3DA II R pipeline (XDS IDXREF all images) selected
Interpreted from image /dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_0001.cbf:
Template BAZ2BA-x828_1_####.cbf
Directory /dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x828
Project: nt5073v16
Heavy atom: s
Crystal: xBAZ2BAx8281
ISPyB XML output set to ispyb.xml
Min No. images / sweep set to 3
XParallel set to -1
Blend mode on
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/Harvest
Created CCP4_SCR: /tmp/4137896.1.medium.q/tmp8Y4qkj
Removing 0 apparently still images
Removing 0 apparently still images
Resetting indexer done as prepare not done
Resetting indexer finish done as index not done
Resetting indexer done as prepare not done
Selected image 1
Selected image 450
Selected image 900
Logfile: labelit.index -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/setup/1_labelit.index.log
Indexing from images:
/dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_0001.cbf
/dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_0450.cbf
/dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_0900.cbf
Overriding value for wavelength SAD to 0.920000
Reading 1800 headers took 3s
Exposure epoch for sweep BAZ2BA-x828_1_####.cbf: 1400120800 1400120890
Using XDS Integrater in new resolution mode
Integrater factory: Setting wavelength: 0.920000
Deleting all stored results.
Using XDS II Indexer
Indexer factory: Setting wavelength: 0.920000
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index
Latest header information for image 1:
beam = (143.99324000000001, 124.99928000000001)
date = Thu May 15 03:26:40 2014
detector = dectris
detector_class = pilatus 2M
distance = 189.45
epoch = 1400120800.0
exposure_time = 0.05
phi_end = 30.1
phi_start = 30.0
phi_width = 0.1
pixel = (0.17200000000000001, 0.17200000000000001)
raw_beam = (143.99324000000001, 124.99928000000001)
size = (1679, 1475)
two_theta = 0.0
wavelength = 0.92
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate
Sweep epoch: 1400120800
Latest header information for image 1:
beam = (143.99324000000001, 124.99928000000001)
date = Thu May 15 03:26:40 2014
detector = dectris
detector_class = pilatus 2M
distance = 189.45
epoch = 1400120800.0
exposure_time = 0.05
phi_end = 30.1
phi_start = 30.0
phi_width = 0.1
pixel = (0.17200000000000001, 0.17200000000000001)
raw_beam = (143.99324000000001, 124.99928000000001)
size = (1679, 1475)
two_theta = 0.0
wavelength = 0.92
Resetting indexer done as prepare not done
Resetting integrater done as prepare not done
Resetting integrater finish done as integrate not done
Resetting indexer done as prepare not done
Resetting integrater done as prepare not done
Resetting indexer done as prepare not done
Preparing to do some integration...
XDS INTEGRATE PREPARE:
Wavelength: 0.920000
Distance: 189.45
Resetting indexer done as prepare not done
Resetting indexer finish done as index not done
Resetting indexer done as prepare not done
XDS INDEX PREPARE:
Wavelength: 0.920000
Distance: 189.45
Adding images for indexer: 1 -> 1800
Logfile: xds -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/2_xds_XYCORR.log
Logfile: xds -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/3_xds_INIT.log
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/4_xds_par_COLSPOT.log
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/5_xds_par_IDXREF.log
Testing II or I indexing
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/6_xds_par_IDXREF.log
Adding images for indexer: 1 -> 5
Adding images for indexer: 451 -> 455
Adding images for indexer: 901 -> 905
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/index/7_xds_par_IDXREF.log
I:  0.86 0.26 0.09
II: 0.87 0.29 0.04
Selecting I or II, chose ii
Ignoring solution with lattice hR
Ignoring solution with lattice hR
Ignoring solution with lattice tP
Ignoring solution with lattice tP
Ignoring solution with lattice oP
Target unit cell: 83.20 96.90 58.00 90.00 90.00 90.00
Chosen unit cell: 83.20 96.90 58.00 90.00 90.00 90.00
Absent: 25  vs.  Present: 41935 Total: 47974
Centring analysis: oC => oC
Low resolution limit assigned as: 50.38
Low resolution set to: 50.3834569922
Files available at the end of XDS integrate prepare:
Y-CORRECTIONS.cbf
SPOT.XDS
BLANK.cbf
X-CORRECTIONS.cbf
XPARM.XDS
BKGINIT.cbf
GAIN.cbf
Doing some integration...
