Hi Young-Jin,
Third, ncs may be the key... I re-processed hkl and cut the resolution
I'm wondering why you cut the resolution?
and did ncs=true. It first generated error message and suggested to put distance limit upto 3.
With ncs=true phenix.refine will determine the NCS groups automatically. Since the currently used algorithm is very simple the NCS groups may not be chosen optimally (making it smart is in to-do list). This is why it is a good idea to check the automatically determined NCS groups, especially when you see a message that asks you to push the distance limit to a larger value. You can look in .geo file (the file that lists all the geometry restraints used in refinement) for something like EXCESSIVE DISTANCE to see affected atoms and then check the map to see if these atoms should be forced to obey NCS and not represent the individuality of NCS related groups and therefore need to be excluded from NCS restraints. Good luck! Pavel.