------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by the Regents of the University of California at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- SOLVE --- * * * * Automated structure solution for MAD and MIR * * * * Please type "solvehelp" for on-line help * * or see "http://solve.lanl.gov" * ******************************************************* (version 2.09 of 25-Apr-2005 / Size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" Dataset title: SOLVE 30-Apr-05 Enter "HELP", commands, or keywords > The date today is 30-apr-05. Your license expires on 15-dec-96. >! mad.script: Command file to read in raw MAD data, scale, analyze and solve it >title 3-wavelength MAD dataset ! a title for this dataset overall title is: 3-wavelength MAD dataset ! a title for this dataset >@solve.setup ! get our standard information read in Opened formatted file: solve.setup Switching to command input from this file... >SYMFILE /usr/local/lib/solve/i4.sym ! symmetry file for this space group symfile set to: /usr/local/lib/solve/i4.sym >! (most common space groups should be in >! this directory) >CELL 113.949 113.949 32.474 90.000 90.000 90.00 Cell = 113.948997 113.948997 32.473999 90. 90. 90. >RESOLUTION 2.1 20 ! Resolution limits in A Resolution limits will be 2.0999999 to 20. A > Closed command file: solve.setup End of command input from this file >logfile mad.logfile ! write out most information to this file. Log file set to: mad.logfile LOG: write output to a log file or change log file name or stop writing output to log file. Opened formatted file: mad.logfile >! summary info will be written to "solve.prt" > >checksolve ! compare solutions to the one input below Input heavy atom parameters will be used to compare to solutions obtained by solve routines. > >mad_atom se ! the anomalously scattering atom is selenium Using values for atom Se for A1 A2 A3 A4 B1 B2 B3 B4 C from International tables for this MAD experiment. "A" values for MAD data are: 17.0006008 5.81960011 3.97309995 4.35430002 "B" values for MAD data are: 2.40980005 0.272599995 15.2371998 43.8162994 "C" value for MAD data is: 2.84089994 > >refscattfactors ! do not refine scattering factors (you can if Refining values of of fprime and fdoubleprime >! you want as long as the data is good) > >readdenzo [ data is from scalepack. Note: for best results data will be read in using DENZO format >[ use "no merge original index" in scalepack >[ Alternative to "readdenzo" is "readformatted"] > >unmerged [ data have not been merged to the asymmetric un data is assumed to be unmerged >[ Alternative to "unmerged" is "premerged"] > > >lambda 1 ! info on wavelength #1 follows Considering set or derivative 1 >label Wavelength # 1 ! a label for this wavelength label( 1) = Wavelength # 1 ! a label for this wavelength >rawmadfile p9_se_w1.sca ! datafile for lambda 1 containing raw Intensitie MAD dataset 1 for lambda 1 is: p9_se_w1.sca > > >! You can have more than >! one datafile per wavelength but you should put >! matching I+/I- data in one datafile > >! All datafiles for all wavelengths >! must be in the same format > >wavelength 0.9790 ! wavelength value wavelength( 1) = 0.978999972 >fprimv_mad -8.52 ! f' value at this wavelength f-prime value for MAD wavelength lambda 1 is: -8.52000046 >fprprv_mad 2.84 ! f" value at this wavelength f" value for MAD wavelength lambda 1 is: 2.83999991 > >! read in coordinates just to refer all the >! solutions to the same origin as used in the pdb >! file. (Not used to find solutions). >atomname se atomname( 1) = Se >xyz 0.9770 0.2439 1.1071 xyz( 1)= 0.976999998 0.243900001 1.10710001 >xyz 1.1877 0.2625 0.9833 atomname( 2) = Se xyz( 2)= 1.18770003 0.262499988 0.983299971 >xyz 1.1669 0.2943 0.9205 atomname( 3) = Se xyz( 3)= 1.16690004 0.29429999 0.92049998 >xyz 1.1142 0.1801 0.5117 atomname( 4) = Se xyz( 4)= 1.1142 0.180099994 0.511699975 > >lambda 2 Number of wavelengths or derivatives set to: 2 Considering set or derivative 2 >rawmadfile p9_se_w2.sca MAD dataset 1 for lambda 2 is: p9_se_w2.sca >wavelength 0.9788 wavelength( 2) = 0.978799999 >fprimv_mad -8.0 f-prime value for MAD wavelength lambda 2 is: -8. >fprprv_mad 4.0 f" value for MAD wavelength lambda 2 is: 4. > >lambda 3 Number of wavelengths or derivatives set to: 3 Considering set or derivative 3 >rawmadfile p9_se_w4.sca MAD dataset 1 for lambda 3 is: p9_se_w4.sca >wavelength 0.9600 wavelength( 3) = 0.959999979 >fprimv_mad -3.16 f-prime value for MAD wavelength lambda 3 is: -3.16000009 >fprprv_mad 3.69 f" value for MAD wavelength lambda 3 is: 3.69000006 > >nres 147 [approx # of residues of protein in asymmetric unit] nres set to: 147 >nanomalous 3 [approx # of anomalously scattering atoms in a.u.] nanomalous set to: 3 > > >SCALE_MAD ! read in and localscale the data Output summary will be written to solve.prt Opened formatted file: solve.prt FOR THIS SPACE GROUP THERE ARE 2 GROUPS OF 4 EQUIVALENT POSITIONS. RELATED BY CENTERING. ALL EQUIV POSITIONS IN GROUP 2 ARE RELATED TO THOSE IN GROUP 1 BY THE TRANSLATION: ( 0.500, 0.500, 0.500) THE FUNDAMENTAL SET OF 4 ROTATION MATRICES AND TRANSLATION VECTORS FOR THIS SPACE GROUP IS: ROTATION MATRIX TRANS ROTATION MATRIX TRANS 1.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0.000 0.000 -1.000 0.000 0.000 0.000 1.