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
