The six separate tail costs do not add to the full tail cost in the tested 6V5D selections.

In Protein Data Bank entry 6V5D, six separate tail-atom alignment costs did not add to the cost of fitting the full tail. Using all 176 models and 76 C-alpha atoms in chain A, we aligned models with generalized Procrustes fitting and measured coordinate variance in residues 1–70. The full-tail cost was 0.18292612791453855 Ų; the six single-atom costs summed to 0.10627480058171263 Ų, leaving a gap of 0.07665132733282592 Ų (41.902886267092876% of the full cost). All 1,462 saved selections of 16 models had a positive gap. For residue 71, the single-atom cost was +0.0011295066016146493 Ų, while its marginal cost after the other five tail atoms was −0.002613625792239116 Ų. These findings describe this alignment calculation on one fixed coordinate ensemble. They do not establish physical interactions, biological causality, or global convergence. The actual refinement groups remain unknown; selections overlap and quantiles are descriptive, not confidence intervals. The work does not measure dynamics or agreement with independent experimental data.

protein structure · ubiquitin · 6V5D · structural alignment · generalized Procrustes · coordinate variance · RMSF · tail atoms · sensitivity analysis · NMR ensemble · Shapley allocation