***** IDXREF ***** (VERSION Nov 1, 2016 BUILT=20161205) 19-Dec-2016 INPUT PARAMETER VALUES ---------------------- NAME_TEMPLATE_OF_DATA_FRAMES=/home/teach02/Data_Protein_FG/2014/Jaromir-Marek/160112-Vyuka-Lyso-HD-/Images/160112-Vyuka-Lyso-HD-1???.img SMV STARTING_ANGLE= -72.8000 STARTING_FRAME= 1 NX= 1042 NY= 1042 QX= 0.090000 QY= 0.090000 DIRECTION_OF_DETECTOR_X-AXIS= -0.95630 0.00000 0.29237 DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000 DETECTOR_DISTANCE= -43.000 ORGX= 523.32 ORGY= 523.14 NUMBER OF DETECTOR SEGMENTS 1 SEGMENT= 1 1042 1 1042 ! x1,x2,y1,y2 (pixel units) SEGMENT_ORGX= 0.00 SEGMENT_ORGY= 0.00 SEGMENT_DISTANCE= 0.00 DIRECTION_OF_SEGMENT_X-AXIS= 1.000000 0.000000 0.000000 DIRECTION_OF_SEGMENT_Y-AXIS= 0.000000 1.000000 0.000000 X-RAY_WAVELENGTH= 1.541870 INCIDENT_BEAM_DIRECTION= 0.000000 0.000000 1.000000 ROTATION_AXIS= 0.000000 1.000000 0.000000 OSCILLATION_RANGE= 0.2000 INDEX_MAGNITUDE= 8 INDEX_ERROR= 0.050 INDEX_QUALITY= 0.80 SEPMIN= 6.00 CLUSTER_RADIUS= 3 MAXIMUM_ERROR_OF_SPOT_POSITION= 3.0 MAXIMUM_ERROR_OF_SPINDLE_POSITION= 2.0 MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.50 TRUSTED_REGION= 0.00 1.42 INCLUDE_RESOLUTION_RANGE= 41.000 1.332 SPACE GROUP AND CELL PARAMETERS ARE UNKNOWN AUTOINDEXING IS BASED ON 49857 OUT OF 49857 SPOTS WITHIN THE ALLOWED RESOLUTION RANGES OF THE FOLLOWING DATA IMAGES: SPOT_RANGE= 1 600 ***** DETERMINATION OF THE RECIPROCAL LATTICE BASIS ****** NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 201 MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels) 3 MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel) 6.0 MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS 0.8145E-02 OBSERVED BASIS CELL VOLUME 0.2330E+06 DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS 3 # COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH 1 -0.0002828 0.0101727-0.0075745 0.0126861 78.83 2 -0.0125335-0.0011688-0.0010983 0.0126357 79.14 3 -0.0033011 0.0158453 0.0213297 0.0267755 37.35 CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS # COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES 1 -0.0002801 0.0101559-0.0075496 2561. 1.00 -0.00 0.00 2 0.0125045 0.0012291 0.0011070 2473. 0.00 -1.00 0.00 3 0.0122467 0.0113086-0.0064675 2414. 1.00 -1.00 -0.00 4 0.0128141-0.0090006 0.0086748 2394. -1.00 -1.00 0.00 5 -0.0005734 0.0203496-0.0151192 2335. 2.00 0.00 0.00 6 -0.0035752 0.0260068 0.0137387 2262. 1.00 -0.00 1.00 7 -0.0032826 0.0158292 0.0213401 2253. -0.00 -0.00 1.00 8 0.0130876-0.0191721 0.0162234 2236. -2.00 -1.00 -0.00 9 0.0092565 0.0170094 0.0224319 2229. -0.00 -1.00 1.00 10 0.0119481 0.0215145-0.0140385 2223. 2.00 -1.00 0.00 11 0.0029986-0.0056583-0.0289053 2215. 1.00 0.00 -1.00 12 0.0089465 0.0271654 0.0148407 2204. 1.00 -1.00 1.00 13 -0.0038526 0.0361893 0.0061794 2197. 2.00 -0.00 1.00 14 -0.0095351-0.0068275-0.0299794 2158. 