Python console duplicates main window

Do you mean your source code gets automatically added to Python Console?

Yes, and I want at left to see only variables. How to move python output down and keep left only variables?

It can't be disabled completely.

You could just resize the Variables and drag it all the way to the left.

You may also want to try our Jupyter support https://www.jetbrains.com/help/pycharm/jupyter-notebook-support.html