I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this: Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 Deciding if we should continue... Recent R change per cycle: 0.0 Ending these build cycles as the recent change in R per cycle has been 0.0 and the required value of change is -0.005 and the R is somewhat acceptable at 0.276670644792 All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 All omit/non-omit regions completed finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 Finishing AutoBuild Run 162 Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat AutoBuild Run 162 Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz Sequence file: /Users/heather/Desktop/M/m.pir Best solution on cycle: 2 R/Rfree=0.26/0.33 Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb --- Model (CIF file) --- cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif --- Refinement log file --- log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine --- Model-building log file --- log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log --- Model-map correlation log file --- log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz You might consider making one very good model now with: phenix.autobuild \ data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \ model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ rebuild_in_place=True \ seq_file=/Users/heather/Desktop/M/m.pir My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed. I am using 1.8.2-1472 if that matters. Thanks, Heather