Dear Veerendra, Based on the very limited information you give, it is hard to figure out what really is the problem. However, here are some comments:
-Molecules in the asymmetric unit: If e.g. there are two molecules in the asu and you searched only for one, you might get good phaser statistics and bad R-factors. In the phaser log file there is an estimate how many molecules phaser would expect in the asu. -Correct space group: Depending on your phaser job, phaser might decide that the true space group is different from the space group used during data processing. If you did not change the space group of your input mtz to the one found by phaser, refinement might have been done with the wrong space group, resulting in catastrophic Rfactors. -Other problems like twinning. Good luck! Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Veerendra KUMAR (IMCB) Gesendet: Freitag, 19. September 2014 11:34 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Phaser MR problem Dear CCP4 members, Recently I have collected native data at 3.3 A resolution. The structure of the protein should have two domains. The structure of c terminal domain from homologous (30 seq similarity) is known. I took n terminal domain from another homologous protein. I ran the phaser using these two ensembles and got the following solutions. # [No title given] SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 0.27592 BFAC 5.82534 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 1.60902 BFAC 5.47988 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy Ala phaser model. The R values are 0.590/0.62. I use the map to build the model in Buccaneer but it did not build anything. Is the pahser solution correct? Why are the R values so high despite the good TFZ score? Any suggestions are greatly appreciated. Thank you Veerendra Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