1.00 1.00 -1.00 15 0.0086569 0.0373514 0.0072598 2157. 2.00 -1.00 1.00 16 -0.0008584 0.0305217-0.0227157 2154. 3.00 0.00 0.00 17 0.0247678 0.0125157-0.0053736 2117. 1.00 -2.00 0.00 18 -0.0158291 0.0146679 0.0202538 2113. -0.00 1.00 1.00 19 0.0253310-0.0078272 0.0097826 2107. -1.00 -2.00 0.00 20 -0.0041384 0.0463307-0.0014087 2107. 3.00 -0.00 1.00 21 0.0250646 0.0023699 0.0022151 2098. 0.00 -2.00 0.00 22 -0.0161059 0.0248381 0.0126533 2092. 1.00 1.00 1.00 23 -0.0155309 0.0044876 0.0278375 2092. -1.00 1.00 1.00 24 0.0026971 0.0044904-0.0364923 2090. 2.00 0.00 -1.00 25 0.0217493 0.0181634 0.0234873 2086. 0.00 -2.00 1.00 26 -0.0133875 0.0293793-0.0237768 2055. 3.00 1.00 0.00 27 0.0083786 0.0475320-0.0002881 2054. 3.00 -1.00 1.00 28 0.0116669 0.0316676-0.0216218 2051. 3.00 -1.00 -0.00 29 0.0256174-0.0180011 0.0173537 2046. -2.00 -2.00 0.00 30 -0.0163801 0.0350323 0.0050722 2045. 2.00 1.00 1.00 31 0.0220477 0.0079987 0.0310540 2040. -1.00 -2.00 1.00 32 0.0214833 0.0283455 0.0159458 2033. 1.00 -2.00 1.00 33 0.0245002 0.0226656-0.0129704 2001. 2.00 -2.00 -0.00 34 0.0152217 0.0056540-0.0354069 1995. 2.00 -1.00 -1.00 35 -0.0044297 0.0565150-0.0089652 1972. 4.00 -0.00 1.00 36 -0.0166721 0.0451890-0.0024990 1959. 3.00 1.00 1.00 37 0.0211920 0.0385313 0.0083711 1954. 2.00 -2.00 1.00 38 -0.0223285 0.0021676-0.0386152 1933. 2.00 2.00 -1.00 39 -0.0011458 0.0406956-0.0302758 1930. 4.00 0.00 0.00 40 -0.0024303-0.0146682 0.0440529 1913. -3.00 -0.00 1.00 41 -0.0259029 0.0281950-0.0248921 1913. 3.00 2.00 0.00 42 0.0080851 0.0577003-0.0078628 1907. 4.00 -1.00 1.00 43 0.0100952-0.0134980 0.0451254 1904. -3.00 -1.00 1.00 44 0.0113929 0.0418512-0.0291745 1903. 4.00 -1.00 0.00 45 0.0136719-0.0395334 0.0313504 1894. -4.00 -1.00 -0.00 46 0.0208977 0.0487116 0.0008217 1885. 3.00 -2.00 1.00 47 0.0242126 0.0328301-0.0205309 1878. 3.00 -2.00 -0.00 48 -0.0149370-0.0158345 0.0430007 1870. -3.00 1.00 1.00 49 0.0283644-0.0135105-0.0191360 1855. -0.00 -2.00 -1.00 50 0.0342863 0.0193487 0.0245892 1854. 0.00 -3.00 1.00 51 -0.0286441 0.0236821 0.0115263 1849. 1.00 2.00 1.00 52 0.0339854 0.0295042 0.0170583 1844. 1.00 -3.00 1.00 53 0.0280729-0.0033196-0.0267384 1841. 1.00 -2.00 -1.00 54 -0.0169605 0.0553820-0.0100686 1839. 4.00 1.00 1.00 55 0.0345639 0.0091688 0.0321393 1831. -1.00 -3.00 1.00 56 0.0289220-0.0338702-0.0039659 1828. -2.00 -2.00 -1.00 57 0.0375923 0.0035350 0.0033045 1818. 0.00 -3.00 0.00 58 -0.0071508 0.0520286 0.0275172 1818. 2.00 -0.00 2.00 59 0.0378786-0.0066422 0.0108888 1815. -1.00 -3.00 0.00 60 0.0053675 0.0532145 0.0286083 1814. 