Your beta and gamma angle in P1 are awfully close to 90 degrees. Are you sure about P1 ? Could it be C2 with beta of 104 ˚ ? I'm assuming the CRYST card below belongs to your structure right ?
Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 19, 2010, at 10:54 PM, 孙庆祥 wrote: > 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。 > > > 网易邮箱，没有垃圾邮件的邮箱。