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0.000 Opened formatted file: /usr/local/lib/solve/i4.sym Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /usr/local/lib/solve/syminfo.lib Resolution range will be from 2.0999999 to 20. Setting up arrays...this may take some time for large unit cells.... SETGRID: set fft and patterson grids (This can take some time for big unit cells) Setting fft grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:27:17 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 SEC STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 0 SEC STATUS The fft containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of map requires 221232 of 1825201 points in unit cell. The fft containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 190 192 0 96 192 0 23 48 The EZD map file containing the output map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 190 0 96 0 23 Setting patt grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:27:20 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 SEC STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 3 SEC STATUS The patterson containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of Patterson map requires 230450 of 1825201 points in unit cell. The patterson containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: PATTGRID 0 190 192 0 96 192 0 24 48 *************************************************************************** SOLVE STATUS 30-apr-05 11:27:22 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 7 SEC STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 5 SEC STATUS This unit cell is not chiral *************************************************************************** SOLVE STATUS 30-apr-05 11:27:22 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 7 SEC STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 0 SEC STATUS Output summary will be written to solve.prt Reading in total of 3 MAD datafiles This is MAD dataset # 1 Opened binary file: scratch_all.drg File 1 with intensity data for lambda 1. This is the 1 th dataset for this wavelength READFILE: read in a file to .drg format Assuming after header with 2*ns+1 lines, this data file contains: h k l hh kk ll i i i i Intensity sigma, not merged (may be multiple observations) and h k l, -h -k -l can both appear Opened formatted file: p9_se_w1.sca 4 i41 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 0 -1 0 1 0 0 0 0 1 0 6 3 0 1 0 -1 0 0 0 0 1 0 6 3 0 0 -4 0 0 4 7 2 1 1 96061.5 10961.7 First 9 lines of data files are assumed to be header and will be ignored. Dorgbn-style file with this data will be: lambda_1_1_i.drg Opened binary file: lambda_1_1_i.drg Total of 113816 records read, with 68289 accepted in the resolution range of 2.0999999 to 20. Resolution range will be from 2.0999999 to 20. Please enter input dorgbn-style file> Opened binary file: lambda_1_1_i.drg This file has 2 columns of data. They are: Col: 0:lambda_1_1_i.drg Col: 1:lambda_1_1_i.drg I obs Col: 2:lambda_1_1_i.drg Sig I obs How many records would you like to see? (if you type "-1" you can enter a particular reflection to look at) > 10records will be listed. H K L Resol Col1 Col2 Col3 Col4 Col5 (etc) 0 0 -4 8.12 96061.50 10961.70 0 0 8 4.06 30367.90 3168.10 0 0 -8 4.06 40557.10 4456.50 0 0 12 2.71 89643.20 9790.10 1 0 3 10.78 14359.40 1832.80 -1 0 3 10.78 15403.50 1741.60 0 -1 3 10.78 15158.00 1720.30 0 1 3 10.78 15210.40 1632.10 -1 0 -3 10.78 12722.70 1362.50 1 0 -3 10.78 12025.40 1297.40 Converting this data from I to F. MATH: Perform simple math operations on dorgbn files. Operation to be performed is :i_to_f Input file > Opened binary file: lambda_1_1_i.drg Input data col 0: lambda_1_1_i.drg Input data col 1: lambda_1_1_i.drg I obs Input data col 2: lambda_1_1_i.drg Sig I obs Output file > Opened binary file: lambda_1_1_f.drg Resolution range will be from 2.0999999 to 20. Number of records written: 65734, number with no data: 2555 number out of resolution range 0 Separating out anomalous pairs. GETMIRROR Maximize overlap of F+ and F- by choosing the right symmetry equivalent for F-. Input file = Resolution range will be from 2.0999999 to 20. Opened binary file: lambda_1_1_f.drg Col: 0: Col: 1: F from I_TO_F Wavelength # 1 ! a label for th Col: 2: SIGMA of F Wavelength # 1 ! a label for th Deriv F from column: 1: F from I_TO_F Wavelength # 1 Sig of Der F from col: 2: SIGMA of F Wavelength # 1 A total of 65185 unique derivative data were found # of F+/F- pairs found using equivalence # 1 is: 22752 # of F+/F- pairs found using equivalence # 2 is: 20885 # of F+/F- pairs found using equivalence # 3 is: 20196 # of F+/F- pairs found using equivalence # 4 is: 20928 Best equivalance (nequiv_separate) = 1 MATH: Perform simple math operations on dorgbn files. Operation to be performed is :separateano Input file > Opened binary file: lambda_1_1_f.drg Input data col 0: Input data col 1: F from I_TO_F Wavelength # 1 ! a label for this wavelength Input data col 2: SIGMA of F Wavelength # 1 ! a label for this wavelength Opened binary file: lambda_1_1_fp.drg Output F+,sig+ written to lambda_1_1_fp.drg Opened binary file: lambda_1_1_fm.drg Output F-,sig- written to lambda_1_1_fm.drg Output HKL for F- will be inverted: If a reflection with indices HKL is read in and determined to be an F-, it will be written out as -H -K -L. Resolution range will be from 2.0999999 to 20. Total records with F+: 39694 Total records with F-: 26040 Number of records written: 65734, number with no data: 0 number out of resolution range 0 Merging data in first file to use as basis for overall scaling of everything MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: scratch_1.mrg How many input files will there be ? > There will be 2 input files What is file name for first file to be merged? > Opened binary file: lambda_1_1_fp.drg Columns 1, 2 assumed to be f,sig. Col: 0 SIGMA of F Wavelength # 1 ! a label for this wavelength Col: 1 F+ from separateano Wavelength # 1 ! a label for this wavelength Col: 2 sig of F+ Wavelength # 1 ! a label for this wavelength Enter next file name : Opened binary file: lambda_1_1_fm.drg Columns 1, 2 assumed to be f,sig. analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.497793347 This will be applied to all sigmas Summary of data: Reflections read : 65734 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 65734 Rejected : |obs-mean|> 4 Sig: 825 Chisqr > 20 : 0 Unique hkl : 12272 overall r-factor on F: 4.6 % overall r-factor on I: 6.9 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 4204 801 4.2 7.4 0.039 2 4.2 4093 763 3.3 5.7 0.038 3 3.7 4044 749 3.5 5.9 0.037 4 3.1 7475 1365 3.8 6.3 0.038 5 2.9 4491 820 4.4 7.0 0.039 6 2.7 6045 1116 4.7 7.6 0.041 7 2.5 8106 1517 5.3 8.6 0.044 8 2.3 11148 2120 5.8 9.4 0.048 9 2.2 6945 1356 6.1 9.8 0.053 10 2.1 8358 1665 6.5 10.6 0.064 Rescaling standard dataset to put it on approximate absolute scale. NRES = 147; expected = 288120. ; observed in lowest resolution shell = 48609.5898 ... Scale factor = 5.92722559 Opened binary file: scratch_1.mrg Opened binary file: scratch.mrg Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_1_1_fm.drg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F- from separateano Wavelength # 1 ! a label for th Col: 2: sig of F- Wavelength # 1 ! a label for th Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano Wavelength # 1 Sig of Der F from col: 2: sig of F- Wavelength # 1 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_1_1_fm.