Nithin, C.; Pilla, S. P.; Kmiecik, S.

CASP16 provided a community-wide benchmark to assess RNA structure prediction across monomeric and multimeric assemblies. In this work, we present the performance of our group (LCBio) as a diagnostic case study to examine the structural and methodological limits of current modeling pipelines. While our workflow achieved top-tier results-ranking first in the RNA multimer category and performing competitively for monomers-achieving high atomic precision remains a significant challenge across the field. We show a hierarchical pattern of predictive breakdown, in which modeling fidelity degrades from reliable local features to increasingly speculative global architectures. Multi-helix junctions emerge as a major transition boundary where 2D topological success often fails to translate into 3D geometric realism, leading to cascading errors in global architecture. Our analysis highlights that, particularly for complex systems, the "hand of the modeler"-through expert-guided curation and template integration-remains important in navigating these limitations. This creates a regime of speculative multimer assembly, where competitive rankings are achieved through correct coarse-grained organization despite persistent subunit-level inaccuracies in interaction geometry. By placing benchmark performance in a direct structural context, this case study helps define the current limits of RNA structure prediction and highlights priorities for improving predictive accuracy.