On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
> 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
I don't know exactly what has gone wrong.
Let's collect some more information.
- When you took the intial TLS parameters from TLSMD server, did you also
take the corresponding modified PDB file?
If not, that could well be the problem.
- It looks from the output that you did not tick the "reset B factors to 20"
box in ccp4i. Can you confirm that?
Ethan
> 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
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
