************ Version 7.0.0 (beta test) for Image plate and CCD data 14th June 2006 *********** A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK E-mail andrew@mrc-lmb.cam.ac.uk New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann (1998) J. Appl. Cryst. 30, 1036-1040 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993), J.Appl.Cryst. 24,795-800.) X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.) (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242. ===> newmat autoindex.mat ===> directory /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1 ===> template ref-AV01-3342167Aa_1_###.img ===> BEST ON ===> prerefine on ****** Keyword NOT RECOGNISED ***** ===> autoindex dps refine image 1 thresh 20.000000 Using DPS code for background indexing Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution ===> autoindex dps refine image 2 thresh 20.000000 Using DPS code for background indexing Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution ===> mosaic estimate ===> go From information in the image file, the detector has been recognized as: ADSC If this is incorrect you must supply a DETECTOR keyword Crystal to detector distance of 287.49mm taken from image header Wavelength of 0.97950A taken from image header Pixel size of 0.1026mm taken from image header. Start and end phi values for image 0 from image header are 0.00 and 1.00 degrees. Oscillation axis set as PHI from image header Main beam position has been calculated as 156.93mm 158.88mm from parameters in the image header. You should check these values carefully as they may be in error! Autoindexing using 2 images Image numbers: 1 2 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_001.img Determining average spot size for spots in centre of image. ========================================================== Determining best threshold for spot finding. Default parameters may be reset with SPOTS keyword. Minimum radius 15.8mm, maximum radius 63.07mm, minimum number of spots 10 Threshold set to 5.0 Threshold set to 5.0 Based on a median spot size of 4 by 3 pixels in X and Y, the measurement box parameters have been set to 15 13 8 5 4 The overall size of the box has been fixed. To prevent this use keywords PROFILE NOFIXBOX. ***** WARNING ***** Lattice type not specified, so assumed primitive Based on a median spot size of 4 by 3 pixels in X and Y, the spot separation parameters (in X and Y) have been set to 0.61 0.51mm. Closest possible spot separation is 0.00mm. Determining best threshold for spot finding. Default parameters may be reset with SPOTS keyword. Minimum radius 15.8mm, maximum radius 63.07mm, minimum number of spots 10 Threshold set to 5.0 Threshold set to 5.0 Finding spots on image 1 (Midpoint of phi 0.500 degrees) Calculating radial background..... The background is radial along the X (slow) direction The average of 51 pixels, excluding outliers, is used The scan is offset by 0.0mm from the image centre in Y to avoid any backstop shadow ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.81mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.91mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.01mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.11mm Radial Background calculation complete RADIUS 15.7 16.1 16.5 16.9 17.3 17.7 18.2 18.6 19.0 19.4 19.8 20.2 BACKG 6714 6520 6319 6127 5982 5841 5657 5504 5382 5259 5139 5028 SIGMA 40 40 39 39 38 38 37 37 36 36 35 35 NREJ 17 18 18 27 18 14 24 30 19 22 12 15 RADIUS 20.6 21.0 21.4 21.9 22.3 22.7 