My understanding is that NCS restraint can significantly enhance the speed
> of calculation, but considering the subunits even with the eactly same
> sequence may not be identical, to have NCS restraint may be not necessary
> or may be not good for the refinement, am I right?
>
Non-crystallographic symmetry (NCS) is one of the sources of a priori
knowledge about your crystal structure that can be used to inform
refinement. Practically NCS can be used as constraints (or strict NCS) or
restraints. In case of constraints all NCS related units are identical. In
case of NCS restraints, NCS related copies are guided to be similar; this
can be done in torsion angle space ("torsion NCS") or in Cartesian space
("Cartesian NCS"). NCS restraints or constraints can be applied to
coordinates, B-factors occupancies, etc all other refinable parameters of
atomic model.
Using Cartesian NCS requires you to be more careful selecting NCS related
groups. Torsion NCS with top-out like restraint potentials make it more
straightforward. Most of todays programs do a good job using NCS more or
less automatically.
Using NCS restraints may slightly increase the time of refinement because
extra calculations are done.
Using NCS constraints may slightly decrease the time of refinement because
even though the minimizer deals with less refinable parameters, Fcalc,
refinement target and gradients are still calculated using all atoms (not
only NCS independent part).
Typically, using NCS in refinement is beneficial at resolutions ~2A and
lower. Technically, torsion NCS with top-out potential should do no harm at
resolutions better than 2A. A rule of thumb, at 2-4A you use NCS restraints
and at resolutions lower than 4A using NCS constraints may be good.
Some helpful reading includes:
Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J.
& Sheldrick, G. M. (1999). Acta Cryst. D55, 1158-1167.
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A.,
Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst.
D67, 355-367.
Smart, O. S., Womack, T. O., Flensburg, C., Keller, P., Paciorek, W.,
Sharff, A., Vonrhein, C. & Bricogne, G. (2012). Acta Cryst. D68, 368-380.
J. J. Headd, N. Echols, P. V. Afonine, N. W. Moriarty, R. J. Gildea and P.
D. Adams. Acta Cryst. (2014). D70, 1346-1356
Pavel