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 25962 unique derivative data were found Total of 12272 native F, 25961 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 79 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 3522 3376 3345 2 3.150 2154 2114 4781 4685 4643 3 2.940 832 820 1839 1806 1790 4 2.783 831 825 1801 1790 1761 5 2.625 1022 1006 2123 2097 2075 6 2.520 813 802 1712 1698 1662 7 2.415 976 964 1971 1959 1926 8 2.310 1173 1156 2346 2326 2253 9 2.205 1382 1356 2680 2678 2605 10 2.100 1702 1665 3186 3183 3053 total 12506 12272 25961 25598 25113 Mean value of Nat/Der for 10 resol ranges: 2.43 2.42 2.43 2.42 2.42 2.43 2.43 2.41 2.41 2.42 A total of 114 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.427 0.000 -0.046 0.000 Overall average scale factor = 0.999725699 for n = 25113 Note that there were 363 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 25840 records written. Of these, 25840 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 25477 had F for native Number of reflns rejected >3sig: 121 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 3347 556.411 0.040 1.000 0.00 32.12 0.00 2 3.150 4659 482.452 0.040 1.000 0.00 27.04 0.00 3 2.940 1797 330.459 0.049 1.000 4.78 19.45 0.25 4 2.783 1781 285.874 0.052 1.000 6.65 17.25 0.39 5 2.625 2090 242.452 0.057 1.000 7.81 15.30 0.51 6 2.520 1689 218.567 0.058 1.000 6.68 14.44 0.46 7 2.415 1952 206.591 0.063 1.000 8.20 14.12 0.58 8 2.310 2318 204.867 0.062 1.000 6.92 14.39 0.48 9 2.205 2669 194.249 0.064 1.000 5.79 14.45 0.40 10 2.100 3175 174.676 0.069 1.000 0.00 15.26 0.00 Total: 25477 315.583 0.049 1.000 0.00 20.85 0.25 Recommended resolution cut-off = 2.10 Opened binary file: lambda_1_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_1_1_fp.drg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano Wavelength # 1 Sig of Der F from col: 2: sig of F+ Wavelength # 1 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_1_1_fp.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 39224 unique derivative data were found Total of 12272 native F, 39223 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 471 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 5068 4924 4854 2 3.150 2154 2114 6904 6799 6717 3 2.940 832 820 2694 2658 2627 4 2.783 831 825 2711 2701 2662 5 2.625 1022 1006 3243 3214 3152 6 2.520 813 802 2569 2553 2502 7 2.415 976 964 3087 3074 2972 8 2.310 1173 1156 3692 3675 3567 9 2.205 1382 1356 4191 4188 4019 10 2.100 1702 1665 5064 5061 4850 total 12506 12272 39223 38847 37922 Mean value of Nat/Der for 10 resol ranges: 2.44 2.44 2.43 2.44 2.44 2.43 2.43 2.44 2.44 2.43 A total of 228 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.442 0.000 -0.039 0.000 Overall average scale factor = 1.0000025 for n = 37922 Note that there were 376 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 38984 records written. Of these, 38984 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 38608 had F for native Number of reflns rejected >3sig: 239 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 4864 538.228 0.033 1.000 0.00 26.44 0.00 2 3.150 6753 475.657 0.034 1.000 0.00 22.71 0.00 3 2.940 2648 331.318 0.041 1.000 3.23 16.80 0.19 4 2.783 2690 288.086 0.042 1.000 3.89 14.85 0.26 5 2.625 3196 240.705 0.047 1.000 5.40 12.98 0.42 6 2.520 2543 212.996 0.051 1.000 6.12 12.20 0.50 7 2.415 3052 203.630 0.053 1.000 6.15 12.19 0.50 8 2.310 3660 200.706 0.054 1.000 5.97 12.32 0.48 9 2.205 4167 192.409 0.056 1.000 5.12 12.62 0.41 10 2.100 5035 172.560 0.061 1.000 0.00 13.22 0.00 Total: 38608 306.153 0.042 1.000 0.00 17.40 0.23 Recommended resolution cut-off = 2.10 Opened binary file: lambda_1_1_fp.scltofp File 2 with intensity data for lambda 2. This is the 1 th dataset for this wavelength READFILE: read in a file to .drg format Assuming after header with 2*ns+1 lines, this data file contains: h k l hh kk ll i i i i Intensity sigma, not merged (may be multiple observations) and h k l, -h -k -l can both appear Opened formatted file: p9_se_w2.sca 4 i41 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 0 -1 0 1 0 0 0 0 1 0 6 3 0 1 0 -1 0 0 0 0 1 0 6 3 0 0 4 0 0 4 188 1 1 1 80331.8 8648.0 First 9 lines of data files are assumed to be header and will be ignored. Dorgbn-style file with this data will be: lambda_2_1_i.drg Opened binary file: lambda_2_1_i.drg Total of 145453 records read, with 88399 accepted in the resolution range of 2.0999999 to 20. Resolution range will be from 2.0999999 to 20. Please enter input dorgbn-style file> Opened binary file: lambda_2_1_i.drg This file has 2 columns of data. They are: Col: 0:lambda_2_1_i.drg Col: 1:lambda_2_1_i.drg I obs Col: 2:lambda_2_1_i.drg Sig I obs How many records would you like to see? (if you type "-1" you can enter a particular reflection to look at) > 10records will be listed. H K L Resol Col1 Col2 Col3 Col4 Col5 (etc) 0 0 4 8.12 80331.80 8648.00 0 0 -4 8.12 104526.70 11623.30 0 0 8 4.06 44883.60 4527.60 0 0 8 4.06 41134.10 4431.90 0 0 -8 4.06 53386.00 5564.10 0 0 -8 4.06 50401.80 5464.60 0 0 12 2.71 119801.40 12231.20 0 0 12 2.71 105312.90 12602.20 1 0 3 10.78 19407.00 2301.40 1 0 3 10.78 19337.00 2204.00 Converting this data from I to F. MATH: Perform simple math operations on dorgbn files. Operation to be performed is :i_to_f Input file > Opened binary file: lambda_2_1_i.drg Input data col 0: lambda_2_1_i.drg Input data col 1: lambda_2_1_i.drg I obs Input data col 2: lambda_2_1_i.drg Sig I obs Output file > Opened binary file: lambda_2_1_f.drg Resolution range will be from 2.0999999 to 20. Number of records written: 85374, number with no data: 3025 number out of resolution range 0 Separating out anomalous pairs. GETMIRROR