Appion

We finally got redux running and can look at the plots from ACE2, and we see surprisingly poor estimations. I am attaching a two 1D plots for comparison of results from ACE2 and from CTFfind, and it is clear that ACE2 is pretty far off. These plots are for what I would consider a good image with Thon rings out to nearly 8 Angstroms.
Additionally, we've noticed that vast majority of images output "!!! WARNING: Image is possibly over-focused" when the 1/30A - 1/10A and 5 peak confidences are being calculated.
Any ideas why we might be having these issues?
running myami r17119

Here's the output for the ACE2 run for this image, but I can send the MRC file if you need it for debugging:

Starting image 1 ( skip:0, remain:0 ) id:696246, file: 12sep10a_01gr_082sq_02hl_02en ... Pixel size: 1.15450433333
... Ace2 executable: /archive/glander/myami/appion/bin/ace2.exe
... running ace2 at Thu Sep 13 08:08:13 2012
/archive/glander/myami/appion/bin/ace2.exe -i /leginon4/glander/12sep10a/rawdata/12sep10a_00001gr_00082sq_v02_00002hl_00002en.mrc -b 2 -c 2.2 -k 120.0 -a 1.15450433333 -e 10.0,0.001 -r 0.0

Program: /archive/glander/myami/appion/bin/ace2.exe in source ace2.m, svn revision 17012,
which was compiled on Aug 9 2012 at 10:54:00.

Reading Image /leginon4/glander/12sep10a/rawdata/12sep10a_00001gr_00082sq_v02_00002hl_00002en.mrc: DONE in 0.12 seconds
Processing image with 4096 4096 pixels
APIX: 1.154504 KV: 120.000000 CS: 2.200000
Binning image by 2 pixels... DONE in 0.05 seconds
Blurring 100 edge pixels... DONE in 0.02 seconds
Generating power spectrum... DONE in 4.31 seconds
post-binning by 2...
Blurring edges by 10.0 pixels...
Finding edges for ellipse fitting... DONE in 0.25 seconds (12495 edges)
Using RANSAC to find ellipse parameters...
RANSAC SUCCESS, 608/12495 (4.87%-99.00%)
DONE in 1.23 seconds
--
... Committing ctf parameters for 12sep10a_01gr_082sq_02hl_02en to database
... Reading image...
[CTF param] def1: 2.42e-06 | def2: 2.47e-06 | angle: 35.2 | ampcontr 0.27 | defratio 1.021
[CTF stats] conf: 0.978 | conf_d: 0.978
Final params: def1: 2.42e-06 | def2: 2.47e-06 | angle: 35.2 | defratio 1.02
... Defocus Astig Percent Diff 1.02 -- 2.419e-06, 2.469e-06
Computing power spectra.........
... Compute PSD with fieldsize 2048 and 9 images complete in 10.34 sec
... Preform a rotational average and remove spikes...
PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE
... Number of available peaks is 250
... Determine and subtract noise model
PART 2: BACKGROUND NOISE SUBTRACTION
... starting peak extension
Peak Extension Complete in 0.98 msec
... Constraint violation: 0.014 < -0.001
... Constraint violation: -0.009 < -0.001
... Constraint violation: -0.028 < -0.001
... Constraint violation: -0.006 < -0.001
Noise Model Complete in 86.04 msec
... Constraint violation: -0.005 < -0.001
-
... Saving 1D graph to file 12sep10a_01gr_082sq_02hl_02en-plots.png
PART 8: NORMALIZE THE 2D IMAGE
PART 9: DRAW THE 2D POWERSPEC IMAGE
... Saving 2D powerspectra to file: 12sep10a_01gr_082sq_02hl_02en-powerspec.jpg
[CTF run] method: ace2 | runname acetwo1
[CTF param] def1: 2.42e-06 | def2: 2.47e-06 | angle: 35.2 | ampcontr 0.27 | defratio 1.021
[CTF stats] conf_30-10: 0.363 | conf_5peak: 0.509 | res_0.8: 100.0A | res_0.5 100.0A
[CTF stats] conf: 0.978 | conf_d: 0.978

SUMMARY: pyace2
    ------------------------------------------
    PEAKS:        0 peaks of 0
    AVG PEAKS:    0.0 +/- 0.0 peaks
    (- ESTIMATE: 0 to 0 total peaks )
    -----------------------------------------
    TIME:         24.83 sec
    AVG TIME:     26.67 +/- 32.91 sec
    ------------------------------------------