1. Go to WHM >> cPanel >> Manage Plugins
2. Install the cronconfig cPanel plugin which allow users to edit cPanel cron settings/program run times.



upcp is the program that updates cPanel and it is recommended to run this script once a day. It has, by default, been set to a random time between 9pm and 6am local time. cpbackupcpbackup is the program used to run backups on your server and set by default to run at 1am. However, it is a good idea to set these cron jobs to run at an off peak time of your site.
Setting cron time – Remember the Hour is always set in military time; Day set to 15 means 15th day of the month; Month is coded as 1=January and 12=December; and weekdays are noted as 0=Sunday and 6=Saturday.
Here is what sample settings mean – Minute = 47; Hour = 1; Day = *; Month = *; Weekday = *. This process would run everyday at 01:47AM. Have you set you server cron functions at non peak hours?