Re: [ccp4bb] Differences in Refmac5 refinement on CCP46.1.1

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Differences in Refmac5 refinement on CCP46.1.1
From: Rafael_Couñago rafael {- dot -} counago {- at -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2009-03-30

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Subject: Re: Question about stereo on LCD monitor
From: Rafal Dolot rdolot {- at -} BIO {- dot -} CBMM {- dot -} LODZ {- dot -} PL
Date: 2009-03-30

Subject: Re: Differences in Refmac5 refinement on CCP46.1.1
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-03-30

Hi Rafael,

>
> Things very different on the "new" version:
> - The rmsANGL shot up (from 2.088 to 3.088);
> - The rmsBOND also shot up (from 0.25 to 0.0468).
>
> As a consequence of having my geometric constrains blown up, the
> Rwork
> went considerably down.
>
> Does anybody have any thoughts on why using the same geometry
> restraints
> led to very different results?

From what you show, the logs are not dramatically different anyway.
In one case Rfree is 20.37% and in the other 20.4%.
Which tells you that loosening geometry is not helping ;-)

What you say about the geometry restraints being the same is not
correct.
The relative weight of geometry terms is the same.
***But you do not mention anything about the relative weight of Xrays
to Geometry, which YOU have to set***
(new REFMAC has an AUTO version which works OK, but not for the very
final rounds, in my opinion)

Would I be right to suspect you have either set the X-ray vs Geometry
weight to the wrong value in the old job (0.3 as default?)
while in the new job AUTO is used?

The rms distance you get in the new job is 0.0468 and the z score is
1.958, clearly indicating that the geometry is far too loose.
In the old job, you had 0.025 and 2.088, which I also think is loose.
(unless you have VERY high resolution .. and even then ... I would
expect a better zBOND).

Aim for tighter geometry and look at Z-bond (0.5 - 1.0) are good
values I think. I personally decided
I prefer the Ian Tickle analysis btw, and I like looking at the
weightB relationship to weightXray.

It was early in the year to have the RMS-bonds discussion... (same as
Jim pointed out for the I/sig(I) discussion).

Best, Tassos

PS This script can be useful to decide what good weight are (need
editing)
btw, I would love to have that type of Job in ccp4i, and its rather
easy to code in Tcl.
Anybody with time to spare on the CCP4 team ? I think it can be useful
to have a job
for optimizing weights extensively (phenix has also that mode and I
like it a lot ... even if its slow).

#!/bin/csh -f
#
echo "xweight bweight rfactor rfree rmszbonds" > stats.log

foreach xweight ( 0.04 0.08 0.12 0.16 0.20 0.25 0.30)
foreach bweight ( 0.1 0.2 0.6 1.0 1.5 2.0 2.5 3.0 )
#
# Define your Input / Output files
#
refmac5 XYZIN "CLIC3_final_2.pdb" XYZOUT "del.tmp" HKLIN
"clic3.mtz" HKLOUT "del.mtz.tmp" TLSIN
"tls_cli3.tls" TLSOUT "del.tls.tmp" LIBOUT "delete.cif" > refmac_$
{xweight}_${bweight}.log <make check NONE
make -
hydrogen ALL -
hout NO -
peptide NO -
cispeptide YES -
ssbridge YES -
symmetry YES -
sugar YES -
connectivity NO -
link NO
refi -
type REST -
resi MLKF -
meth CGMAT -
bref ISOT
refi tlsc 10
temp set 20.0
ncyc 10
scal -
type SIMP -
reso 2.210 38.691 -
LSSC -
ANISO -
EXPE
solvent YES -
VDWProb 1.2 -
IONProb 0.8 -
RSHRink 0.8
weight -
MATRIX ${xweight}
monitor MEDIUM -
torsion 10.0 -
distance 10.0 -
angle 10.0 -
plane 10.0 -
chiral 10.0 -
bfactor 10.0 -
bsphere 10.0 -
rbond 10.0 -
ncsr 10.0
labin FP=F_Unspecified SIGFP=SIGF_Unspecified -
FREE=FreeR_flag
labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
PHDELWT=PHDELWT FOM=FOM
temp ${bweight} 2.0 3.0 2.0 3.0
PNAME fox
DNAME 040808
RSIZE 80
USECWD
END
EOF

echo -n ${xweight} ${bweight} >> stats.log
awk '(NF=11){if ($1==20) print $2, $3, $8}' refmac_${xweight}_$
{bweight}.log >> stats.log
end

end

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Differences in Refmac5 refinement on CCP46.1.1
From: Rafael_Couñago rafael {- dot -} counago {- at -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2009-03-30

Next message:
Subject: Re: Question about stereo on LCD monitor
From: Rafal Dolot rdolot {- at -} BIO {- dot -} CBMM {- dot -} LODZ {- dot -} PL
Date: 2009-03-30