23.1 23.5 23.9 24.3 24.7 25.1 BACKG 4892 4771 4666 4567 4470 4377 4271 4186 4100 4029 3943 3858 SIGMA 34 34 34 33 33 33 32 32 32 31 31 31 NREJ 17 22 20 14 17 16 24 18 14 8 10 15 RADIUS 25.5 26.0 26.4 26.8 27.2 27.6 28.0 28.4 28.8 29.2 29.6 30.1 BACKG 3771 3695 3632 3564 3510 3422 3365 3308 3253 3183 3129 3087 SIGMA 30 30 30 29 29 29 29 28 28 28 27 27 NREJ 27 22 14 9 6 19 18 18 13 11 14 8 RADIUS 30.5 30.9 31.3 31.7 32.1 32.5 32.9 33.3 33.8 34.2 34.6 35.0 BACKG 3014 2970 2920 2868 2838 2784 2741 2670 2639 2603 2562 2523 SIGMA 27 27 27 26 26 26 26 25 25 25 25 25 NREJ 19 18 16 14 7 8 14 17 14 10 11 19 RADIUS 35.4 35.8 36.2 36.6 37.0 37.4 37.9 38.3 38.7 39.1 39.5 39.9 BACKG 2482 2436 2401 2367 2335 2299 2263 2232 2191 2155 2138 2107 SIGMA 24 24 24 24 24 23 23 23 23 23 23 22 NREJ 12 17 17 13 11 11 8 8 11 20 13 17 RADIUS 40.3 40.7 41.1 41.5 42.0 42.4 42.8 43.2 43.6 44.0 44.4 44.8 BACKG 2076 2042 2017 1990 1956 1914 1890 1876 1857 1819 1801 1774 SIGMA 22 22 22 22 22 21 21 21 21 21 21 21 NREJ 10 8 9 8 10 17 20 9 8 18 12 14 RADIUS 45.2 45.7 46.1 46.5 46.9 47.3 47.7 48.1 48.5 48.9 49.3 49.8 BACKG 1738 1723 1693 1681 1661 1644 1611 1593 1575 1554 1536 1516 SIGMA 20 20 20 20 20 20 20 19 19 19 19 19 NREJ 23 14 22 10 11 10 13 12 15 11 10 13 RADIUS 50.2 50.6 51.0 51.4 51.8 52.2 52.6 53.0 53.4 53.9 54.3 54.7 BACKG 1510 1489 1462 1435 1435 1387 1390 1384 1365 1354 1325 1311 SIGMA 19 19 19 18 18 18 18 18 18 18 18 18 NREJ 14 15 16 13 51 15 13 12 10 7 12 10 RADIUS 55.1 55.5 55.9 56.3 56.7 57.1 57.6 58.0 58.4 58.8 59.2 59.6 BACKG 1303 1293 1274 1258 1249 1230 1218 1206 1199 1175 1157 1162 SIGMA 18 17 17 17 17 17 17 17 17 17 17 17 NREJ 13 10 10 14 8 13 17 17 13 15 22 15 RADIUS 60.0 60.4 60.8 61.2 61.7 62.1 62.5 62.9 63.3 63.7 64.1 64.5 BACKG 1157 1140 1137 1126 1112 1102 1094 1074 1063 1052 1043 1044 SIGMA 17 16 16 16 16 16 16 16 16 16 16 16 NREJ 14 21 17 14 10 12 9 13 16 12 20 16 RADIUS 64.9 65.3 65.8 66.2 66.6 67.0 67.4 67.8 68.2 68.6 69.0 69.5 BACKG 1034 1020 1024 1015 1008 1001 1001 993 988 975 967 952 SIGMA 16 15 15 15 15 15 15 15 15 15 15 15 NREJ 17 21 10 11 9 16 10 9 7 12 18 14 RADIUS 69.9 70.3 70.7 71.1 71.5 71.9 72.3 72.7 73.1 73.6 74.0 74.4 BACKG 956 947 937 938 926 934 919 909 911 903 900 905 SIGMA 15 15 15 15 15 15 15 15 15 15 15 15 NREJ 12 11 8 9 16 9 19 16 12 17 17 11 RADIUS 74.8 75.2 75.6 76.0 76.4 76.8 77.2 77.7 78.1 78.5 78.9 79.3 BACKG 903 899 885 886 878 878 878 870 868 857 852 840 SIGMA 15 14 14 14 14 14 14 14 14 14 14 14 NREJ 13 11 24 14 22 19 23 22 17 12 12 15 RADIUS 79.7 80.1 80.5 80.9 81.4 81.8 82.2 82.6 83.0 83.4 83.8 84.2 BACKG 842 828 825 824 819 813 798 799 784 779 770 765 SIGMA 14 14 14 14 14 14 14 14 14 13 13 13 NREJ 14 16 13 5 10 12 16 12 19 15 17 15 RADIUS 84.6 85.0 85.5 85.9 86.3 86.7 87.1 87.5 87.9 88.3 88.7 89.1 BACKG 763 753 742 737 736 725 719 709 697 698 681 681 SIGMA 13 13 13 13 13 13 13 13 13 13 13 13 NREJ 15 10 22 14 13 15 9 12 16 9 20 9 RADIUS 89.6 90.0 90.4 90.8 91.2 91.6 92.0 92.4 92.8 93.3 93.7 94.1 BACKG 672 661 657 652 653 645 636 625 613 613 607 597 SIGMA 12 12 12 12 12 12 12 12 12 12 12 12 NREJ 15 21 17 14 6 7 9 15 15 11 8 15 RADIUS 94.5 94.9 95.3 95.7 96.1 96.5 96.9 97.4 97.8 98.2 98.6 99.0 BACKG 592 584 584 580 568 571 559 560 554 541 540 540 SIGMA 12 12 12 12 11 11 11 11 11 11 11 11 NREJ 13 21 13 11 17 8 18 10 11 18 17 15 RADIUS 99.4 99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9 BACKG 535 528 519 513 510 513 500 486 492 485 480 477 SIGMA 11 11 11 11 11 11 11 11 11 11 10 10 NREJ 10 8 13 14 18 11 18 22 13 18 18 10 RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8 BACKG 473 470 467 465 460 452 446 443 444 444 436 430 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 16 19 18 13 10 12 21 16 10 13 14 17 RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8 BACKG 431 428 418 417 415 414 413 413 406 405 406 403 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 11 10 14 10 12 11 9 11 15 12 7 9 RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7 BACKG 395 395 396 389 386 384 376 377 378 373 374 377 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 18 9 12 14 15 12 25 17 10 13 15 8 RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6 BACKG 368 369 364 358 359 359 353 351 355 356 348 350 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 19 9 15 13 7 10 10 12 7 13 15 14 RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5 BACKG 348 344 342 339 338 339 333 336 335 337 331 328 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 10 13 15 11 17 14 20 13 9 10 12 15 RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5 BACKG 330 328 324 325 328 322 322 319 318 317 316 314 SIGMA 9 9 9 9 9 8 8 8 8 8 8 8 NREJ 10 18 16 12 10 15 8 10 13 13 13 11 RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4 BACKG 315 311 310 311 305 303 305 308 311 302 299 300 SIGMA 8 8 8 8 8 8 8 8 8 8 8 8 NREJ 8 11 8 9 17 11 11 11 7 14 20 12 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7 BACKG 300 302 299 298 298 299 295 73 SIGMA 8 8 8 8 8 8 8 2 NREJ 14 11 10 7 9 7 12 3 Starting spot search... Number of spots excluded from possible ice rings: 521 Median spot size is 7 x 6 pixels, mode size is 6 by 5 Total number of spots found:2297 Number rejected as too small on X: 234 Number rejected as too small on Y: 48 Number rejected as too big on X: 47 Number rejected as too big on Y: 8 Number too close (SEPARATION keyword): 135 (currently SEPARATION 0.61 0.51) Number stored as OK: 805 highest resolution is 2.16 Angstrom 99% have resolution less than 2.21 Angstrom Number of spots found in each bin 68 12 18 34 33 19 19 52 108 21 16 32 25 11 25 109 256 4 3 11 4 2 9 236 293 0 0 0 0 0 5 198 152 0 0 0 0 0 2 109 image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_002.img Finding spots on image 2 (Midpoint of phi 90.500 degrees) Calculating radial background..... The background is radial along the X (slow) direction The average of 51 pixels, excluding outliers, is used The scan is offset by 0.0mm from the image centre in Y to avoid any backstop shadow ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.81mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 51.91mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.01mm ** WARNING ** Fewer than 17 pixels with values greater than 0 (keyword NULLPIX) at a radius of 52.11mm Radial Background calculation complete RADIUS 15.7 16.1 16.5 16.9 17.3 17.7 18.2 18.6 19.0 19.4 19.8 20.2 BACKG 6750 6555 6336 6167 6023 5855 5716 5580 5428 5303 5186 5043 SIGMA 41 40 39 39 38 38 37 37 36 36 36 35 NREJ 17 22 30 28 24 23 14 17 20 13 14 20 RADIUS 20.6 21.0 21.4 21.9 22.3 22.7 23.1 23.5 23.9 24.3 24.7 25.1 BACKG 4930 4823 4696 4613 4516 4420 4317 4186 4136 4050 3956 3889 SIGMA 35 34 34 33 33 33 32 32 32 31 31 31 NREJ 19 12 17 10 8 8 15 20 18 13 17 19 RADIUS 25.5 26.0 26.4 26.8 27.2 27.6 28.0 28.4 28.8 29.2 29.6 30.1 BACKG 3809 3717 3664 3581 3526 3462 3388 3328 3256 3199 3165 3110 SIGMA 30 30 30 29 29 29 29 28 28 28 28 27 NREJ 19 26 11 14 10 13 19 15 22 21 8 10 RADIUS 30.5 30.9 31.3 31.7 32.1 32.5 32.9 33.3 33.8 34.2 34.6 35.0 BACKG 