From Moon of Alabama:

U.S. State Department Daily Press Briefing September 28 2016 – Spokesperson John Kirby

QUESTION: But what I don’t think we have heard here is, so what are the consequences for Russia if this agreement falls through beyond some interagency discussions about options that have not yet been chosen? What are the consequences for Russia other than Secretary Kerry won’t talk to them on this particular issue going forward?

MR KIRBY: The consequences are that the civil war will continue in Syria, that extremists and extremists groups will continue to exploit the vacuums that are there in Syria to expand their operations, which will include, no question, attacks against Russian interests, perhaps even Russian cities, and Russia will continue to send troops home in body bags, and they will continue to lose resources – even, perhaps, more aircraft.

The Russian Federation interpreted that not as a prediction or warning, but as a direct threat.