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Automated Validation of NMR Structures
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Entry too large or a bug #249

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. PDB-CING the entry.

What is the expected output? What do you see instead?
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r792)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd              on: nmr.cmbi.umcn.nl (darwin/32bit)               at: Wed 
Jun  9 13:47:28 2010
DEBUG: Using:
DEBUG: inputDir:             
file:///Users/jd/wattosTestingPlatform/pdb/data/structures/divided/pdb/uv
DEBUG: outputDir:            /Library/WebServer/Documents/PDB-CING/data/uv/2uva
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          PDB
DEBUG: modelCount:           None
Enforcing a redo
copying file: 
//Users/jd/wattosTestingPlatform/pdb/data/structures/divided/pdb/uv/pdb2uva.ent.
gz to: pdb2uva.ent.gz
DEBUG: Removing file: pdb2uva.ent.gz
==> Parsing pdbFile "2uva.pdb" ... 
PDB parser: unknown record type: SPLIT 
Non-standard (residues and their) atoms to add:
FMN : C1'  C10  C2   C2'  C3'  C4   C4'  C4A  C5'  C5A  C6   C7   C7M  C8   C8M 
 C9   C9A  N1   N10  N3   N5   O1P  O2   O2'  O2P  O3'  O3P  O4   O4'  O5'  P   
 [ 3079]
DEBUG: Residue.addDihedralD1: skipping non N-terminal residue without doublet 
<Residue GLN19> (missing preceding neighbor but not N-terminal)
DEBUG: Residue.addDihedralD1: skipping residue <Residue GLY29> because of 
missing atoms

...

DEBUG: chk 1 ssType   res    <Residue GLU2078> mdl 0 a2   183.38 a1   193.07 
c_av       38 c_sd       40 ck        7 zk    -0.77 h-        0 h+      140 z-  
  -0.95 z+     2.58
DEBUG: Expected exactly one but Found 0 histogram for <Residue GLU2078>; 
skipping
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
Python(38268) malloc: *** mmap(size=4894720) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
CING started at : Wed Jun  9 13:47:24 2010
CING stopped at : Wed Jun  9 14:24:21 2010
CING took       : 2216.779 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 344, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 262, in main
    doWattos=doWattos, doTalos=doTalos):
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 960, in validate
    doWattos = doWattos, doTalos = doTalos)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 105, in validate
    project.runCingChecks(toFile=True, ranges=ranges)
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 963, in runCingChecks
    return runCingChecks(self, toFile=toFile, ranges = ranges)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 69, in runCingChecks
    project.checkForSaltbridges(toFile)
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 966, in checkForSaltbridges
    return checkForSaltbridges(self, cutoff = cutoff, toFile = toFile)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 817, in checkForSaltbridges
    result.append( s )
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/NTutils.py", line 202, in append
    list.append(self, item)
MemoryError

Original issue reported on code.google.com by jurge...@gmail.com on 9 Jun 2010 at 12:31

GoogleCodeExporter commented 9 years ago 
It seems to be simply getting out of memory resources even though there's like 
16 Gigs physically in nmr. In the shell executing the python code there are no 
limits set on memory:

jd:nmr/~/ limit
cputime      unlimited
filesize     unlimited
datasize     6144 kbytes
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
descriptors  256 
memorylocked unlimited
maxproc      266 

Processes:  113 total, 5 running, 1 stuck, 107 sleeping... 481 threads          

      14:38:54
Load Avg:  0.38,  0.52,  0.97    CPU usage:  0.57% user,  0.79% sys, 98.64% idle
SharedLibs: num =   21, resident =   52M code, 2108K data, 4016K linkedit.
MemRegions: num = 18007, resident =  702M +   47M private,  314M shared.
PhysMem: 1072M wired, 1275M active,  128M inactive, 2473M used,   14G free.
VM: 8875M + 384M   1329704(0) pageins, 22(0) pageouts

I need some help with this.

Original comment by jurge...@gmail.com on 9 Jun 2010 at 12:39

GoogleCodeExporter commented 9 years ago 
Alan, is this something we wouldn't face with a 64 bit Python? 
With machines getting bigger, it might make sense to use it. How has your 
experience with 64 bit CING been?

