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Two defects in percycle_phenix, both long-standing (the 0.6.3 archive carries the same values), which together removed phenix from the convergence panel: 1. The per-macrocycle R-factors were divided by 100. The log prints fractions -- " 0.3234 0.3388 0.0154 0.014 1.3" under "work free delta bonds angl", against that same log's "Final R-work = 0.2212" -- so every phenix trajectory came out at ~0.003. Its total apparent R-free improvement was then ~0.0009, below the panel's guard, and the curve was dropped with the legend reading n=0. 2. Each block holds one row, the state at the START of that macrocycle, so block i is cycle i. Emitting block 0 a second time as cycle 1 gave phenix a flat first macrocycle -- it appeared to achieve nothing in the cycle where it moves most. The end of the final macrocycle appears only in the summary line, never in a block, and was missing entirely; it is now read from "Final R-work =". 1A0F now traces 0.3388 -> 0.2509 across cycles 0-10, landing exactly on the value the log reports for itself. Median fraction of total R-free improvement by macrocycle 2: torchref 0.814, phenix 0.766, refmac 0.596. Panel D previously showed no phenix curve at all. Figure 2C keeps the carried-over 0.6.3 runtimes; re-aggregating rewrites fig_runtime.csv, so it was restored from the archive again afterwards. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_018QVRRkhcy5omKhb5a8TM8H
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Two defects in percycle_phenix, both long-standing (the 0.6.3 archive carries the same values), which together removed phenix from the convergence panel: