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[ccp4bb]: We are having problems with newer versions of refmac5



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Hi all

This message is two things.

It is a plea for suggestions/insight/clues on what we might be doing
wrong in using newer refmac versions.

It is also a heads-up notice that at least in our hands refmac 5.1.x
is not always refining as well as the earlier version 5.0.36 (the one 
included in CCP4 4.1.1). We see this for all newer versions we have tried 
up to and including 5.1.80.  I am concerned that other groups may be 
suffering from similar problems, but may not have noticed.

We first encountered this problem when trying to reproduce refinement
runs of a pair of high resolution (~1A) structures. The original refinements
had been done in parallel in shelxl and refmac 5.0.36 using full aniso
treatment.  The shelxl and refmac runs agreed well with each other.
The same structures fail to refine as well in refmac 5.1.x.

In our problem cases, the final model after refinement in 5.1.x 
looks OK on its own.  But when the restraint weights are set to yield
acceptable measures of quality (DPI, geometric residuals, anisotropy) 
the R and Rfree residuals are noticeably poorer than those for the final 
model from version 5.0.36.  If we had not set out to
replicate an earlier refinement we might never have noticed something
was wrong.

We have tried other, simpler, test cases which do refine OK in both the
new and the old refmac5, so the problem is not universal.
But we have not been able to pin down what it is about the failing cases 
that is making them fail.


General summary
------------------
Running the exact input scripts, mtz files, and starting models originally
used with refmac 5.0.36 through newer refmac5 versions causes the refinement
to blow up (atoms lost, residuals diverge, floating exceptions, all-around
bad behaviour).  Some exploration of the code and new documentation clued us
in that the interpretation of weighting parameters has changed in the new
versions. We therefore systematically searched for revised weighting
parameters that would yield behaviour equivalent to our original nice runs.
At the same time we sought for other possible sources of error, either in
our input or in the newer program source code.  Unfortunately after several
weeks of looking we have not been able to find any set of weighting 
parameters, refinement options, or input *.cif library files that yield
results from version 5.1.x quite as nice as the ones from 5.0.36. 

We have confirmed that the difference between versions 5.0.36 and 5.1.x
persists across tests
 - under linux (g77 or ifc compilers) or alpha (DU4.0D)
 - with or without generation of hydrogen atoms
 - aniso or iso refinement of the model
 - inclusion or exclusion of all ligand atoms other than metals
 - varying the Shannon sampling interval for the FFT grid

The 5.1.x versions are much more sensitive to weighting parameters than
5.0.36 was, especially MATRix.  This sensitivity is somewhat less on the 
[64-bit] alpha than on linux/x86, which suggests to me that maybe there
is an ill-conditioned matrix somewhere.


Details
-------
Below I give a summary of 1A refinement runs of Carbonic Anhydrase I
as reported by refmac 5.0.36 and by the "best" run we were able to 
obtain from version 5.1.80.  The input model and *.mtz files were 
identical.  Both these runs included generation of hydrogens and a fully
anisotropic model.

Difference in final R values
	version		R	Rfree
	5.0.36		0.1362	0.1502
	5.1.80		0.1450	0.1563

RMS Difference in final coordinates
	 529 CA atoms  0.0198A
	2511 all atoms 0.0624A     [>2x the ESU from Cruickshank DPI]
	

Differences we do not understand, which may or may not contribute to the 
observed difference in refinement results:

 - the count of VDW terms is radically different in the new version

 - the count of "free" atoms is also radically different

 - HBOND and period 3 torsion terms are no longer reported

 - despite our best efforts to find appropriate weighting parameters, 
   the B restraints terms and gradient do not match very well between
   the new and old runs

 - notice that the ratio of X-ray gradient to Geometric gradient is
   roughly 2:1 in the 'old' run and roughly 1:1 in the 'new' run.
   One would think that increasing the MATRix weight in the new run
   to up-weight the X-ray term would improve R at the cost of the resulting 
   geometry.  It doesn't.  An otherwise identical run of 5.1.80 with only 
   the MATRix weight changed to balance the two gradients yields both 
   worse R and Rfree and worse geometry.

 - 5.1.x seems to have convergence problems.  In many (most?) runs, 
   R and Rfree reach a minimum after 3-10 cycles, and then get worse again 
   before converging to something higher.  By contrast, 5.0.36 converges 
   to the minimum and is stable there for at least the 25 cycles over 
   which we tracked it.

 - 5.1.x reports a very small scale factor for the Babinet solvent correction
   (0 in the example below; near 0 in most other runs).  Does this mean that
   it essentially not making a solvent correction?  That right there might 
   explain the difference. Why would the Babinet correction be so different
   between the new and old versions of refmac?

