I have read and understood the problem and the answer. I have a similar problem : in one template there is a ligand and in the second there is no ligand, and thus i think this error is generated... (the relevant ligand is an ATP and MG which are present in one template and absent in the other). I use gaps to compensate the missing ligands and I still get the error messages

Dynamically allocated memory at amprmcns [B,kB,MB]: 16912855 16516.461 16.129 make_re_417_> Restraint type to be calculated: distance r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 .....

r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 stdevs__397E> STDEV < 0: -0.2287 Set to 1E-5. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 16912855 16516.461 16.129 Starting time : 2004/07/22 14:48:09.689 Closing time : 2004/07/22 14:48:45.264 Total CPU time [seconds] : 0.00

This error message is usually encountered when two residues in the target sequence are aligned with two or more template distances that are very different, so that the corresponding combined restraint cannot be reproduced accurately by a cubic spline. Almost invariably, this error occurs when there is an error in the alignment (ie, one template 'says' a particular

target distance should be close to 10A and the other template says it should be 20A). But in your case, it seems something else may be wrong, because

stdev is less than 0. Would you please modify file $MODINSTALL6v2/modlib/messages.lib from

M 644 3 1 Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2

To (add @S1 in the fourth line, and keep a blank line after the @S1):

M 644 3 1 Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 @S1

And email me the log file output.

I know the message should be more informative and it should print what the violating distance is, and some day we will get there ;-)

I hope this helps.

Best, Andrej

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org

> -----Original Message----- > From: owner-modeller_usage@salilab.org > [">mailto:owner-modeller_usage@salilab.org] On Behalf Of Guittet, Muriel > Sent: Friday, March 21, 2003 12:32 PM > To: modeller_usage@salilab.org > Subject: error STDEV < 0: > > > Dear Modellers, > > I saw that someone already encoutered that error in the > modeller digest .. but unfortunately there was no answer (or > just to use the "output='long'" command what I did without > any answer) I try to model a protein structure, using 4 > different templates with about 30% of sequence identity with > the target. > > Modeller always send me the same error message: > r_dista_644W> Two basis restraints have means too far apart: > > ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 > > stdevs__397E> STDEV < 0: -0.1509 > > Set to 1E-5. > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Could someone explain me the meaning of this and how to fix it? > > thanks a lot for your help. > > Muriel > >

-- Jacques Zylberg - Prof. B. Fischer's lab Chemistry Department Bar-Ilan University Ramat-Gan, Israel

e-mail: zylbergj@noamy.ch.biu.ac.il Phone: +972-3-5317785