Hi everyone,
I have a 3.3A cryoEM map and I use the refmac5 in CCPEM for the model refinement. The B-factor of the refined.pdb goes to very low (2~10). If I run one more round of refmac5, B-factors for all residues are 2. Why the B-factor keep decreasing? The parameters I used in refmac5:
resolution: 3.3
20 cycles.
weight: 1
map sharpen 40
Set input model B-factor: 40
local refinement: 3A
with external restraints (RNA packing and secondary structure)
weight matrix: 0.001
Results:
Average FSC: 87.14
Rms BondLength: 0.0060
Rms BondAngle: 1.0862
And the validation from half maps looks normal.
Thanks,
Fuxing
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