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[ccp4bb]: Refmac5 refinement of residues having alternate locations
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Dear All,
The question is about Refmac5 refinement of residues having
alternate locations.
The input pdb file is like:
........
ATOM 50 O GLY A 6 161.528 26.356 120.426 1.00 9.11 8
ATOM 51 N LYS A 7 160.374 27.641 119.021 1.00 9.68 7
ATOM 52 CA LYS A 7 160.767 28.872 119.659 1.00 11.39 6
ATOM 53 CB ALYS A 7 160.663 30.041 118.686 0.50 12.85 6
ATOM 54 CB BLYS A 7 160.683 30.038 118.701 0.50 12.85 6
ATOM 55 CG ALYS A 7 159.228 30.228 118.136 0.50 20.50 6
ATOM 56 CG BLYS A 7 161.638 29.910 117.525 0.50 20.50 6
ATOM 57 CD ALYS A 7 159.134 30.983 116.801 0.50 27.69 6
ATOM 58 CD BLYS A 7 161.417 31.016 116.509 0.50 27.69 6
ATOM 59 CE ALYS A 7 157.756 30.775 116.166 0.50 31.56 6
ATOM 60 CE BLYS A 7 162.153 30.728 115.210 0.50 31.56 6
ATOM 61 NZ ALYS A 7 157.377 31.895 115.260 0.50 34.80 7
ATOM 62 NZ BLYS A 7 161.539 31.436 114.054 0.50 34.80 7
ATOM 63 C LYS A 7 159.836 29.082 120.876 1.00 11.28 6
ATOM 64 O LYS A 7 158.964 28.253 121.142 1.00 10.30 8
ATOM 65 N LEU A 8 160.021 30.172 121.607 1.00 10.71 7
........
after 3~5 cycles' refinemenit, the atoms of LYS7 went out of the
density (but other part of the structure looked OK) and the R-factor/
Free-R-factor increased.
5-fold NCS restraint (tight) for main chain and side chains was used.
Can anybody give me a suggestion?
Thanks a lot!
Xiaofeng Zhang
P.S.
side chain atoms at alternate locations are NCS-related.
-----------------------------------------------------------
Xiaofeng Zhang Ph.D. Student
Department of Bioscience
Karolinska Institute, NOVUM
141 57 Huddinge
Email: xiaofeng.zhang@biosci.ki.se
http://www.csb.ki.se/users/xray/xiaofeng/xiaofeng.html
Tel: +46-(0)8-6089177 Fax: +46-(0)8-6089290
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