I'm not quite at the stage of sending out queries for my novel yet. But I am drafting the agent query letter, which has turned out to be a pretty enlightening process.
The guidance I've found most helpful so far comes from agent Noah Lukeman, who has written a free e-book on query letters. He advises keeping the summary of your novel to one paragraph, three sentences long. Seems like an extremely tall order, but, with the help of some swift comparisons, it's actually doable. (The Brothers Karamazov meets A Canticle for Leibowitz! OK, I didn't use that one...)
I remember the agonies I went through trying to write the abstract for my dissertation, and it's safe to say I *never* succeeded in getting at the heart of what I was writing about. But maybe that's because I had 1-2 pages to work with, instead of three sentences. Actually writing it in one sentence first is even better (this is called the "log line" or "hook," I've learned).
Yes, your novel is complicated, but if you can't summarize it in one or three sentences--I mean literally cannot, after weeks of effort--you do have a problem. It means your purpose in writing your novel is not clear to you. And that means it will be unclear, not only in your synopsis or log line, but in the novel itself.
For me, the process of drafting the query has involved a dialog between the novel and the query. Between query drafts, I've found myself returning to the novel and revising. Not massively, but enough to clarify issues that caused the synopsis I was trying to write to sound false. In other words, I'd write a synopsis that seemed like it should be true, but I realized in the novel that it wasn't. I asked myself why not, and often decided the synopsis version was the better one. Writing the synopsis helped me figure out something that didn't yet make sense in the novel.
There must be a point when it is too early to try to write a synopsis and log line, but it seems to be a very helpful tool in later-stage revisions.