Original comment by jurge...@gmail.com on 9 Jun 2010 at 12:50

GoogleCodeExporter commented 9 years ago 
considering 
http://code.google.com/p/cing/wiki/MacInstallationGuideForFinkIn64Bits

Original comment by jurge...@gmail.com on 9 Jun 2010 at 12:51

GoogleCodeExporter commented 9 years ago 
Let me try to run this example here.

Where can I get the input file?

Original comment by alanwil...@gmail.com on 9 Jun 2010 at 12:58

GoogleCodeExporter commented 9 years ago 
pdb ;-)
then just initPdb cing with it and run
project.validate()

Original comment by jurge...@gmail.com on 9 Jun 2010 at 1:04

GoogleCodeExporter commented 9 years ago 
Rev. 796

After 60 hours running for a real time cpu usage of ~170 min using 2.88 Gb Real 
mem and 4.65 Virtual mem (swapping almost all the time), I stopped the 
programme. It seemed to have reached further than Jurgen's test.

amadeus[2009]:~/Downloads% cing -n 2uva --initPDB 2UVA.pdb.txt --validate -v 9
/sw/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets 
module is deprecated
  from sets import Set
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9               
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: alan            on: Unknown host (darwin/64bit)                   at: Fri 
Jun 11 19:41:23 2010
DEBUG: 
Version:           0.900
Revision:          None (http://code.google.com/p/cing/source/detail?r=None)
Date:              21 April 2010
Database:          INTERNAL_0
SML:               0.230

CING root:         /Users/alan/workspace/cingWork
CING tmp:          /var/folders/+m/+meU9wCwHYKwh16Rr5-GsE+++TM/-Tmp-/cing

