There are a large number of PAK clashes, I would regard this "solution" with caution. Have you inspected the solution to see where these clashes are occurring? If they are from long flexible loops or the termini, perhaps if you would trim the model to remove those clashes and re-run the MR calculation, you might wind up with a better solution that will refine.
I also second the re-building option. Run density modification with the MR solution, then try both Phenix AutoBuild and also Buccaneer. For a 3.0 Å dataset, I would expect that Buccaneer would be more likely to work (and certainly give you an answer in less time). If Buccaneer can't give you a solution after using your "solution" for density modification and re-building, I would regard this as an unusable solution. The R-factors you quote after refinement indicate that the solution is not correct, or at least not correct enough to converge to the true solution. Since it is a multi-domain protein, perhaps try the MR search with individual domains. Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Sharan Karade <sharankar...@gmail.com> Sent: Tuesday, February 16, 2021 12:38 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Challenging Molecular Replacement EXTERNAL MAIL Hi, Looks like, you have the solution. Have you tried the Phenix AutoBuild module? sometimes it works well. Best luck On Tue, Feb 16, 2021 at 1:21 PM Muhammad Bashir Khan <m...@ualberta.ca<mailto:m...@ualberta.ca>> wrote: Dear All; I have data set of about 3.0A. It's a multidomain protein. I tried several options with MR but it's was not working. I trimmed one of the search models, it does not give any solution using CCP4 molrep. I used Phenix phaser it gives a solution after several hours with the following output. ** SINGLE solution ** Solution written to PDB file: MgtA_phaser.1.pdb ** Solution written to MTZ file: MgtA_phaser.1.mtz Solution annotation (history): SOLU SET RFZ=2.7 TFZ=6.3 PAK=6 LLG=62 TFZ==6.5 RFZ=2.2 TFZ=28.0 PAK=9 LLG=1207 TFZ==42.0 LLG=1370 TFZ==41.8 PAK=9 LLG=1370 TFZ==41.8 SOLU SPAC P 21 2 21 SOLU 6DIM ENSE ense_1 EULER 269.0 80.4 177.3 FRAC 0.24 -0.22 -0.07 BFAC -1.51 #TFZ==6.5 SOLU 6DIM ENSE ense_1 EULER 89.0 80.4 177.3 FRAC 0.26 -1.01 -0.07 BFAC 2.26 #TFZ==41.8 SOLU ENSEMBLE ense_1 VRMS DELTA -0.7291 #RMSD 1.50 #VRMS 1.23 Running Phenix refine on the solution gives a breakup map and the R factors are not decreasing below 47.61 and 50.94. Thank you for any suggestions in advance 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<mailto: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 -- Sharan Karade Postdoc-fellow IBBR-UMD, 9600 Gudelsky Dr, Rockville Maryland 20850 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## 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/
