3v Running Log for JobId '2019.aug24.455'

Program is still running, progress is shown below

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  • host ip address=200.44.65.90 (Sat Aug 24 23:01:28 2019)
  • converting pdb into xyzr (Sat Aug 24 23:01:28 2019)
  • completed conversion of PDB file: 2019.aug24.455.pdb (size: 141k) (Sat Aug 24 23:01:31 2019)
  • converted 4505 atoms of 4505 atoms (Sat Aug 24 23:01:31 2019)
  • found 4505 atoms in pdb (Sat Aug 24 23:01:31 2019)
  • starting probe size 0.000 (Sat Aug 24 23:01:31 2019)
  • running 3v volume program (Sat Aug 24 23:01:31 2019)
  • smoothing out volume (Sat Aug 24 23:01:31 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:01:31 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:01:42 2019)
  • compressing 2019.aug24.455-0.0.obj (Sat Aug 24 23:01:42 2019)
  • UCSF Chimera completed in 10.76 sec (Sat Aug 24 23:01:42 2019)
  • analyzing volume (Sat Aug 24 23:01:42 2019)
  • normal CoM (-0.1, -1.8, -1.0) Å (Sat Aug 24 23:01:44 2019)
  • reduced center failed (Sat Aug 24 23:01:44 2019)
  • volume analysis completed in 2.04 sec (Sat Aug 24 23:01:44 2019)
  • compressing 2019.aug24.455-0.0.mrc (Sat Aug 24 23:01:44 2019)
  • starting probe size 3.000 (Sat Aug 24 23:01:44 2019)
  • running 3v volume program (Sat Aug 24 23:01:44 2019)
  • smoothing out volume (Sat Aug 24 23:01:45 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:01:45 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:01:55 2019)
  • compressing 2019.aug24.455-3.0.obj (Sat Aug 24 23:01:55 2019)
  • UCSF Chimera completed in 10.95 sec (Sat Aug 24 23:01:56 2019)
  • analyzing volume (Sat Aug 24 23:01:56 2019)
  • normal CoM (-4.0, -1.8, 1.1) Å (Sat Aug 24 23:01:58 2019)
  • reduced center failed (Sat Aug 24 23:01:58 2019)
  • volume analysis completed in 2.77 sec (Sat Aug 24 23:01:58 2019)
  • compressing 2019.aug24.455-3.0.mrc (Sat Aug 24 23:01:58 2019)
  • starting probe size 6.000 (Sat Aug 24 23:01:59 2019)
  • running 3v volume program (Sat Aug 24 23:01:59 2019)
  • smoothing out volume (Sat Aug 24 23:01:59 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:01:59 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:02:09 2019)
  • compressing 2019.aug24.455-6.0.obj (Sat Aug 24 23:02:09 2019)
  • UCSF Chimera completed in 10.63 sec (Sat Aug 24 23:02:10 2019)
  • analyzing volume (Sat Aug 24 23:02:10 2019)
  • normal CoM (-2.0, -1.8, -2.9) Å (Sat Aug 24 23:02:13 2019)
  • reduced center failed (Sat Aug 24 23:02:13 2019)
  • volume analysis completed in 3.47 sec (Sat Aug 24 23:02:13 2019)
  • compressing 2019.aug24.455-6.0.mrc (Sat Aug 24 23:02:13 2019)
  • starting probe size 9.000 (Sat Aug 24 23:02:13 2019)
  • running 3v volume program (Sat Aug 24 23:02:13 2019)
  • smoothing out volume (Sat Aug 24 23:02:14 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:02:14 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:02:25 2019)
  • compressing 2019.aug24.455-9.0.obj (Sat Aug 24 23:02:25 2019)
  • UCSF Chimera completed in 10.67 sec (Sat Aug 24 23:02:25 2019)
  • analyzing volume (Sat Aug 24 23:02:25 2019)
  • normal CoM (-0.0, -3.7, -3.0) Å (Sat Aug 24 23:02:28 2019)
  • reduced center failed (Sat Aug 24 23:02:29 2019)
  • volume analysis completed in 4.04 sec (Sat Aug 24 23:02:29 2019)
  • compressing 2019.aug24.455-9.0.mrc (Sat Aug 24 23:02:29 2019)
  • tarring file list (Sat Aug 24 23:02:29 2019)
  • compressing 2019.aug24.455-0.0.mrc (Sat Aug 24 23:02:29 2019)
  • compressing 2019.aug24.455-3.0.mrc (Sat Aug 24 23:02:29 2019)
  • compressing 2019.aug24.455-6.0.mrc (Sat Aug 24 23:02:29 2019)
  • compressing 2019.aug24.455-9.0.mrc (Sat Aug 24 23:02:29 2019)
  • FINISHED (Sat Aug 24 23:02:29 2019)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2019/aug24/455/2019.aug24.455-9.0.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.aug24.455-9.0.obj 
Message: UCSF Chimera completed in 10.67 sec 
OBJFILE /var/www/html/3vee/output/2019/aug24/455/2019.aug24.455-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-0.0, -3.7, -3.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 4.04 sec 
Message: compressing 2019.aug24.455-9.0.mrc 
Message: tarring file list 
Message: compressing 2019.aug24.455-0.0.mrc 
Message: compressing 2019.aug24.455-3.0.mrc 
Message: compressing 2019.aug24.455-6.0.mrc 
Message: compressing 2019.aug24.455-9.0.mrc 
Message: FINISHED 
		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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