3v Running Log for JobId '2019.sep10.70b'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=195.209.233.168 (Tue Sep 10 05:45:53 2019)
  • waiting for system load (3.05) to calm down, total wait time: 8.72 sec (Tue Sep 10 05:45:53 2019)
  • waiting for system load (2.81) to calm down, total wait time: 14.74 sec (Tue Sep 10 05:46:02 2019)
  • running now (Tue Sep 10 05:46:08 2019)
  • downloading pdb file (Tue Sep 10 05:46:08 2019)
  • waiting for system load (2.38) to calm down, total wait time: 17.47 sec (Tue Sep 10 05:46:08 2019)
  • running now (Tue Sep 10 05:46:10 2019)
  • failed to download pdb id: 4pqe (Tue Sep 10 05:46:10 2019)
  • waiting for system load (2.38) to calm down, total wait time: 20.2 sec (Tue Sep 10 05:46:10 2019)
  • running now (Tue Sep 10 05:46:13 2019)
  • trying download pdb id again without bio unit (Tue Sep 10 05:46:15 2019)
  • waiting for system load (2.35) to calm down, total wait time: 22.76 sec (Tue Sep 10 05:46:15 2019)
  • running now (Tue Sep 10 05:46:18 2019)
  • waiting for system load (2.32) to calm down, total wait time: 25.16 sec (Tue Sep 10 05:46:18 2019)
  • running now (Tue Sep 10 05:46:20 2019)
  • completed download of PDB id 4pqe (size: 365 k, 4611 lines) (Tue Sep 10 05:46:21 2019)
  • waiting for system load (2.32) to calm down, total wait time: 27.56 sec (Tue Sep 10 05:46:21 2019)
  • running now (Tue Sep 10 05:46:23 2019)
  • converting pdb into xyzr (Tue Sep 10 05:46:23 2019)
  • waiting for system load (2.13) to calm down, total wait time: 29.1 sec (Tue Sep 10 05:46:23 2019)
  • running now (Tue Sep 10 05:46:24 2019)
  • completed conversion of PDB file: 4pqe-2019.sep10.70b.pdb (size: 128k) (Tue Sep 10 05:46:27 2019)
  • converted 4087 atoms of 4087 atoms (Tue Sep 10 05:46:27 2019)
  • found 4087 atoms in pdb (Tue Sep 10 05:46:27 2019)
  • waiting for system load (2.13) to calm down, total wait time: 30.65 sec (Tue Sep 10 05:46:27 2019)
  • running now (Tue Sep 10 05:46:29 2019)
  • running 3v volume program (Tue Sep 10 05:46:29 2019)
  • waiting for system load (2.04) to calm down, total wait time: 31.87 sec (Tue Sep 10 05:46:29 2019)
  • running now (Tue Sep 10 05:46:30 2019)
  • waiting for system load (3.16) to calm down, total wait time: 42.05 sec (Tue Sep 10 05:46:36 2019)
  • waiting for system load (3.26) to calm down, total wait time: 53.69 sec (Tue Sep 10 05:46:46 2019)
  • running now (Tue Sep 10 05:46:57 2019)
  • smoothing out volume (Tue Sep 10 05:46:57 2019)
  • waiting for system load (2.76) to calm down, total wait time: 59.24 sec (Tue Sep 10 05:46:57 2019)
  • running now (Tue Sep 10 05:47:03 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 10 05:47:03 2019)
  • UCSF Chimera created Jmol compatible file (Tue Sep 10 05:47:37 2019)
  • compressing 4pqe-2019.sep10.70b.obj (Tue Sep 10 05:47:37 2019)
  • waiting for system load (7.46) to calm down, total wait time: 5 min 29 sec (Tue Sep 10 05:47:37 2019)
  • running now (Tue Sep 10 05:52:07 2019)
  • UCSF Chimera completed in 5 min 31 sec (Tue Sep 10 05:52:07 2019)
  • analyzing volume (Tue Sep 10 05:52:07 2019)
  • normal CoM (-5.4, -3.6, 0.7) Å (Tue Sep 10 05:52:09 2019)
  • reduced center failed (Tue Sep 10 05:52:09 2019)
  • volume analysis completed in 2.4 sec (Tue Sep 10 05:52:09 2019)
  • compressing 4pqe-2019.sep10.70b.mrc (Tue Sep 10 05:52:09 2019)
  • FINISHED (Tue Sep 10 05:52:09 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: waiting for system load (3.26) to calm down, total wait time: 53.69 sec 
Message: running now 
Message: smoothing out volume 
Message: waiting for system load (2.76) to calm down, total wait time: 59.24 sec 
Message: running now 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 4pqe-2019.sep10.70b.obj 
Message: waiting for system load (7.46) to calm down, total wait time: 5 min 29 sec 
Message: running now 
Message: UCSF Chimera completed in 5 min 31 sec 
OBJFILE /var/www/html/3vee/output/2019/sep10/70b/4pqe-2019.sep10.70b.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.4, -3.6, 0.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.4 sec 
Message: compressing 4pqe-2019.sep10.70b.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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