3v Running Log for JobId '2023.jan23.502'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=132.183.4.6 (Mon Jan 23 18:29:04 2023)
  • converting pdb into xyzr (Mon Jan 23 18:29:04 2023)
  • completed conversion of PDB file: 2023.jan23.502.pdb (size: 110k) (Mon Jan 23 18:29:07 2023)
  • converted 3518 atoms of 3518 atoms (Mon Jan 23 18:29:07 2023)
  • found 3518 atoms in pdb (Mon Jan 23 18:29:07 2023)
  • starting probe size 0.000 (Mon Jan 23 18:29:07 2023)
  • running 3v volume program (Mon Jan 23 18:29:07 2023)
  • smoothing out volume (Mon Jan 23 18:29:08 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:29:09 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:29:24 2023)
  • compressing 2023.jan23.502-0.0.obj (Mon Jan 23 18:29:24 2023)
  • UCSF Chimera completed in 19.82 sec (Mon Jan 23 18:29:28 2023)
  • analyzing volume (Mon Jan 23 18:29:28 2023)
  • normal CoM (3.8, -0.8, -5.6) Å (Mon Jan 23 18:30:18 2023)
  • reduced center failed (Mon Jan 23 18:30:25 2023)
  • volume analysis completed in 57.51 sec (Mon Jan 23 18:30:25 2023)
  • compressing 2023.jan23.502-0.0.pdb (Mon Jan 23 18:30:25 2023)
  • compressing 2023.jan23.502-0.0.mrc (Mon Jan 23 18:30:29 2023)
  • starting probe size 1.000 (Mon Jan 23 18:30:33 2023)
  • running 3v volume program (Mon Jan 23 18:30:33 2023)
  • smoothing out volume (Mon Jan 23 18:30:35 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:30:36 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:30:50 2023)
  • compressing 2023.jan23.502-1.0.obj (Mon Jan 23 18:30:50 2023)
  • UCSF Chimera completed in 19.13 sec (Mon Jan 23 18:30:54 2023)
  • analyzing volume (Mon Jan 23 18:30:54 2023)
  • normal CoM (1.8, -0.9, -3.6) Å (Mon Jan 23 18:31:45 2023)
  • reduced center failed (Mon Jan 23 18:31:55 2023)
  • volume analysis completed in 61.35 sec (Mon Jan 23 18:31:55 2023)
  • compressing 2023.jan23.502-1.0.pdb (Mon Jan 23 18:31:55 2023)
  • compressing 2023.jan23.502-1.0.mrc (Mon Jan 23 18:31:58 2023)
  • starting probe size 2.000 (Mon Jan 23 18:32:03 2023)
  • running 3v volume program (Mon Jan 23 18:32:03 2023)
  • smoothing out volume (Mon Jan 23 18:32:05 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:32:06 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:32:20 2023)
  • compressing 2023.jan23.502-2.0.obj (Mon Jan 23 18:32:20 2023)
  • UCSF Chimera completed in 18.53 sec (Mon Jan 23 18:32:23 2023)
  • analyzing volume (Mon Jan 23 18:32:23 2023)
  • normal CoM (3.8, -1.0, -5.6) Å (Mon Jan 23 18:33:19 2023)
  • reduced center failed (Mon Jan 23 18:33:31 2023)
  • volume analysis completed in 67.36 sec (Mon Jan 23 18:33:31 2023)
  • compressing 2023.jan23.502-2.0.pdb (Mon Jan 23 18:33:31 2023)
  • compressing 2023.jan23.502-2.0.mrc (Mon Jan 23 18:33:34 2023)
  • starting probe size 3.000 (Mon Jan 23 18:33:38 2023)
  • running 3v volume program (Mon Jan 23 18:33:38 2023)
  • smoothing out volume (Mon Jan 23 18:33:41 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:33:42 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:33:57 2023)
  • compressing 2023.jan23.502-3.0.obj (Mon Jan 23 18:33:57 2023)
  • UCSF Chimera completed in 18.16 sec (Mon Jan 23 18:34:00 2023)
  • analyzing volume (Mon Jan 23 18:34:00 2023)
  • normal CoM (1.7, -1.1, -3.5) Å (Mon Jan 23 18:34:57 2023)
  • reduced center failed (Mon Jan 23 18:35:09 2023)
  • volume analysis completed in 69.83 sec (Mon Jan 23 18:35:09 2023)
  • compressing 2023.jan23.502-3.0.pdb (Mon Jan 23 18:35:09 2023)
  • compressing 2023.jan23.502-3.0.mrc (Mon Jan 23 18:35:12 2023)
  • starting probe size 4.000 (Mon Jan 23 18:35:16 2023)
  • running 3v volume program (Mon Jan 23 18:35:16 2023)
  • waiting for system load (2.27) to calm down, total wait time: 2.15 sec (Mon Jan 23 18:35:31 2023)
  • running now (Mon Jan 23 18:35:33 2023)
  • smoothing out volume (Mon Jan 23 18:35:33 2023)
  • waiting for system load (2.17) to calm down, total wait time: 3.85 sec (Mon Jan 23 18:35:33 2023)
  • running now (Mon Jan 23 18:35:34 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:35:36 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:35:50 2023)
  • compressing 2023.jan23.502-4.0.obj (Mon Jan 23 18:35:50 2023)
  • waiting for system load (2.06) to calm down, total wait time: 5.14 sec (Mon Jan 23 18:35:50 2023)
  • running now (Mon Jan 23 18:35:51 2023)
  • waiting for system load (2.06) to calm down, total wait time: 6.43 sec (Mon Jan 23 18:35:51 2023)
  • running now (Mon Jan 23 18:35:52 2023)
  • UCSF Chimera completed in 24.58 sec (Mon Jan 23 18:35:55 2023)
