SIMPLE Test Report - apof

SIMPLE test run

Execution times

1h 29m 33.4sTotal across 10 timed test steps

Test step	Program	Duration
10_refine3D_auto	refine3D_auto	51m 34.5s3094.5 seconds
9_abinitio3D	abinitio3D	20m 43.8s1243.8 seconds
8_abinitio3D_cavgs	abinitio3D_cavgs	7m 52.1s472.1 seconds
7_model_cavgs_rejection	model_cavgs_rejection	0.7s0.7 seconds
6_abinitio2D	abinitio2D	2m 59.9s179.9 seconds
5_extract	extract	3.1s3.1 seconds
4_pick	pick	55.5s55.5 seconds
3_ctf_estimate	ctf_estimate	0.1s0.1 seconds
2_motion_correct	motion_correct	5m 03.2s303.2 seconds
1_import_movies	import_movies	20.5s20.5 seconds

Total is the sum of execution times recorded by SIMPLE in this test LOG.

10_refine3D_auto51m 34.5s

orientations_distribution_state01.jpg

orthogonal_reprojs_state01.jpg

LOG summary: PROGRAM refine3D_auto

>>> % SEARCH SPACE SCANNED   AVG/SDEV/MIN/MAX:      100.000        0.000      100.000      100.000
>>> MATCHING  LOW-PASS LIMIT (THIS ITERATION)         2.600
>>> NU HANDOFF LP (NEXT)     AVG/SDEV/MIN/MAX:        2.600        0.000        2.600        2.600
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        2.600        0.000        2.600        2.600
>>> RESOLUTION @ FSC=0.5     AVG/SDEV/MIN/MAX:        2.936        0.000        2.936        2.936
>>> SCORE [0,1]              AVG/SDEV/MIN/MAX:        0.384        0.004        0.372        0.401
>>> -------------------- SETTINGS --------------------
>>> | REFINEMENT MODE               | prob_neigh
>>> | PROB NEIGH MODE               | state
>>> | NSPACE PROJECTION DIRECTIONS  | 20000
>>> | GAU REGULARIZATION            | off
>>> | ML  REGULARIZATION            | on, TAU: 1.00000000
>>> | CONICAL REGULARIZATION        | off
>>> | ICM REGULARIZATION            | off
>>> | AUTOMASKING                   | on, MODE: yes
>>> | FILTER MODE                   | nonuniform
>>> --------------------------------------------------
>>> CONVERGED: yes
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_REFINE3D NORMAL STOP ****
>>>
>>> RECONSTRUCTION AT ORIGINAL SAMPLING
>>>
>>> FINAL RECONSTRUCTION SAMPLING: box=192 smpd=  1.3000
>>> FINAL RECONSTRUCTION: reusing committed canonical sigmas
>>> # SHARED-MEMORY THREADS USED BY rec3D MASTER PROCESS:      8
>>> RECONSTRUCT3D: 10 PART(S) COMPLETED IN     17.0 s
>>> AUTOMASKING LOW-PASS/DILATION LAYERS/EDGE:   20.00 A/  6 voxels/  6 voxels
>>> FOUND:       1 CONNECTED COMPONENT(S)
>>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=density phase_randomization=yes
>>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE  1:   0.9531
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
>>> POSTPROCESS: FSC from fsc_state01.bin, 0.5/0.143 at   2.94/  2.60 A
>>> B-FACTOR (UNFILTERED PAIR) DETERMINED TO:   -75.19
>>> POSTPROCESS: B   -75.19 capped at the cutoff shell: gain  16.13 from shell 96 to Nyquist
>>> POSTPROCESS: ML-regularized map (solve_kind=gridding_regularized), its prior already FSC-weighted it: no FSC weighting
>>> POSTPROCESS: B-sharpened, then Butterworth low-pass at   2.60 A
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:  3094.5 seconds