Default verbosity: 3

DEBUG: options: {'test2': None, 'old': None, 'docdoc': None, 'export': False, 
'nosave': None, 'xeasyPeaks': None, 'generatePeaks': None, 'xeasy': None, 
'moleculeName': None, 'script': None, 'init': None, 'initCcpn': None, 'test': 
None, 'new': None, 'shiftx': False, 'ensemble': None, 'ranges': None, 
'superpose': False, 'ipython': None, 'validate': True, 'info': None, 'name': 
'2uva', 'yasara': None, 'doc': None, 'verbosity': 9, 'pydoc': None, 'merge': 
None, 'initPDB': '2UVA.pdb.txt', 'initBMRB': None}
DEBUG: args: []
==> Parsing pdbFile "2UVA.pdb.txt" ... 
PDB parser: unknown record type: SPLIT 
Non-standard (residues and their) atoms to add:
FMN : C1'  C10  C2   C2'  C3'  C4   C4'  C4A  C5'  C5A  C6   C7   C7M  C8   C8M 
 C9   C9A  N1   N10  N3   N5   O1P  O2   O2'  O2P  O3'  O3P  O4   O4'  O5'  P   
 [ 3079]
DEBUG: Residue.addDihedralD1: skipping non N-terminal residue without doublet 
<Residue GLN19> (missing preceding neighbor but not N-terminal)
DEBUG: Residue.addDihedralD1: skipping residue <Residue GLY29> because of 
missing atoms
DEBUG: and so on for a total of 1680 messages
==> Molecule 2UVA.pdb: No potential disulfide bridged residues found
Calculating rmsd's (residues: 19-2078,3079, models: 0-0)
----------- Project: 2uva -----------
created:    Fri Jun 11 19:41:23 2010
molecules:  [<Molecule "2UVA.pdb" (C:6,R:12366,A:273984,M:1)>]
peaks:      []
distances:  []
dihedrals:  []
rdcs:       []
coplanars:  []
-------------------------------------
==> Executing script 
"/Users/alan/workspace/cingWork/python/cing/Scripts/doValidate.py"
==> Running shiftx
runShiftx: non-protein residues [<Residue 2UVA.pdb.G.FMN3079 (355404)>, 
<Residue 2UVA.pdb.H.FMN3079 (498582)>, <Residue 2UVA.pdb.I.FMN3079 (641760)>, 
<Residue 2UVA.pdb.J.FMN3079 (784938)>, <Residue 2UVA.pdb.K.FMN3079 (928116)>, 
<Residue 2UVA.pdb.L.FMN3079 (1071294)>] will be skipped.
0
==> calculating Q-factors for chemical shift
==> Calculating secondary structure by DSSP
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.G.FMN3079 (355404)> 
found and will be written out for What If
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.H.FMN3079 (498582)> 
found and will be written out for What If
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.I.FMN3079 (641760)> 
found and will be written out for What If
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.J.FMN3079 (784938)> 
found and will be written out for What If
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.K.FMN3079 (928116)> 
found and will be written out for What If
WARNING: runWhatif: non-standard residue <Residue 2UVA.pdb.L.FMN3079 (1071294)> 
found and will be written out for What If
==> Running What If checks on 12366 residues for an estimated (7 residues/s): 
1766 seconds; please wait
0ERROR: Whatif._parseCheckdb: file "2uva.cing/2UVA.pdb/Whatif/check_000.db" not 
found.
ERROR: 
runWhatif: Failed to parse check db check_000.db
==> Running procheck_nmr
No DR lists to export
No DR lists to export
==> Parsing procheck results
==> Finished procheck_nmr successfully
Failed to find ccpn attribute project. Happens when no CCPN project was read 
first.
Failed to nmrStar.toNmrStarFile (fine if there wasn't a CCPN project to start 
with)
RunTalosPlus: No resonances defined so no sense in running.
==> Analyzing restraints
==> validateRestraints, output to 2uva.cing/2UVA.pdb/Cing/restraints.txt
DEBUG: chk 1 ssType   res      <Residue GLN19> mdl 0 a2   203.02 a1   252.74 
c_av       36 c_sd       37 ck        1 zk    -0.95 h-        0 h+      115 z-  
  -0.97 z+     2.13
DEBUG: chk 0 ssType   res      <Residue SER20> mdl 0 a2    84.06 a1  -147.23 
c_av       47 c_sd       45 ck        2 zk    -1.00 h-        0 h+      157 z-  
  -1.03 z+     2.45
DEBUG: chk 2 ssType   res      <Residue SER20> mdl 0 a2   124.54 a1   339.03 
c_av     3048 c_sd     2049 ck      165 zk    -1.41 h-        8 h+     8855 z-  
  -1.48 z+     2.83
DEBUG: chk 0 ssType   res      <Residue LEU21> mdl 0 a2   127.61 a1  -138.90 
c_av       28 c_sd       21 ck        4 zk    -1.15 h-        0 h+       72 z-  
  -1.37 z+     2.11
DEBUG: chk 1 ssType   res      <Residue LEU21> mdl 0 a2   189.41 a1   279.79 
c_av      205 c_sd      168 ck        6 zk    -1.18 h-        0 h+      487 z-  
  -1.22 z+     1.67
DEBUG: chk 2 ssType   res      <Residue LEU21> mdl 0 a2   168.38 a1   124.54 
c_av     5220 c_sd     3356 ck      739 zk    -1.34 h-        6 h+    14168 z-  
  -1.55 z+     2.67
DEBUG: chk 0 ssType S res      <Residue ARG22> mdl 0 a2   109.22 a1  -141.49 
c_av       20 c_sd       12 ck        8 zk    -1.00 h-        0 h+       40 z-  
  -1.67 z+     1.73
DEBUG: chk 1 ssType S res      <Residue ARG22> mdl 0 a2   212.28 a1   289.02 
c_av       24 c_sd       18 ck        0 zk    -1.28 h-        0 h+       57 z-  
  -1.28 z+     1.80
DEBUG: chk 2 ssType S res      <Residue ARG22> mdl 0 a2   244.57 a1   168.38 
c_av     4626 c_sd     3576 ck     4808 zk     0.05 h-        0 h+    12688 z-  
  -1.29 z+     2.25
DEBUG: chk 0 ssType S res      <Residue PRO23> mdl 0 a2   108.12 a1   -59.95 
c_av       31 c_sd       21 ck        0 zk    -1.48 h-        0 h+       70 z-  
  -1.48 z+     1.86
DEBUG: chk 1 ssType S res      <Residue PRO23> mdl 0 a2    35.72 a1   334.82 
c_av       58 c_sd       37 ck       31 zk    -0.73 h-        0 h+       99 z-  
  -1.58 z+     1.12
DEBUG: chk 2 ssType S res      <Residue PRO23> mdl 0 a2   171.62 a1   244.57 
c_av     2840 c_sd     2178 ck     2669 zk    -0.08 h-        0 h+     7644 z-  
  -1.30 z+     2.21
DEBUG: chk 0 ssType S res      <Residue LEU24> mdl 0 a2   120.79 a1  -110.44 
c_av       47 c_sd       31 ck       96 zk     1.61 h-        0 h+       98 z-  
  -1.53 z+     1.67
DEBUG: chk 1 ssType S res      <Residue LEU24> mdl 0 a2   185.33 a1   253.36 
c_av      126 c_sd       96 ck        1 zk    -1.30 h-        0 h+      256 z-  
  -1.31 z+     1.35
...

