sorry for late reply.
@Garikai_Dzoma hmm that could be hard. since there are approximately 10 websites on that. the things i changed was OS (debian to Ubuntu) moved to another VPS provider. And php cron jobs order. i am not sure if i made php cron jobs not to cross each other time lines.
i attached the graphs. i may miss some points but i didn't see any relativity between cpu and network and disk operations.
this is CPU Monthly graph.
this is network Monthly graph.
this is IPv6 Monthly graph.
And disk IO graphs. 
@virtubox indeed. i did the reboot but the issue persists.
i was using debian OS before with the same sites and there weren't such problems. moved the VPS to another provider and installed the sites on Ubuntu this time and the issues started to occur.