you payed my attention to something i did

in first round of refinment after molecular replacment

i used
1- output.sca
2- MR.1.pdb
3- MR.1.mtz

as input files

then i proceded with the output of this round of refinment to other

because you sayed ((do not use MR.mtz for refinement!*))

1- in this case should i start agian from the begining or it does not matter because .sca was included.

2- how can i know form the output files of this first run, if both .sca and MR.1.mtz were used or only one was used in refinment

I just tried this, and if you added the Scalepack file first (which, FYI, would get done for you automatically if you clicked the "Run phenix.refine" button in the AutoMR or Phaser GUIs), then MR.1.mtz will be used as experimental phase restraints, but nothing else. This isn't appropriate (you should only use genuine experimental phases for this, not model-based phases), but it doesn't negate the results of the refinement. However, you really need to look at the log file from refinement to be certain - it will state which parameters each reflection file were used for. Could you please send the log to nechols@lbl.gov (not the entire list)?

-Nat