Maximize overlap of F+ and F- by choosing the right symmetry equivalent for F-. Input file = Resolution range will be from 2.0999999 to 20. Opened binary file: lambda_2_1_f.drg Col: 0: Output of MATH routine from HEAVY Col: 1: F from I_TO_F set 2 Col: 2: SIGMA of F set 2 Deriv F from column: 1: F from I_TO_F set 2 Sig of Der F from col: 2: SIGMA of F set 2 A total of 78729 unique derivative data were found # of F+/F- pairs found using equivalence # 1 is: 31787 # of F+/F- pairs found using equivalence # 2 is: 31655 # of F+/F- pairs found using equivalence # 3 is: 31167 # of F+/F- pairs found using equivalence # 4 is: 31214 Best equivalance (nequiv_separate) = 1 MATH: Perform simple math operations on dorgbn files. Operation to be performed is :separateano Input file > Opened binary file: lambda_2_1_f.drg Input data col 0: Output of MATH routine from HEAVY Input data col 1: F from I_TO_F set 2 Input data col 2: SIGMA of F set 2 Opened binary file: lambda_2_1_fp.drg Output F+,sig+ written to lambda_2_1_fp.drg Opened binary file: lambda_2_1_fm.drg Output F-,sig- written to lambda_2_1_fm.drg Output HKL for F- will be inverted: If a reflection with indices HKL is read in and determined to be an F-, it will be written out as -H -K -L. Resolution range will be from 2.0999999 to 20. Total records with F+: 49259 Total records with F-: 36115 Number of records written: 85374, number with no data: 0 number out of resolution range 0 Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_2_1_fm.drg Col: 0: SIGMA of F set 2 Col: 1: F- from separateano set 2 Col: 2: sig of F- set 2 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano set 2 Sig of Der F from col: 2: sig of F- set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_2_1_fm.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 35868 unique derivative data were found Total of 12272 native F, 35867 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 248 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 4705 4510 4473 2 3.150 2154 2114 6501 6377 6312 3 2.940 832 820 2526 2487 2463 4 2.783 831 825 2519 2507 2476 5 2.625 1022 1006 2980 2945 2906 6 2.520 813 802 2397 2376 2326 7 2.415 976 964 2773 2756 2703 8 2.310 1173 1156 3312 3289 3225 9 2.205 1382 1356 3724 3703 3608 10 2.100 1702 1665 4430 4406 4270 total 12506 12272 35867 35356 34762 Mean value of Nat/Der for 10 resol ranges: 2.16 2.14 2.15 2.15 2.14 2.15 2.15 2.15 2.15 2.16 A total of 171 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.148 0.000 0.027 0.000 Overall average scale factor = 0.999759972 for n = 34762 Note that there were 511 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 35684 records written. Of these, 35684 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 35173 had F for native Number of reflns rejected >3sig: 183 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 4477 548.627 0.042 1.000 0.00 34.57 0.00 2 3.150 6334 478.748 0.041 1.000 0.00 29.31 0.00 3 2.940 2477 323.685 0.050 1.000 0.00 20.59 0.00 4 2.783 2493 281.717 0.053 1.000 4.46 18.29 0.24 5 2.625 2933 238.533 0.058 1.000 6.54 16.24 0.40 6 2.520 2362 210.764 0.063 1.000 7.16 15.07 0.48 7 2.415 2745 201.925 0.065 1.000 6.99 14.77 0.47 8 2.310 3273 199.878 0.064 1.000 6.25 14.84 0.42 9 2.205 3691 188.627 0.067 1.000 5.99 14.85 0.40 10 2.100 4388 171.391 0.073 1.000 0.00 15.60 0.00 Total: 35173 308.387 0.051 1.000 0.00 22.10 0.20 Recommended resolution cut-off = 2.10 Opened binary file: lambda_2_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_2_1_fp.drg Col: 0: SIGMA of F set 2 Col: 1: F+ from separateano set 2 Col: 2: sig of F+ set 2 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano set 2 Sig of Der F from col: 2: sig of F+ set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_2_1_fp.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 42862 unique derivative data were found Total of 12272 native F, 42861 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 6398 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 5818 5638 5575 2 3.150 2154 2114 7618 7497 7405 3 2.940 832 820 2909 2872 2829 4 2.783 831 825 2944 2927 2887 5 2.625 1022 1006 3514 3473 3413 6 2.520 813 802 2763 2743 2684 7 2.415 976 964 3336 3314 3227 8 2.310 1173 1156 3922 3896 3796 9 2.205 1382 1356 4569 4537 4389 10 2.100 1702 1665 5468 5420 5212 total 12506 12272 42861 42317 41417 Mean value of Nat/Der for 10 resol ranges: 2.17 2.16 2.17 2.16 2.16 2.17 2.17 2.17 2.17 2.18 A total of 292 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.169 0.000 0.007 0.000 Overall average scale factor = 1.00044417 for n = 41417 Note that there were 544 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 42546 records written. Of these, 42546 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 42002 had F for native Number of reflns rejected >3sig: 315 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 5581 534.767 0.037 1.000 0.00 29.22 0.00 2 3.150 7439 473.972 0.034 1.000 0.00 25.04 0.00 3 2.940 2852 328.939 0.043 1.000 0.00 18.30 0.00 4 2.783 2913 283.543 0.043 1.000 0.00 15.92 0.00 5 2.625 3441 239.313 0.047 1.000 2.68 13.94 0.19 6 2.520 2722 209.674 0.053 1.000 5.83 12.85 0.45 7 2.415 3288 200.447 0.055 1.000 5.32 12.82 0.42 8 2.310 3876 199.157 0.057 1.000 5.94 12.92 0.46 9 2.205 4505 188.841 0.060 1.000 5.63 13.08 0.43 10 2.100 5385 170.342 0.064 1.000 0.00 13.71 0.00 Total: 42002 306.360 0.044 1.000 0.00 19.03 0.17 Recommended resolution cut-off = 2.10 Opened binary file: lambda_2_1_fp.scltofp File 3 with intensity data for lambda 3. This is the 1 th dataset for this wavelength READFILE: read in a file to .drg format Assuming after header with 2*ns+1 lines, this data file contains: h k l hh kk ll i i i i Intensity sigma, not merged (may be multiple observations) and h k l, -h -k -l can both appear Opened formatted file: p9_se_w4.sca 4 i41 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 0 -1 0 1 0 0 0 0 1 0 6 3 0 1 0 -1 0 0 0 0 1 0 6 3 0 0 4 0 0 4 14 1 0 1 86926.2 9343.9 First 9 lines of data files are assumed to be header and will be ignored. Dorgbn-style file with this data will be: lambda_3_1_i.drg Opened binary file: lambda_3_1_i.drg Total of 