*** Entries to program alignframes ***
  InputFile = 540_001.tif
  OutputImageFile = W:/Modis_02July2018/images/540_001_ali.mrc
  AlignAndSumBinning = 4 1
  ScalingOfSum = 12.225000
  GainReferenceFile = CountRef_58-4_001.dm4
  RotationAndFlip = -1
  CameraDefectFile = defects_455_001.txt
  PairwiseFrames = 40
  ShiftLimit = 20
  GroupSize = 1
  FilterRadius2 = 0.060000
  VaryFilter = 0.060000
  RefineAlignment = 5
  StopIterationsAtShift = 0.100000
  RefineRadius2 = 0.060000
  MinForSplineSmoothing = 0
  UseGPU = 0
  AntialiasFilter = 4
  FilterSigma2 = 0.008574
*** End of entries ***

Assuming binning of 1.0 instead of a small subarea;
    use the -imagebinned option to set a binning if this is incorrect.
File 1 (540_001.tif): 40 frames
  Weighted residual mean = 11.354, SD = 4.323, mean max = 16.59, max max = 16.59
  Max unweighted resid mean = 36.98, max = 36.98   Dist = 497.35, smoothed = 189.27
 FRC crossings 0.5: 0.0112  0.25: 0.0192  0.125: 0.0271  is 0.0004 at 0.25/pix
SUCCESSFULLY COMPLETED