[ccp4bb] unstable refinement error in SHELXL
Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? *For more information*: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)* the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the* not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu
Re: [ccp4bb] unstable refinement error in SHELXL
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lu Yu, your wR2 in the first log-extract seems very high (43%) - it might simply be that you model is still not good enough to refine the data anisotropically. Does it work if you refine the model isotropically? If so, improve the model as much as possible before going anisotropically. You might also want to include more reflections - with SHEL 10 0.1 you leave out all data with d10A which might be quite a few important reflections. It is difficult to go into more detail without knowing the exact content of the output (lst-files), especially in the second case where the listing file tells you that something is wrong with the 'ISOR'-command. Regards, Tim On 03/19/12 17:00, Lu Yu wrote: Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? *For more information*: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)* the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the* not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPZ1pBUxlJ7aRr7hoRAvZRAJ9TKlJLQjho67GGxZAyHIcioDcnrwCeIYjy 4rL0aiefine9z1LcQ3SSGno= =aoDC -END PGP SIGNATURE-
Re: [ccp4bb] unstable refinement error in SHELXL
Dear Lu Yu, SHELXL is usually very stable so there must be an error in your .ins file, but it is difficult fo us to guess what it is without seeing the full file. A common error that can cause such instability is caused by a long-standing bug in Coot, which sets some occupancies in the .ins file to 1.0 (meaning that they can be refined freely starting at 1.0) rather than the usual 11.0 (which means that they should be fixed at 1.0; you can add 10 to a parameter to fix it). Another possibility is that Coot has not understood a 'free variable' that has been used for e.g. occupancy refinement. The small molecule people use other graphical GUIs for SHELXL (shelXle, WinGX, Olex2, System-S, XSEED, Oscail, XSHELL etc.) that make far fewer mistakes. The .ins files written by Coot should always be checked carefully and if necessary edited before running SHELXL. Best wishes, George On 03/19/2012 05:00 PM, Lu Yu wrote: Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? _For more information_: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)*the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the*not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
