*** Entries to program beadtrack *** InputSeedModel = WTI042413_1series4.seed OutputModel = WTI042413_1series4.fid ImageFile = WTI042413_1series4.preali ImagesAreBinned = 1 RotationAngle = 168.0 TiltFile = WTI042413_1series4.rawtlt TiltDefaultGrouping = 7 MagDefaultGrouping = 5 RotDefaultGrouping = 1 MinViewsForTiltalign = 4 BeadDiameter = 14.84 FillGaps = 1 MaxGapSize = 5 MinTiltRangeToFindAxis = 10.0 MinTiltRangeToFindAngles = 20.0 BoxSizeXandY = 48,48 RoundsOfTracking = 2 LocalAreaTracking = 0 LocalAreaTargetSize = 1000 MinBeadsInArea = 8 MinOverlapBeads = 5 MaxBeadsToAverage = 4 PointsToFitMaxAndMin = 7,3 DensityRescueFractionAndSD = 0.6,1.0 DistanceRescueCriterion = 10.0 RescueRelaxationDensityAndDistance = 0.7,0.9 PostFitRescueResidual = 2.5 DensityRelaxationPostFit = 0.9 MaxRescueDistance = 2.5 ResidualsToAnalyzeMaxAndMin = 9,5 DeletionCriterionMinAndSD = 0.04,2.0 *** End of entries *** RO image file on unit 1 : WTI042413_1series4.preali Size= 204763 K Number of columns, rows, sections ..... 1852 1856 61 Map mode .............................. 0 (byte) Start cols, rows, sects, grid x,y,z ... 0 0 0 1852 1856 61 Pixel spacing (Angstroms).............. 6.740 6.740 6.740 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 0.000 0.000 Minimum density ....................... 0.0000 Maximum density ....................... 249.72 Mean density .......................... 82.064 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 0 854 0 0 4 Titles : SerialEM: Digitized on Janelia Krios 26-Apr-13 14:20:21 Tilt axis angle = 168.0, binning = 2 spot = 7 camera = 3 CCDERASER: Bad points replaced with interpolated values 26-Apr-13 17:17:47 NEWSTACK: Images copied, transformed, floated to means 26-Apr-13 17:18:40 FORMATTED ro file opened: /groups/sciserv/home/delacruzm/cindi/WTI042413_1/series4/WTI042413_1series4.rawtlt Starting object 1, round 1, 21 contours view 30, pass 1, 21 points (- 0), mean, sd, max dev: 1.56 1.01 4.13 view 29, pass 1, 21 points (- 0), mean, sd, max dev: 2.30 1.49 5.43 view 28, pass 1, 21 points (- 0), mean, sd, max dev: 0.77 0.37 1.49 4 views, 15 cycles, F = 0.9916712E-05, mean residual = 0.38 view 27, pass 1, 21 points (- 0), mean, sd, max dev: 0.63 0.39 1.62 5 views, 31 cycles, F = 0.1484409E-04, mean residual = 0.42 view 26, pass 1, 21 points (- 0), mean, sd, max dev: 0.67 0.31 1.14 6 views, 18 cycles, F = 0.2123202E-04, mean residual = 0.47 view 25, pass 1, 21 points (- 0), mean, sd, max dev: 0.56 0.34 1.22 7 views, 12 cycles, F = 0.2497386E-04, mean residual = 0.47 view 24, pass 1, 21 points (- 0), mean, sd, max dev: 0.78 0.40 1.69 8 views, 72 cycles, F = 0.3000078E-04, mean residual = 0.48 view 23, pass 1, 21 points (- 0), mean, sd, max dev: 0.63 0.37 1.47 9 views, 28 cycles, F = 0.3463817E-04, mean residual = 0.49 view 22, pass 1, 21 points (- 0), mean, sd, max dev: 0.52 0.28 1.02 10 views, 30 cycles, F = 0.3856427E-04, mean residual = 0.49 view 21, pass 1, 21 points (- 0), mean, sd, max dev: 0.66 0.37 1.62 11 