[phenixbb] Re: Seeking Advice on Difficult MR Case: TFZ 6–8 for All Search Models, R-free ~0.50

Thank you for the suggestion. I did use phenix.process_predicted_model on the AlphaFold model before MR. I tested both the processed full-length model and the resulting domain-partitioned models. Unfortunately, the results were very similar to those obtained with manually trimmed/domain-separated models. TFZ values remain in the 6–8 range and subsequent refinement stalls with R-free around 0.50. Therefore, I suspect there may be a larger issue than simply search-model preparation.