[mjslee0921]

A deposited covalent bond at an oxygen can replace an entire unobserved CCD branch. The existing non-CCD reconstruction fallback only considers immediate terminal neighbors, so it regenerates a missing phosphate at an already bonded nucleotide O5′.

Extend that fallback with a conservative heavy-atom graph check: neutral oxygen, two CCD single bonds, one retained external single bond to a nonmetal, a unique wholly unobserved acyclic side, and observed support on the retained connected side. Equivalent observed copies must agree; any deposited branch atom in the entity site vetoes removal. Protection concerns retained raw atoms and bonds, not unrepresented struct_conn declarations. Existing terminal-neighbor behavior remains unchanged. Native confidence slots already use canonical atom-name indices.

Validation: 16 focused tests and scoped hooks passed. Actual same-input 4N48 reconstruction removes only P/OP1/OP2/OP3 from G1 in chains C and D, preserving every surviving atom annotation, coordinate and bond; named confidence slots are unchanged. The 237,550-atom 6D9J reconstruction is unchanged. These controls cover reconstruction before assembly/cropping; revised full-panel and final-consumer validation remain outstanding.

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