9_abinitio3D20m 43.8s

orientations_distribution_state01.jpg

orientations_distribution_state01_stage04.jpg

orientations_distribution_state01_stage05.jpg

orientations_distribution_state01_stage06.jpg

orientations_distribution_state01_stage07.jpg

orientations_distribution_state01_stage08.jpg

orthogonal_reprojs_state01.jpg

orthogonal_reprojs_state01_stage04.jpg

orthogonal_reprojs_state01_stage05.jpg

orthogonal_reprojs_state01_stage06.jpg

orthogonal_reprojs_state01_stage07.jpg

orthogonal_reprojs_state01_stage08.jpg

LOG summary: PROGRAM abinitio3D

Recent FSC=0.143 resolution estimates:
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.800        0.000        4.800        4.800
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.800        0.000        4.800        4.800
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.800        0.000        4.800        4.800
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.800        0.000        4.800        4.800
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.457        0.000        4.457        4.457
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.457        0.000        4.457        4.457
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.457        0.000        4.457        4.457
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        4.160        0.000        4.160        4.160
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        3.900        0.000        3.900        3.900
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        3.900        0.000        3.900        3.900
>>> RESOLUTION @ FSC=0.143   AVG/SDEV/MIN/MAX:        3.900        0.000        3.900        3.900

Status:
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_POSTPROCESS NORMAL STOP ****
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_REFINE3D NORMAL STOP ****
**** SIMPLE_CALC_PSPEC_ASSEMBLE NORMAL STOP ****
**** SIMPLE_CALC_PSPEC NORMAL STOP ****
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_REFINE3D NORMAL STOP ****
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
**** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP ****
**** SIMPLE_ABINITIO3D NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:  1243.8 seconds

8_abinitio3D_cavgs7m 52.1s

orientations_distribution_state01.jpg

LOG summary: PROGRAM abinitio3D_cavgs

**** SIMPLE_CALC_PSPEC NORMAL STOP ****
>>> BOOTSTRAP_REC3D: GRIDDING ML-REGULARIZED BOOTSTRAP MAP ON THE IMAGE-POWER SEED, SIGMA ITERATION 83
>>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=none phase_randomization=no
>>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE  1:   0.0000
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
>>> BOOTSTRAP_REC3D: RESIDUAL SIGMA2 PASS AGAINST THE BOOTSTRAP MAP, ITERATION 83
>>> SIGMA2 INIT: reusing committed canonical state
>>>
>>> ITERATION     83
>>>
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_REFINE3D NORMAL STOP ****
>>> BOOTSTRAP_REC3D: EUCLID ML-REGULARIZED RECONSTRUCTION ON RESIDUAL SIGMAS, SIGMA ITERATION 84
>>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=none phase_randomization=no
>>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE  1:   0.0000
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
**** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP ****
>>>
>>> RE-PROJECTION OF THE FINAL VOLUME
>>>
>>> GENERATING PROJECTIONS
**** SIMPLE_REPROJECT NORMAL STOP ****
>>> SHIFTING IMAGES
CLASS:    70 RANK:     1 CORR:   0.77
CLASS:    61 RANK:     2 CORR:   0.77
CLASS:    28 RANK:     3 CORR:   0.77
CLASS:    11 RANK:     4 CORR:   0.75
CLASS:    21 RANK:     5 CORR:   0.75
CLASS:     5 RANK:     6 CORR:   0.75
CLASS:    33 RANK:     7 CORR:   0.75
CLASS:    90 RANK:     8 CORR:   0.72
CLASS:    75 RANK:     9 CORR:   0.72
CLASS:    64 RANK:    10 CORR:   0.72
CLASS:    79 RANK:    11 CORR:   0.00
**** SIMPLE_RANK_CAVGS NORMAL STOP ****
**** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:   472.1 seconds

