3v Running Log for JobId '2017.oct12.109'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=193.60.81.5 (Thu Oct 12 09:22:18 2017)
  • converting pdb into xyzr (Thu Oct 12 09:22:20 2017)
  • completed conversion of PDB file: 2017.oct12.109.pdb (size: 3016k) (Thu Oct 12 09:23:27 2017)
  • converted 96527 atoms of 96527 atoms (Thu Oct 12 09:23:27 2017)
  • found 96527 atoms in pdb (Thu Oct 12 09:23:27 2017)
  • starting probe size 0.000 (Thu Oct 12 09:23:27 2017)
  • waiting for system load (2.36) to calm down, total wait time: 2.62 sec (Thu Oct 12 09:23:27 2017)
  • running now (Thu Oct 12 09:23:29 2017)
  • running 3v volume program (Thu Oct 12 09:23:29 2017)
  • waiting for system load (2.25) to calm down, total wait time: 4.67 sec (Thu Oct 12 09:23:29 2017)
  • running now (Thu Oct 12 09:23:32 2017)
  • waiting for system load (2.47) to calm down, total wait time: 7.95 sec (Thu Oct 12 09:23:35 2017)
  • running now (Thu Oct 12 09:23:38 2017)
  • smoothing out volume (Thu Oct 12 09:23:38 2017)
  • waiting for system load (2.47) to calm down, total wait time: 11.22 sec (Thu Oct 12 09:23:38 2017)
  • running now (Thu Oct 12 09:23:42 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 09:23:42 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 09:23:56 2017)
  • compressing 2017.oct12.109-0.0.obj (Thu Oct 12 09:23:56 2017)
  • waiting for system load (2.19) to calm down, total wait time: 13.01 sec (Thu Oct 12 09:23:56 2017)
  • running now (Thu Oct 12 09:23:57 2017)
  • waiting for system load (2.19) to calm down, total wait time: 14.79 sec (Thu Oct 12 09:23:57 2017)
  • running now (Thu Oct 12 09:23:59 2017)
  • UCSF Chimera completed in 25.52 sec (Thu Oct 12 09:24:00 2017)
  • analyzing volume (Thu Oct 12 09:24:00 2017)
  • normal CoM (17.0, 32.8, -2.6) Å (Thu Oct 12 09:24:08 2017)
  • reduced center failed (Thu Oct 12 09:24:09 2017)
  • volume analysis completed in 8.41 sec (Thu Oct 12 09:24:09 2017)
  • compressing 2017.oct12.109-0.0.mrc (Thu Oct 12 09:24:09 2017)
  • waiting for system load (2.08) to calm down, total wait time: 16.15 sec (Thu Oct 12 09:24:09 2017)
  • running now (Thu Oct 12 09:24:10 2017)
  • waiting for system load (2.08) to calm down, total wait time: 17.51 sec (Thu Oct 12 09:24:10 2017)
  • running now (Thu Oct 12 09:24:12 2017)
  • starting probe size 3.000 (Thu Oct 12 09:24:13 2017)
  • waiting for system load (2.08) to calm down, total wait time: 18.87 sec (Thu Oct 12 09:24:13 2017)
  • running now (Thu Oct 12 09:24:15 2017)
  • running 3v volume program (Thu Oct 12 09:24:15 2017)
  • waiting for system load (2.08) to calm down, total wait time: 20.23 sec (Thu Oct 12 09:24:20 2017)
  • running now (Thu Oct 12 09:24:22 2017)
  • smoothing out volume (Thu Oct 12 09:24:22 2017)
  • waiting for system load (2.08) to calm down, total wait time: 21.59 sec (Thu Oct 12 09:24:22 2017)
  • running now (Thu Oct 12 09:24:23 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 09:24:23 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 09:24:35 2017)
  • compressing 2017.oct12.109-3.0.obj (Thu Oct 12 09:24:35 2017)
  • UCSF Chimera completed in 16.05 sec (Thu Oct 12 09:24:36 2017)
  • analyzing volume (Thu Oct 12 09:24:36 2017)
  • normal CoM (12.9, 28.5, 5.3) Å (Thu Oct 12 09:24:59 2017)
