Hi Amit Most likely nothing is going wrong. Your final Rfree looks quite respectable for 2.8 Ang. data. It's meaningless to compare the Rfree at the beginning of a refinement with that at the end. Rfree is only meaningful if the refinement has converged. So it is valid to compare the Rfree at the end of one refinement with the Rfree at the end of another refinement (e.g. if you changed the restraints or the weights), to decide which starting conditions are optimal.
HTH -- Ian On 7 May 2014 16:11, Amit Kumar <[email protected]> wrote: > > Hello, > > I have a 2.8 angstrom structure of a protein ligand complex. The R/R free > before adding the ligand was 0.21614/0.27760 and after adding the ligand, > the R/Rfree is 0.2030/0.2691. > . > However while refining the structure by Refmac 5, I see a decrease in R > factor but an increase in R free as number of cycles increase. What could > be going wrong here? > > Below is the tail of the log. > > Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ > $$ > 0 0.2218 0.2606 0.797 32405. 3572.4 0.0103 0.517 1.503 0.675 0.074 > 1 0.2106 0.2599 0.799 32189. 3565.2 0.0108 0.536 1.504 0.668 0.075 > 2 0.2062 0.2600 0.801 32122. 3563.5 0.0105 0.525 1.519 0.673 0.071 > 3 0.2044 0.2607 0.801 32083. 3562.7 0.0104 0.519 1.528 0.676 0.070 > 4 0.2030 0.2615 0.802 32057. 3562.9 0.0104 0.517 1.530 0.677 0.070 > 5 0.2025 0.2631 0.801 32048. 3563.9 0.0104 0.516 1.528 0.677 0.071 > 6 0.2023 0.2647 0.800 32055. 3566.1 0.0103 0.514 1.525 0.676 0.071 > 7 0.2025 0.2668 0.799 32067. 3569.0 0.0103 0.513 1.523 0.676 0.071 > 8 0.2026 0.2676 0.798 32077. 3571.1 0.0102 0.509 1.521 0.674 0.070 > 9 0.2027 0.2685 0.798 32094. 3573.8 0.0102 0.507 1.520 0.674 0.069 > 10 0.2030 0.2691 0.797 32109. 3575.6 0.0101 0.505 1.519 0.672 0.069 > $$ > $TEXT:Result: $$ Final results $$ > Initial Final > R factor 0.2218 0.2030 > R free *0.2606* *0.2691* > Rms BondLength 0.0103 0.0101 > Rms BondAngle 1.5033 1.5193 > Rms ChirVolume 0.0735 0.0689 > > Best, > Amit >