3046 2995 2935 2907 2858 2802 2745 2702 2663 2618 2585 2542 SIGMA 27 27 27 26 26 26 26 25 25 25 25 25 NREJ 15 15 18 9 10 12 9 18 15 12 9 10 RADIUS 35.4 35.8 36.2 36.6 37.0 37.4 37.9 38.3 38.7 39.1 39.5 39.9 BACKG 2516 2473 2414 2380 2358 2316 2283 2248 2220 2188 2157 2131 SIGMA 25 24 24 24 24 24 23 23 23 23 23 23 NREJ 13 13 26 22 17 17 13 15 13 16 22 15 RADIUS 40.3 40.7 41.1 41.5 42.0 42.4 42.8 43.2 43.6 44.0 44.4 44.8 BACKG 2088 2062 2028 2008 1976 1941 1920 1893 1871 1848 1830 1804 SIGMA 22 22 22 22 22 22 21 21 21 21 21 21 NREJ 15 8 13 14 13 12 12 10 13 13 12 17 RADIUS 45.2 45.7 46.1 46.5 46.9 47.3 47.7 48.1 48.5 48.9 49.3 49.8 BACKG 1770 1734 1731 1702 1678 1661 1650 1622 1593 1571 1555 1531 SIGMA 21 20 20 20 20 20 20 20 19 19 19 19 NREJ 10 16 11 12 15 11 6 11 14 12 15 16 RADIUS 50.2 50.6 51.0 51.4 51.8 52.2 52.6 53.0 53.4 53.9 54.3 54.7 BACKG 1518 1507 1488 1454 1443 1432 1414 1417 1393 1379 1360 1353 SIGMA 19 19 19 19 18 18 18 18 18 18 18 18 NREJ 18 13 18 19 51 21 19 9 19 19 20 10 RADIUS 55.1 55.5 55.9 56.3 56.7 57.1 57.6 58.0 58.4 58.8 59.2 59.6 BACKG 1340 1328 1304 1289 1281 1255 1253 1241 1221 1208 1204 1192 SIGMA 18 18 18 17 17 17 17 17 17 17 17 17 NREJ 7 7 10 14 16 20 14 12 16 19 11 11 RADIUS 60.0 60.4 60.8 61.2 61.7 62.1 62.5 62.9 63.3 63.7 64.1 64.5 BACKG 1178 1175 1172 1162 1157 1145 1143 1140 1135 1136 1135 1129 SIGMA 17 17 17 17 17 16 16 16 16 16 16 16 NREJ 12 13 10 10 16 13 4 10 11 8 14 21 RADIUS 64.9 65.3 65.8 66.2 66.6 67.0 67.4 67.8 68.2 68.6 69.0 69.5 BACKG 1121 1125 1124 1117 1103 1083 1069 1061 1063 1042 1026 1018 SIGMA 16 16 16 16 16 16 16 16 16 16 16 15 NREJ 19 17 16 10 7 12 10 14 16 21 21 15 RADIUS 69.9 70.3 70.7 71.1 71.5 71.9 72.3 72.7 73.1 73.6 74.0 74.4 BACKG 1010 1006 1002 993 996 980 977 972 970 974 973 973 SIGMA 15 15 15 15 15 15 15 15 15 15 15 15 NREJ 17 20 14 19 10 18 19 12 14 14 7 9 RADIUS 74.8 75.2 75.6 76.0 76.4 76.8 77.2 77.7 78.1 78.5 78.9 79.3 BACKG 967 973 969 982 974 976 972 977 973 963 960 949 SIGMA 15 15 15 15 15 15 15 15 15 15 15 15 NREJ 9 11 14 12 17 13 13 10 10 14 16 13 RADIUS 79.7 80.1 80.5 80.9 81.4 81.8 82.2 82.6 83.0 83.4 83.8 84.2 BACKG 933 931 924 915 898 891 873 867 851 844 834 823 SIGMA 15 15 15 15 14 14 14 14 14 14 14 14 NREJ 19 13 14 12 18 15 20 9 16 14 12 13 RADIUS 84.6 85.0 85.5 85.9 86.3 86.7 87.1 87.5 87.9 88.3 88.7 89.1 BACKG 815 807 797 785 774 766 761 747 746 736 731 722 SIGMA 14 14 14 14 13 13 13 13 13 13 13 13 NREJ 12 13 13 15 18 18 12 17 12 10 7 7 RADIUS 89.6 90.0 90.4 90.8 91.2 91.6 92.0 92.4 92.8 93.3 93.7 94.1 BACKG 702 701 696 690 679 669 654 652 645 641 633 630 SIGMA 13 13 13 13 13 12 12 12 12 12 12 12 NREJ 16 12 11 6 11 10 20 11 20 22 15 14 RADIUS 94.5 94.9 95.3 95.7 96.1 96.5 96.9 97.4 97.8 98.2 98.6 99.0 BACKG 617 618 612 606 597 589 582 584 582 575 568 563 SIGMA 12 12 12 12 12 12 12 12 12 11 11 11 NREJ 22 14 11 10 19 18 17 8 10 10 10 12 RADIUS 99.4 99.8 100.2 100.6 101.0 101.5 101.9 102.3 102.7 103.1 103.5 103.9 BACKG 552 546 545 541 528 531 525 515 515 512 511 504 SIGMA 11 11 11 11 11 11 11 11 11 11 11 11 NREJ 15 12 10 11 20 10 10 18 22 17 12 15 RADIUS 104.3 104.7 105.2 105.6 106.0 106.4 106.8 107.2 107.6 108.0 108.4 108.8 BACKG 494 491 487 482 477 470 469 467 470 462 454 451 SIGMA 11 11 11 10 10 10 10 10 10 10 10 10 NREJ 14 12 15 13 8 13 11 13 8 10 18 16 RADIUS 109.3 109.7 110.1 110.5 110.9 111.3 111.7 112.1 112.5 112.9 113.4 113.8 BACKG 454 446 445 445 440 437 436 429 427 424 417 420 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 9 13 12 12 12 14 10 15 22 13 20 