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> >