7_model_cavgs_rejection0.7s

LOG summary: PROGRAM model_cavgs_rejection

 >>> PROGRAM: model_cavgs_rejection
>>> EXECUTION DIRECTORY: 7_model_cavgs_rejection
>>> CAVG QUALITY MODEL          : chunk100mics
>>> CAVG QUALITY MODEL SOURCE   : built-in preset chunk100mics
>>> CAVG QUALITY MODEL CONTEXT  : chunk
>>> CAVG HARD-GATE CONTEXT      : chunk
>>> CAVG HARD-GATE SOURCE       : model artifact
>>> DEFAULT HARD GATES REJECTED:     71
>>> CAVG QUALITY SELECTED / REJECTED :     11 /     79
>>> CAVG QUALITY THRESHOLD RAW / OFFSET / EFFECTIVE :    0.350 /    0.000 /    0.350
>>> CAVG QUALITY SEPARATION / USED THRESHOLD :    0.000 USED=T
>>> WROTE cavgs_quality_features.txt
>>> WROTE quality_selected_cavgs.mrc #CAVGS:     11
>>> WROTE quality_rejected_cavgs.mrc #CAVGS:     79
>>> WROTE hard_gate_rejections.mrc #CAVGS:     71
>>> WROTE quality_ranked_cavgs.mrc #CAVGS:     90
>>> WROTE quality_ranked_cavgs.txt
**** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:     0.7 seconds

6_abinitio2D2m 59.9s

cavgs_iter027.jpg

LOG summary: PROGRAM abinitio2D

Final class ranking and status:
CLASS:    70 RANK:     1 POP:  472 RES:   3.73
CLASS:    64 RANK:     2 POP:  553 RES:   3.73
CLASS:    33 RANK:     3 POP:  459 RES:   3.90
CLASS:     5 RANK:     4 POP:  476 RES:   3.96
CLASS:    61 RANK:     5 POP:  390 RES:   4.03
CLASS:    90 RANK:     6 POP:  538 RES:   4.03
CLASS:    11 RANK:     7 POP:  477 RES:   4.03
CLASS:    21 RANK:     8 POP:  494 RES:   4.16
CLASS:    75 RANK:     9 POP:  337 RES:   4.30
CLASS:    86 RANK:    10 POP:  303 RES:   5.67
CLASS:    28 RANK:    11 POP:  391 RES:   6.09
CLASS:    63 RANK:    12 POP:   30 RES:  14.68
CLASS:    53 RANK:    13 POP:   32 RES:  15.60
CLASS:    65 RANK:    14 POP:   46 RES:  16.64
CLASS:    23 RANK:    15 POP:   32 RES:  19.20
CLASS:    20 RANK:    16 POP:   19 RES:  20.80
CLASS:    51 RANK:    17 POP:   86 RES:  22.69
CLASS:    44 RANK:    18 POP:   41 RES:  22.69
CLASS:    56 RANK:    19 POP:    3 RES:  24.96
CLASS:    87 RANK:    20 POP:   29 RES:  24.96
CLASS:    45 RANK:    21 POP:    9 RES:  24.96
CLASS:    62 RANK:    22 POP:   67 RES:  24.96
CLASS:    79 RANK:    23 POP:   27 RES:  24.96
CLASS:    39 RANK:    24 POP:   12 RES:  27.73
CLASS:    34 RANK:    25 POP:   24 RES:  27.73
CLASS:    43 RANK:    26 POP:   11 RES:  31.20
CLASS:    71 RANK:    27 POP:    9 RES:  35.66
CLASS:    24 RANK:    28 POP:   12 RES:  41.60
CLASS:    58 RANK:    29 POP:   13 RES:  41.60
CLASS:    60 RANK:    30 POP:   33 RES:  41.60
CLASS:    89 RANK:    31 POP:   10 RES:  41.60
CLASS:     4 RANK:    32 POP:   12 RES:  41.60
CLASS:    54 RANK:    33 POP:    6 RES:  49.92
CLASS:    50 RANK:    34 POP:    5 RES:  49.92
CLASS:    81 RANK:    35 POP:    9 RES:  49.92
CLASS:    77 RANK:    36 POP:    7 RES:  49.92
CLASS:    18 RANK:    37 POP:    9 RES:  49.92
CLASS:    37 RANK:    38 POP:   45 RES:  62.40
CLASS:    36 RANK:    39 POP:    7 RES:  62.40
CLASS:    84 RANK:    40 POP:   26 RES:  62.40
CLASS:    31 RANK:    41 POP:   18 RES: 124.80
CLASS:    26 RANK:    42 POP:   26 RES: 124.80
CLASS:    85 RANK:    43 POP:    6 RES: 124.80
CLASS:    42 RANK:    44 POP:    2 RES: 249.60
CLASS:    68 RANK:    45 POP:    5 RES: 249.60
CLASS:     1 RANK:    46 POP:    5 RES: 249.60