124360 records read, with 77544 accepted in the resolution range of 2.0999999 to 20. Resolution range will be from 2.0999999 to 20. Please enter input dorgbn-style file> Opened binary file: lambda_3_1_i.drg This file has 2 columns of data. They are: Col: 0:lambda_3_1_i.drg Col: 1:lambda_3_1_i.drg I obs Col: 2:lambda_3_1_i.drg Sig I obs How many records would you like to see? (if you type "-1" you can enter a particular reflection to look at) > 10records will be listed. H K L Resol Col1 Col2 Col3 Col4 Col5 (etc) 0 0 4 8.12 86926.20 9343.90 0 0 4 8.12 89485.30 9839.50 0 0 -4 8.12 103852.10 12904.70 0 0 -4 8.12 105556.70 11864.20 0 0 8 4.06 45349.30 4771.20 0 0 8 4.06 45157.00 4948.50 0 0 -8 4.06 50322.60 5698.80 0 0 -8 4.06 52261.90 5704.70 0 0 12 2.71 108173.80 11427.50 0 0 12 2.71 109819.80 11575.20 Converting this data from I to F. MATH: Perform simple math operations on dorgbn files. Operation to be performed is :i_to_f Input file > Opened binary file: lambda_3_1_i.drg Input data col 0: lambda_3_1_i.drg Input data col 1: lambda_3_1_i.drg I obs Input data col 2: lambda_3_1_i.drg Sig I obs Output file > Opened binary file: lambda_3_1_f.drg Resolution range will be from 2.0999999 to 20. Number of records written: 74926, number with no data: 2618 number out of resolution range 0 Separating out anomalous pairs. GETMIRROR Maximize overlap of F+ and F- by choosing the right symmetry equivalent for F-. Input file = Resolution range will be from 2.0999999 to 20. Opened binary file: lambda_3_1_f.drg Col: 0: Output of MATH routine from HEAVY Col: 1: F from I_TO_F set 3 Col: 2: SIGMA of F set 3 Deriv F from column: 1: F from I_TO_F set 3 Sig of Der F from col: 2: SIGMA of F set 3 A total of 41723 unique derivative data were found # of F+/F- pairs found using equivalence # 1 is: 13258 # of F+/F- pairs found using equivalence # 2 is: 5264 # of F+/F- pairs found using equivalence # 3 is: 10461 # of F+/F- pairs found using equivalence # 4 is: 7952 Best equivalance (nequiv_separate) = 1 MATH: Perform simple math operations on dorgbn files. Operation to be performed is :separateano Input file > Opened binary file: lambda_3_1_f.drg Input data col 0: Output of MATH routine from HEAVY Input data col 1: F from I_TO_F set 3 Input data col 2: SIGMA of F set 3 Opened binary file: lambda_3_1_fp.drg Output F+,sig+ written to lambda_3_1_fp.drg Opened binary file: lambda_3_1_fm.drg Output F-,sig- written to lambda_3_1_fm.drg Output HKL for F- will be inverted: If a reflection with indices HKL is read in and determined to be an F-, it will be written out as -H -K -L. Resolution range will be from 2.0999999 to 20. Total records with F+: 40528 Total records with F-: 34398 Number of records written: 74926, number with no data: 0 number out of resolution range 0 Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_3_1_fm.drg Col: 0: SIGMA of F set 3 Col: 1: F- from separateano set 3 Col: 2: sig of F- set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano set 3 Sig of Der F from col: 2: sig of F- set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_3_1_fm.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 18635 unique derivative data were found Total of 12272 native F, 18634 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 15764 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 2462 2364 2334 2 3.150 2154 2114 3360 3301 3281 3 2.940 832 820 1256 1236 1228 4 2.783 831 825 1288 1281 1266 5 2.625 1022 1006 1521 1505 1488 6 2.520 813 802 1234 1223 1197 7 2.415 976 964 1459 1450 1434 8 2.310 1173 1156 1715 1700 1680 9 2.205 1382 1356 1988 1969 1929 10 2.100 1702 1665 2351 2338 2292 total 12506 12272 18634 18367 18129 Mean value of Nat/Der for 10 resol ranges: 2.21 2.18 2.18 2.18 2.17 2.17 2.18 2.17 2.17 2.18 A total of 79 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.198 0.000 -0.238 0.000 Overall average scale factor = 1.00008857 for n = 18129 Note that there were 267 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 18547 records written. Of these, 18547 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 18280 had F for native Number of reflns rejected >3sig: 87 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 2332 548.542 0.047 1.000 15.24 29.21 0.52 2 3.150 3290 471.164 0.044 1.000 10.26 24.42 0.42 3 2.940 1232 312.488 0.054 1.000 12.58 17.07 0.74 4 2.783 1273 275.619 0.056 1.000 11.99 15.43 0.78 5 2.625 1498 234.357 0.063 1.000 12.09 13.79 0.88 6 2.520 1216 206.839 0.065 1.000 10.82 12.86 0.84 7 2.415 1449 198.222 0.067 1.000 10.83 12.64 0.86 8 2.310 1695 194.767 0.067 1.000 10.40 12.85 0.81 9 2.205 1961 182.557 0.067 1.000 8.12 13.03 0.62 10 2.100 2334 167.484 0.072 1.000 6.31 13.55 0.47 Total: 18280 302.736 0.055 1.000 10.98 18.67 0.64 Recommended resolution cut-off = 2.10 Opened binary file: lambda_3_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_3_1_fp.drg Col: 0: SIGMA of F set 3 Col: 1: F+ from separateano set 3 Col: 2: sig of F+ set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano set 3 Sig of Der F from col: 2: sig of F+ set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_3_1_fp.scltofp Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12272 unique reflections for native Summary of data for derivative : A total of 23089 unique derivative data were found Total of 12272 native F, 23088 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 17440 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1564 2973 2875 2848 2 3.150 2154 2114 4044 3990 3949 3 2.940 832 820 1536 1517 1500 4 2.783 831 825 1612 1601 1585 5 2.625 1022 1006 1977 1956 1930 6 2.520 813 802 1553 1541 1515 7 2.415 976 964 1846 1834 1801 8 2.310 1173 1156 2136 2117 2078 9 2.205 1382 1356 2471 2448 2374 10 2.100 1702 1665 2940 2910 2815 total 12506 12272 23088 22789 22395 Mean value of Nat/Der for 10 resol ranges: 2.23 2.20 2.19 2.18 2.19 2.19 2.19 2.20 2.19 2.19 A total of 124 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.217 0.000 -0.304 0.000 Overall average scale factor = 1.00052929 for n = 22395 There were 3 reflections that could not be scaled due to the presence of too few nearby reflections. An overall scale was used for these. Note