3v Running Log for JobId '2019.sep10.256'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=195.209.233.168 (Tue Sep 10 05:43:25 2019)
  • waiting for system load (6.02) to calm down, total wait time: 2 min 7 sec (Tue Sep 10 05:43:26 2019)
  • waiting for system load (4.51) to calm down, total wait time: 2 min 50 sec (Tue Sep 10 05:45:32 2019)
  • running now (Tue Sep 10 05:46:16 2019)
  • downloading pdb file (Tue Sep 10 05:46:16 2019)
  • waiting for system load (2.35) to calm down, total wait time: 2 min 53 sec (Tue Sep 10 05:46:16 2019)
  • running now (Tue Sep 10 05:46:18 2019)
  • failed to download pdb id: 4pqe (Tue Sep 10 05:46:18 2019)
  • waiting for system load (2.32) to calm down, total wait time: 2 min 55 sec (Tue Sep 10 05:46:18 2019)
  • running now (Tue Sep 10 05:46:21 2019)
  • trying download pdb id again without bio unit (Tue Sep 10 05:46:23 2019)
  • waiting for system load (2.13) to calm down, total wait time: 2 min 56 sec (Tue Sep 10 05:46:23 2019)
  • running now (Tue Sep 10 05:46:25 2019)
  • waiting for system load (2.13) to calm down, total wait time: 2 min 58 sec (Tue Sep 10 05:46:25 2019)
  • running now (Tue Sep 10 05:46:26 2019)
  • completed download of PDB id 4pqe (size: 365 k, 4611 lines) (Tue Sep 10 05:46:26 2019)
  • waiting for system load (2.13) to calm down, total wait time: 2 min 60 sec (Tue Sep 10 05:46:26 2019)
  • running now (Tue Sep 10 05:46:28 2019)
  • converting pdb into xyzr (Tue Sep 10 05:46:28 2019)
  • waiting for system load (2.04) to calm down, total wait time: 3 min 1 sec (Tue Sep 10 05:46:28 2019)
  • running now (Tue Sep 10 05:46:29 2019)
  • completed conversion of PDB file: 4pqe-2019.sep10.256.pdb (size: 128k) (Tue Sep 10 05:46:35 2019)
  • converted 4087 atoms of 4087 atoms (Tue Sep 10 05:46:35 2019)
  • found 4087 atoms in pdb (Tue Sep 10 05:46:35 2019)
  • waiting for system load (3.16) to calm down, total wait time: 3 min 11 sec (Tue Sep 10 05:46:35 2019)
  • waiting for system load (3.26) to calm down, total wait time: 3 min 23 sec (Tue Sep 10 05:46:45 2019)
  • running now (Tue Sep 10 05:46:57 2019)
  • running 3v volume program (Tue Sep 10 05:46:57 2019)
  • waiting for system load (2.76) to calm down, total wait time: 3 min 28 sec (Tue Sep 10 05:46:57 2019)
  • running now (Tue Sep 10 05:47:03 2019)
  • waiting for system load (2.34) to calm down, total wait time: 3 min 31 sec (Tue Sep 10 05:47:03 2019)
  • running now (Tue Sep 10 05:47:05 2019)
  • smoothing out volume (Tue Sep 10 05:47:05 2019)
  • waiting for system load (2.34) to calm down, total wait time: 3 min 33 sec (Tue Sep 10 05:47:05 2019)
  • waiting for system load (3.43) to calm down, total wait time: 3 min 48 sec (Tue Sep 10 05:47:08 2019)
  • waiting for system load (5.44) to calm down, total wait time: 5 min 15 sec (Tue Sep 10 05:47:22 2019)
  • running now (Tue Sep 10 05:48:50 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 10 05:48:50 2019)
  • UCSF Chimera created Jmol compatible file (Tue Sep 10 05:49:00 2019)
  • compressing 4pqe-2019.sep10.256.obj (Tue Sep 10 05:49:00 2019)
  • waiting for system load (2.83) to calm down, total wait time: 5 min 21 sec (Tue Sep 10 05:49:00 2019)
  • waiting for system load (2.61) to calm down, total wait time: 5 min 26 sec (Tue Sep 10 05:49:06 2019)
  • running now (Tue Sep 10 05:49:10 2019)
  • waiting for system load (2.40) to calm down, total wait time: 5 min 29 sec (Tue Sep 10 05:49:10 2019)
  • running now (Tue Sep 10 05:49:13 2019)
  • UCSF Chimera completed in 2 min 10 sec (Tue Sep 10 05:49:13 2019)
  • analyzing volume (Tue Sep 10 05:49:13 2019)
  • normal CoM (-5.4, -3.6, 0.7) Å (Tue Sep 10 05:49:15 2019)
  • reduced center failed (Tue Sep 10 05:49:16 2019)
  • volume analysis completed in 2.32 sec (Tue Sep 10 05:49:16 2019)
  • compressing 4pqe-2019.sep10.256.mrc (Tue Sep 10 05:49:16 2019)
  • waiting for system load (2.21) to calm down, total wait time: 5 min 30 sec (Tue Sep 10 05:49:16 2019)
  • running now (Tue Sep 10 05:49:17 2019)
  • waiting for system load (2.21) to calm down, total wait time: 5 min 32 sec (Tue Sep 10 05:49:17 2019)
  • running now (Tue Sep 10 05:49:19 2019)
  • FINISHED (Tue Sep 10 05:49:19 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 4pqe-2019.sep10.256.obj 
Message: waiting for system load (2.83) to calm down, total wait time: 5 min 21 sec 
Message: waiting for system load (2.61) to calm down, total wait time: 5 min 26 sec 
Message: running now 
Message: waiting for system load (2.40) to calm down, total wait time: 5 min 29 sec 
Message: running now 
Message: UCSF Chimera completed in 2 min 10 sec 
OBJFILE /var/www/html/3vee/output/2019/sep10/256/4pqe-2019.sep10.256.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.4, -3.6, 0.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.32 sec 
Message: compressing 4pqe-2019.sep10.256.mrc 
Message: waiting for system load (2.21) to calm down, total wait time: 5 min 30 sec 
Message: running now 
Message: waiting for system load (2.21) to calm down, total wait time: 5 min 32 sec 
Message: running now 
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
Download source code
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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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