STENCIL: Alignment Fidelity Outweighs Template Selection in Retrieval-Augmented Protein Inverse Folding

Retrieval-augmented inverse folding conditions design on similar templates, and recent work invests in retrieving more and better ones. Within the template-retrieval setting studied here, candidate discovery already provides informative structural evidence. We therefore focus on the next post-retrieval bottleneck: conditional on an admissible template, can its residues be registered precisely at the target positions? STENCIL addresses this question by exhaustively re-aligning retained candidates by exact structural superposition, using a single template, and decoding in one deterministic pass with 3.2M parameters. On split-safe CATH 4.2 it reaches 69.342% residue-pooled recovery, the highest among methods with runnable deterministic re-evaluations under our protocol. The decisive test leaves the template, its coverage, its TM-score and its composition untouched, and permutes only where its residues land; that alone costs 26.95 recovery points. A complete-case paired 2x2 analysis finds that the alignment contrast is statistically larger than the selection contrast. The sequence-identity analysis bounds the regime in which retrieval helps.