that there were 299 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 22949 records written. Of these, 22949 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 22650 had F for native Number of reflns rejected >3sig: 139 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 2847 539.486 0.046 1.000 11.89 29.54 0.40 2 3.150 3967 465.610 0.040 1.000 0.00 24.41 0.00 3 2.940 1508 316.931 0.049 1.000 8.37 17.75 0.47 4 2.783 1589 268.838 0.049 1.000 6.32 15.16 0.42 5 2.625 1942 228.941 0.055 1.000 7.23 13.94 0.52 6 2.520 1537 198.788 0.059 1.000 7.24 12.82 0.57 7 2.415 1828 189.513 0.062 1.000 6.84 12.97 0.53 8 2.310 2107 187.008 0.063 1.000 7.30 12.99 0.56 9 2.205 2429 174.123 0.066 1.000 5.52 13.32 0.41 10 2.100 2896 159.984 0.070 1.000 0.00 13.99 0.00 Total: 22650 294.259 0.051 1.000 6.38 18.77 0.33 Recommended resolution cut-off = 2.10 Opened binary file: lambda_3_1_fp.scltofp MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: scratch.mrg Overwriting this file. How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: scratch_all.drg Columns 1, 2 assumed to be f,sig. Col: 0 all data dump for scale_mad. F and sigma Col: 1 all data dump for scale_mad. F and sigma Col: 2 all data dump for scale_mad. F and sigma analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.397521973 This will be applied to all sigmas Summary of data: Reflections read : 184550 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 184550 Rejected : |obs-mean|> 4 Sig: 4344 Chisqr > 20 : 0 Unique hkl : 12166 overall r-factor on F: 4.4 % overall r-factor on I: 6.6 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 9653 766 4.0 7.2 0.034 2 4.2 9659 745 3.2 5.5 0.033 3 3.7 9473 727 3.3 5.5 0.032 4 3.1 17504 1335 3.6 6.0 0.033 5 2.9 10398 798 4.3 6.8 0.033 6 2.7 14445 1106 4.5 7.3 0.034 7 2.5 19492 1506 5.1 8.3 0.037 8 2.3 27114 2118 5.6 9.0 0.040 9 2.2 17212 1373 5.9 9.4 0.043 10 2.1 20840 1692 6.4 10.3 0.052 Opened binary file: scratch_all.drg Overwriting this file. Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_1_1_fm.drg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F- from separateano Wavelength # 1 ! a label for th Col: 2: sig of F- Wavelength # 1 ! a label for th Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano Wavelength # 1 Sig of Der F from col: 2: sig of F- Wavelength # 1 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_1_1_fm.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 25962 unique derivative data were found Total of 12166 native F, 25961 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 79 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 3522 3282 3247 2 3.150 2154 2062 4781 4592 4554 3 2.940 832 798 1839 1752 1737 4 2.783 831 818 1801 1763 1736 5 2.625 1022 1000 2123 2070 2049 6 2.520 813 794 1712 1661 1626 7 2.415 976 964 1971 1946 1916 8 2.310 1173 1154 2346 2305 2233 9 2.205 1382 1373 2680 2668 2597 10 2.100 1702 1692 3186 3173 3042 total 12506 12166 25961 25212 24737 Mean value of Nat/Der for 10 resol ranges: 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.41 2.41 2.41 A total of 114 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.430 0.000 -0.129 0.000 Overall average scale factor = 0.999860585 for n = 24737 Note that there were 749 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 25846 records written. Of these, 25846 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 25097 had F for native Number of reflns rejected >3sig: 115 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 3257 567.136 0.038 1.000 0.00 32.40 0.00 2 3.150 4567 488.523 0.037 1.000 0.00 27.14 0.00 3 2.940 1747 335.284 0.046 1.000 0.00 19.38 0.00 4 2.783 1756 287.850 0.049 1.001 4.13 17.02 0.24 5 2.625 2065 244.144 0.053 1.002 6.42 14.96 0.43 6 2.520 1652 220.252 0.055 1.002 5.93 14.12 0.42 7 2.415 1936 206.270 0.060 1.000 7.29 13.64 0.53 8 2.310 2295 204.941 0.060 0.999 6.32 14.03 0.45 9 2.205 2659 193.922 0.063 0.997 5.72 14.01 0.41 10 2.100 3163 173.955 0.069 0.997 0.00 14.94 0.00 Total: 25097 317.687 0.047 0.999 0.00 20.72 0.21 Recommended resolution cut-off = 2.10 Opened binary file: lambda_1_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_1_1_fp.drg Col: 0: SIGMA of F Wavelength # 1 ! a label for th Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano Wavelength # 1 Sig of Der F from col: 2: sig of F+ Wavelength # 1 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_1_1_fp.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 39224 unique derivative data were found Total of 12166 native F, 39223 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 471 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 5068 4782 4725 2 3.150 2154 2062 6904 6631 6551 3 2.940 832 798 2694 2581 2552 4 2.783 831 818 2711 2670 2635 5 2.625 1022 1000 3243 3177 3120 6 2.520 813 794 2569 2508 2460 7 2.415 976 964 3087 3053 2957 8 2.310 1173 1154 3692 3642 3540 9 2.205 1382 1373 4191 4172 4006 10 2.100 1702 1692 5064 5050 4841 total 12506 12166 39223 38266 37387 Mean value of Nat/Der for 10 resol ranges: 2.43 2.44 2.44 2.44 2.44 2.43 2.43 2.43 2.43 2.42 A total of 191 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.444 0.000 -0.081 0.000 Overall average scale factor = 0.999961436 for n = 37387 Note that there were 957 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 39036 records written. Of these, 39036 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 38079 had F for native Number of reflns rejected >3sig: 187 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 4738 550.371 0.037 0.998 0.00 30.07 0.00 2 3.150 6592 484.303 0.037 1.003 0.00 25.66 0.00 3 2.940 2570 336.414 0.044 1.002 0.00 18.71 0.00 4 2.783 2663 289.966 0.047 1.002 4.62 16.47 0.28 5 2.625 3167 242.412 0.052 1.001 6.69 14.25 0.47 6 2.520 2498 213.839 0.056 1.000 6.85 13.40 0.51 7 2.415 3033 203.694 0.059 0.999 7.29 13.30 0.55 8 2.310 3634 200.803 0.060 0.999 6.93 13.47 0.51 9 2.205 4155 192.416 0.062 0.999 5.35 13.80 0.39 10 2.100 5029 171.820 0.067 0.998 0.00 14.56 0.00 Total: 38079 308.567 0.047 1.000 0.00 19.44 0.23 Recommended resolution cut-off = 2.10 Opened binary file: lambda_1_1_fp.scltofp Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_2_1_fm.drg Col: 0: SIGMA of F set 2 Col: 1: F- from separateano set 2 Col: 2: sig of F- set 2 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano set 2 Sig of Der F from col: 2: sig of F- set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_2_1_fm.