Hi All, I am working on a dataset diffracted to ~2.8 A and the highest template identity is about 12%. I am trying MR_Rosetta following the online manual with the following command, hhr file and fragment files are prepared as online manual suggested. phenix.mr_rosetta seq_file=../seq.dat data=../in.mtz hhr_files=../xxx-align.hhr read_hhpred.number_of_models=1 read_hhpred.number_of_models_to_skip=0 already_placed=False fragment_files=../aat000_03_05.200_v1_3 fragment_files=../aat000_09_05.200_v1_3 rescore_mr.relax=False ncs_copies=2 use_all_plausible_sg=True nproc=8 group_run_command=sh resolution=4.5 place_model.mr_resolution=4.5 rosetta_modeling.map_resolution=4.5 run_prerefine=true number_of_prerefine_models=1000 >& log this run ends up with the error message like this, Trying to adjust the PDB sequence from alignment file: ---------------------------------------------------------------------------------KMNSKELSLKGLCLR--DDGPGIIIVVGNEKSCKFYENLVMK-------------------DMHNNSISKTWEGYLQDCKFKGWFMKVCNDQDSLLRTLGQ------------ to match the actual PDB sequence: KMNSKELSLKGLCLRIRDDGPGIIIVVGNEKSCKFYENLVMKDMHNNSISKTWEGYLQDCKFKGWFMKVCNDQDSLLRTLGQ New alignment line 4 for PDB: 0 ---------------------------------------------------------------------------------KMNSKELSLKGLCLR--DDGPGIIIVVGNEKSCKFYENLVMK-------------------DMHNNSISKTWEGYLQDCKFKGWFMKVCNDQDSLLRTLGQ------------ Sorry: Sorry, please supply an alignment file for this job. mr_rosetta cannot automatically generate alignments where there are deletions required from the PDB file This only happens when I set ncs_copies=2. If i change ncs_copies=1, no such error. When I looked at the output file with ncs_copies=2, I find a MR solution with very high TFZ (~16) and high LLG (>500). So I re-run with ncs_copies=2 with the mr_rosetta_params.eff file in the first run, the program ends at the same point. But the MR solutions all have low TFZ (~5) and small LLG (<60). Here are my two questions, 1) Why does the program stop if i set ncs_copies=2 but not ncs_copies=1? 2) Why the re-run on same data with same parameters give different result? Thanks in advance for helping me on these problems. Regards, Fengyun