Dear all
I have found some issues in REFMAC5 output files (I am using version
5.8.0158)
1) when I use the "pdbout shifts" instruction, the "TLS ORIGIN" values
in the TLSOUT file and the "REMARK 3" PDB records do not take into
account the applied origin shift
2) when I :
- do zero refinement cycles ("ncycles 0", just to calculate R-factors
and other statistics)
- set TLSIN = TLSOUT from a previous run
- do NOT use the "TLS ADDU" instruction
then the B factor values in the output PDB file will nevertheless
contain the contribution from the TLS tensors (not just the residuals B
factors). However, a "REMARK 3 U VALUES : RESIDUAL ONLY" card in the
output PDB file will be found. I have run some tests using coordinates
and structure factors from PDB entry 2pm1. You will find here below some
excerpts from the REFMAC5 log and output PDB files:
#================================================================================
## RUN 0 : TLS + Biso refinement + TLSOUT addU
# refmac5 xyzin 2pm1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.0.pdb
# hklout refine.0.mtz
# tlsout refine.0.tls
#
./refine.0.log: Data line--- refi type rest reso 1.6
./refine.0.log: Data line--- refi bref iso
./refine.0.log: Data line--- bfactor set 20
./refine.0.log: Data line--- refi tlsc 20
./refine.0.log: Data line--- ncycl 50
./refine.0.log: Data line--- tlsout addu
./refine.0.log: Data line--- END
./refine.0.pdb:REMARK 3 U VALUES : WITH TLS ADDED
./refine.0.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 24.39 N
./refine.0.pdb:ANISOU 1 N ALA A 1 3480 3008 2779 -684 -267 -1026 N
./refine.0.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 21.59 C
./refine.0.pdb:ANISOU 2 CA ALA A 1 2947 2814 2439 -575 -360 -773 C
./refine.0.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 22.81 C
./refine.0.pdb:ANISOU 3 CB ALA A 1 3184 3199 2282 -488 -498 -713 C
./refine.0.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 18.64 C
./refine.0.pdb:ANISOU 4 C ALA A 1 2551 2314 2214 -438 -179 -575 C
./refine.0.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 19.23 O
./refine.0.pdb:ANISOU 5 O ALA A 1 2730 2280 2294 -344 -6 -574 O
================================================================================
## RUN 1 : TLS+Biso refinement; no TLSOUT addU
# refmac5 xyzin 2pm1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.1.pdb
# hklout refine.1.mtz
# tlsout refine.1.tls
#
./refine.1.log: Data line--- refi type rest reso 1.6
./refine.1.log: Data line--- refi bref iso
./refine.1.log: Data line--- bfactor set 20
./refine.1.log: Data line--- refi tlsc 20
./refine.1.log: Data line--- ncycl 50
./refine.1.log: Data line--- END
./refine.1.pdb:REMARK 3 U VALUES : RESIDUAL ONLY
./refine.1.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 11.25 N
./refine.1.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 10.71 C
./refine.1.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 11.12 C
./refine.1.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 10.38 C
./refine.1.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 11.15 O
================================================================================
## RUN 2a : run 0 TLScycles + 0 REFI cycles starting from run 1 output
# refmac5 xyzin refine.1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.2a.pdb
# hklout refine.2a.mtz
# tlsin refine.1.tls
# tlsout refine.2a.tls
#
./refine.2a.log: Data line--- refi type rest reso 1.6
./refine.2a.log: Data line--- refi bref iso
./refine.2a.log: Data line--- refi tlsc 0
./refine.2a.log: Data line--- ncycl 0
./refine.2a.log: Data line--- END
./refine.2a.log: Data line--- REFMAC_5.8.0158
./refine.2a.log: Data line--- TLS From REFMAC
./refine.2a.log: Data line--- RANGE 'A 1.' 'A 83.' ALL
./refine.2a.log: Data line--- ORIGIN 14.408 -11.294 0.204
./refine.2a.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132
0.0145
./refine.2a.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778
0.8265
./refine.2a.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451
0.0292 0.2475 -0.3305
./refine.2a.pdb:REMARK 3 U VALUES : RESIDUAL ONLY
./refine.2a.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 24.39 N
./refine.2a.pdb:ANISOU 1 N ALA A 1 3480 3008 2779 -684 -267 -1026 N
./refine.2a.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 21.59 C
./refine.2a.pdb:ANISOU 2 CA ALA A 1 2948 2814 2439 -575 -360 -773 C
./refine.2a.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 22.81 C
./refine.2a.pdb:ANISOU 3 CB ALA A 1 3185 3198 2282 -488 -498 -713 C
./refine.2a.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 18.64 C
./refine.2a.pdb:ANISOU 4 C ALA A 1 2552 2314 2214 -438 -179 -576 C
./refine.2a.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 19.23 O
./refine.2a.pdb:ANISOU 5 O ALA A 1 2731 2281 2295 -344 -7 -574 O
