Hello List, I am very new to using Phenix/Rosetta to solve MR. I just finished a job by following the procedures described on phenix-online.org using Phenix GUI. The program reported that no solution was found, but when I went through the RUN_FILE_*.log, I found that despite all the log files ended with the following sentences: Stage to relax: refined_rescored_rosetta_solution No solutions to relax No autobuilt solutions to iterate... Finishing up mr_rosetta... one solution had a Rfree of 0.48 with correct number of molecules in ASU. When I refined that solution using phenix, Rfree went down further, proving to be a correct one. So my question is: why phenix.mr_rosetta did not report this solution as a good one? My second question is regarding model rebuild using phenix/rosetta. No matter I used the GUI or command lines copied from phenix-online like the following: phenix.mr_rosetta \ seq_file=~/MA/Mpa.pir \ data=~/MA/MA.mtz \ search_models=~/MA/refine_6.pdb \ already_placed=True \ fragment_files = ~/MA/MA-3mer \ fragment_files = ~/MA/MA-9mer \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=6 \ space_group="C 1 2 1" \ use_all_plausible_sg=False \ nproc=4 the program always fails. The log files have the following messages: Sorry, a subprocess has failed... ...... Sorry: Failed to run REBUILD...see log file in MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log They pointed to rebuild.log files, but these files don't contain error message and they ended with the following seemingly innocuous lines: protocols.relax.FastRelax: CMD: accept_to_best -3682.86 0.994359 0.994359 0.44 core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. protocols.relax.FastRelax: CMD: endrepeat -3682.86 0.994359 0.994359 0.44 protocols::checkpoint: Deleting checkpoints of FastRelax protocols::checkpoint: Deleting checkpoints of FastRelax protocols.jd2.JobDistributor: S_MA_R_0005 reported success in 4573 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 20716 seconds I would appreciate it if you could tell me what could be the causes of the failures. Thank in advance, Yonglin