The manuscript is mostly written already; but some parts of the Results are still up in the air because they were waiting for some final data. It also needs polishing and some revising to incorporate results from a Neisseria uptake sequence paper that came out a few months ago.
To cope with all the data we've been occasionally creating 'Flow of Results' pages that summarize our results and conclusions, in the order we think the paper should present them. Yesterday we began our final push by going through the most recent version of the Flow of Results'. I'm not sure we have everything in the perfect order, but we have an order that's good enough, with each result triggering a question that's addressed by the next result.