Well - you are a long way from a solution! All those rotation angles are close to each other..
What is the cell? How similar is the model to your structure? Have you looked at the self rotation function? Eleanor On Thu, 25 Feb 2021 at 20:54, Muhammad Bashir Khan <m...@ualberta.ca> wrote: > *Hello everyone;* > > > *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: m...@ualberta.ca <cbroo...@ualberta.ca> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
