Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
After an initial round of TLS refinement Refmac stops and and claims a problem
but nevertheless writes at the end "Task completed successfully" and does not
write any file despite it claims to have it done. I copied a part of the log
file at the end of the mail
Could anyone point me to the mistake i made probably?
Thanks in advance
Christian
#CCP4I VERSION CCP4Interface 2.0.6
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 11 Oct 2010 17:37:30
#CCP4I USER roth
#CCP4I PROJECT sharpoutputrefinement
#CCP4I JOB_ID 19
#CCP4I SCRATCH /tmp
#CCP4I HOSTNAME bbzws339.bbz.uni-leipzig.de
#CCP4I PID 13018
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.1: Refmac_5.5.0109 version 5.5.0109 : 13/10/09##
###############################################################
User: unknown Run date: 11/10/2010 Run time: 17:37:30
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
$TEXT:Reference1: $$ comment $$
"Refinement of Macromolecular Structures by the Maximum-Likelihood Method:"
G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
Acta Crystallogr. D53, 240-255
EU Validation contract: BIO2CT-92-0524
$$
$SUMMARY :Reference1: $$ Refmac: $$
:TEXT:Reference1: $$
Data line--- make check NONE
Data line--- make hydrogen ALL hout NO peptide NO cispeptide
NO ssbridge YES symmetry YES sugar YES connectivity NO
link NO
Data line--- refi type REST PHASE SCBL BBLU resi MLKF meth
CGMAT bref ISOT
Data line--- refi tlsc 10
Data line--- ncyc 25
Data line--- scal type SIMP LSSC ANISO EXPE
Data line--- solvent YES
Data line--- weight MATRIX 0.1
Data line--- 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
Data line--- labin FP=FP SIGFP=SIGFP HLA=HLA HLB=HLB HLC=HLC HLD=HLD
FREE=FreeR_flag
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
Data line--- PNAME sharpoutputrefinement
Data line--- DNAME hrsync
Data line--- RSIZE 80
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /homes/roth/dlhdata/sharp/eden_unique.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
/software/linuxsoft/ccp4/ccp4-6.1.3/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name -
/homes/roth/dlhdata/sharp/shrefmac9.pdb
Output coordinate file. Logical name - XYZOUT actual file name -
/homes/roth/dlhdata/sharp/shrefmac10.pdb
Input reflection file. Logical name - HKLIN actual file name -
/homes/roth/dlhdata/sharp/eden_unique.mtz
Output reflection file. Logical name - HKLOUT actual file name -
/homes/roth/dlhdata/sharp/eden_refmac3.mtz
Cell from mtz : 61.560 69.500 133.350 90.000 90.000 90.000
Space group from mtz: number - 19; name - P 21 21 21
Refinement type : Restrained
***TLS refinement cycle*** 2
1
0.1153065 0.1254572 0.1168760 1.2506233E-02 2.1331017E-03
1.5424690E-04
-1.4598943E-02 -3.3578421E-03 -1.7373050E-02 -3.3114674E-03 -1.3628958E-02
-2.4346421E-03
-8.4016532E-02 4.1347187E-02 -0.1191208 -0.1013065 -0.1222848
0.1371335 -0.2420141 5.1373582E-02
-0.3787168
Problem
xyz 1107 48.64835 38.25826 83.76399 -34.85817
8.685342 -6.930134 -12.26284 -18.79212 3.157892
19.69073 -34.85817 0.6871372 23.66340 -0.3420097
-0.5949482 0.7273692
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final coordinates (XYZOUT) to /homes/roth/dlhdata/sharp/shrefmac10.pdb
***************************************************************************
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final phases (HKLOUT) to /homes/roth/dlhdata/sharp/eden_refmac3.mtz
***************************************************************************
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final TLS (TLSOUT) to /homes/roth/dlhdata/sharp/dlhtls_refmac1.tls
***************************************************************************
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 11 Oct 2010 17:42:38
#CCP4I TERMINATION OUTPUT_FILES
/homes/roth/dlhdata/sharp/sharpoutputrefinement_19_hrsync.refmac.cif
sharpoutputrefinement
#CCP4I MESSAGE Task completed successfully