Status:
**** SIMPLE_CAVGASSEMBLE NORMAL STOP ****
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_PROB_ALIGN2D NORMAL STOP ****
**** SIMPLE_CAVGASSEMBLE NORMAL STOP ****
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_CLUSTER2D NORMAL STOP ****
**** SIMPLE_CAVGASSEMBLE NORMAL STOP ****
**** SIMPLE_DISTR_MAKE_CAVGS NORMAL STOP ****
**** SIMPLE_RANK_CAVGS NORMAL STOP ****
**** SIMPLE_ABINITIO2D NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:   179.9 seconds

5_extract3.1s

ptcls_sample.jpg

ptcls_sample_lp.jpg

LOG summary: PROGRAM extract

100. percent micrographs marker not found; recent extract diagnostics:
>>> EXTRACT: 8 PART(S) COMPLETED IN      2.0 s
**** SIMPLE_EXTRACT_DISTR NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:     3.1 seconds

4_pick55.5s

LOG summary: PROGRAM pick

100. percent micrographs marker not found; recent pick diagnostics:
>>> PICK: 5 PART(S) COMPLETED IN     55.0 s
**** SIMPLE_DISTR_PICK NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:    55.5 seconds

3_ctf_estimate0.1s

FoilHole_14491433_Data_14487171_14487173_20221214_121942_EER_ctf_estimate_diag.jpg

FoilHole_14491478_Data_14487165_14487167_20221214_123819_EER_ctf_estimate_diag.jpg

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FoilHole_15510394_Data_14487165_14487167_20221215_015304_EER_ctf_estimate_diag.jpg

LOG summary: PROGRAM ctf_estimate

100. percent marker not found; recent CTF diagnostics:
>>> CTF_ESTIMATE: 5 PART(S) COMPLETED IN     20.0 s
**** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:    20.1 seconds
AVERAGE CTF RESOLUTION               :     4.34
STANDARD DEVIATION OF CTF RESOLUTION :     6.60
MINIMUM CTF RESOLUTION (BEST)        :     2.80
MAXIMUM CTF RESOLUTION (WORST)       :    50.00
**** SIMPLE_ORISTATS NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:     0.1 seconds

2_motion_correct5m 03.2s

FoilHole_14491433_Data_14487171_14487173_20221214_121942_EER_thumb.jpg

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$FoilHole_14509189_Data_14487171_14487173_20221214_151711_EER_thumb.jpg$ FoilHole_14509189_Data_14487171_14487173_20221214_151711_EER_thumb.jpg

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LOG summary: PROGRAM motion_correct

100. percent marker not found; recent motion-correction diagnostics:
**** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:   303.2 seconds

1_import_movies20.5s

movthumb1.jpg

LOG summary: PROGRAM import_movies

>>> IMPORTED     50 MOVIE(S)
>>> TOTAL NUMBER OF MOVIE(S):    50
**** IMPORT_MOVIES NORMAL STOP ****
**** SIMPLE Git Commit:  3cad71a1
**** Execution time:    20.5 seconds