 - The reported "Partial structure 1" scales are also different. 
   What does this refer to?

 - The reported Overall figure of merit is better in 5.1.x.
   How exactly is this quantity calculated?


                                          ******  REFMAC 5.0.36  ******          ******   REFMAC 5.1.80   ******
----------------------------------------------------------------------------    ------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)   N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2233     0.014     0.021               2233     0.013     0.021
Bond distances: others                         1942     0.001     0.020               1942     0.005     0.020
Bond angles  : refined atoms                   3024     2.190     1.966               3024     2.280     1.966
Bond angles  : others                          4590     1.059     3.000               4590     2.444     3.000
Torsion angles, period  1. refined              258     6.011     3.000                258     6.797     5.000
Torsion angles, period  3. refined              417    19.851    15.000
Chiral centres: refined atoms                   317     0.125     0.200                314     0.113     0.200 
Planar groups: refined atoms                   2415     0.009     0.020               2415     0.008     0.020
Planar groups: others                           434     0.004     0.020                434     0.004     0.020
VDW repulsions: refined atoms                   489     0.374     0.300                936     0.275     0.200
VDW repulsions: others                         2009     0.245     0.300               6658     0.426     0.200
VDW; torsion: refined atoms                       4     0.724     0.500                640     0.108     0.200
VDW; torsion: others                              5     0.984     0.500               4483     0.283     0.200
HBOND: refined atoms                            273     0.172     0.500              
HBOND: others                                     1     0.158     0.500              
Metal-ion: refined atoms                          6     0.401     0.500                  6     0.566     0.200
VDW repulsions; symmetry: refined atoms          17     0.257     0.300                114     0.315     0.200
VDW repulsions; symmetry: others                 64     0.254     0.300                276     0.374     0.200
HBOND; symmetry: refined atoms                   37     0.256     0.500              
M. chain bond B values: refined atoms          1297     1.785     1.000               1297     1.218     1.000
M. chain bond B values: others                  522     1.650     1.000                522     1.164     1.000
M. chain angle B values: refined atoms         2110     2.698     1.500               2110     1.883     1.500
M. chain angle B values: others                1794     2.557     1.500               1794     1.804     1.500
S. chain bond B values: refined atoms           936     3.333     2.000                936     2.236     2.000
S. chain bond B values: others                 1420     1.859     2.000               1420     1.273     2.000
S. chain angle B values: refined atoms          915     4.737     3.000                915     3.262     3.000
S. chain angle B values: others                2796     2.820     3.000               2796     1.953     3.000
Sphericity. Free atoms                            1     0.833     8.000                337    11.448     8.000
Sphericity. Bonded atoms                       2138     6.441     8.000               2174     4.558     8.000
Rigid bond restraints                          2198     0.773     0.500               2233     0.517     0.500
----------------------------------------------------------------------------    ------------------------------------

Resolution limits                    =     15.000     1.000                       15.000     1.000
Number of used reflections           =     121649                                 121649
Percentage observed                  =    98.2038                                98.2038
Percentage of free reflections       =     3.9684                                 3.9684
Overall R factor                     =     0.1362                                 0.1450
Free R factor                        =     0.1502                                 0.1563
Overall weighted R factor            =     0.1243                                 0.1308
Free weighted R factor               =     0.1378                                 0.1443
Overall correlation coefficient      =     0.9752                                 0.9694
Free correlation coefficient         =     0.9694                                 0.9628
Cruickshanks DPI for coordinate error=     0.0269                                 0.0262
Overall figure of merit              =     0.9179                                 0.9336

----------------------------------------------------------------------------    ------------------------------------
Norm of X_ray positional gradient                44.1                                    28.4
Norm of Geom. positional gradient                27.2                                    31.1
Norm of X_ray B-factor gradient                 0.171E+04                                898.
Norm of Geom. B-factor gradient                  292.                                    300.
Product of X_ray and Geom posit. gradients     -0.930E+07                              -0.403E+07
 Cosine of angle between them                      -0.581                                  -0.341
Product of X_ray and Geom B-fact gradients      0.258E+08                               0.227E+08
 Cosine of angle between them                       0.003                                   0.005

----------------------------------------------------------------------------    ------------------------------------

Overall               :      scale =   1.079, B  =   0.014                       scale =    1.071, B  =   0.003
Babinet"s bulk solvent:      scale =   0.112, B  = 174.346                       scale =    0.000, B  = 196.718
Partial structure    1:      scale =   1.985, B  =  31.170                       scale =    0.388, B  = 128.847
Overall anisotropic scale factors
   B11 =  0.10 B22 =  0.12 B33 = -0.27 B12 =  0.00 B13 = -0.11 B23 =  0.00		(identical)
 


	yours in puzzlement,

		Ethan

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195