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 35868 unique derivative data were found Total of 12166 native F, 35867 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 248 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 4705 4358 4312 2 3.150 2154 2062 6501 6240 6173 3 2.940 832 798 2526 2422 2395 4 2.783 831 818 2519 2476 2445 5 2.625 1022 1000 2980 2911 2871 6 2.520 813 794 2397 2339 2289 7 2.415 976 964 2773 2745 2693 8 2.310 1173 1154 3312 3268 3201 9 2.205 1382 1373 3724 3712 3614 10 2.100 1702 1692 4430 4415 4274 total 12506 12166 35867 34886 34267 Mean value of Nat/Der for 10 resol ranges: 2.16 2.14 2.15 2.15 2.14 2.15 2.15 2.14 2.14 2.15 A total of 197 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.152 0.000 -0.060 0.000 Overall average scale factor = 0.999862552 for n = 34267 Note that there were 981 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 35669 records written. Of these, 35669 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 34688 had F for native Number of reflns rejected >3sig: 198 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 4319 560.489 0.034 1.001 0.00 29.66 0.00 2 3.150 6198 485.730 0.033 0.998 0.00 25.12 0.00 3 2.940 2411 327.724 0.041 0.999 0.00 17.44 0.00 4 2.783 2462 282.967 0.044 1.000 2.36 15.35 0.15 5 2.625 2900 239.991 0.047 1.000 4.74 13.49 0.35 6 2.520 2324 211.426 0.052 1.001 5.90 12.49 0.47 7 2.415 2732 201.510 0.055 1.000 6.67 12.10 0.55 8 2.310 3248 199.493 0.054 1.000 5.64 12.22 0.46 9 2.205 3702 187.698 0.057 1.000 5.47 12.14 0.45 10 2.100 4392 170.142 0.061 1.000 0.00 12.90 0.00 Total: 34688 309.791 0.042 1.000 0.00 18.66 0.21 Recommended resolution cut-off = 2.10 Opened binary file: lambda_2_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_2_1_fp.drg Col: 0: SIGMA of F set 2 Col: 1: F+ from separateano set 2 Col: 2: sig of F+ set 2 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano set 2 Sig of Der F from col: 2: sig of F+ set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_2_1_fp.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 42862 unique derivative data were found Total of 12166 native F, 42861 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 6398 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 5818 5452 5383 2 3.150 2154 2062 7618 7314 7224 3 2.940 832 798 2909 2792 2748 4 2.783 831 818 2944 2902 2862 5 2.625 1022 1000 3514 3442 3379 6 2.520 813 794 2763 2701 2642 7 2.415 976 964 3336 3300 3207 8 2.310 1173 1154 3922 3870 3758 9 2.205 1382 1373 4569 4551 4398 10 2.100 1702 1692 5468 5453 5238 total 12506 12166 42861 41777 40839 Mean value of Nat/Der for 10 resol ranges: 2.17 2.17 2.17 2.17 2.16 2.17 2.17 2.17 2.17 2.17 A total of 302 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.166 0.000 0.065 0.000 Overall average scale factor = 1.00005031 for n = 40839 Note that there were 1084 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 42561 records written. Of these, 42561 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 41477 had F for native Number of reflns rejected >3sig: 300 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 5398 547.963 0.033 0.999 0.00 27.61 0.00 2 3.150 7257 481.999 0.032 1.001 0.00 23.51 0.00 3 2.940 2772 333.741 0.039 1.001 0.00 16.94 0.00 4 2.783 2889 284.864 0.041 1.000 0.00 14.62 0.00 5 2.625 3415 240.547 0.044 0.999 4.17 12.70 0.33 6 2.520 2683 210.387 0.050 0.999 6.01 11.69 0.51 7 2.415 3275 200.418 0.052 1.000 6.28 11.54 0.54 8 2.310 3844 198.739 0.052 1.000 5.60 11.66 0.48 9 2.205 4522 187.795 0.054 1.001 5.08 11.78 0.43 10 2.100 5422 168.507 0.059 1.001 0.00 12.46 0.00 Total: 41477 307.953 0.040 1.000 0.00 17.63 0.19 Recommended resolution cut-off = 2.10 Opened binary file: lambda_2_1_fp.scltofp Scaling F- to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_3_1_fm.drg Col: 0: SIGMA of F set 3 Col: 1: F- from separateano set 3 Col: 2: sig of F- set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F- from separateano set 3 Sig of Der F from col: 2: sig of F- set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_3_1_fm.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 18635 unique derivative data were found Total of 12166 native F, 18634 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 15764 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 2462 2275 2240 2 3.150 2154 2062 3360 3223 3203 3 2.940 832 798 1256 1204 1196 4 2.783 831 818 1288 1267 1247 5 2.625 1022 1000 1521 1484 1467 6 2.520 813 794 1234 1203 1177 7 2.415 976 964 1459 1442 1424 8 2.310 1173 1154 1715 1691 1667 9 2.205 1382 1373 1988 1982 1943 10 2.100 1702 1692 2351 2343 2293 total 12506 12166 18634 18114 17857 Mean value of Nat/Der for 10 resol ranges: 2.21 2.18 2.18 2.18 2.17 2.17 2.17 2.17 2.16 2.17 A total of 94 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.202 0.000 -0.345 0.000 Overall average scale factor = 1.00016797 for n = 17857 Note that there were 520 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 18534 records written. Of these, 18534 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 18014 had F for native Number of reflns rejected >3sig: 100 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 2245 563.106 0.036 1.002 0.00 26.72 0.00 2 3.150 3212 478.957 0.034 0.997 0.00 22.37 0.00 3 2.940 1201 316.671 0.041 0.998 6.16 15.23 0.40 4 2.783 1258 277.439 0.044 1.000 6.55 13.71 0.48 5 2.625 1476 235.569 0.047 1.000 7.11 11.98 0.59 6 2.520 1194 207.435 0.050 1.001 6.44 11.23 0.57 7 2.415 1437 198.031 0.052 1.001 7.25 10.85 0.67 8 2.310 1680 193.931 0.052 1.002 6.31 11.11 0.57 9 2.205 1977 181.332 0.053 1.002 4.54 11.15 0.41 10 2.100 2334 166.021 0.057 1.002 0.00 11.77 0.00 Total: 18014 304.411 0.042 1.000 1.16 16.72 0.30 Recommended resolution cut-off = 2.10 Opened binary file: lambda_3_1_fm.scltofp Scaling F+ to scratch.mrg LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: scratch.mrg Col: 