Before asking this question I searched as well as I could in the explanatory pages, as well as discussion threads.

In the bottom-right segment of the Rosetta graphic, which shows the combined "Accepted Energy" plus "RMSD", occasionally there are small red squares. What do they indicate?

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AFAIK:

"The red dots are the lowest energy structures of each completed trajectory." --David Kim, Project scientist

"Alright, just for clarity, each folding run generates a low energy 'red dot' in the local graph on local system. There are generally multiple folding runs per work unit so multiple 'red dots' are expected, just not all visible at the same time due to the shifting of the local splatter graph window to accommodate the range of energy levels. The resulting 'red dots' are sent back to rosetta to be consolidated into the 'results' splatter graph along with other completed WUs. All the 'green points' the local computer has generated in the local splatter graph are discarded." -- cruncher

(Source: Graphics thread)

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