How to optimize Scanning/Indexing in PyCharm?

Question

PyCharm

A completely incomprehensible situation happens to me with PyCharm 2017.1.5 on Ubuntu 16.04 (I suspect that the problem may occur on the entire JetBrains IDE line, so I put the appropriate tags).
After doing "File" -> "Invalidate Caches / Restart", pycharm decided to crawl and index everything! . The Scanning files for Indexing
stage lasted for 20 minutes , and now I have been watching Indexing for half an hour, and I see that it scans not only the current project, but also others that are in a completely different place, and the contents of my home folder that are in no way related to development (~/.cache, ~/.config). Vine indexes the file system. Even saw how he climbed into "/lib/...". In general, almost everything is real, 99% of which I definitely don’t need in a specific python project.
He doesn't care about my settings in "File -> Settings -> Project Structure", where I added almost everything to Excluded, except for the code. And I did not find other settings on this topic at all.