I have tried to run Sharepoint site collection. When I went to site settings I have got an error message "File not found", but which file? I said ok, I want to be clever, then I went to Event Log where I found error message from Sharepoint: "Error: Failure in loading assembly: Microsoft.SharePoint, Version=184.108.40.206, Culture=neutral, PublicKeyToken=71e9bce111e9429c" after crawling for a while I found the solution (and cause).
When You edit Your web.config using nice IIS pluggedin editor, this editor add namespace declaration xmlns="http://schemas.microsoft.com/.NetConfiguration/v2.0" which is wrong here for some reasons. Just remove this namespace and be happy You have fixed Your problem.