Timeout with Snapshot

I am getting this error when running Snapshot on our client's site:

This request takes too long to process, it is timed out by the server. If it should not be timed out, please contact administrator of this web site to increase 'Connection Timeout'.

It's hitting the uploads/2016/12 folder and crashing.

I already increased max_execution_time to 600 but it's not getting anywhere near 10 minutes before showing this error.

The folder it crashes on has some files up to 7Mb individually, but the whole folder is around 160Mb in total size and contains about 4000 files.

Any idea?