Saturday, 19 November 2011

refmac 5.6 ccp4 6.2.0

From: Kenneth A. Satyshur
Date: 28 October 2011 02:48


Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24 A,
aniso with H in riding position and it just exploded! I get error in distances such as

                        Standard  External       All
                Bonds:      3270         0      3270
               Angles:      4923         0      4923
              Chirals:       214         0       214
               Planes:       368         0       368
             Torsions:       957         0       957
---------------------------------------

 Number of reflections in file      90428
 Number of reflections read          90428


     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A      5 PRO C   A - A      5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015 sig.= 0.014
A      5 PRO C   B - A      5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668 sig.= 0.014
A      5 PRO HB1 A - A      5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834 sig.= 0.021
A      5 PRO HB1 A - A      6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547 sig.= 0.020
A      5 PRO HB1 B - A      5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789 sig.= 0.021
A      5 PRO HB1 B - A      6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669 sig.= 0.020
A      5 PRO HG1 A - A      5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287 sig.= 0.020
A      5 PRO HG1 A - A      6 LEU N   A mod.= 4.860 id.= 1.530 dev= -3.330 sig.= 0.020
A      5 PRO HG1 A - A      6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604 sig.= 0.021
A      5 PRO HG1 B - A      5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256 sig.= 0.020
A      5 PRO HG1 B - A      6 LEU N   B mod.= 4.922 id.= 1.530 dev= -3.392 sig.= 0.020
A      5 PRO HG1 B - A      6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139 sig.= 0.021
A      6 LEU N   A - A      6 LEU CA  A mod.= 1.467 id.= 0.970 dev= -0.497 sig.= 0.020
A      6 LEU N   A - A      6 LEU HA  A mod.= 2.005 id.= 0.970 dev= -1.035 sig.= 0.020
A      6 LEU N   A - A      6 LEU CB  A mod.= 2.497 id.= 1.530 dev= -0.967 sig.= 0.020
A      6 LEU N   B - A      6 LEU CA  B mod.= 1.469 id.= 0.970 dev= -0.499 sig.= 0.020
A      6 LEU N   B - A      6 LEU HA  B mod.= 2.032 id.= 0.970 dev= -1.062 sig.= 0.020
A      6 LEU N   B - A      6 LEU CB  B mod.= 2.446 id.= 1.530 dev= -0.916 sig.= 0.020
A      6 LEU CB  A - A      6 LEU HB2 A mod.= 0.969 id.= 1.521 dev=  0.552 sig.= 0.020
A

Rfree goes form 17 to 28 and R from 15 to 25.
Coot map looks like a bunch of busted insect parts.


I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is good. I am forced to use the
old ccp4 and refmac to publish. Rf 17 R 15.
thanks

--
Kenneth A. Satyshur, M.S.,Ph.D.
Associate Scientist
University of Wisconsin


----------
From: Tim Gruene



Dear Kenneth A. Satyshur,

what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower that value until the explosion stops.

If this happens at low matrix values (at 1.24A it should be way above 5
or 10 for a well refined structure), your resolution might not be 1.24A,
i.e., you may have integrated noise (check I/sigI over resolution shells).

Tim

P.S.: I wonder what power somebody might have to _force_ you use a
specific software version...
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen




----------
From: Robbie Joosten


Hi Kenneth,

This looks like an off-by-one bug in the restraint generation. Typical sources are weird LINKs, wrong atom names and bad luck. I suggest you make sure you have the very latest Refmac and dictionary and try setting up a new refinement instead of recycling an old job. If that doesn't work, we may need a closer look at your input model.

Cheers,
Robbie



----------
From: LEGRAND Pierre


Hi Kenneth,

I am experiencing exactly the same problem, in similar conditions: refinement with H at 0.84 A resolution.
From a bunch of tests made yesterday, I have found that it is linked to incompatibilities between   cif dictionaries definitions and H names in the input PDB.
For me, one simple solution to that problem, was to remove all H atoms from my input pdb and let refmac rebuild them (MAKE HYDR ALL).
I hope the trick will work for you.

