[phenixbb] Problem avoiding real space refinement

Jerome Nwachukwu JNwachuk at scripps.edu
Thu Oct 27 08:31:08 PDT 2011


Hi:
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.
Is there a way to correct this, or to ensure that real space refinement is not performed during refinement?

Thank you,
-Jerome

Jerome C. Nwachukwu, PhD
Dept. of Cancer Biology
The Scripps Research Institute-Florida

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