14 RADIUS 114.2 114.6 115.0 115.4 115.8 116.2 116.6 117.1 117.5 117.9 118.3 118.7 BACKG 418 414 409 407 403 401 402 397 395 389 389 390 SIGMA 10 10 10 10 10 10 10 9 9 9 9 9 NREJ 8 9 18 12 14 16 8 8 11 16 11 9 RADIUS 119.1 119.5 119.9 120.3 120.7 121.2 121.6 122.0 122.4 122.8 123.2 123.6 BACKG 388 383 382 380 379 378 372 368 370 368 365 366 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 13 12 10 9 8 11 10 17 11 13 15 8 RADIUS 124.0 124.4 124.8 125.3 125.7 126.1 126.5 126.9 127.3 127.7 128.1 128.5 BACKG 367 362 359 358 358 359 352 351 349 351 357 350 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 7 9 17 15 14 11 17 18 18 15 9 11 RADIUS 129.0 129.4 129.8 130.2 130.6 131.0 131.4 131.8 132.2 132.6 133.1 133.5 BACKG 349 341 345 344 343 345 340 338 341 341 339 335 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 11 19 14 18 18 13 19 18 12 15 12 17 RADIUS 133.9 134.3 134.7 135.1 135.5 135.9 136.3 136.7 137.2 137.6 138.0 138.4 BACKG 331 330 330 330 332 326 329 326 324 323 324 321 SIGMA 9 9 9 9 9 9 9 9 9 8 9 8 NREJ 15 15 12 11 8 19 11 9 14 14 10 14 RADIUS 138.8 139.2 139.6 140.0 140.4 140.9 141.3 141.7 BACKG 320 320 319 316 318 311 313 79 SIGMA 8 8 8 8 8 8 8 2 NREJ 11 13 10 15 12 18 14 1 Starting spot search... Number of spots excluded from possible ice rings: 236 Median spot size is 8 x 6 pixels, mode size is 6 by 5 Total number of spots found:1920 Number rejected as too small on X: 119 Number rejected as too small on Y: 31 Number rejected as too big on X: 28 Number rejected as too big on Y: 9 Number too close (SEPARATION keyword): 143 (currently SEPARATION 0.61 0.51) Number stored as OK: 696 highest resolution is 2.16 Angstrom 99% have resolution less than 2.31 Angstrom Number of spots found in each bin 37 8 19 36 32 10 8 51 135 2 18 31 17 8 4 76 257 0 8 7 1 0 2 217 269 0 4 0 0 0 0 169 132 0 0 0 0 0 0 78 FORMATTED UNKNOWN file opened on unit 10 Logical name: ref-AV01-3342167Aa_1.spt, Filename: ref-AV01-3342167Aa_1.spt 805 spots written for image 1 696 spots written for image 2 A total of 1501 spots were written to file FORMATTED OLD file opened on unit 10 Logical name: ref-AV01-3342167Aa_1.spt, Filename: ref-AV01-3342167Aa_1.spt DPS Indexing using 583 reflections with I >= 20 I/sigma(I) DPS Indexing at Two-theta = 0.00 with 583 reflections (minimum spot separation = 0.62mm. Maximum expected cell edge 293.51, Beam position is 156.93 158.88 Generating direct lattice vectors (This may take some time): |-----------------| .................. Refining 30 direct space vectors: |----------------------------| .............................. selected 9 CELL(start) = 78.671 78.736 105.662 90.02 90.09 72.42 CELL(finis) = 78.600 78.647 105.627 89.97 89.99 72.51 Using 532 out of 583 reflections List of possible Laue groups, sorted on penalty index. The lower the PENALTY, the better No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups 44 999 unrefined hR 186.09 131.73 78.60 79.7 80.3 88.5 H3,H32 (hexagonal settings of R3 and R32) IN CONRHO, BAD ACOS ARG (TARRAY5) -1.3427 140.71 78.65 105.63 90.0 90.0 121.4 R3,R32 (primitive rhombohedral cell) 43 969 unrefined cF 140.71 165.00 140.75 118.7 82.7 118.7 F23,F432,F4132 42 968 unrefined tI 131.66 140.75 78.60 67.0 100.3 111.6 I4,I41,I422,I4122 41 878 unrefined cI 131.67 92.99 131.66 69.3 57.6 69.4 I23,I213,I432,I4132 40 758 unrefined tI 131.67 92.99 131.66 69.3 57.6 69.4 I4,I41,I422,I4122 39 725 unrefined hR 78.60 92.99 341.26 90.0 107.4 126.2 H3,H32 (hexagonal settings of R3 and R32) 105.63 131.65 131.66 