2.00 -1.00 2.00 PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES) 37.35 78.83 79.14 90.01 90.10 90.09 # COORDINATES OF REC. BASIS VECTOR REDUCED CELL INDICES 1 -0.0002828 0.0101727-0.0075745 0.00 -1.00 0.00 2 -0.0125335-0.0011688-0.0010983 -0.00 0.00 1.00 3 -0.0033011 0.0158453 0.0213297 -1.00 -0.00 -0.00 ***** RESULTS FROM LOCAL INDEXING OF 3000 OBSERVED SPOTS ***** MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED 8 MAXIMUM ALLOWED DEVIATION FROM INTEGERAL INDICES 0.050 MIMINUM QUALITY OF INDICES FOR EACH SPOT IN A SUBTREE 0.80 QUALITY OF INDICES REQUIRED TO INCLUDE SECOND SUBTREE 0.00 NUMBER OF SUBTREES 66 SUBTREE POPULATION 1 2927 2 2 3 2 4 2 5 2 6 2 7 2 8 2 9 2 10 1 NUMBER OF ACCEPTED SPOTS FROM LARGEST SUBTREE 2927 ***** SELECTION OF THE INDEX ORIGIN OF THE REFLECTIONS ***** The origin of the reflection indices determined so far is 0,0,0 by default which is usually correct. In certain critical cases it may happen that this automatic choice is wrong which leads to misindexing of the reflections by a constant offset. You may replace the default by specifying INDEX_ORIGIN= h k l in the input file "XDS.INP" and rerun the IDXREF step. Below you find a list of possible alternatives together with a measure of their likelihood. QUALITY small values mean a high likelihood for this offset DELTA is the angle between given and refined beam direction XD,YD computed direct beam position (pixels) on detector given beam position (pixel): 669.39 523.14 X,Y,Z computed coordinates of the direct beam wave vector DH,DK,DL mean absolute difference between observed and fitted indices INDEX_ QUALITY DELTA XD YD X Y Z DH DK DL ORIGIN 0 0 0 1.7 0.2 670.6 524.8 -0.0015 0.0021 0.6486 0.01 0.03 0.03 0 0 1 71.1 0.8 662.8 525.6 0.0082 0.0033 0.6485 0.14 0.24 0.39 SELECTED: INDEX_ORIGIN= 0 0 0 ***** REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 ***** REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 2924 INDEXED SPOTS REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL STANDARD DEVIATION OF SPOT POSITION (PIXELS) 0.68 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 1.00 SPACE GROUP NUMBER 1 UNIT CELL PARAMETERS 37.278 78.801 79.070 89.834 90.293 90.000 REC. CELL PARAMETERS 0.026826 0.012690 0.012647 90.166 89.707 90.001 COORDINATES OF UNIT CELL A-AXIS 4.724 -22.124 -29.628 COORDINATES OF UNIT CELL B-AXIS 1.681 -62.997 47.309 COORDINATES OF UNIT CELL C-AXIS -78.459 -7.298 -6.550 CRYSTAL MOSAICITY (DEGREES) 0.227 LAB COORDINATES OF ROTATION AXIS -0.004160 0.999987 -0.002857 DIRECT BEAM COORDINATES (REC. ANGSTROEM) -0.001506 0.002138 0.648558 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 670.60 524.79 DETECTOR ORIGIN (PIXELS) AT 523.32 523.14 CRYSTAL TO DETECTOR DISTANCE (mm) -43.00 LAB COORDINATES OF DETECTOR X-AXIS -0.956305 0.000000 0.292372 LAB COORDINATES OF DETECTOR Y-AXIS 0.000000 1.000000 0.000000 ***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP # 1 ***** 36444 OUT OF 49857 SPOTS INDEXED. 