Starting image 2 ( skip:8, remain:2 ) id:695438, file: 17may02a_e6f_012gr_01sq_014hl_01en-a ... Pixel size: 1.2 Found 0 ctf values !!! WARNING: no best CTF value for image 17may02a_e6f_012gr_01sq_014hl_01en-a !!! WARNING: Defocus minimum is less than zero Defocus search range: 1000 A to 45000 A (0.10 to 4.50 um) ... running ctf estimation at Tue May 2 13:28:47 2017 input = 17may02a_e6f_012gr_01sq_014hl_01en-a.mrc output = 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc apix = 1.2 kv = 200.0 cs = 2.7 ampcontrast = 0.1 fieldsize = 1024 resmin = 50.0 resmax = 4.0 defmin = 1000.0 defmax = 45000.0 defstep = 1000.0 known_astig = no exhaustive_astig_search = no restrain_astig = yes expect_astig = 500.0 phase = yes min_phase_shift = 0.174532925199 max_phase_shift = 2.96705972839 phase_search_step = 0.174532925199 expert_opts = no newline = /data/software/repo/ctffind4/4.0.16/ctffind4 17may02a_e6f_012gr_01sq_014hl_01en-a.mrc 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc 1.2 200.0 2.7 0.1 1024 50.0 4.0 1000.0 45000.0 1000.0 no no yes 500.0 yes 0.174532925199 2.96705972839 0.174532925199 no ** Welcome to CTFFind ** Version - 4.0.16 Input Mode: Batch Date & Time: 2017-05-02 13:28:47 Copyright 2015 Howard Hughes Medical Institute. All rights reserved. Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html ) Input image file name [17may02a_e6f_012gr_01sq_013hl_01en-a.mrc] : 17may02a_e6f_012gr_01sq_014hl_01en-a.mrc Output diagnostic filename [17may02a_e6f_012gr_01sq_013hl_01en-a-pow.mrc] : 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc Pixel size [1.2] : 1.2 Acceleration voltage [200.0] : 200.0 Spherical aberration [2.7] : 2.7 Amplitude contrast [0.1] : 0.1 Size of power spectrum to compute [1024] : 1024 Minimum resolution [50.0] : 50.0 Maximum resolution [4.0] : 4.0 Minimum defocus [1000.0] : 1000.0 Maximum defocus [45000.0] : 45000.0 Defocus search step [1000.0] : 1000.0 Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : yes Please enter a valid number! Expected (tolerated) astigmatism [500.0] : 500.0 Find additional phase shift? [yes] : yes Minimum phase shift [0.174532925199] : 0.174532925199 Maximum phase shift [2.96705972839] : 2.96705972839 Phase shift search step [0.174532925199] : 0.174532925199 Summary information for file 17may02a_e6f_012gr_01sq_014hl_01en-a.mrc Number of columns, rows, sections: 3710 3838 1 MRC data mode: 2 Bit depth: 32 Pixel size: 1.000 1.000 1.000 Working on micrograph 1 of 1 100% [==============================] done! Estimated defocus values : 20788.59 , 20508.88 Angstroms Estimated azimuth of astigmatism: -65.43 degrees Additional phase shift : 1.121 (.36 pi) Score : .09671 Thon rings with good fit up to : 3.6 Angstroms Summary of results : 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.txt Diagnostic images : 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc Detailled results, including 1D fit profiles: 17may02a_e6f_012gr_01sq_014hl_01en-a-pow_avrot.txt Use this command to plot 1D fit profiles : ctffind_plot_results.sh 17may02a_e6f_012gr_01sq_014hl_01en-a-pow_avrot.txt Total execution time : 1 minute and 56 seconds 2017-05-02 13:30:43 : CTFFind finished cleanly. ... ctf estimation completed in 1 min 56 sec ... reading 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.txt ... reading MRC: 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc size:(1024, 1024) dtype:float32 ... writing JPEG: 17may02a_e6f_012gr_01sq_014hl_01en-a-pow.jpg ==== Committing data to database ==== ... Committing ctf parameters for 17may02a_e6f_012gr_01sq_014hl_01en-a to database ... Reading image... [CTF param] def1: 2.051 um | def2: 2.079 um | angle: 24.6 | ampcontr 0.10 | defratio 1.014 [CTF param] additional phase shift: 64.2 degrees Final params: def1: 2.051 um | def2: 2.079 um | angle: 24.6 | defratio 1.01 ... Defocus Astig Percent Diff 0.68 -- 2.051, 2.079 um Computing power spectra in 2048x2048 blocks........ ... Compute PSD with 8 subfields and fieldsize 2048 complete in 5.11 sec * correlation 1: 0.04181 -> contribution: 0.1303 * correlation 2: 0.03923 -> contribution: 0.1223 * correlation 3: 0.04326 -> contribution: 0.1348 * correlation 4: 0.04218 -> contribution: 0.1314 * correlation 5: 0.04049 -> contribution: 0.1262 * correlation 6: 0.03840 -> contribution: 0.1197 * correlation 7: 0.03809 -> contribution: 0.1187 * correlation 8: 0.03742 -> contribution: 0.1166 Using 8 of 8 subfields in final power spectra ... Preform a rotational average and remove spikes... PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE Resolution range for the data is 1/68.5A to 1/2.0A ... far from focus images, increasing number of extrema (100) ... Number of available peaks is 117 ... setting the number of sections to default: 6 ... Determine and subtract noise model PART 2: BACKGROUND NOISE SUBTRACTION ... starting peak extension Peak Extension Complete in 1.87 msec PART 3: ENVELOPE NORMALIZATION ... Setting last 3 values to -3.2 (test = -3.2) ... starting peak extension Peak Extension Complete in 1.92 msec PART 3B: BAND-PASS FILTER PART 4: PEAK EXTENSION ... starting peak extension Peak Extension Complete in 1.78 msec ... starting peak extension Peak Extension Complete in 1.79 msec PART 5: CTF FIT AND CONFIDENCE 1/30A - 1/10A confidence is 0.989 (overfocus 0.156) 1/30A - 1/10A confidence is 0.989 (overfocus 0.156) 5 peak confidence is 0.979 (overfocus 0.066) PART 6: CTF RESOLUTION LIMITS [ 0.898 0.763 0.764 -0.076 0.062 0.091 0.188 0.199 0.245 0.279 0.269 0.262 0.193 0.176 0.151] !!! WARNING: Res calc: Negative values in first 10 values [ 0.898 0.763 0.764 -0.076 0.062 0.091 0.188 0.199 0.245 0.279 0.269 0.262 0.193 0.176 0.151] !!! WARNING: Res calc: Negative values in first 10 values Resolution limit is 4.01 at 0.8 and 3.56 at 0.5 PART 7: MAKE 1D PLOT SUMMARY FIGURE ... Saving 1D graph to file 17may02a_e6f_012gr_01sq_014hl_01en-a-plots.png PART 8: NORMALIZE THE 2D IMAGE ... converting 1d arrays to 2d and normalizing .................. ... 2d image normalization complete ... Resolution ring of the edge of the image 2.84 ... Resolution ring of 25th valley 6.400 (5.0, 4.0086544986979424, 3.5551356021786837, 6.3996785830426726) ... Final resolution ring of 2D Plot: 4.621 PART 9: DRAW THE 2D POWERSPEC IMAGE ... Saving 2D powerspectra to file: 17may02a_e6f_012gr_01sq_014hl_01en-a-powerspec.jpg Full CTF display makeCtfImages routine complete in 16.45 sec 17may02a_e6f_012gr_01sq_014hl_01en-a-powerspec.jpg [CTF run] method: unknown | runname ctffind4run1 [CTF param] def1: 2.051 um | def2: 2.079 um | angle: 24.6 | ampcontr 0.10 | defratio 1.014 [CTF param] additional phase shift: 64.2 degrees [CTF stats] conf_30-10: 0.989 | conf_5peak: 0.979 | res_0.8: 4.0A | res_0.5 3.6A SUMMARY: ctffind4 ------------------------------------------ TIME: 2 min 13 sec AVG TIME: 1.5 +/- 0.55 min (- REMAINING TIME: 2 min 3 sec for 1 images -) ------------------------------------------ Starting image 3 ( skip:8, remain:1 ) id:695440, file: 17may02a_e6f_012gr_01sq_015hl_01en-a ... Pixel size: 1.2 Found 0 ctf values !!! WARNING: no best