[sharp-discuss] H32 SHARP-ARP/wARP-Refmac problem?
Ole Kristensen
OleK@sc.dfh.dk
Tue, 10 Dec 2002 11:22:04 +0100
In a current case, I got so far as to run the arp/warp step from autosharp
(SHARP 2.0.0, Sushi 3.0.14). Despite good phases I got stuck. Here is the
log output:
MTZ file :
/home/sharp/users/olek/None.sharp/logfiles/tig118.5/eden_flat_34.5pc.mtz
$warpbin : /a/xtal/linux/arp_warp_6.0/bin/Linux
Cell : 71.6440 71.6440 375.4090 90.0000 90.0000 120.0000
Spacegroup : H32 (155)
Wilson B-Factor : 38.419
Protein size : 2952
Sequence file : <wARP_34.5pc/seq.pir>
Resolution : 30.000 2.30
Asymmetric unit : 0.00000 1.00000 0.00000 1.00000 0.00000 1.00000
2. Generating "warp.par" for ARP/wARP version 6.0
(details) <wARP_34.5pc/warp.par> (directory index) <wARP_34.5pc>
3. Running "arpwarp.sh"
1. reading warp.par (for ARP/wARP version 6.0)
2. Building free atoms model
2.1 calculating initial map
2.2 expanding map to ARP limits
2.3 building initial model
Note: Had to go as low as 0.80 sigma, to complete atoms search.
Note: Remove atoms if below 1.0 sigmas in 2mFoDFc map.
Add atoms in density above 3.2 sigmas in mFoDFc map.
A maximum of 100 ARP refinement cycles will be run in total.
Rebuilding of the model will happen every 10 cycles.
3. running warpNtrace loop
Note: using fixed weight in REFMAC of 0.5 - check geometry afterwards!
Note: automatically adjusting phase blurring in REFMAC
16247 reflections ( 99.99 % complete ) and 0 restraint used, for
refining 3310 atoms.
Observations/parameters ratio is 1.23 (~1.23 with restraints).
Starting model : R = 0.341 (Rfree = 0.331)
Cycle 1 : After refmac : R = 0.314 (Rfree = 0.320)
Found 21 (21 requested) and removed 15 (16 requested) atoms.
Cycle 2 : After refmac : R = 0.297 (Rfree = 0.321)
Found 21 (21 requested) and removed 2 (16 requested) atoms.
Cycle 3 : After refmac : R = 0.286 (Rfree = 0.324)
Found 21 (21 requested) and removed 5 (18 requested) atoms.
Cycle 4 : After refmac : R = 0.278 (Rfree = 0.322)
Found 22 (22 requested) and removed 9 (21 requested) atoms.
Cycle 5 : After refmac : R = 0.271 (Rfree = 0.321)
Found 22 (22 requested) and removed 10 (22 requested) atoms.
Cycle 6 : After refmac : R = 0.265 (Rfree = 0.317)
Found 22 (22 requested) and removed 13 (22 requested) atoms.
Cycle 7 : After refmac : R = 0.260 (Rfree = 0.315)
Found 22 (22 requested) and removed 20 (22 requested) atoms.
Cycle 8 : After refmac : R = 0.255 (Rfree = 0.312)
Found 22 (22 requested) and removed 12 (22 requested) atoms.
Cycle 9 : After refmac : R = 0.253 (Rfree = 0.313)
Found 22 (22 requested) and removed 21 (22 requested) atoms.
Cycle 10 : After refmac : R = 0.249 (Rfree = 0.309)
Found 22 (22 requested) and removed 7 (22 requested) atoms.
Building Cycle 1
Round 1 : 291 peptides in 22 chains.
Round 2 : 312 peptides in 14 chains.
Chains 14, Residues 298 [out of 369], Connectivity Index 0.91
Cycle 11 : After refmac : R = 0.339 (Rfree = 0.384)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 12 : After refmac : R = 0.317 (Rfree = 0.375)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 13 : After refmac : R = 0.303 (Rfree = 0.366)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 14 : After refmac : R = 0.293 (Rfree = 0.359)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 15 : After refmac : R = 0.283 (Rfree = 0.348)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 16 : After refmac : R = 0.277 (Rfree = 0.345)
Found 16 (16 requested) and removed 8 (8 requested) atoms.