2792 REJECTED REFLECTIONS (REASON: OVERLAP) 10621 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION) EXPECTED ERROR IN SPINDLE POSITION 0.339 DEGREES EXPECTED ERROR IN DETECTOR POSITION 1.30 PIXELS ***** DIFFRACTION PARAMETERS USED AT START OF INTEGRATION ***** REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 36444 INDEXED SPOTS REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL STANDARD DEVIATION OF SPOT POSITION (PIXELS) 1.29 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 0.34 SPACE GROUP NUMBER 1 UNIT CELL PARAMETERS 37.195 78.831 79.106 90.078 90.140 90.082 REC. CELL PARAMETERS 0.026885 0.012685 0.012641 89.922 89.859 89.918 COORDINATES OF UNIT CELL A-AXIS 4.643 -21.979 -29.645 COORDINATES OF UNIT CELL B-AXIS 1.798 -63.106 47.209 COORDINATES OF UNIT CELL C-AXIS -78.493 -7.151 -6.749 CRYSTAL MOSAICITY (DEGREES) 0.227 LAB COORDINATES OF ROTATION AXIS -0.000824 0.999995 -0.003007 DIRECT BEAM COORDINATES (REC. ANGSTROEM) -0.000803 0.001860 0.648560 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 670.03 524.57 DETECTOR ORIGIN (PIXELS) AT 523.32 523.14 CRYSTAL TO DETECTOR DISTANCE (mm) -43.00 LAB COORDINATES OF DETECTOR X-AXIS -0.956305 0.000000 0.292372 LAB COORDINATES OF DETECTOR Y-AXIS 0.000000 1.000000 0.000000 *********** DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE *********** The CHARACTER OF A LATTICE is defined by the metrical parameters of its reduced cell as described in the INTERNATIONAL TABLES FOR CRYSTALLOGRAPHY Volume A, p. 746 (KLUWER ACADEMIC PUBLISHERS, DORDRECHT/BOSTON/LONDON, 1989). Note that more than one lattice character may have the same BRAVAIS LATTICE. A lattice character is marked "*" to indicate a lattice consistent with the observed locations of the diffraction spots. These marked lattices must have low values for the QUALITY OF FIT and their implicated UNIT CELL CONSTANTS should not violate the ideal values by more than MAXIMUM_ALLOWED_CELL_AXIS_RELATIVE_ERROR= 0.03 MAXIMUM_ALLOWED_CELL_ANGLE_ERROR= 3.0 (Degrees) LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) CHARACTER LATTICE OF FIT a b c alpha beta gamma * 44 aP 0.0 37.2 78.8 79.1 90.1 90.1 90.1 * 31 aP 1.5 37.2 78.8 79.1 89.9 89.9 90.1 * 35 mP 4.1 78.8 37.2 79.1 90.1 90.1 90.1 * 33 mP 4.6 37.2 78.8 79.1 90.1 90.1 90.1 * 34 mP 5.7 37.2 79.1 78.8 90.1 90.1 90.1 * 32 oP 7.2 37.2 78.8 79.1 90.1 90.1 90.1 * 25 mC 16.8 111.6 111.8 37.2 90.0 90.2 89.8 * 23 oC 19.8 111.6 111.8 37.2 90.0 90.2 89.8 * 20 mC 19.9 111.6 111.8 37.2 90.0 90.2 90.2 * 21 tP 22.9 78.8 79.1 37.2 90.1 90.1 90.1 37 mC 248.9 162.4 37.2 78.8 90.1 90.1 76.9 39 mC 251.1 161.9 37.2 79.1 90.1 90.1 76.8 36 oC 252.0 37.2 162.4 78.8 89.9 90.1 103.1 28 mC 252.7 37.2 162.4 78.8 89.9 89.9 76.9 38 oC 254.2 37.2 161.9 79.1 89.9 90.1 103.2 29 mC 254.8 37.2 162.0 79.1 90.0 90.1 76.6 27 mC 500.4 162.0 37.2 111.6 90.2 133.4 76.6 19 oI 516.1 37.2 111.6 117.8 89.9 71.6 90.2 26 oF 622.3 37.2 162.0 162.4 86.9 103.1 103.4 18 tI 638.0 111.6 117.8 37.2 