Diagnosing and narrowing the simulation-to-real gap in powder X-ray diffraction with a wet-dry agentic loop

Powder X-ray diffraction (PXRD) is the routine probe of crystalline matter, yet its analysis is the rate-limiting step as laboratories automate acquisition. Deep-learning analyzers excel on simulated patterns and degrade on measured ones. This simulation-to-real gap is structural, not additive: synthetic denoising gives no measurable lift on real spectra, whereas correcting a small peak-position drift more than doubles median retrieval correlation. Real-spectrum fine-tuning, peak-aligned reranking, and recalibration narrow what remains and restore the coverage synthetic anchors lose. Xtalyst integrates these in an agent-orchestrated system spanning phase identification, refinement, and calibrated property prediction. On a frozen held-out partition (n=534) each module measured on both splits reproduces its development finding -- including the synthetic-anchor under-coverage, whose magnitude differs between the two pools -- while held-out refinement converges and preserves symmetry without reaching profile-quality fits, and on a diffractometer its wet-dry recommend-rescan-reanalyze loop flips a blinded silicon standard to a gated PASS and changes which minor phase is resolved on a multi-metal alloy.