Hi Dale, my experience is that high-B regions may become "visible" in maps only late in refinement. So my answer to the original poster would be - "both global reciprocal-space (phase quality) and local real-space (high mobility) features contribute to a region not appearing ordered in the map". This would be supported by your experience if those residues that you could not model in 3BCL had high (or at least higher) B-factors compared to the rest of the model. Is that so?
best, Kay