  • reduced center failed (Thu Oct 12 09:25:01 2017)
  • volume analysis completed in 25.11 sec (Thu Oct 12 09:25:01 2017)
  • compressing 2017.oct12.109-3.0.mrc (Thu Oct 12 09:25:01 2017)
  • waiting for system load (2.27) to calm down, total wait time: 23.74 sec (Thu Oct 12 09:25:02 2017)
  • running now (Thu Oct 12 09:25:04 2017)
  • waiting for system load (2.17) to calm down, total wait time: 25.44 sec (Thu Oct 12 09:25:04 2017)
  • running now (Thu Oct 12 09:25:05 2017)
  • starting probe size 6.000 (Thu Oct 12 09:25:07 2017)
  • waiting for system load (2.17) to calm down, total wait time: 27.14 sec (Thu Oct 12 09:25:07 2017)
  • running now (Thu Oct 12 09:25:09 2017)
  • running 3v volume program (Thu Oct 12 09:25:09 2017)
  • waiting for system load (2.08) to calm down, total wait time: 28.5 sec (Thu Oct 12 09:25:09 2017)
  • running now (Thu Oct 12 09:25:10 2017)
  • waiting for system load (2.53) to calm down, total wait time: 32.18 sec (Thu Oct 12 09:25:20 2017)
  • running now (Thu Oct 12 09:25:24 2017)
  • smoothing out volume (Thu Oct 12 09:25:24 2017)
  • waiting for system load (2.41) to calm down, total wait time: 35.09 sec (Thu Oct 12 09:25:24 2017)
  • running now (Thu Oct 12 09:25:27 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 09:25:27 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 09:25:43 2017)
  • compressing 2017.oct12.109-6.0.obj (Thu Oct 12 09:25:43 2017)
  • waiting for system load (2.25) to calm down, total wait time: 37.14 sec (Thu Oct 12 09:25:43 2017)
  • running now (Thu Oct 12 09:25:45 2017)
  • waiting for system load (2.15) to calm down, total wait time: 38.76 sec (Thu Oct 12 09:25:45 2017)
  • running now (Thu Oct 12 09:25:47 2017)
  • UCSF Chimera completed in 27.0 sec (Thu Oct 12 09:25:47 2017)
  • analyzing volume (Thu Oct 12 09:25:47 2017)
  • normal CoM (8.8, 28.0, 5.2) Å (Thu Oct 12 09:25:57 2017)
  • reduced center failed (Thu Oct 12 09:25:59 2017)
  • volume analysis completed in 11.15 sec (Thu Oct 12 09:25:59 2017)
  • compressing 2017.oct12.109-6.0.mrc (Thu Oct 12 09:25:59 2017)
  • waiting for system load (2.12) to calm down, total wait time: 40.27 sec (Thu Oct 12 09:25:59 2017)
  • running now (Thu Oct 12 09:26:00 2017)
  • waiting for system load (2.03) to calm down, total wait time: 41.46 sec (Thu Oct 12 09:26:00 2017)
  • running now (Thu Oct 12 09:26:01 2017)
  • starting probe size 9.000 (Thu Oct 12 09:26:02 2017)
  • waiting for system load (2.03) to calm down, total wait time: 42.65 sec (Thu Oct 12 09:26:02 2017)
  • running now (Thu Oct 12 09:26:04 2017)
  • running 3v volume program (Thu Oct 12 09:26:04 2017)
  • waiting for system load (2.42) to calm down, total wait time: 45.61 sec (Thu Oct 12 09:26:19 2017)
  • running now (Thu Oct 12 09:26:21 2017)
  • smoothing out volume (Thu Oct 12 09:26:21 2017)
  • waiting for system load (2.31) to calm down, total wait time: 47.96 sec (Thu Oct 12 09:26:21 2017)
  • running now (Thu Oct 12 09:26:24 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 09:26:24 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 09:26:37 2017)
  • compressing 2017.oct12.109-9.0.obj (Thu Oct 12 09:26:37 2017)
  • waiting for system load (2.34) to calm down, total wait time: 50.47 sec (Thu Oct 12 09:26:37 2017)
  • running now (Thu Oct 12 09:26:40 2017)