DEBUG: chk 0 ssType   res    <Residue TYR2077> mdl 0 a2     7.26 a1   -98.99 
c_av       10 c_sd        8 ck       12 zk     0.17 h-        0 h+       31 z-  
  -1.38 z+     2.71
DEBUG: chk 1 ssType   res    <Residue TYR2077> mdl 0 a2    97.45 a1   305.27 
c_av       18 c_sd       16 ck        8 zk    -0.63 h-        0 h+       58 z-  
  -1.14 z+     2.58
DEBUG: chk 2 ssType   res    <Residue TYR2077> mdl 0 a2   200.93 a1    44.72 
c_av     1698 c_sd     1445 ck     2011 zk     0.22 h-        0 h+     6298 z-  
  -1.18 z+     3.18
DEBUG: chk 1 ssType   res    <Residue GLU2078> mdl 0 a2   183.38 a1   193.07 
c_av       38 c_sd       40 ck        7 zk    -0.77 h-        0 h+      140 z-  
  -0.95 z+     2.58
DEBUG: Expected exactly one but Found 0 histogram for <Residue GLU2078>; 
skipping
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>
DEBUG: Failed to getDsspSecStructConsensus from validateDihedralCombinations 
for residue; skipping: <Residue FMN3079>

Original comment by alanwil...@gmail.com on 14 Jun 2010 at 7:42

GoogleCodeExporter commented 9 years ago 
Thanks for checking Alan! Looks like 64 bits isn't making the biggest 
difference on your 3 G machine.
This problem might slip through to another time.

Original comment by jurge...@gmail.com on 14 Jun 2010 at 7:49

GoogleCodeExporter commented 9 years ago 
Well, the difference I see is that 64 bits at least didn't crash (although I 
stopped the test), so if I had like 8Gb of Ram, it probably would work much 
faster and I would have the chance to see it finish.

Besides, which Mac OSX is the iCing server using?

Original comment by alanwil...@gmail.com on 14 Jun 2010 at 8:56

GoogleCodeExporter commented 9 years ago 
Right.
It's using 10.5.8.
Thanks!

Original comment by jurge...@gmail.com on 14 Jun 2010 at 9:06

GoogleCodeExporter commented 9 years ago 
This issue comes up for entry 2ku2 as well. 50 models with each ~250 AA.

==> RunTalosPlus: No resonances defined so no sense in running.
==> Analyzing restraints
==> validateRestraints, output to 2ku2.cing/2ku2/Cing/restraints.txt
Python(32801) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
CING started at : Tue Sep 21 01:05:23 2010
CING stopped at : Tue Sep 21 04:27:53 2010
CING took       : 12149.965 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 348, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 255, in main
    doWattos=doWattos, doTalos=doTalos):
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 964, in validate
    doWattos = doWattos, doTalos = doTalos)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 108, in validate
    project.runCingChecks(toFile=True, ranges=ranges)
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 967, in runCingChecks
    return runCingChecks(self, toFile=toFile, ranges = ranges)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 71, in runCingChecks
    project.checkForSaltbridges(toFile)
  File "/Users/jd/workspace35/cingStable/python/cing/core/classes.py", line 970, in checkForSaltbridges
    return checkForSaltbridges(self, cutoff = cutoff, toFile = toFile)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 772, in checkForSaltbridges
    s = validateSaltbridge(res1,res2)
  File "/Users/jd/workspace35/cingStable/python/cing/core/validate.py", line 971, in validateSaltbridge
    'criteria: %(criterium1)s, %(criterium2)s\n'
  File "/Users/jd/workspace35/cingStable/python/cing/Libs/NTutils.py", line 1270, in __init__
    dict.__init__(self, *args, **kwds)
MemoryError
Python(32801) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Exception MemoryError: MemoryError() in <module 'threading' from 
'/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/threa
ding.pyc'> ignored
Python(32801) malloc: *** mmap(size=2097152) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error in sys.exitfunc:
MemoryError