views, 112 cycles, F = 0.4466640E-04, mean residual = 0.50 view 20, pass 1, 21 points (- 0), mean, sd, max dev: 0.55 0.20 0.91 12 views, 31 cycles, F = 0.4924980E-04, mean residual = 0.51 1 pts deleted for pass 2, conts: 17 12 views, 4 cycles, F = 0.4883137E-04, mean residual = 0.51 1 pts added on pass 2, conts: 17 view 20, pass 2, 21 points (- 0), mean, sd, max dev: 0.47 0.17 0.82 12 views, 3 cycles, F = 0.4924694E-04, mean residual = 0.51 1 pts deleted, big mean residual, conts: 17 12 views, 1 cycles, F = 0.4887112E-04, mean residual = 0.51 view 19, pass 1, 21 points (- 0), mean, sd, max dev: 0.66 0.43 1.58 13 views, 111 cycles, F = 0.5440963E-04, mean residual = 0.51 view 18, pass 1, 21 points (- 0), mean, sd, max dev: 0.67 0.55 2.17 14 views, 30 cycles, F = 0.6179458E-04, mean residual = 0.52 2 pts deleted for pass 2, conts: 4 8 14 views, 13 cycles, F = 0.5871880E-04, mean residual = 0.51 2 pts added on pass 2, conts: 4 8 view 18, pass 2, 21 points (- 0), mean, sd, max dev: 0.57 0.50 1.84 14 views, 2 cycles, F = 0.6211058E-04, mean residual = 0.52 1 pts deleted, big mean residual, conts: 4 14 views, 3 cycles, F = 0.6060703E-04, mean residual = 0.52 view 17, pass 1, 21 points (- 0), mean, sd, max dev: 0.68 0.43 1.80 15 views, 35 cycles, F = 0.6734099E-04, mean residual = 0.53 view 16, pass 1, 21 points (- 0), mean, sd, max dev: 0.55 0.47 2.25 16 views, 31 cycles, F = 0.7394556E-04, mean residual = 0.53 view 15, pass 1, 21 points (- 0), mean, sd, max dev: 0.66 0.40 1.87 17 views, 72 cycles, F = 0.8057988E-04, mean residual = 0.54 view 14, pass 1, 21 points (- 0), mean, sd, max dev: 0.58 0.39 1.72 18 views, 41 cycles, F = 0.8473564E-04, mean residual = 0.53 1 pts deleted for pass 2, conts: 15 18 views, 3 cycles, F = 0.8416583E-04, mean residual = 0.53 1 pts added on pass 2, conts: 15 view 14, pass 2, 21 points (- 0), mean, sd, max dev: 0.50 0.35 1.62 18 views, 1 cycles, F = 0.8460095E-04, mean residual = 0.53 view 13, pass 1, 21 points (- 0), mean, sd, max dev: 0.61 0.29 1.22 19 views, 63 cycles, F = 0.9121538E-04, mean residual = 0.54 view 12, pass 1, 21 points (- 0), mean, sd, max dev: 0.65 0.35 1.50 20 views, 45 cycles, F = 0.9821195E-04, mean residual = 0.55 1 pts deleted for pass 2, conts: 13 20 views, 9 cycles, F = 0.9733722E-04, mean residual = 0.55 1 pts added on pass 2, conts: 13 view 12, pass 2, 21 points (- 0), mean, sd, max dev: 0.57 0.32 1.43 20 views, 3 cycles, F = 0.9825113E-04, mean residual = 0.55 1 pts deleted, big mean residual, conts: 13 20 views, 1 cycles, F = 0.9738479E-04, mean residual = 0.55 view 11, pass 1, 21 points (- 0), mean, sd, max dev: 0.56 0.38 1.54 21 views, 58 cycles, F = 0.1034511E-03, mean residual = 0.55 view 10, pass 1, 21 points (- 0), mean, sd, max dev: 0.62 0.42 1.95 22 views, 34 cycles, F = 0.1103644E-03, mean residual = 0.55 1 pts deleted for pass 2, conts: 15 22 views, 9 cycles, F = 0.1093253E-03, mean residual = 0.55 1 pts added on pass 2, conts: 15 view 10, pass 2, 21 points (- 0), mean, sd, max