<div dir="ltr">Dear All;<div><br></div><div><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i>I collected data set which can be easily processed in a space grouop P21 (P1211)</i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i>at approx 3.7A. I procedeed with MR using phaser in phenix which give a solution with two copies.
</i><i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">** There were 8 solutions<br><br>** Pdb and/or Mtz files have been written with results for 1 of these solutions<br><br>** Solution #1 written to PDB file: Khan_phaser.1.pdb<br>** Solution #1 written to MTZ file: Khan_phaser.1.mtz<br> Solution #1 annotation (history):<br> 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<br> LLG=1210 TFZ==36.8<br> SOLU SPAC P 1 2 1<br> 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<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64<br><br> Solution #2 annotation (history):<br> 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<br> TFZ==34.0<br> SOLU SPAC P 1 2 1<br> SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00 0.14 BFAC -3.15<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65<br><br> Solution #3 annotation (history):<br> 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<br> TFZ==39.2<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00 0.01 BFAC -1.69<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64<br><br> Solution #4 annotation (history):<br> 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<br> TFZ==33.6<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00 0.47 BFAC -2.89<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64<br><br> Solution #5 annotation (history):<br> 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<br> TFZ==33.6<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00 0.47 BFAC -1.57<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64<br><br> Solution #6 annotation (history):<br> 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<br> TFZ==34.6<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01 0.03 BFAC -2.58<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66<br><br> Solution #7 annotation (history):<br> 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<br> TFZ==34.5<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01 0.03 BFAC -1.93<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65<br><br> Solution #8 annotation (history):<br> 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<br> TFZ==38.5<br> SOLU SPAC P 1 21 1<br> SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00 0.00 BFAC -1.77<br> 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<br> SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65<br><br>CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs)<br>Finished: Tue Feb 16 23:27:36 2021<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i>Got the following warnings:</i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">WARNINGS<br>--------<br><br>------------------------------------------------------------------------------------------<br>Warning: Intensity moments suggest possibility of twinning. Tests based on possible twin<br>laws will be more definitive.<br>------------------------------------------------------------------------------------------<br><br>------------------------------------------------------------------------------------------<br>Warning: The composition you have entered gives a solvent content of 87%, which is<br>extremely unlikely. You should increase the composition.<i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">After running xtraige for the .mtz, I get this warning about NCS<i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Frac. coord. : 0.157 -0.000 -0.333<i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Distance to origin : 119.294<i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Height relative to origin : 33.056 %<i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">p_value(height) : 8.504e-04.<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">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.<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Upon an attempt at initial refinement with different stratageis, the R-fators are stuck at<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Start R-work = 0.5066, R-free = 0.5233<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Final R-work = 0.4831, R-free = 0.4965<br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><br></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">The question is that there is something that is not being recognized
for example merohedral twinning or that the NCS/pseudosymmetry is not <span style="font-family:Arial,Helvetica,sans-serif">being addressed</span></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"> correctly. Any suggestions would be highly appreciated.</pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Regards;</pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)"><i><br></i></pre><pre style="white-space:pre-wrap;color:rgb(0,0,0)">Bashir</pre></div><div><div>-- <br></div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><span style="font-family:Helvetica;font-size:medium">------------------------------------------------------</span></div><span style="font-family:Helvetica;font-size:medium">Muhammad Bashir Khan, Ph.D.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Research Associate</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Department of Biochemistry</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Medical Science Bldg.</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Lab 3-27</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">University of Alberta</span><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Edmonton AB, T6G 2H7</span><br style="font-family:Helvetica;font-size:medium"><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">Phone: </span><a value="+17804923465" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium">780-492-4577-</a><br style="font-family:Helvetica;font-size:medium"><span style="font-family:Helvetica;font-size:medium">e-mail: </span><a href="mailto:cbrooks1@ualberta.ca" style="color:rgb(17,85,204);font-family:Helvetica;font-size:medium" target="_blank">mbk@ualberta.ca</a><br></div></div></div></div></div></div>