, or buggy plugin. One plugin that is known to cause these errors is Permissions 3.x.
Note: It is recommended to use an alternative permissions plugin that is actually up to date.
In most cases, a server restart will fix the issue. However, to prevent it from happening again, troubleshoot the server plugins. One basic method of troubleshooting is to remove plugins one at a time and let the server run for a while to see if the issue stops. It is also recommended to update all plugins and remove any out-of-date plugins during this testing period.