  • analyzing volume (Mon Jan 23 18:35:55 2023)
  • normal CoM (3.5, -1.0, -5.4) Å (Mon Jan 23 18:36:57 2023)
  • reduced center failed (Mon Jan 23 18:37:11 2023)
  • volume analysis completed in 1 min 16 sec (Mon Jan 23 18:37:11 2023)
  • compressing 2023.jan23.502-4.0.pdb (Mon Jan 23 18:37:11 2023)
  • waiting for system load (2.29) to calm down, total wait time: 8.68 sec (Mon Jan 23 18:37:11 2023)
  • running now (Mon Jan 23 18:37:13 2023)
  • waiting for system load (2.11) to calm down, total wait time: 10.15 sec (Mon Jan 23 18:37:13 2023)
  • running now (Mon Jan 23 18:37:14 2023)
  • compressing 2023.jan23.502-4.0.mrc (Mon Jan 23 18:37:17 2023)
  • starting probe size 5.000 (Mon Jan 23 18:37:22 2023)
  • running 3v volume program (Mon Jan 23 18:37:22 2023)
  • waiting for system load (3.14) to calm down, total wait time: 20.05 sec (Mon Jan 23 18:37:44 2023)
  • waiting for system load (2.73) to calm down, total wait time: 25.32 sec (Mon Jan 23 18:37:54 2023)
  • running now (Mon Jan 23 18:37:59 2023)
  • smoothing out volume (Mon Jan 23 18:37:59 2023)
  • waiting for system load (2.51) to calm down, total wait time: 28.87 sec (Mon Jan 23 18:37:59 2023)
  • running now (Mon Jan 23 18:38:03 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 18:38:04 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 18:38:18 2023)
  • compressing 2023.jan23.502-5.0.obj (Mon Jan 23 18:38:18 2023)
  • waiting for system load (2.30) to calm down, total wait time: 31.16 sec (Mon Jan 23 18:38:18 2023)
  • running now (Mon Jan 23 18:38:21 2023)
  • waiting for system load (2.30) to calm down, total wait time: 33.46 sec (Mon Jan 23 18:38:21 2023)
  • running now (Mon Jan 23 18:38:23 2023)
  • UCSF Chimera completed in 42.08 sec (Mon Jan 23 18:38:26 2023)
  • analyzing volume (Mon Jan 23 18:38:26 2023)
  • normal CoM (1.4, -0.9, -3.4) Å (Mon Jan 23 18:39:30 2023)
  • reduced center failed (Mon Jan 23 18:39:44 2023)
  • volume analysis completed in 1 min 18 sec (Mon Jan 23 18:39:44 2023)
  • compressing 2023.jan23.502-5.0.pdb (Mon Jan 23 18:39:44 2023)
  • waiting for system load (2.20) to calm down, total wait time: 35.29 sec (Mon Jan 23 18:39:44 2023)
  • running now (Mon Jan 23 18:39:46 2023)
  • waiting for system load (2.20) to calm down, total wait time: 37.12 sec (Mon Jan 23 18:39:46 2023)
  • running now (Mon Jan 23 18:39:48 2023)
  • compressing 2023.jan23.502-5.0.mrc (Mon Jan 23 18:39:51 2023)
  • waiting for system load (2.03) to calm down, total wait time: 38.31 sec (Mon Jan 23 18:39:51 2023)
  • running now (Mon Jan 23 18:39:52 2023)
  • tarring file list (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-0.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-0.0.mrc (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-1.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-1.0.mrc (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-2.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-2.0.mrc (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-3.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-3.0.mrc (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-4.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-4.0.mrc (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-5.0.pdb (Mon Jan 23 18:39:56 2023)
  • compressing 2023.jan23.502-5.0.mrc (Mon Jan 23 18:39:56 2023)
  • FINISHED (Mon Jan 23 18:39:56 2023)

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Log file display

Show last lines of log file  
Terminal display
		
Message: running now 
Message: waiting for system load (2.20) to calm down, total wait time: 37.12 sec 
Message: running now 
Message: compressing 2023.jan23.502-5.0.mrc 
Message: waiting for system load (2.03) to calm down, total wait time: 38.31 sec 
Message: running now 
Message: tarring file list 
Message: compressing 2023.jan23.502-0.0.pdb 
Message: compressing 2023.jan23.502-0.0.mrc 
Message: compressing 2023.jan23.502-1.0.pdb 
Message: compressing 2023.jan23.502-1.0.mrc 
Message: compressing 2023.jan23.502-2.0.pdb 
Message: compressing 2023.jan23.502-2.0.mrc 
Message: compressing 2023.jan23.502-3.0.pdb 
Message: compressing 2023.jan23.502-3.0.mrc 
Message: compressing 2023.jan23.502-4.0.pdb 
Message: compressing 2023.jan23.502-4.0.mrc 
Message: compressing 2023.jan23.502-5.0.pdb 
Message: compressing 2023.jan23.502-5.0.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
Download source code
Help
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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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