For some reason after upgrading to Sierra some of self signed certificates stopped being trusted.
Keychain Access was hanging and guru meditating while trying to delete/reinstall certificate.
this helps to reinstall self signed certificate:
0. find your certificate among installed
security find-certificate -a -Z|grep -e "SHA\|alis"
1. remove cert with
security delete-certificate -Z certSha
2. install cert via command line
sudo security add-trusted-cert -d -r trustAsRoot -p ssl myCoolSelfSigned.cer
3. in Keychain Access in system keychain open certificate and select "Always Trust"
as well this tool does magick
sudo certtool i myCert.crt