[ccp4bb]: infinite loops in refmac?

[Mark DePristo <mdepristo@cryst.bioc.cam.ac.uk>]

Hello everyone,

I've been experiencing some odd behavior with refmac5.  On some input files, refmac5 will enter into something like an infinite loop, never terminating.  Things start to go bad from the start (the nan values for bond length and angle RMS deltas):

    CGMAT cycle number =      1


-------------------------------------------------------------------------------
Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   827     1.891     0.022
Bond angles  : refined atoms                   1124       nan     1.942
-------------------------------------------------------------------------------


-----------------------------------------------------------------------------
Overall               : scale =    1.014, B  =  -1.043
Babinet"s bulk solvent: scale =    0.764, B  =  50.000
Partial structure    1: scale =    0.143, B  =  30.515
Overall anisotropic scale factors
B11 =  0.01 B22 = -0.09 B33 =  0.07 B12 =  0.00 B13 = -0.01 B23 =  0.00
-----------------------------------------------------------------------------


-----------------------------------------------------------------------------
Overall R factor                     =     0.4249
Free R factor                        =     0.5012
Overall figure of merit              =     0.4024
-----------------------------------------------------------------------------








CGMAT cycle number =      2


-------------------------------------------------------------------------------
Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   827       nan     0.022
Bond angles  : refined atoms                   1124       nan     1.942

The program never gets past this last line.  The input PDB file is the result of 20 steps of unrestrained refinement against a 1.31 Å dataset with refmac5.  The behavior is simple to reproduce, just run:

.../refine refine-2-1.pdb refine-2-1.mtz RESTrained 20 output.pdb output.mtz weak isotropic 0.75

meaning approximately to refine refine-2-1.pdb against refine-2-1.mtz with 20 steps of restrained refinement with weight matrix 0.75, weak restraints and isotropic b-factors.

The refine script and input files can be found at:

http://raven.bioc.cam.ac.uk/~mdepristo/refmac/refine-2-1.pdb
http://raven.bioc.cam.ac.uk/~mdepristo/refmac/refine-2-1.mtz
http://raven.bioc.cam.ac.uk/~mdepristo/refmac/refine

I've had this crop up a couple of times already and it's starting to become a serious nuisance.  Has anyone else experienced this?  Is there a workaround?

Thanks, 

Mark

Mark DePristo
Ph.D. Candidate
Dept. of Biochemistry
Cambridge University
mdepristo@cryst.bioc.cam.ac.uk
http://www-cryst.bioc.cam.ac.uk/~mdepristo/