dev: 0.54 0.36 1.67 22 views, 1 cycles, F = 0.1097189E-03, mean residual = 0.55 view 9, pass 1, 21 points (- 0), mean, sd, max dev: 0.61 0.26 1.16 23 views, 30 cycles, F = 0.1154660E-03, mean residual = 0.55 view 8, pass 1, 21 points (- 0), mean, sd, max dev: 0.64 0.32 1.50 24 views, 36 cycles, F = 0.1214768E-03, mean residual = 0.56 1 pts deleted for pass 2, conts: 16 24 views, 2 cycles, F = 0.1201444E-03, mean residual = 0.56 1 pts added on pass 2, conts: 16 view 8, pass 2, 21 points (- 0), mean, sd, max dev: 0.55 0.23 1.05 24 views, 2 cycles, F = 0.1205192E-03, mean residual = 0.56 view 7, pass 1, 21 points (- 0), mean, sd, max dev: 0.88 0.52 2.09 25 views, 55 cycles, F = 0.1315003E-03, mean residual = 0.57 1 pts deleted for pass 2, conts: 6 25 views, 10 cycles, F = 0.1291237E-03, mean residual = 0.57 1 pts added on pass 2, conts: 6 view 7, pass 2, 21 points (- 0), mean, sd, max dev: 0.79 0.44 1.93 25 views, 8 cycles, F = 0.1311375E-03, mean residual = 0.57 1 pts deleted, big mean residual, conts: 6 25 views, 8 cycles, F = 0.1291214E-03, mean residual = 0.57 view 6, pass 1, 21 points (- 0), mean, sd, max dev: 0.53 0.32 1.33 26 views, 35 cycles, F = 0.1359274E-03, mean residual = 0.57 view 5, pass 1, 21 points (- 0), mean, sd, max dev: 0.71 0.27 1.59 27 views, 35 cycles, F = 0.1441033E-03, mean residual = 0.58 1 pts deleted for pass 2, conts: 20 27 views, 15 cycles, F = 0.1413606E-03, mean residual = 0.57 1 pts added on pass 2, conts: 20 view 5, pass 2, 21 points (- 0), mean, sd, max dev: 0.66 0.28 1.61 27 views, 28 cycles, F = 0.1431126E-03, mean residual = 0.57 1 pts deleted, big mean residual, conts: 20 27 views, 24 cycles, F = 0.1408577E-03, mean residual = 0.57 view 4, pass 1, 21 points (- 5), mean, sd, max dev: 0.62 0.31 1.32 28 views, 35 cycles, F = 0.1861873E-03, mean residual = 0.60 3 pts deleted for pass 2, conts: 13 14 16 28 views, 36 cycles, F = 0.1469043E-03, mean residual = 0.57 3 pts added on pass 2, conts: 13 14 16 view 4, pass 2, 21 points (- 0), mean, sd, max dev: 0.63 0.31 1.72 28 views, 8 cycles, F = 0.1482865E-03, mean residual = 0.57 view 3, pass 1, 21 points (- 5), mean, sd, max dev: 0.53 0.28 1.03 29 views, 46 cycles, F = 0.1716299E-03, mean residual = 0.59 5 pts deleted for pass 2, conts: 4 2 17 19 18 29 views, 3 cycles, F = 0.1529705E-03, mean residual = 0.58 5 pts added on pass 2, conts: 4 2 17 19 18 view 3, pass 2, 21 points (- 0), mean, sd, max dev: 0.93 0.75 2.59 29 views, 3 cycles, F = 0.1661025E-03, mean residual = 0.59 4 pts deleted, big mean residual, conts: 4 17 19 18 29 views, 1 cycles, F = 0.1547195E-03, mean residual = 0.58 view 2, pass 1, 21 points (- 5), mean, sd, max dev: 0.72 0.36 1.39 30 views, 48 cycles, F = 0.1778737E-03, mean residual = 0.60 3 pts deleted for pass 2, conts: 6 20 16 30 views, 3 cycles, F = 0.1640567E-03, mean residual = 0.59 3 pts added on pass 2, conts: 6 20 16 view 2, pass 2, 21 points (- 0), mean, sd, max dev: 1.08 0.63 3.26 30 views, 3 cycles, F = 0.1750852E-03, mean