If you have sub-plots going nowhere, scenes that advance nothing or characters that fail to come alive; if parts of your story are told in the wrong sequence, you’ve begun it too early or dragged on the ending too long: this is where it should be picked up. At this stage, you want someone who can judge the MS as a whole, and who knows the rules and standards of your genre (and in this context, lit fic is a genre).
Good beta-readers can be excellent at this – however, bear in mind that they are READERS, not necessarily writers or editors. They can tell you where part of your book is not working for them, but they probably won’t suggest how to fix it.
If your book is NON-FICTION then you may choose work with a structural editor at a much earlier stage, when you are working out how to construct your book, how to order and present your ideas.