By the way, I am facing an other problem: Clashes in inter residues H-bonds between H and acceptor atoms. What is the correct way to define these. The HYDBND pdb definition doesn't seems to work. Do I need to use LINK definitions ? Is there a way to do that automatically ?

Cheers,
Pierre




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From: Garib N Murshudov

Hi All

I think that is the reason. In version of refmac (with new dictio uses new pdb v3 hydrogen naming and there are a lot of differences. 

regards
Garib

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology




----------
From: Ed Pozharski


Just to verify, is this by any chance *unrestrained* refinement?

----------
From: LEGRAND Pierre


Dear Ed,
Not in my case. I still do *restrained* refinement.
I use:
refi type REST -
   resi MLKF -
   meth CGMAT -
   bref MIXED
ncyc 10
blim 0.1 200.0

With both: weight MATRIX 50 or weight AUTO it gives the same problem.
I have also tested the latest refmac5 version (Refmac_5.6.0119) and latest dictionaries (refmac_dictionary_v5.31), but it still produce the same error, directly from the first cycle.

I can give more details and files off-list if requested.
Cheers,
Pierre



----------
From: Tim Gruene

Dear all,

If those hydrogens are in riding position, their coordinates are
calculated and should not be refined at all, isn't it? Hence they should
appear in the list of deviations at all.

Are the hydrogens present in the PDB file? Does it work to delete them all?

Tim


----------
From: Stefan Gerhardt

Hi my two cents ...

At I would use full anisotropic refinement only with
relaxed weights on B values. Weight "50" seems to me very
very loose (but I haven't seen the log file). I would use
weight auto and then look at the refmac log file. The Log
file tells you what is the weight matrix being used. For
the next refmac run -> use half of THAT weight matrix from
the "weight auto" run before !

cheers
Stefan




----------
From: Tim Gruene


Sorry, "should NOT appear in the list of deviations", of course!



----------
From: Garib N Murshudov


Dear Pierre

Resolution seems to be good enough for full anisotropic refinement. Why don't you try this and see if it stabilises refinement.

regards
Garib

----------
From: LEGRAND Pierre


Thanks all for your suggestions,

Here's a little summary of my recent tests.
I am currently using "WEIGHT AUTO" and BREF MIXED with a pdb file that contains ANISOU definition for all atoms except hydrogens.

Final results for "BREF MIXED" refinement :

                     Initial    Final
          R factor    0.0880   0.0867
            R free    0.0932   0.0925
    Rms BondLength    0.0174   0.0189
     Rms BondAngle    2.8613   2.8740
    Rms ChirVolume    0.1076   0.1146

Final results for "BREF ANISO" refinement:

                     Initial    Final
          R factor    0.0880   0.0874
            R free    0.0932   0.0956
    Rms BondLength    0.0174   0.0189
     Rms BondAngle    2.8613   2.8683
    Rms ChirVolume    0.1076   0.1151

In the "WEIGHT AUTO" run refmac5 uses:  "Weight matrix    137.7641"
Final results for "WEIGHT MATRIX 60" refinement:

                     Initial    Final
          R factor    0.0880   0.0872
            R free    0.0932   0.0922
    Rms BondLength    0.0174   0.0181
     Rms BondAngle    2.8613   2.8632
    Rms ChirVolume    0.1076   0.1134

I have just sent Garib different data files so that he can reproduce the problem one can have with H naming/dictionaries definitions.
When it happens, from the same initial pdb with "WEIGHT AUTO" and "BREF MIXED" but a differente cif definition (from the latest refmac_dictionary_v5.31) here what it gives:

                     Initial    Final
          R factor    0.0880   0.1820
            R free    0.0932   0.1869
    Rms BondLength    2.8573   2.3884
     Rms BondAngle   35.7010  34.7547
    Rms ChirVolume   10.5335   4.2429

I hope it helps to clarify the situation,
Cheers,
Pierre




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