# How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA

In the tutorial of RNAfold it states,

RNAfold reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in dot-bracket notation and its free energy to stdout.

In the example using the -p --MEA options, the

• MFE = -5.00 and the
• ensemble Free Energy = -5.72.

How can the free energy of the ensemble be lower than the minimum free energy?

• @MichaelG. First, thank you. I read and learn from your comments and answers. Second: I tried with CUACGGCGCGGCGC and I get: structure=.....(((...))) with -0.40 kcal/mol for the MFE and for the probab. representation of the ensemble, structu=.....,,,...)), with -1.10 kcal/mol. I don't see pseudoknots there (should I?). – aerijman Apr 15 '19 at 18:49
• @MichaelG. 1st: Thank you! I feel honored!! 2nd: I think (and I could be wrong) that the only tool in Vienna that predicts pseudoknots is RNAPKplex (I am too far from being expert in the topic, I just googled it -couldn't find that info as fast in Vienna documentation-). 3rd: I am perplexed... I don't know how is this possible – aerijman Apr 22 '20 at 16:26