CTF value for image 17may02a_e6f_012gr_01sq_015hl_01en-a !!! WARNING: Defocus minimum is less than zero Defocus search range: 1000 A to 45000 A (0.10 to 4.50 um) ... running ctf estimation at Tue May 2 13:31:00 2017 input = 17may02a_e6f_012gr_01sq_015hl_01en-a.mrc output = 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc apix = 1.2 kv = 200.0 cs = 2.7 ampcontrast = 0.1 fieldsize = 1024 resmin = 50.0 resmax = 4.0 defmin = 1000.0 defmax = 45000.0 defstep = 1000.0 known_astig = no exhaustive_astig_search = no restrain_astig = yes expect_astig = 500.0 phase = yes min_phase_shift = 0.174532925199 max_phase_shift = 2.96705972839 phase_search_step = 0.174532925199 expert_opts = no newline = /data/software/repo/ctffind4/4.0.16/ctffind4 17may02a_e6f_012gr_01sq_015hl_01en-a.mrc 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc 1.2 200.0 2.7 0.1 1024 50.0 4.0 1000.0 45000.0 1000.0 no no yes 500.0 yes 0.174532925199 2.96705972839 0.174532925199 no ** Welcome to CTFFind ** Version - 4.0.16 Input Mode: Batch Date & Time: 2017-05-02 13:31:00 Copyright 2015 Howard Hughes Medical Institute. All rights reserved. Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html ) Input image file name [17may02a_e6f_012gr_01sq_014hl_01en-a.mrc] : 17may02a_e6f_012gr_01sq_015hl_01en-a.mrc Output diagnostic filename [17may02a_e6f_012gr_01sq_014hl_01en-a-pow.mrc] : 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc Pixel size [1.2] : 1.2 Acceleration voltage [200.0] : 200.0 Spherical aberration [2.7] : 2.7 Amplitude contrast [0.1] : 0.1 Size of power spectrum to compute [1024] : 1024 Minimum resolution [50.0] : 50.0 Maximum resolution [4.0] : 4.0 Minimum defocus [1000.0] : 1000.0 Maximum defocus [45000.0] : 45000.0 Defocus search step [1000.0] : 1000.0 Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : yes Please enter a valid number! Expected (tolerated) astigmatism [500.0] : 500.0 Find additional phase shift? [yes] : yes Minimum phase shift [0.174532925199] : 0.174532925199 Maximum phase shift [2.96705972839] : 2.96705972839 Phase shift search step [0.174532925199] : 0.174532925199 Summary information for file 17may02a_e6f_012gr_01sq_015hl_01en-a.mrc Number of columns, rows, sections: 3710 3838 1 MRC data mode: 2 Bit depth: 32 Pixel size: 1.000 1.000 1.000 Working on micrograph 1 of 1 100% [==============================] done! Estimated defocus values : 22200.57 , 21926.01 Angstroms Estimated azimuth of astigmatism: -54.36 degrees Additional phase shift : 1.489 (.47 pi) Score : .09369 Thon rings with good fit up to : 3.9 Angstroms Summary of results : 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.txt Diagnostic images : 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc Detailled results, including 1D fit profiles: 17may02a_e6f_012gr_01sq_015hl_01en-a-pow_avrot.txt Use this command to plot 1D fit profiles : ctffind_plot_results.sh 17may02a_e6f_012gr_01sq_015hl_01en-a-pow_avrot.txt Total execution time : 1 minute and 57 seconds 2017-05-02 13:32:57 : CTFFind finished cleanly. ... ctf estimation completed in 1 min 58 sec ... reading 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.txt ... reading MRC: 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc size:(1024, 1024) dtype:float32 ... writing JPEG: 17may02a_e6f_012gr_01sq_015hl_01en-a-pow.jpg ==== Committing data to database ==== ... Committing ctf parameters for 17may02a_e6f_012gr_01sq_015hl_01en-a to database ... Reading image... [CTF param] def1: 2.193 um | def2: 2.220 um | angle: 35.6 | ampcontr 0.10 | defratio 1.013 [CTF param] additional phase shift: 85.3 degrees Final params: def1: 2.193 um | def2: 2.220 um | angle: 35.6 | defratio 1.01 ... Defocus Astig Percent Diff 0.62 -- 2.193, 2.220 um Computing power spectra in 2048x2048 blocks........ ... Compute PSD with 8 subfields and fieldsize 2048 complete in 5.0 sec * correlation 1: 0.03175 -> contribution: 0.1312 * correlation 2: 0.03356 -> contribution: 0.1386 * correlation 3: 0.02944 -> contribution: 0.1216 * correlation 4: 0.02893 -> contribution: 0.1195 * correlation 5: 0.02790 -> contribution: 0.1153 * correlation 6: 0.02753 -> contribution: 0.1137 * correlation 7: 0.03229 -> contribution: 0.1334 * correlation 8: 0.03070 -> contribution: 0.1268 Using 8 of 8 subfields in final power spectra ... Preform a rotational average and remove spikes... PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE ERROR !!! WARNING: Logging images failing CtfdisplayTool to /data/microscopes/appion/17may02a/ctf/ctffind4run1/failed_ctfdisplay_images.txt [CTF run] method: unknown | runname ctffind4run1 [CTF param] def1: 2.193 um | def2: 2.220 um | angle: 35.6 | ampcontr 0.10 | defratio 1.013 [CTF param] additional phase shift: 85.3 degrees SUMMARY: ctffind4 ------------------------------------------ TIME: 2 min 7 sec AVG TIME: 1.55 +/- 0.55 min ------------------------------------------ !!! WARNING: skipped total of 8 images. ... to process them again, remove 'continue' option and run ctffind4 again. ... Finished all images, checking for more ... Querying database for preset 'en-a' images from session '17may02a' ... ... 14 images recevied in 13.65 msec ... Found 14 images in 13.72 msec ... Remove processed images skipping processed images ............ ... finished skipping in 14.07 msec !!! WARNING: skipped 12 of 14 images ... [[ 0 no reprocess | 0 rejected | 0 wrong tilt | 12 in donedict ]] ... Process images old to new Beginning Main Loop Starting image 0 ( skip:12, remain:2 ) id:695442, file: 17may02a_e6f_012gr_01sq_016hl_01en-a ... Pixel size: 1.2 Found 0 ctf values !!! WARNING: no best CTF value for image 17may02a_e6f_012gr_01sq_016hl_01en-a !!! WARNING: Defocus minimum is less than zero Defocus search range: 1000 A to 45000 A (0.10 to 4.50 um) ... running ctf estimation at Tue May 2 13:33:06 2017 input = 17may02a_e6f_012gr_01sq_016hl_01en-a.mrc output = 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.mrc apix = 1.2 kv = 200.0 cs = 2.7 ampcontrast = 0.1 fieldsize = 1024 resmin = 50.0 resmax = 4.0 defmin = 1000.0 defmax = 45000.0 defstep = 1000.0 known_astig = no exhaustive_astig_search = no restrain_astig = yes expect_astig = 500.0 phase = yes min_phase_shift = 0.174532925199 max_phase_shift = 2.96705972839 phase_search_step = 0.174532925199 expert_opts = no newline = /data/software/repo/ctffind4/4.0.16/ctffind4 17may02a_e6f_012gr_01sq_016hl_01en-a.mrc 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.mrc 1.2 200.0 2.7 0.1 1024 50.0 4.0 1000.0 45000.0 1000.0 no no yes 500.0 yes 0.174532925199 2.96705972839 0.174532925199 no ** Welcome to CTFFind ** Version - 4.0.16 Input Mode: Batch Date & Time: 2017-05-02 13:33:06 Copyright 2015 Howard Hughes Medical Institute. All rights reserved. Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html ) Input image file name [17may02a_e6f_012gr_01sq_015hl_01en-a.mrc] : 17may02a_e6f_012gr_01sq_016hl_01en-a.mrc Output diagnostic filename [17may02a_e6f_012gr_01sq_015hl_01en-a-pow.mrc] : 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.mrc Pixel size [1.2] : 1.2 Acceleration voltage [200.0] : 200.0 Spherical aberration [2.7] : 2.7 Amplitude contrast [0.1] : 0.1 Size of power spectrum to compute [1024] : 1024 Minimum resolution [50.0] : 50.0 Maximum resolution [4.0] : 4.0 Minimum defocus [1000.0] : 1000.0 Maximum defocus [45000.0] : 45000.0 Defocus search step [1000.0] : 1000.0 Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : no Please enter a valid number! Expected (tolerated) astigmatism [500.0] : yes Please enter a valid number! Expected (tolerated) astigmatism [500.0] : 500.0 Find additional phase shift? [yes] : yes Minimum phase shift [0.174532925199] : 0.174532925199 Maximum phase shift [2.96705972839] : 2.96705972839 Phase shift search step [0.174532925199] : 0.174532925199 Summary information for file 17may02a_e6f_012gr_01sq_016hl_01en-a.mrc Number of columns, rows, sections: 3710 3838 1 MRC data mode: 2 Bit depth: 32 Pixel size: 1.000 1.000 1.000 Working on micrograph 1 of 1 100% [==============================] done! Estimated defocus values : 23427.16 , 23135.30 Angstroms Estimated azimuth of astigmatism: -81.92 degrees Additional phase shift : 1.643 (.52 pi) Score : .08659 Thon rings with good fit up to : 17.1 Angstroms Summary of results : 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.txt Diagnostic images : 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.mrc Detailled results, including 1D fit profiles: 17may02a_e6f_012gr_01sq_016hl_01en-a-pow_avrot.txt Use this command to plot 1D fit profiles : ctffind_plot_results.sh 17may02a_e6f_012gr_01sq_016hl_01en-a-pow_avrot.txt Total execution time : 1 minute and 56 seconds 2017-05-02 13:35:04 : CTFFind finished cleanly. ... ctf estimation completed in 1 min 58 sec ... reading 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.txt ... reading MRC: 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.mrc size:(1024, 1024) dtype:float32 ... writing JPEG: 17may02a_e6f_012gr_01sq_016hl_01en-a-pow.jpg ==== Committing data to database ==== ... Committing ctf parameters for 17may02a_e6f_012gr_01sq_016hl_01en-a to database ... Reading image... [CTF param] def1: 2.314 um | def2: 2.343 um | angle: 8.1 | ampcontr 0.10 | defratio 1.013 [CTF param] additional phase shift: 94.1 degrees Final params: def1: 2.314 um | def2: 2.343 um | angle: 8.1 | defratio 1.01 ... Defocus Astig Percent Diff 0.63 -- 2.314, 2.343 um Computing power spectra in 2048x2048 blocks........ ... Compute PSD with 8 subfields and fieldsize 2048 complete in 5.11 sec * correlation 1: 0.02584 -> contribution: 0.1422 * correlation 2: 0.02471 -> contribution: 0.1359 * correlation 3: 0.02521 -> contribution: 0.1387 * correlation 4: 0.01857 -> contribution: 0.1022 * correlation 5: 0.02517 -> contribution: 0.1385 * correlation 6: 0.02021 -> contribution: 0.1112 * correlation 7: 0.02322 -> contribution: 0.1278 * correlation 8: 0.01885 -> contribution: 0.1037 Using 8 of 8 subfields in final power spectra ... Preform a rotational average and remove spikes... PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE ERROR !!! WARNING: Logging images failing CtfdisplayTool to /data/microscopes/appion/17may02a/ctf/ctffind4run1/failed_ctfdisplay_images.txt [CTF run] method: unknown | runname ctffind4run1 [CTF param] def1: 2.314 um | def2: 2.343 um | angle: 8.1 | ampcontr 0.10 | defratio 1.013 [CTF param] additional phase shift: 94.1 degrees SUMMARY: ctffind4 ------------------------------------------ TIME: 2 min 7 sec AVG TIME: 1.59 +/- 0.55 min (- REMAINING TIME: 2 min 8 sec for 1 images -) ------------------------------------------