Logfile: xds -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/8_xds_DEFPIX.log
Setting low resolution limit in DEFPIX to 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/9_xds_par_INTEGRATE.log
Xparallel: -1 using 6 chunks
Mosaic spread range: 0.085 0.109 0.141
Resetting integrater, to ensure refined orientation is used
Using low resolution limit: 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/10_xds_par_CORRECT.log
XDS applied reindex: -2 0 0 0 0 -2 0 0 0 0 2 0
Postrefinement in P1 results:
83.172  96.886  58.005  89.975  90.010  89.919
0.028   0.034   0.020   0.006   0.020   0.009
Deviations: 0.30 pixels 0.04 degrees
Using low resolution limit: 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/11_xds_par_CORRECT.log
Setting spacegroup to: 20
Setting cell to: 83.20 96.90 58.00 90.00 90.00 90.00
XDS applied reindex: 2 0 0 0 0 2 0 0 0 0 2 0
Postrefinement in "correct" spacegroup results:
83.091  96.792  57.950  90.000  90.000  90.000
0.065   0.031   0.017   0.000   0.000   0.000
Deviations: 0.37 pixels 0.04 degrees
Error correction parameters: A=1.000 B=0.000
Axis misalignment 0.00 degrees
RMSD ratio: 1.23
RMSPhi ratio: 0.62
Wrote 0 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Resetting integrater finish done as integrate not done
Doing some integration...
Logfile: xds -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/12_xds_DEFPIX.log
Setting low resolution limit in DEFPIX to 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/13_xds_par_INTEGRATE.log
Using globally refined parameters
Xparallel: -1 using 6 chunks
Mosaic spread range: 0.063 0.063 0.063
Using low resolution limit: 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/14_xds_par_CORRECT.log
Setting spacegroup to: 20
Setting cell to: 83.20 96.90 58.00 90.00 90.00 90.00
XDS applied reindex: 2 0 0 0 0 2 0 0 0 0 2 0
Postrefinement in "correct" spacegroup results:
83.091  96.794  57.951  90.000  90.000  90.000
0.066   0.032   0.018   0.000   0.000   0.000
Deviations: 0.37 pixels 0.04 degrees
Error correction parameters: A=1.000 B=0.000
Axis misalignment 0.00 degrees
0 alien reflections are already removed
Wrote 500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Scaler reset
Using XDSA Scaler
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale
Scaler reset
Resetting Scaler done as prepare not done
Called scaler done from Schema.Interfaces.Scaler 394 (False)
Resetting scaler finish done as scaling not done
Called scaler finish done from Schema.Interfaces.Scaler 401 (False)
Resetting Scaler done as prepare not done
Called scaler done from Schema.Interfaces.Scaler 394 (False)
For EPOCH 1400120800 have:
ID = nt5073v16/xBAZ2BAx8281/SAD
SWEEP = SWEEP1
Doses scaled by 1.00e+00
Logfile: pointless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/15_pointless.log
Scaling intensities by factor 1.000000e+00
Logfile: pointless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/16_pointless.log
Possible lattices (pointless):
oC mC aP
Agreed lattice oC
Pointless analysis of /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/SWEEP1-combat.mtz
Pointgroup: C 2 2 2 (h,k,l)
Composing x,y,z and h,k,l -> x,y,z
Deleting REMOVE.HKL as reindex op set.