  • waiting for system load (2.47) to calm down, total wait time: 53.75 sec (Thu Oct 12 09:26:40 2017)
  • running now (Thu Oct 12 09:26:43 2017)
  • UCSF Chimera completed in 25.33 sec (Thu Oct 12 09:26:44 2017)
  • analyzing volume (Thu Oct 12 09:26:44 2017)
  • normal CoM (12.9, 32.4, 5.6) Å (Thu Oct 12 09:26:55 2017)
  • reduced center failed (Thu Oct 12 09:26:57 2017)
  • volume analysis completed in 12.97 sec (Thu Oct 12 09:26:57 2017)
  • compressing 2017.oct12.109-9.0.mrc (Thu Oct 12 09:26:57 2017)
  • waiting for system load (2.49) to calm down, total wait time: 57.15 sec (Thu Oct 12 09:26:57 2017)
  • running now (Thu Oct 12 09:27:00 2017)
  • waiting for system load (2.37) to calm down, total wait time: 59.82 sec (Thu Oct 12 09:27:00 2017)
  • running now (Thu Oct 12 09:27:03 2017)
  • tarring file list (Thu Oct 12 09:27:04 2017)
  • waiting for system load (2.34) to calm down, total wait time: 62.33 sec (Thu Oct 12 09:27:04 2017)
  • running now (Thu Oct 12 09:27:06 2017)
  • waiting for system load (2.34) to calm down, total wait time: 64.84 sec (Thu Oct 12 09:27:06 2017)
  • running now (Thu Oct 12 09:27:09 2017)
  • compressing 2017.oct12.109-0.0.mrc (Thu Oct 12 09:27:09 2017)
  • waiting for system load (2.23) to calm down, total wait time: 66.8 sec (Thu Oct 12 09:27:09 2017)
  • running now (Thu Oct 12 09:27:11 2017)
  • compressing 2017.oct12.109-3.0.mrc (Thu Oct 12 09:27:11 2017)
  • waiting for system load (2.23) to calm down, total wait time: 68.76 sec (Thu Oct 12 09:27:11 2017)
  • running now (Thu Oct 12 09:27:13 2017)
  • compressing 2017.oct12.109-6.0.mrc (Thu Oct 12 09:27:13 2017)
  • waiting for system load (2.23) to calm down, total wait time: 1 min 11 sec (Thu Oct 12 09:27:13 2017)
  • running now (Thu Oct 12 09:27:15 2017)
  • compressing 2017.oct12.109-9.0.mrc (Thu Oct 12 09:27:15 2017)
  • waiting for system load (2.13) to calm down, total wait time: 1 min 12 sec (Thu Oct 12 09:27:15 2017)
  • running now (Thu Oct 12 09:27:16 2017)
  • FINISHED (Thu Oct 12 09:27:16 2017)

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Log file display

Show last lines of log file 
Terminal display
		
Message: waiting for system load (2.37) to calm down, total wait time: 59.82 sec 
Message: running now 
Message: tarring file list 
Message: waiting for system load (2.34) to calm down, total wait time: 62.33 sec 
Message: running now 
Message: waiting for system load (2.34) to calm down, total wait time: 64.84 sec 
Message: running now 
Message: compressing 2017.oct12.109-0.0.mrc 
Message: waiting for system load (2.23) to calm down, total wait time: 66.8 sec 
Message: running now 
Message: compressing 2017.oct12.109-3.0.mrc 
Message: waiting for system load (2.23) to calm down, total wait time: 68.76 sec 
Message: running now 
Message: compressing 2017.oct12.109-6.0.mrc 
Message: waiting for system load (2.23) to calm down, total wait time: 1 min 11 sec 
Message: running now 
Message: compressing 2017.oct12.109-9.0.mrc 
Message: waiting for system load (2.13) to calm down, total wait time: 1 min 12 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
Help
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If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
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