Hi Tongqing, can be a number of reasons, including: - refinement did not converge (need to run more macro-cycles); - choice of TLS groups is not optimal; - side-chains are partially occupied (need to use partial occupancy or model multiple occupancies); - see recent discussion on ccp4b about disulfides showing lots of residual density. To tell more I will need to see data and model, focusing on residues/ligands in question. Pavel On 6/8/14, 5:32 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Dear colleagues,
I am refining one structure at 1.94 A with phenix.refine with individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 19.8%. But when inspecting the maps, I noticed that the sidechain tip of some residues showed positive density and the b-factor for those atoms were very high while those for the other atoms of the same residues were normal; The b-factors for newly added ligands were also not refined well showing high b-value and positive density at the same time; the disulfide bonds also show positive density and high B. The occupancy were all set to 1.
Please give suggestions. Thanks!
Best regards,
**
*Tongqing*
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*Tongqing Zhou, Ph.D.*
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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