[phenixbb] NCS/pseudo-symmetry
Muhammad Bashir Khan
mbk at ualberta.ca
Thu Feb 25 12:56:12 PST 2021
Dear All;
*I collected data set which can be easily processed in a space grouop
P21 (P1211)*
*at approx 3.7A. I procedeed with MR using phaser in phenix which give
a solution with two copies.
*
** There were 8 solutions
** Pdb and/or Mtz files have been written with results for 1 of these solutions
** Solution #1 written to PDB file: Khan_phaser.1.pdb
** Solution #1 written to MTZ file: Khan_phaser.1.mtz
Solution #1 annotation (history):
SOLU SET RFZ=3.4 TFZ=4.2 PAK=0 LLG=15 TFZ==5.5 RFZ=2.8 TFZ=27.6
PAK=5 LLG=1173 TFZ==36.5 LLG=1210 TFZ==36.8 PAK=6
LLG=1210 TFZ==36.8
SOLU SPAC P 1 2 1
SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.3 FRAC 0.20 0.00
0.18 BFAC -1.90 #TFZ==5.5
SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.2 FRAC 0.05 0.00
0.51 BFAC 1.60 #TFZ==36.8
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64
Solution #2 annotation (history):
SOLU SET RFZ=3.0 TFZ=5.5 PAK=0 LLG=10 RFZ=2.7 TFZ=25.6 PAK=0
LLG=1165 TFZ==34.8 LLG=1198 TFZ==34.0 PAK=4 LLG=1198
TFZ==34.0
SOLU SPAC P 1 2 1
SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00
0.14 BFAC -3.15
SOLU 6DIM ENSE ense_1 EULER 169.3 96.4 357.9 FRAC 0.91 -0.00
0.52 BFAC 1.82 #TFZ==34.0
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65
Solution #3 annotation (history):
SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=34.6 PAK=1
LLG=1146 TFZ==39.7 LLG=1185 TFZ==39.2 PAK=3 LLG=1186
TFZ==39.2
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00
0.01 BFAC -1.69
SOLU 6DIM ENSE ense_1 EULER 8.3 86.4 2.0 FRAC -0.14 -0.00
0.34 BFAC 1.72 #TFZ==39.2
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64
Solution #4 annotation (history):
SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=2.9 TFZ=30.5 PAK=6
LLG=1156 TFZ==34.4 LLG=1183 TFZ==33.6 PAK=7 LLG=1183
TFZ==33.6
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00
0.47 BFAC -2.89
SOLU 6DIM ENSE ense_1 EULER 359.5 82.1 2.8 FRAC -0.02 -0.00
0.14 BFAC 2.57 #TFZ==33.6
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64
Solution #5 annotation (history):
SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=3.0 TFZ=29.0 PAK=6
LLG=1115 TFZ==34.1 LLG=1178 TFZ==33.6 PAK=7 LLG=1178
TFZ==33.6
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00
0.47 BFAC -1.57
SOLU 6DIM ENSE ense_1 EULER 180.1 99.2 180.7 FRAC 0.34 0.50
0.20 BFAC 2.47 #TFZ==33.6
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64
Solution #6 annotation (history):
SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=36.2 PAK=1
LLG=1136 TFZ==35.0 LLG=1169 TFZ==34.6 PAK=1 LLG=1169
TFZ==34.6
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01
0.03 BFAC -2.58
SOLU 6DIM ENSE ense_1 EULER 359.2 82.9 1.4 FRAC -0.09 0.01
0.36 BFAC 2.08 #TFZ==34.6
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66
Solution #7 annotation (history):
SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=35.3 PAK=1
LLG=1122 TFZ==35.4 LLG=1149 TFZ==34.5 PAK=1 LLG=1148
TFZ==34.5
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01
0.03 BFAC -1.93
SOLU 6DIM ENSE ense_1 EULER 180.8 97.5 182.4 FRAC 0.78 -0.49
0.31 BFAC 2.44 #TFZ==34.5
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65
Solution #8 annotation (history):
SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=33.9 PAK=1
LLG=1083 TFZ==38.5 LLG=1146 TFZ==38.5 PAK=4 LLG=1146
TFZ==38.5
SOLU SPAC P 1 21 1
SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00
0.00 BFAC -1.77
SOLU 6DIM ENSE ense_1 EULER 8.1 86.2 2.6 FRAC 0.17 -0.00
-0.33 BFAC 1.66 #TFZ==38.5
SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65
CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs)
Finished: Tue Feb 16 23:27:36 2021
*Got the following warnings:*
WARNINGS
--------
------------------------------------------------------------------------------------------
Warning: Intensity moments suggest possibility of twinning. Tests
based on possible twin
laws will be more definitive.
------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------
Warning: The composition you have entered gives a solvent content of
87%, which is
extremely unlikely. You should increase the composition.
After running xtraige for the .mtz, I get this warning about NCS
Frac. coord. : 0.157 -0.000 -0.333
Distance to origin : 119.294
Height relative to origin : 33.056 %
p_value(height) : 8.504e-04.
Translational pseudo-symmetry is very likely present in these data.
Be aware that this will change the intensity statistics and may impact
subsequent analyses, and in practice may lead to higher R-factors in
refinement.
Upon an attempt at initial refinement with different stratageis, the
R-fators are stuck at
Start R-work = 0.5066, R-free = 0.5233
Final R-work = 0.4831, R-free = 0.4965
The question is that there is something that is not being recognized
for example merohedral twinning or that the NCS/pseudosymmetry is not
being addressed
correctly. Any suggestions would be highly appreciated.
Regards;
Bashir
--
------------------------------------------------------
Muhammad Bashir Khan, Ph.D.
Research Associate
Department of Biochemistry
Medical Science Bldg.
Lab 3-27
University of Alberta
Edmonton AB, T6G 2H7
Phone: 780-492-4577-
e-mail: mbk at ualberta.ca <cbrooks1 at ualberta.ca>
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