Because I haven't yet find answer to my question and I have tried everything, I need to ask questions here again.
I created clean project using different manuals but somehow I end up always to the same problem.
Example guide what I have used:
I can create custom site collection and when I open it, it gives me 404 error message.
I can access settings page, when I write /_layouts/settings.aspx
Here is source code:
source
Here is log file: log