Hi, Collins, Thanks for the valuable comments. I tried refineing using 2.0A cutoff, but the problem persists. (No Molrep solution is found with R less than 0.7, ).
Could you please show me how can I indentify and eliminate the catastrophic error that I'm having with the data? Regards, At 2010-07-19 19:48:35，"Collins, Edward J" <edward_coll...@med.unc.edu> wrote: Right. So, you have a good map (not perfect since your CC in fo-fc map is in 80% range- should be in 90%s, but lousy overall statistics. What do the R factors/Rfree look like as a function of resolution? Later in this output file, there are those statistics after each cycle. I just want to know if you have a good R factor and Rfree at low resolution but really bad at high resolution? It is possible, based on the postrefine statistics that you chose to use all of your data, but there was really only good data to about 2.0 angstroms. Depending on how bad the statistics are at high resolution, you could get this bad of an Rfree, but that would be strange. At least, I have never seen the Rfactor at 40% in such a case. high 30% would be more likely. The one bin showed in this file is for the highest resolution (50%) which is pretty bad. If you make your resolution cutoff 20-2.0 angstroms and run for a few cycles, you would see if this is a function of resolution. If those statistics look similar (that is, the low resolution R factor and Rfree are bad too), you have a catastrophic error in your data somewhere. It could be pseudo symmetry/wrong space group identification. It could be misindexing in some weird way. It could be a second crystal that unfortunately for you had a series of overlaps -especially on high intensity reflections. Good luck, -ed On Jul 19, 2010, at 3:41 AM, 孙庆祥 wrote: Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADER SWISS-MODEL SERVER ( pa-JAN-g) XXXX COMPND SS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE (WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.522 REMARK 3 BIN RESOLUTION RANGE LOW : 1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.45 REMARK 3 B22 (A**2) : -12.86 REMARK 3 B33 (A**2) : 4.41 REMARK 3 B12 (A**2) : 0.51 REMARK 3 B13 (A**2) : -1.32 REMARK 3 B23 (A**2) : -8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1016 ; 0.008 ; 0.022 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 1.482 ; 1.974 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 122 ; 9.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;33.363 ;26.087 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 176 ;21.472 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;13.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 144 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 774 ; 0.007 ; 0.022 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 624 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 1.686 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 392 ; 1.691 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 362 ; 2.734 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1016 ; 0.952 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 4 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.307 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, K, -K-L REMARK 3 TWIN FRACTION : 0.191 REMARK 3 TWIN DOMAIN : 3 REMARK 3 TWIN OPERATOR : -H, -K, K+L REMARK 3 TWIN FRACTION : 0.198 REMARK 3 TWIN DOMAIN : 4 REMARK 3 TWIN OPERATOR : H, -K, -L REMARK 3 TWIN FRACTION : 0.304 REMARK 3 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 3 SSBOND 1 CYS A 3 CYS A 24 SSBOND 2 CYS A 17 CYS A 41 SSBOND 3 CYS A 43 CYS A 54 SSBOND 4 CYS A 55 CYS A 60 SSBOND 5 CYS B 3 CYS B 24 SSBOND 6 CYS B 17 CYS B 41 SSBOND 7 CYS B 43 CYS B 54 SSBOND 8 CYS B 55 CYS B 60 CRYST1 18.232 39.633 77.526 104.82 90.08 90.04 P 1 SCALE1 0.054849 0.000038 0.000087 0.00000 SCALE2 0.000000 0.025232 0.006677 0.00000 SCALE3 0.000000 0.000000 0.013343 0.00000 >when you say that the Rfree is 0.4, what statistic are you quoting? For all of >your data or the highest shell It is clear from the data reduction statistics >that your data do not go to 1.57 angstroms. There are no data at that >resolution. The <I> is 1/2 of the error; <I> 24 and error about 40. The >Rmerge for the shell is 59% which is close enough to random for me to have >little confidence in it. >It would help us if you just cut and paste the statistics into the question. >You are right, the density looks great. There is something funny about the >statistics if this is a normal 2fo-fc map. >cheers, >-ed collins > >On Jul 18, 2010, at 10:39 PM, 孙庆祥 wrote: > >> <Density over model.png> > 您想拥有和网易免费邮箱一样强大的软件吗？ 网易邮箱，没有垃圾邮件的邮箱。
