How to do a complete refresh in Safari 10.1.1 on MacOS Sierra
Shift-click the refresh button, or choose View → Reload Page From Origin (⌥⌘R) to refresh ignoring cached resources for the current domain. You can observe the effect in the Web Inspector's Network tab.

                                                            


What I suspect is catching you out here is how a force refresh only bypasses cache for the same domain as the site you're refreshing. Even with a force refresh, resources may still be cached, such as from CDN domains.

                                                                       

To bypass cache for all resources, open the web inspector, choose the Network tab, then select ‘Ignore the resource cache when loading resources’. Refresh the page normally (all refreshes ignore cache now, not just ⇧-refresh) and all resources will be loaded from origin.