41.4 50.0 49.9 R3,R32 (primitive rhombohedral cell) 38 725 unrefined oF 78.60 153.26 225.39 85.9 110.4 101.8 F222 37 696 unrefined tI 78.60 78.65 230.79 76.2 76.2 107.5 I4,I41,I422,I4122 36 696 unrefined oI 78.60 78.65 230.79 103.8 103.8 107.5 I222,I212121 35 667 unrefined oI 92.99 131.67 131.66 57.6 69.3 69.4 I222,I212121 34 667 unrefined tI 131.66 131.67 92.99 69.4 69.3 57.6 I4,I41,I422,I4122 33 666 unrefined oI 78.60 131.66 140.75 68.4 67.0 79.7 I222,I212121 32 637 unrefined hP 78.65 105.63 78.60 90.0 107.5 90.0 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221 P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322 31 635 unrefined mI 92.99 230.79 78.60 103.8 126.2 66.3 C2 (transformed from I2) 30 424 unrefined oF 92.99 126.80 230.79 90.0 113.7 90.0 F222 29 424 unrefined mC 126.80 92.99 131.67 69.4 118.8 90.0 C2 28 423 unrefined mC 153.26 78.60 131.66 79.7 121.4 78.2 C2 27 394 unrefined oC 78.65 225.38 78.60 84.0 107.5 110.4 C222,C2221 26 394 unrefined mC 225.39 78.60 78.65 107.5 96.0 69.6 C2 25 394 unrefined oC 78.60 225.39 78.65 84.0 107.5 110.4 C222,C2221 24 393 unrefined mC 78.60 225.39 78.65 96.0 107.5 69.6 C2 23 393 unrefined mC 78.60 225.39 78.65 96.0 107.5 69.6 C2 22 393 unrefined mC 225.38 78.65 78.60 107.5 96.0 69.6 C2 21 335 unrefined cP 78.60 78.65 105.63 90.0 90.0 107.5 P23,P213,P432,P4232,P4332,P4132 20 335 unrefined hR 126.80 131.65 140.71 111.6 90.0 118.8 H3,H32 (hexagonal settings of R3 and R32) 78.65 78.60 105.63 90.0 90.0 102.9 R3,R32 (primitive rhombohedral cell) 19 335 unrefined mC 131.66 131.73 78.60 79.7 100.3 73.3 C2 18 335 unrefined tP 78.65 105.63 78.60 90.0 107.5 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 17 335 unrefined hR 92.99 131.65 165.07 98.3 90.0 110.7 H3,H32 (hexagonal settings of R3 and R32) 78.65 78.60 105.63 90.0 90.0 77.1 R3,R32 (primitive rhombohedral cell) 16 335 unrefined oC 131.66 131.73 78.60 79.7 100.3 73.3 C222,C2221 15 334 unrefined mC 131.73 131.66 78.60 100.3 100.3 106.7 C2 14 121 0.723 0.98 mC 78.60 153.26 105.63 90.0 90.0 78.2 C2 13 121 0.721 0.98 oC 78.60 153.26 105.63 90.0 90.0 101.8 C222,C2221 12 121 0.551 0.99 mC 153.26 78.60 105.63 90.0 90.0 78.2 C2 11 121 1.137 0.99 hP 78.60 78.65 105.63 90.0 90.0 107.5 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221 P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322 10 92 0.969 0.98 tP 78.60 78.65 105.63 90.0 90.0 107.5 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 9 91 0.977 0.98 mP 78.60 78.65 105.63 90.0 90.0 107.5 P2,P21 8 91 0.958 0.99 mP 78.65 78.60 105.63 90.0 90.0 107.5 P2,P21 7 91 0.974 0.98 oP 78.60 78.65 105.63 90.0 90.0 107.5 P222,P2221,P21212,P212121 6 1 0.114 0.93 mC 92.99 126.80 105.63 90.0 90.0 90.0 C2 5 1 0.113 0.93 oC 92.99 126.80 105.63 90.0 90.0 90.0 C222,C2221 4 1 0.112 0.93 mC 126.80 92.99 105.63 90.0 90.0 90.0 C2 3 0 0.103 0.92 aP 78.60 78.65 105.63 90.0 90.0 72.5 P1 2 0 0.106 0.92 mP 78.60 105.63 78.65 90.0 107.5 90.0 P2,P21 1 0 0.103 0.92 aP 78.60 78.65 105.63 90.0 90.0 107.5 P1 No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups Suggested Solution: 5 C222 penalty: 1 cell: 92.992 126.804 105.627 90.03 90.02 89.96 regularized cell: 92.992 126.804 105.627 90.00 90.00 90.00 Symmetry: oC (C Centred Orthorhombic) Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-6.0/lib/data/syminfo.lib Mosflm has chosen solution 5 from the list automatically. You may want to re-run the autoindexing and choose a solution yourself. The solution and direct beam position will now be refined; reflections