71.6 89.8 90.1 1 cF 999.0 117.7 117.5 117.8 95.9 95.6 143.1 2 hR 999.0 87.2 87.3 117.8 118.4 61.9 100.5 3 cP 999.0 37.2 78.8 79.1 90.1 90.1 90.1 5 cI 999.0 87.3 87.1 111.6 50.4 50.2 79.7 4 hR 999.0 87.2 87.5 117.5 118.3 61.9 100.5 6 tI 999.0 111.6 87.3 87.1 79.7 50.4 50.2 7 tI 999.0 87.3 87.1 111.6 50.4 50.2 79.7 8 oI 999.0 87.1 87.3 111.6 50.2 50.4 79.7 9 hR 999.0 37.2 87.2 252.6 102.7 98.3 115.3 10 mC 999.0 87.1 87.2 79.1 90.0 90.1 129.5 11 tP 999.0 37.2 78.8 79.1 90.1 90.1 90.1 12 hP 999.0 37.2 78.8 79.1 90.1 90.1 90.1 13 oC 999.0 87.1 87.2 79.1 90.0 90.1 50.5 15 tI 999.0 37.2 78.8 180.4 64.2 78.3 90.1 16 oF 999.0 87.1 87.2 180.4 107.9 118.7 50.5 14 mC 999.0 87.1 87.2 79.1 90.0 90.1 50.5 17 mC 999.0 87.2 87.1 87.3 79.7 100.5 50.5 22 hP 999.0 78.8 79.1 37.2 90.1 90.1 90.1 24 hR 999.0 180.1 111.8 37.2 90.0 78.2 107.9 30 mC 999.0 78.8 176.7 37.2 89.8 89.9 63.6 40 oC 999.0 78.8 176.7 37.2 89.8 90.1 116.4 42 oI 999.0 37.2 78.8 180.4 115.8 101.7 90.1 41 mC 999.0 176.7 78.8 37.2 90.1 90.2 63.6 43 mI 999.0 87.1 180.4 78.8 115.8 154.7 61.3 For protein crystals the possible space group numbers corresponding to each Bravais-type are given below for your convenience. Note, that reflection integration is based only on orientation and metric of the lattice. It does not require knowledge of the correct space group! Thus, if no such information is provided by the user in XDS.INP, reflections are integrated assuming a triclinic reduced cell lattice; the space group is assigned automatically or by the user in the last step (CORRECT) when integrated intensities are available. ****** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY ****** BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS TYPE [SPACE GROUP NUMBER,SYMBOL] aP [1,P1] mP [3,P2] [4,P2(1)] mC,mI [5,C2] oP [16,P222] [17,P222(1)] [18,P2(1)2(1)2] [19,P2(1)2(1)2(1)] oC [21,C222] [20,C222(1)] oF [22,F222] oI [23,I222] [24,I2(1)2(1)2(1)] tP [75,P4] [76,P4(1)] [77,P4(2)] [78,P4(3)] [89,P422] [90,P42(1)2] [91,P4(1)22] [92,P4(1)2(1)2] [93,P4(2)22] [94,P4(2)2(1)2] [95,P4(3)22] [96,P4(3)2(1)2] tI [79,I4] [80,I4(1)] [97,I422] [98,I4(1)22] hP [143,P3] [144,P3(1)] [145,P3(2)] [149,P312] [150,P321] [151,P3(1)12] [152,P3(1)21] [153,P3(2)12] [154,P3(2)21] [168,P6] [169,P6(1)] [170,P6(5)] [171,P6(2)] [172,P6(4)] [173,P6(3)] [177,P622] [178,P6(1)22] [179,P6(5)22] [180,P6(2)22] [181,P6(4)22] [182,P6(3)22] hR [146,R3] [155,R32] cP [195,P23] [198,P2(1)3] [207,P432] [208,P4(2)32] [212,P4(3)32] [213,P4(1)32] cF [196,F23] [209,F432] [210,F4(1)32] cI [197,I23] [199,I2(1)3] [211,I432] [214,I4(1)32] Maximum oscillation range to prevent angular overlap at high resolution limit assuming zero (!) mosaicity. Maximum oscillation range High resolution limit (degrees) (Angstrom) 2.91 4.00 2.18 3.00 1.45 2.00 0.73 1.00 cpu time used 16.6 sec elapsed wall-clock time 6.7 sec