Cycle 17 : After refmac : R = 0.270 (Rfree = 0.323)
Found 17 (17 requested) and removed 8 (8 requested) atoms.
Cycle 18 : After refmac : R = 0.263 (Rfree = 0.321)
Found 17 (17 requested) and removed 8 (8 requested) atoms.
Cycle 19 : After refmac : R = 0.258 (Rfree = 0.317)
Found 17 (17 requested) and removed 8 (8 requested) atoms.
Cycle 20 : After refmac : R = 0.251 (Rfree = 0.316)
Found 17 (17 requested) and removed 8 (8 requested) atoms.
Building Cycle 2
Round 1 : 285 peptides in 14 chains.
Round 2 : 307 peptides in 13 chains.
Chains 10, Residues 285 [out of 369], Connectivity Index 0.92
Note: had to fix PDB file "./files/reshuffle_cycle20.pdb" for RES. numbering
- please check programs!
ERROR : program terminated in REFMAC5 (see refmac_cycle21.log
<wARP_34.5pc/refmac_cycle21.log>)
The ./files/reshuffle_cycle20.pdb looks okay. Refmac seems to be the
problem. I tried
both the refmac5 version from ccp4-4.2.2 and garib's latest version. Here,
is a bit
of my latest attempt:
###############################################################
###############################################################
###############################################################
### CCP4 4.2: Refmac_5.2.00 version 5.2.00 : 31/10/01##
###############################################################
User: Run date: 9/12/02 Run time:23:43:19
......
Data line--- MAKE HYDR N
Data line--- MAKE CHECK 0
Data line--- LABI FP=FPsha SIGFP=SIGFPsha FREE=FreeR_flag HLA=HLAdm
HLB=HLBdm HLC=HLCdm HLD=HLDdm
Data line--- LABO FC=FC PHIC=PHIC FWT=2FOFCWT PHWT=PH2FOFCWT
DELFWT=FOFCWT PHDELWT=PHFOFCWT
Data line--- REFI RESOLUTION 30.000 2.30 TYPE RESTR
Data line--- REFI RESI MLKF PHASed SCBLurred 0.34
Data line--- REFI BREF ISOTROPIC METH CGMAT
Data line--- WEIG MATRIX 0.5
Data line--- DAMP 1.0 1.0
Data line--- SCAL TYPE BULK LSSC ANIS FIXBulk
Data line--- SCAL MLSC FIXBulk
Comment line--- ! maybe only at later stages?
Data line--- SOLVENT YES
Data line--- NCYC 1
Data line--- MONI MANY
Data line--- BLIMI 2 80
Data line--- BINS 20
Data line--- VDWR SIGMA DUMMY 50.0 INCREMENT DUMMY -1.0
Data line--- VDWR 0.0
Data line--- END
.....
.....
CGMAT cycle number = 1
Too many atoms in one brick.
Maximum allowed in one brick = 60
Check symmetry, cell dimensions
===> Error: CREATE_NET failed
Refmac_5.2.00: CREATE_NET failed
Times: User: 5.0s System: 0.7s Elapsed: 0:13
Any ideas about how to get around this? I was wondering if it is related to
the asymmetric unit being defined as:
Asymmetric unit : 0.00000 1.00000 0.00000 1.00000 0.00000 1.00000
Clemens has previously pointed out that one could possibly change the
settings in
$BDG_home/database/lists/symm.dat. Will it work to change the field 10 for
spacegroup
H32 to something smaller than the 0 1 0 1 0 1 limits distributed?
When I simply take the starting file eden_flat_34.5pc.mtz and run arpwarp
just from the
ccp4i with default settings a smaller asu seems to be used and thing run
without error.
Best regards,
Ole Kristensen
Denmark