Why atop shows high CPU but sum of individual processes %CPU far smaller?
Solution 1:
That's because the sum of all of the processes gives you a user load, while you also have disturbingly high system load, which comprises all of the OS kernel operations, such as (but not limited to) context switching, network packet handling and so on.
It's hard to guess what's causing high system load from the screenshot provided. Not the network definitely though.