residual = 0.60 3 pts deleted, big mean residual, conts: 6 20 16 30 views, 3 cycles, F = 0.1638159E-03, mean residual = 0.59 view 1, pass 1, 21 points (- 5), mean, sd, max dev: 0.69 0.29 1.16 31 views, 41 cycles, F = 0.1806997E-03, mean residual = 0.60 4 pts deleted for pass 2, conts: 2 15 12 18 31 views, 1 cycles, F = 0.1716901E-03, mean residual = 0.59 3 pts added on pass 2, conts: 2 15 18 view 1, pass 2, 20 points (- 0), mean, sd, max dev: 0.81 0.36 1.45 31 views, 1 cycles, F = 0.1775236E-03, mean residual = 0.60 3 pts deleted, big mean residual, conts: 2 15 18 31 views, 1 cycles, F = 0.1716329E-03, mean residual = 0.59 31 views, 3 cycles, F = 0.1712316E-03, mean residual = 0.59 view 32, pass 1, 21 points (- 5), mean, sd, max dev: 0.46 0.23 0.81 32 views, 50 cycles, F = 0.1786334E-03, mean residual = 0.59 1 pts deleted for pass 2, conts: 4 32 views, 2 cycles, F = 0.1760921E-03, mean residual = 0.59 1 pts added on pass 2, conts: 4 view 32, pass 2, 21 points (- 0), mean, sd, max dev: 0.58 0.33 1.50 32 views, 1 cycles, F = 0.1775564E-03, mean residual = 0.59 view 33, pass 1, 21 points (- 0), mean, sd, max dev: 0.71 0.32 1.29 33 views, 54 cycles, F = 0.1905691E-03, mean residual = 0.60 view 34, pass 1, 21 points (- 0), mean, sd, max dev: 0.87 0.58 2.35 34 views, 50 cycles, F = 0.2014395E-03, mean residual = 0.61 1 pts deleted for pass 2, conts: 4 34 views, 3 cycles, F = 0.1988154E-03, mean residual = 0.61 1 pts added on pass 2, conts: 4 view 34, pass 2, 21 points (- 0), mean, sd, max dev: 0.69 0.39 1.41 34 views, 1 cycles, F = 0.1992749E-03, mean residual = 0.61 view 35, pass 1, 21 points (- 0), mean, sd, max dev: 0.83 0.43 1.66 35 views, 41 cycles, F = 0.2089702E-03, mean residual = 0.61 view 36, pass 1, 21 points (- 0), mean, sd, max dev: 0.70 0.38 1.38 36 views, 51 cycles, F = 0.2149973E-03, mean residual = 0.61 view 37, pass 1, 21 points (- 0), mean, sd, max dev: 0.62 0.41 1.40 37 views, 58 cycles, F = 0.2226868E-03, mean residual = 0.61 view 38, pass 1, 21 points (- 0), mean, sd, max dev: 0.80 0.33 1.44 38 views, 43 cycles, F = 0.2334410E-03, mean residual = 0.62 view 39, pass 1, 21 points (- 0), mean, sd, max dev: 0.58 0.35 1.76 39 views, 59 cycles, F = 0.2405173E-03, mean residual = 0.62 view 40, pass 1, 21 points (- 0), mean, sd, max dev: 0.50 0.33 1.18 40 views, 67 cycles, F = 0.2455889E-03, mean residual = 0.62 view 41, pass 1, 21 points (- 0), mean, sd, max dev: 0.68 0.39 1.51 41 views, 67 cycles, F = 0.2552030E-03, mean residual = 0.63 view 42, pass 1, 21 points (- 0), mean, sd, max dev: 0.56 0.31 1.09 42 views, 51 cycles, F = 0.2620516E-03, mean residual = 0.63 view 43, pass 1, 21 points (- 0), mean, sd, max dev: 0.58 0.33 1.50 43 views, 54 cycles, F = 0.2683803E-03, mean residual = 0.63 view 44, pass 1, 21 points (- 0), mean, sd, max dev: 0.41 0.35 1.63 44 views, 53 cycles, F = 0.2735069E-03, mean residual = 0.62 view 45, pass 1, 21 points (- 0), mean, sd, max dev: 0.53 0.26 1.14 45 views, 54 cycles, F = 0.2833469E-03, mean