Messed up my keychain and certificates, how I can put it all in factory settings?

I had some problem with SSL authentification in homebrew program and follow a stackoverflow advice to delete Digicert certificates in my keychain, which helped, but since then I couldn't open certain https websites in Safari. I then followed another advice to reset my keychain and restart computer, but apart from the obvious downsides of resetting my keychain, I still can't open for exemple facebook.com in browser (right now in any browser).

I was also tinkering with system time yesterday, I don't know if there is any connection.

So my question is, how do I reset everything so the keychain downloads and saves new certificates?