================================================================================
## RUN 2b : run 1 TLS cycle + 1 REFI cycle starting from run 1 output
# refmac5 xyzin refine.1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.2b.pdb
# hklout refine.2b.mtz
# tlsin refine.1.tls
# tlsout refine.2b.tls
#
./refine.2b.log: Data line--- refi type rest reso 1.6
./refine.2b.log: Data line--- refi bref iso
./refine.2b.log: Data line--- refi tlsc 1
./refine.2b.log: Data line--- ncycl 1
./refine.2b.log: Data line--- END
./refine.2b.log: Data line--- REFMAC_5.8.0158
./refine.2b.log: Data line--- TLS From REFMAC
./refine.2b.log: Data line--- RANGE 'A 1.' 'A 83.' ALL
./refine.2b.log: Data line--- ORIGIN 14.408 -11.294 0.204
./refine.2b.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132
0.0145
./refine.2b.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778
0.8265
./refine.2b.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451
0.0292 0.2475 -0.3305
./refine.2b.pdb:REMARK 3 U VALUES : RESIDUAL ONLY
./refine.2b.pdb:ATOM 1 N ALA A 1 19.624 -3.183 8.094 1.00 11.31 N
./refine.2b.pdb:ATOM 2 CA ALA A 1 19.857 -4.525 7.537 1.00 10.72 C
./refine.2b.pdb:ATOM 3 CB ALA A 1 19.749 -5.555 8.682 1.00 11.14 C
./refine.2b.pdb:ATOM 4 C ALA A 1 18.904 -4.806 6.397 1.00 10.38 C
./refine.2b.pdb:ATOM 5 O ALA A 1 17.697 -4.379 6.389 1.00 11.21 O
================================================================================
## RUN 2c : run 1 TLS cycle + 0 REFI cycle starting from run 1 output
# refmac5 xyzin refine.1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.2c.pdb
# hklout refine.2c.mtz
# tlsin refine.1.tls
# tlsout refine.2c.tls
#
./refine.2c.log: Data line--- refi type rest reso 1.6
./refine.2c.log: Data line--- refi bref iso
./refine.2c.log: Data line--- refi tlsc 1
./refine.2c.log: Data line--- ncycl 0
./refine.2c.log: Data line--- END
./refine.2c.log: Data line--- REFMAC_5.8.0158
./refine.2c.log: Data line--- TLS From REFMAC
./refine.2c.log: Data line--- RANGE 'A 1.' 'A 83.' ALL
./refine.2c.log: Data line--- ORIGIN 14.408 -11.294 0.204
./refine.2c.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132
0.0145
./refine.2c.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778
0.8265
./refine.2c.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451
0.0292 0.2475 -0.3305
./refine.2c.pdb:REMARK 3 U VALUES : RESIDUAL ONLY
./refine.2c.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 24.22 N
./refine.2c.pdb:ANISOU 1 N ALA A 1 3456 2974 2771 -686 -241 -1002 N
./refine.2c.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 21.45 C
./refine.2c.pdb:ANISOU 2 CA ALA A 1 2928 2783 2437 -578 -335 -755 C
./refine.2c.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 22.64 C
./refine.2c.pdb:ANISOU 3 CB ALA A 1 3156 3160 2286 -496 -469 -696 C
./refine.2c.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 18.57 C
./refine.2c.pdb:ANISOU 4 C ALA A 1 2540 2292 2220 -439 -161 -563 C
./refine.2c.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 19.18 O
./refine.2c.pdb:ANISOU 5 O ALA A 1 2718 2262 2304 -345 8 -562 O
================================================================================
## RUN 2d : run 0 TLS cycle + 1 REFI cycle starting from run 1 output
# refmac5 xyzin refine.1.pdb
# hklin 2pm1_unique.mtz
# xyzout refine.2d.pdb
# hklout refine.2d.mtz
# tlsin refine.1.tls
# tlsout refine.2d.tls
#
./refine.2d.log: Data line--- refi type rest reso 1.6
./refine.2d.log: Data line--- refi bref iso
./refine.2d.log: Data line--- refi tlsc 0
./refine.2d.log: Data line--- ncycl 1
./refine.2d.log: Data line--- END
./refine.2d.log: Data line--- REFMAC_5.8.0158
./refine.2d.log: Data line--- TLS From REFMAC
./refine.2d.log: Data line--- RANGE 'A 1.' 'A 83.' ALL
./refine.2d.log: Data line--- ORIGIN 14.408 -11.294 0.204
./refine.2d.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132
0.0145
./refine.2d.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778
0.8265
./refine.2d.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451
0.0292 0.2475 -0.3305
./refine.2d.pdb:REMARK 3 U VALUES : RESIDUAL ONLY
./refine.2d.pdb:ATOM 1 N ALA A 1 19.621 -3.183 8.093 1.00 11.24 N
./refine.2d.pdb:ATOM 2 CA ALA A 1 19.857 -4.524 7.537 1.00 10.69 C
./refine.2d.pdb:ATOM 3 CB ALA A 1 19.748 -5.555 8.682 1.00 11.10 C
./refine.2d.pdb:ATOM 4 C ALA A 1 18.905 -4.806 6.397 1.00 10.36 C
./refine.2d.pdb:ATOM 5 O ALA A 1 17.698 -4.380 6.390 1.00 11.19 O
--
Stefano Trapani
Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-------------------------------------
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France
Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-------------------------------------
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-------------------------------------
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