[phenixbb] Problem avoiding real space refinement

[Nathaniel Echols]

On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu <JNwachuk at scripps.edu> wrote:
> We noticed that in some of our refinements, real space refinement was
> performed even though we chose not to do this.
> I tried to opt out of real space refinement as follows:
> " refine {
>     strategy = *individual_sites individual_sites_real_space rigid_body \
>                *individual_adp group_adp *tls *occupancies group_anomalous
> ..."
> however, the R-free is identical whether we select real space refinement or
> not, and the logfile shows
> " Validate:
>                 |--------START--------|  |--------FINAL--------|
>      residue    map_cc 2mFo-DFc mFo-DFc  map_cc 2mFo-DFc mFo-DFc
>   "LYS A  18 "  0.9359    16.78    0.00  0.9107    17.60    0.00
>   "ARG A  19 "  0.9513    21.82    0.00  0.9470    20.97   -6.52  <<<
>   "ARG A  26 "  0.9440    26.72    0.00  0.9474    27.33   -2.43
>   "ARG A  69 "  0.9685    31.36    0.00  0.9659    32.58    0.00
>   "GLN A  86 "  0.9681    23.57   -5.81  0.8850    19.29  -18.27  <<<
>   "GLU A  89 "  0.9689    26.30   -4.43  0.8977    23.67  -11.59  <<<
>   "LYS A  93 "  0.9746    25.19    0.00  0.9682    26.47    2.90
>      ... "
> and  suggesting that real space refinement was performed.

That's the rotamer fitting - technically, it's an independent step
(fix_rotamers=True)  The individual_sites_real_space strategy only
performs global real-space refinement.

-Nat