which deviate by more than the sigma cutoff from their calculated position will be excluded from the refinement. Refining solution # 5 with C2221 (number 20) symmetry imposed Initial cell (before refinement) is 92.9923 126.8040 105.6273 90.000 90.000 90.000 Using 542 indexed reflections (out of 583 spots used in indexing, {delta(XY) <= 2.5 sigma}), final sd in spot positions is 0.11mm and in phi 0.42 degrees Refined cell parameters 93.00 126.76 105.63 90.00 90.00 90.00 Beam coordinates of 156.93 158.88 have been refined to 156.92 158.80 This is a shift of 0.07mm or 0.033 times the minimum spot separation of ca 2.22mm. Final cell (after refinement) is 92.9987 126.7649 105.6320 90.000 90.000 90.000 FORMATTED UNKNOWN file opened on unit 12 Logical name: autoindex.mat, Filename: autoindex.mat image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_002.img **** Information **** **** Information **** **** Information **** The cell derived from autoindexing will override that given on the CELL keyword. To force the program to use the input cell, add the keyword KEEP. eg: CELL KEEP 74.2 74.2 35.1 90 90 90 **** WARNING **** Because input wavelength ( 0.9795) is not CuKa (1.5418) or Mo (0.7107), source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords. Title for MTZ and GENERATE Files (TITLE): . Crystal identifier (IDENT): ref-AV01-3342167Aa_1 Warning: No PROTEIN NAME given by KeyWord PNAME It has been set to "Unspecified" Warning: No CRYSTAL NAME given by KeyWord XNAME It has been set to "ref-AV01-3342167Aa_1" Warning: No DATASET NAME given by KeyWord DNAME It has been set to "Unspecified" PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000 MAX. No. of Active Reflections= 55 Beam divergence refinement Beam divergence refinement Refining DIV with stepsize 0.01 Degrees Divergence 0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800 Divergence 1.900 2.000 No gained 0 338 387 356 360 391 369 379 388 375 383 7 0 6 10 6 4 5 2 No gained 6 2 Total intensity 60127 69378 76225 82573 87402 90771 94942 96441 97509 98822 99991 99999 99999 99977 99946 99547 99533 99490 99490 Total intensity 99482 99461 SD of intensity 662 675 691 705 721 723 729 729 729 730 730 730 730 730 730 730 730 730 730 SD of intensity 730 730 The mosaicity has been estimated as ---> 0.60 <--- for this image only; This value can be used cautiously as an initial estimate. Storing space group from DPS autoindexing: C2221 number 20 Storing space group from DPS autoindexing: C2221 number 20 ===> BEST OFF ===> xgui on New gui stuff switched on ===> image 1 ===> go Start and end phi values for image 1 from image header are 0.00 and 1.00 degrees. Oscillation axis set as PHI from image header ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** Input beam coordinates 156.92mm 158.80mm DO NOT agree with those calculated from the image header ( 156.93mm 158.88mm) Warning - resetting the iseg value to zero because gui_switch = .true. image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_001.img NeoCtrl => ===> predict_spots Predicted 414 fulls 4652 partials 42 wides 10 overlaps NeoCtrl => ===> create_image binary true filename ref-AV01-3342167Aa_1_001.jpg Output filename set to ref-AV01-3342167Aa_1_001.jpg Beam centre = 156.923599 158.803085 Calling write_jpeg with arg list: trc = 0 0 blc = 3072 3072 factor = 1 write_jpeg -1 3072 3072 0 0 1 0 0 3072 3072 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.915 Returning from CREATE_IMAGE after 2.173 seconds NeoCtrl => ===> create_image prediction on binary true filename ref-AV01-3342167Aa_1_001_pred.jpg Output filename set to ref-AV01-3342167Aa_1_001_pred.jpg Beam centre = 156.923599 158.803085 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 7 6 zoom is 1 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 2.290 seconds NeoCtrl => ===> create_image zoom -4 binary true filename ref-AV01-3342167Aa_1_001_small.jpg Output filename set to ref-AV01-3342167Aa_1_001_small.jpg Beam centre = 156.923599 158.803085 Calling write_jpeg with arg list: trc = 0 0 blc = 3072 3072 factor = -4 write_jpeg -1 3072 3072 0 0 -4 0 0 3072 3072 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.055 Returning from CREATE_IMAGE after 0.288 seconds NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-AV01-3342167Aa_1_001_pred_small.jpg Output filename set to ref-AV01-3342167Aa_1_001_pred_small.jpg Beam centre = 156.923599 158.803085 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 1 1 zoom is -4 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 0.311 seconds NeoCtrl => ===> return New gui stuff switched off ===> xgui off New gui stuff switched off ===> xgui on New gui stuff switched on ===> image 2 ===> go Start and end phi values for image 2 from image header are 90.00 and 91.00 degrees. Oscillation axis set as PHI from image header ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** Input beam coordinates 156.92mm 158.80mm DO NOT agree with those calculated from the image header ( 156.93mm 158.88mm) Warning - resetting the iseg value to zero because gui_switch = .true. image FILENAME: /scisoft/users/svensson/tmp/dataBenchmark/AV01-3342167Aa_1/ref-AV01-3342167Aa_1_002.img NeoCtrl => ===> predict_spots Predicted 434 fulls 4617 partials 32 wides 16 overlaps NeoCtrl => ===> create_image binary true filename ref-AV01-3342167Aa_1_002.jpg Output filename set to ref-AV01-3342167Aa_1_002.jpg binary true filename ref-AV01-3342167Aa_1_001_pred_small.jpg Beam centre = 156.923599 158.803085 Calling write_jpeg with arg list: trc = 0 0 blc = 3072 3072 factor = 1 write_jpeg -1 3072 3072 0 0 1 0 0 3072 3072 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.913 Returning from CREATE_IMAGE after 2.171 seconds NeoCtrl => ===> create_image prediction on binary true filename ref-AV01-3342167Aa_1_002_pred.jpg Output filename set to ref-AV01-3342167Aa_1_002_pred.jpg filename ref-AV01-3342167Aa_1_001_pred_small.jpg Beam centre = 156.923599 158.803085 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 7 6 zoom is 1 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 2.293 seconds NeoCtrl => ===> create_image zoom -4 binary true filename ref-AV01-3342167Aa_1_002_small.jpg Output filename set to ref-AV01-3342167Aa_1_002_small.jpg filename ref-AV01-3342167Aa_1_001_pred_small.jpg Beam centre = 156.923599 158.803085 Calling write_jpeg with arg list: trc = 0 0 blc = 3072 3072 factor = -4 write_jpeg -1 3072 3072 0 0 -4 0 0 3072 3072 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.055 Returning from CREATE_IMAGE after 0.286 seconds NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-AV01-3342167Aa_1_002_pred_small.jpg Output filename set to ref-AV01-3342167Aa_1_002_pred_small.jpg Beam centre = 156.923599 158.803085 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 1 1 zoom is -4 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 0.313 seconds NeoCtrl => ===> return New gui stuff switched off ===> xgui off New gui stuff switched off *********** END OF PROCESSING *****************