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Dear all,
I am refining a structure (almost 1100 residues in the au) at 1.6 A with
refmac5. I could model a number of water molecules. At RCSB validation, I
see several close contacts (in the same asymmetric unit) between water
molecules (both at 1.00 occupancy). To investigate further, I used at
refmac5:
MONITOR MANY VDWR 1.5
In fact this lists several "bad" contacts including those reported by
RCSB validation. Also, at refmac5 output, I see that 2.740 is considered to
be the ideal distance between O's from water molecules, but it reports the
several negative deviations (and several distance values below 2.2, 2.1 and
even 2.0 A). I went to inspect maps and the model in coot. Interestingly,
coot at its "check waters" tool does not list several of these "water close
contacts" even when I ask it to list the ones lower than 2.2 A (does this
distance work there also for between water molecules ? I could not find this
at RTFM), but at measuring the distances there they are (even in the same
au). In coot, I could see a number of cases where there is room for the
molecule to go to "somewhere else" to avoid the bump at 2.2 A (distance used
by RCSB).
I thought this might be due to the fact that I am using higher weights
(around 0.9) because of the resolution (and this gives me very good rms for
bond angles and lengths). I lowered the weight to 0.3 and the problem
persists (although a little less serious). I also made a test, put the same
model into CNS and asked for only the water molecules to be refined. Then,
no close contacts between water molecules at all !
I had never seen this problem (this is the first time I have a structure
at 1.6 A).
My questions are:
a) How does refmac5 treat the distances between water molecules ? What is
the weight imposed to this ? Has this something to do with the fact that the
structure is 1.6 resolution and the weight is high ? If this is the case,
how to use a high general weight (which gives better statistics at rms's and
R factors) and not to have this problem with water molecules ? Has this
something to do with the fact that I have a good number of waters (also
because of the resolution) ?
b) How to overcome this ? What I know is that arp might deal with this in
real space, but there might still remain the fact thhat the new arp waters
is further refined in refmac5 to distances lower than 2.2.
Thanks,
Jorge