Set spacegroup as 21
Using low resolution limit: 50.38
Logfile: xds_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/17_xds_par_CORRECT.log
XDS applied reindex: 2 0 0 0 0 2 0 0 0 0 2 0
Postrefinement in "correct" spacegroup results:
83.091  96.794  57.951  90.000  90.000  90.000
0.066   0.032   0.018   0.000   0.000   0.000
Deviations: 0.37 pixels 0.04 degrees
Error correction parameters: A=1.000 B=0.000
Axis misalignment 0.00 degrees
Wrote 0 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Copying /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/SAD/SWEEP1/integrate/XDS_ASCII.HKL to /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/SAD_SWEEP1.HKL
Cell for SWEEP1: 83.09 96.79 57.95 90.00 90.00 90.00
=> 340434 reflections
Determined unit cell: 83.09 96.79 57.95 90.00 90.00 90.00
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/18_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.746760e+03
Wrote 0 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/19_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.830050e+03
0 alien reflections are already removed
Wrote 500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/20_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.409840e+03
0 alien reflections are already removed
Wrote 1000 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/21_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 9.868800e+02
0 alien reflections are already removed
Wrote 1500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/22_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.137380e+03
0 alien reflections are already removed
Wrote 2000 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/23_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.079310e+03
0 alien reflections are already removed
Wrote 2500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/24_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.298050e+03
0 alien reflections are already removed
Wrote 3000 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/25_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.715430e+03
0 alien reflections are already removed
Wrote 3500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/26_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 1.790360e+03
0 alien reflections are already removed
Wrote 4000 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/27_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 2.863640e+03
0 alien reflections are already removed
Wrote 4500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/28_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 2.870290e+03
0 alien reflections are already removed
Wrote 5000 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 500 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 92472
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/29_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 92472
XSCALE scale factor found to be: 2.870290e+03
500 alien reflections are already removed
Wrote 5500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 0 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
RAM usage at XDSScalerA.py 876: 92472
RAM usage at XDSScalerA.py 923: 92472
Set 1 is from data SAD_SWEEP1.HKL
Set 1 wavelength 0.920000
Logfile: pointless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/30_pointless.log
Scaling intensities by factor 3.483969e-04
RAM usage at XDSScalerA.py 947: 131704
Resolution analysis: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/SCALED_SAD_SWEEP1.mtz nbins=100 isigma=1.000000 misigma=2.000000
Called scaler done from Modules.Scaler.XDSScalerA 1031 (False)
RAM usage at XDSScalerA.py 1037: 131704
Returning as scaling not finished...
RAM usage at XDSScalerA.py 722: 131704
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/31_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 131704
XSCALE scale factor found to be: 8.216420e+02
0 alien reflections are already removed
Wrote 5500 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 3 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Called scaler done from Modules.Scaler.XDSScalerA 865 (False)
RAM usage at XDSScalerA.py 722: 131704
Logfile: xscale_par -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/32_xscale_par.log
Set CELL: 83.09 96.79 57.95 90.00 90.00 90.00
Set SPACEGROUP_NUMBER: 21
Gathering measurements for scaling
Epoch: 1400120800
HKL: SAD_SWEEP1.HKL (SAD/SWEEP1)
RAM usage at XDSScalerA.py 773: 131704
XSCALE scale factor found to be: 8.216420e+02
3 alien reflections are already removed
Wrote 5503 old reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
Wrote 0 new reflections to REMOVE.HKL
Rejected 0 as z < 0.000000
RAM usage at XDSScalerA.py 876: 131704
RAM usage at XDSScalerA.py 923: 131704
Set 1 is from data SAD_SWEEP1.HKL
Set 1 wavelength 0.920000
Logfile: pointless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/33_pointless.log
Scaling intensities by factor 1.217075e-03
RAM usage at XDSScalerA.py 947: 131704
Resolution analysis: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/SCALED_SAD_SWEEP1.mtz nbins=100 isigma=1.000000 misigma=2.000000
RAM usage at XDSScalerA.py 1037: 131704
Logfile: pointless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/34_pointless.log
Updating unit cell to 83.09 96.79 57.95 90.00 90.00 90.00
Logfile: sortmtz -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/35_sortmtz.log
Scaler highest resolution set to  1.90
Logfile: aimless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/36_aimless.log
Run 1 corresponds to sweep SWEEP1
Aimless status: okey dokey
Logfile: aimless -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/37_aimless.log
Run 1 corresponds to sweep SWEEP1
Aimless status: okey dokey
Logfile: mtz2various -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/38_mtz2various.log
Running anomalous signal analysis on /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/nt5073v16_xBAZ2BAx8281_scaled.mtz
Logfile: ctruncate -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/39_ctruncate.log
0 absent reflections in SAD removed
Logfile: freerflag -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/40_freerflag.log
Logfile: freerflag -> /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/41_freerflag.log
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles
Directory exists: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles
Directory exists: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles
Directory exists: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/LogFiles
Directory exists: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles
Making directory: /dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/DataFiles/Integrate