residual = 0.63 view 46, pass 1, 21 points (- 0), mean, sd, max dev: 0.58 0.42 1.66 46 views, 60 cycles, F = 0.2939719E-03, mean residual = 0.63 view 47, pass 1, 21 points (- 0), mean, sd, max dev: 0.58 0.33 1.49 47 views, 59 cycles, F = 0.3045751E-03, mean residual = 0.63 view 48, pass 1, 21 points (- 0), mean, sd, max dev: 0.68 0.34 1.33 48 views, 56 cycles, F = 0.3174688E-03, mean residual = 0.64 view 49, pass 1, 21 points (- 0), mean, sd, max dev: 0.62 0.30 1.21 49 views, 52 cycles, F = 0.3282371E-03, mean residual = 0.65 view 50, pass 1, 21 points (- 0), mean, sd, max dev: 0.73 0.39 1.66 50 views, 52 cycles, F = 0.3424857E-03, mean residual = 0.65 view 51, pass 1, 21 points (- 0), mean, sd, max dev: 0.65 0.34 1.42 51 views, 52 cycles, F = 0.3565702E-03, mean residual = 0.66 view 52, pass 1, 21 points (- 0), mean, sd, max dev: 0.76 0.38 1.40 52 views, 53 cycles, F = 0.3719415E-03, mean residual = 0.67 view 53, pass 1, 21 points (- 0), mean, sd, max dev: 0.85 0.41 1.74 53 views, 59 cycles, F = 0.3919038E-03, mean residual = 0.68 view 54, pass 1, 21 points (- 0), mean, sd, max dev: 0.64 0.32 1.53 54 views, 53 cycles, F = 0.4100145E-03, mean residual = 0.69 1 pts deleted for pass 2, conts: 20 54 views, 1 cycles, F = 0.4051965E-03, mean residual = 0.68 1 pts added on pass 2, conts: 20 view 54, pass 2, 21 points (- 0), mean, sd, max dev: 0.64 0.35 1.51 54 views, 1 cycles, F = 0.4114669E-03, mean residual = 0.69 view 55, pass 1, 21 points (- 0), mean, sd, max dev: 0.68 0.29 1.32 55 views, 56 cycles, F = 0.4264250E-03, mean residual = 0.69 view 56, pass 1, 21 points (- 0), mean, sd, max dev: 0.82 0.41 1.52 56 views, 57 cycles, F = 0.4423569E-03, mean residual = 0.70 1 pts deleted for pass 2, conts: 1 56 views, 1 cycles, F = 0.4383706E-03, mean residual = 0.69 1 pts added on pass 2, conts: 1 view 56, pass 2, 21 points (- 0), mean, sd, max dev: 0.77 0.37 1.41 56 views, 1 cycles, F = 0.4398457E-03, mean residual = 0.70 view 57, pass 1, 21 points (- 5), mean, sd, max dev: 0.67 0.22 1.07 57 views, 56 cycles, F = 0.4573232E-03, mean residual = 0.70 view 58, pass 1, 21 points (- 5), mean, sd, max dev: 0.60 0.26 1.05 58 views, 62 cycles, F = 0.4838085E-03, mean residual = 0.71 3 pts deleted for pass 2, conts: 1 20 18 58 views, 2 cycles, F = 0.4685470E-03, mean residual = 0.71 3 pts added on pass 2, conts: 1 20 18 view 58, pass 2, 21 points (- 0), mean, sd, max dev: 0.88 0.60 2.96 58 views, 2 cycles, F = 0.4833965E-03, mean residual = 0.71 view 59, pass 1, 21 points (- 5), mean, sd, max dev: 0.54 0.19 0.86 59 views, 58 cycles, F = 0.5076491E-03, mean residual = 0.72 2 pts deleted for pass 2, conts: 1 20 59 views, 3 cycles, F = 0.4977157E-03, mean residual = 0.72 2 pts added on pass 2, conts: 1 20 view 59, pass 2, 21 points (- 5), mean, sd, max dev: 0.49 0.19 0.79 59 views, 3 cycles, F = 0.5113267E-03, mean residual = 0.72 1 pts deleted, big mean residual, conts: 20 59 views, 3 cycles, F = 0.5029445E-03, mean residual = 0.72 view 60, pass 1, 