Dear Phenix community, I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on linux. However, I noticed 2 weird things: 1st, Phenix seems that can not handle with alignment between the residues from pdb and sequence.seq, flagging the "Rebuild in place not recommended as identity * fraction_aligned is 0.0%" message but still trying to build the structure with the option "include_input_model=False" I guess(?)... and 2nd, after quite a while I obtained the following error message: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1' /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log: File exists. ******************************************************************************** The alignment between MR.1.pdb and sequence.seq should be something like 80%+! Also tried to run using the followed command line: phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True n_cycle_rebuild_max=5 seq_file=sequence.seq Same problem as above. Could anyone please tell me what to do to prevent this error and get phenix get its job finished? Many thanks in advance, Joao.