We consider the proof complexity of the minimal complete fragment, KS, of standard deep inference systems for propositional logic. To examine the size of proofs we employ atomic flows, diagrams that trace structural changes through a proof but ignore logical information. As results we obtain a polynomial simulation of versions of Resolution, along with some extensions. We also show that these systems, as well as bounded-depth Frege systems, cannot polynomially simulate KS, by giving polynomial-size proofs of certain variants of the propositional pigeonhole principle in KS.

**NB: ** * This is a long version of the conference paper Complexity of deep inference via atomic flows. Importantly, this version resolves some errors in the proofs and statements of the conference version.*