21 points (- 5), mean, sd, max dev: 0.65 0.28 1.21 60 views, 59 cycles, F = 0.5232785E-03, mean residual = 0.73 1 pts deleted for pass 2, conts: 1 60 views, 1 cycles, F = 0.5179224E-03, mean residual = 0.72 1 pts added on pass 2, conts: 1 view 60, pass 2, 21 points (- 0), mean, sd, max dev: 0.90 0.53 2.20 60 views, 1 cycles, F = 0.5232847E-03, mean residual = 0.73 view 61, pass 1, 21 points (- 5), mean, sd, max dev: 0.49 0.25 0.94 61 views, 66 cycles, F = 0.5440774E-03, mean residual = 0.73 1 pts deleted for pass 2, conts: 1 61 views, 1 cycles, F = 0.5388014E-03, mean residual = 0.73 1 pts added on pass 2, conts: 1 view 61, pass 2, 21 points (- 5), mean, sd, max dev: 0.47 0.25 0.90 61 views, 1 cycles, F = 0.5422129E-03, mean residual = 0.73 For object 1, round 1: 21 contours, points missing = 17 61 views, 1 cycles, F = 0.5422082E-03, mean residual = 0.73 view 1, pass 1, 21 points (- 0), mean, sd, max dev: 1.24 0.52 2.27 61 views, 1 cycles, F = 0.5486304E-03, mean residual = 0.73 view 2, pass 1, 21 points (- 0), mean, sd, max dev: 1.29 0.82 3.56 61 views, 1 cycles, F = 0.5634537E-03, mean residual = 0.74 1 pts deleted for pass 2, conts: 16 61 views, 1 cycles, F = 0.5524556E-03, mean residual = 0.74 1 pts added on pass 2, conts: 16 view 2, pass 2, 21 points (- 0), mean, sd, max dev: 1.19 0.60 2.31 61 views, 1 cycles, F = 0.5553994E-03, mean residual = 0.74 view 3, pass 1, 21 points (- 0), mean, sd, max dev: 1.00 0.54 2.59 61 views, 1 cycles, F = 0.5612777E-03, mean residual = 0.74 1 pts deleted for pass 2, conts: 18 61 views, 1 cycles, F = 0.5561111E-03, mean residual = 0.74 1 pts added on pass 2, conts: 18 view 3, pass 2, 21 points (- 0), mean, sd, max dev: 0.90 0.43 1.71 61 views, 1 cycles, F = 0.5575045E-03, mean residual = 0.74 view 5, pass 1, 21 points (- 0), mean, sd, max dev: 0.89 0.53 2.05 61 views, 1 cycles, F = 0.5608379E-03, mean residual = 0.74 view 7, pass 1, 21 points (- 0), mean, sd, max dev: 0.97 0.46 2.22 61 views, 1 cycles, F = 0.5641349E-03, mean residual = 0.74 view 12, pass 1, 21 points (- 0), mean, sd, max dev: 0.61 0.30 1.39 61 views, 1 cycles, F = 0.5642328E-03, mean residual = 0.74 view 18, pass 1, 21 points (- 0), mean, sd, max dev: 0.49 0.29 1.35 61 views, 1 cycles, F = 0.5641917E-03, mean residual = 0.74 view 20, pass 1, 21 points (- 0), mean, sd, max dev: 0.50 0.26 1.08 61 views, 1 cycles, F = 0.5642760E-03, mean residual = 0.74 61 views, 1 cycles, F = 0.5642411E-03, mean residual = 0.74 view 59, pass 1, 21 points (- 5), mean, sd, max dev: 0.53 0.16 0.76 61 views, 1 cycles, F = 0.5686064E-03, mean residual = 0.74 1 pts deleted for pass 2, conts: 20 61 views, 1 cycles, F = 0.5641702E-03, mean residual = 0.74 1 pts added on pass 2, conts: 20 view 59, pass 2, 21 points (- 4), mean, sd, max dev: 0.52 0.22 1.02 61 views, 15 cycles, F = 0.5705173E-03, mean residual = 0.74 For object 1, round 2: 21 contours, points missing = 0 Obj cont: Views on which points are missing Total points missing = 0 SUCCESSFULLY COMPLETED