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
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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