Original comment by jurge...@gmail.com on 21 Sep 2010 at 12:54

GoogleCodeExporter commented 9 years ago 
- It's taking 2 Mb chunks of memory at a time. size=2097152.
- Python can easily go over 2 Gb. I had a test program go to 3 Gb.
- It's not hardware related as it crashes on the exact same spot. 
- Also, memtester shows no mistakes after:
memtester 1G 1
- It's weird that this happens so early in the CING validation. 
- The CCPN file reads fine into Analysis. It shows only the hydrogen bond 
restraints without assigned atoms. Maybe that's the problem?

Original comment by jurge...@gmail.com on 22 Sep 2010 at 3:34

GoogleCodeExporter commented 9 years ago 
Geerten, can you have a quick peak at your saltbridge checking code. Does it 
explode with large entries?
I had a brief look but couldn't spot any such case.

Original comment by jurge...@gmail.com on 4 Jan 2011 at 11:53

GoogleCodeExporter commented 9 years ago 
Trying debug again with with:
cing -n 2ku2 --initPDB pdb2ku2_001.ent --validateFastest -v 9

Works fine with just one model:

DEBUG: >> <Residue G.ASP225> <Residue G.LYS231>
DEBUG: ------------------ Saltbridge ------------------
residues:          <Residue G.ASP225> <Residue G.LYS231>
r (av,sd,min,max): (9.3, nan, 9.3, 9.3)
theta (av,sd):     (143.8, nan)
types:             [('saltbridge', 0), ('C-C bridge', 0), ('N-O bridge', 0), 
('ion pair', 1), ('not observed', 0)]

DEBUG: Ending checkForSaltbridges
==> Calculating rmsd's (ranges: 
A.-3-233,B.-3-233,C.-3-233,D.-3-233,E.-3-233,F.-3-233,G.-3-233, models: 0-0)
==> Disulfide analysis, output to 2ku2.cing/pdb2ku2_001/Cing/disulfides.txt
==> Found assigned/overall/fraction for spins:    13C 0/8071/0.00   15N 
0/2184/0.00   1H 0/11179/0.00
==> Only spins with fraction >= 0.85 will be flagged when missing: {'13C': 
False, '1H': False, '15N': False}
==> Criticizing project: output to "2ku2.cing/pdb2ku2_001/Cing/ROG.txt"
==> summary, output to 2ku2.cing/pdb2ku2_001/Cing/summary.txt
==> Generating Macros
==> Initializing HTML objects
==> Generating CING HTML code.
0...
0..
Creating Procheck html
0.........1.......
Creating Wattos html
0
Html for chain A and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain B and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain C and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain D and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain E and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain F and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for chain G and its residues
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3.........4.........5.........6.........7.........
8.........9.........
0.........1.........2.........3......
Html for dihedrals by Project and Residue
Html for atoms and models
Html for peaks and restraints

==> Rendering HTML pages
Done with overall validation
-------------------------------------------------------
==> Saving <Project 2ku2>
==> Saved <Molecule "pdb2ku2_001" (C:7,R:1659,A:30121,M:1)> to 
"2ku2.cing/Data/Molecules/pdb2ku2_001"
CING started at : Tue Feb  1 16:06:03 2011
CING stopped at : Tue Feb  1 16:09:57 2011
CING took       : 234.916 s

It's taking plenty long now with all models.

Original comment by jurge...@gmail.com on 1 Feb 2011 at 3:22

GoogleCodeExporter commented 9 years ago 
But 2ku2's PDB file is running through validateFastest without error. Strange. 
Regular run from CCPN with all checks is still running on nmr.

Original comment by jurge...@gmail.com on 2 Feb 2011 at 10:17

GoogleCodeExporter commented 9 years ago 
Don't know how but fixed:

http://nmr.cmbi.ru.nl/NRG-CING/data/ku/2ku2/log_validateEntry/2ku2_2011-02-02_05
-29-06.log

Leaving X-ray 2uva for later.

Original comment by jurge...@gmail.com on 4 Feb 2011 at 3:20