Dear all,
Recently, I refine two low resolution structures in refmac 5.5. Their
resolutions are 3A and 3.5A respectively.
For 3A structure, after MR by phaser and rigidbody refinement&restraint
refinement by refmac5.5, I got R factor 25% and R free 35%. And then
each time, after my model building in coot and restraint refinement by
refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%.
For 3.5A structure, the R factor stays 27%, but R free increases from
37% to 42% after my slightly model building in coot.
Could you help me to find the reason?
Maybe the reason is the overfit of the structure? I found that new
version of refmac 5.6 has many new features for low resolution
refinement, such as jelly boy, secondary structure restraints. But I
don't know how to use these new features in old version ccp4i (6.1.13)?
I also used phenix.refine with the "reference model" ( I have high
resolution model for one domain of the low resolution protein) and
"secondary structure restraints", but it seams the same. Any suggestion?
BTW, is that simulator annealing not suitable for low resolution
structure? I used the simulator annealing method of CNS and
phenix.refine, but the geometry of the structure is always destroyed
seriously.
Could you help me?
Thank you very much!