0: all data dump for scale_mad. F and sigma Col: 1: all data dump for scale_mad. F and sigma Col: 2: all data dump for scale_mad. F and sigma Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: all data dump for scale_mad. F and sigma Sig of Nat F from col: 2: all data dump for scale_mad. F and sigma What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: lambda_3_1_fp.drg Col: 0: SIGMA of F set 3 Col: 1: F+ from separateano set 3 Col: 2: sig of F+ set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 1: F+ from separateano set 3 Sig of Der F from col: 2: sig of F+ set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: lambda_3_1_fp.scltofp Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12166 unique reflections for native Summary of data for derivative : A total of 23089 unique derivative data were found Total of 12166 native F, 23088 deriv F observed Additionally, 0 native and 0 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 17440 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1511 2973 2769 2736 2 3.150 2154 2062 4044 3886 3844 3 2.940 832 798 1536 1483 1468 4 2.783 831 818 1612 1591 1572 5 2.625 1022 1000 1977 1939 1910 6 2.520 813 794 1553 1521 1496 7 2.415 976 964 1846 1830 1795 8 2.310 1173 1154 2136 2110 2064 9 2.205 1382 1373 2471 2463 2391 10 2.100 1702 1692 2940 2934 2828 total 12506 12166 23088 22526 22104 Mean value of Nat/Der for 10 resol ranges: 2.22 2.20 2.19 2.19 2.19 2.19 2.18 2.19 2.18 2.18 A total of 148 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 2.215 0.000 -0.283 0.000 Overall average scale factor = 1.00026381 for n = 22104 There were 3 reflections that could not be scaled due to the presence of too few nearby reflections. An overall scale was used for these. Note that there were 562 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 22952 records written. Of these, 22952 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 22390 had F for native Number of reflns rejected >3sig: 136 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 2745 553.915 0.037 1.001 6.43 25.25 0.25 2 3.150 3863 473.796 0.033 1.000 0.00 20.74 0.00 3 2.940 1475 321.547 0.040 0.999 7.22 14.74 0.49 4 2.783 1578 269.719 0.040 0.998 5.94 12.41 0.48 5 2.625 1927 230.434 0.046 0.998 6.86 11.30 0.61 6 2.520 1515 199.286 0.049 0.999 6.35 10.41 0.61 7 2.415 1825 189.085 0.051 1.001 6.49 10.36 0.63 8 2.310 2101 186.147 0.052 1.002 6.46 10.42 0.62 9 2.205 2445 173.245 0.055 1.002 5.22 10.69 0.49 10 2.100 2916 158.378 0.057 1.001 0.00 11.36 0.00 Total: 22390 295.588 0.042 1.000 4.89 15.62 0.35 Recommended resolution cut-off = 2.10 Opened binary file: lambda_3_1_fp.scltofp MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: scratch.mrg Overwriting this file. How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: scratch_all.drg Columns 1, 2 assumed to be f,sig. Col: 0 all data dump for scale_mad. F and sigma Col: 1 all data dump for scale_mad. F and sigma Col: 2 all data dump for scale_mad. F and sigma analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.372454733 This will be applied to all sigmas Summary of data: Reflections read : 184598 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 184598 Rejected : |obs-mean|> 4 Sig: 4366 Chisqr > 20 : 0 Unique hkl : 12166 overall r-factor on F: 4.4 % overall r-factor on I: 6.5 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 9675 768 4.0 7.0 0.033 2 4.2 9668 745 3.2 5.4 0.032 3 3.7 9384 720 3.2 5.3 0.031 4 3.1 17556 1338 3.6 5.9 0.032 5 2.9 10375 797 4.2 6.8 0.032 6 2.7 14447 1106 4.5 7.2 0.033 7 2.5 19521 1508 5.1 8.2 0.036 8 2.3 27085 2116 5.6 8.9 0.039 9 2.2 17260 1376 5.9 9.3 0.042 10 2.1 20847 1692 6.3 10.2 0.050 *************************************************************************** SOLVE STATUS 30-apr-05 11:28:54 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:28:54 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS Merging scaled data in F+ at lambda 1 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_1_0_fp.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_1_1_fp.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F+ from separateano Wavelength # 1 ! a label for this wavelength Col: 2 sig of F+ Wavelength # 1 ! a label for this wavelength analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.200898424 This will be applied to all sigmas Summary of data: Reflections read : 39036 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 39036 Rejected : |obs-mean|> 4 Sig: 4 Chisqr > 20 : 0 Unique hkl : 12319 overall r-factor on F: 2.8 % overall r-factor on I: 4.1 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 2619 834 1.9 3.5 0.025 2 4.2 2405 779 1.7 3.1 0.024 3 3.7 2389 763 2.1 3.3 0.024 4 3.1 4473 1376 2.3 3.8 0.024 5 2.9 2683 828 2.7 4.2 0.025 6 2.7 3634 1124 2.9 4.6 0.026 7 2.5 4862 1513 3.4 5.3 0.028 8 2.3 6751 2116 3.9 6.2 0.031 9 2.2 4174 1344 4.3 6.6 0.034 10 2.1 5042 1642 4.8 7.6 0.040 Merging scaled data in F- at lambda 1 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_1_0_fm.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_1_1_fm.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F- from separateano Wavelength # 1 ! a label for this wavelength Col: 2 sig of F- Wavelength # 1 ! a label for this wavelength analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.204944611 This will be applied to all sigmas Summary of data: Reflections read : 25846 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 25846 Rejected : |obs-mean|> 4 Sig: 7 Chisqr > 20 : 0 Unique hkl : 10967 overall r-factor on F: 2.5 % overall r-factor on I: 3.8 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 1757 659 1.8 3.2 0.025 2 4.2 1740 677 1.8 3.3 0.024 3 3.7 1717 682 1.9 3.3 0.024 4 3.1 3032 1227 2.1 3.6 0.025 5 2.9 1834 740 2.5 3.9 0.025 6 2.7 2421 1018 2.6 4.2 0.026 7 2.5 3194 1379 3.0 4.7 0.028 8 2.3 4297 1907 3.5 5.4 0.030 9 2.2 2671 1216 3.7 5.7 0.032 10 2.1 3176 1462 4.3 6.7 0.039 Combining all data in one file with F+,sig,F-,sig at lambda 1 Run_filemerge: files to merge are: lambda_1_0_fp.mrg lambda_1_0_fm.mrg Output file is: lambda_1_0_fpfm.scl Opened binary file: lambda_1_0_fp.mrg Opened binary file: lambda_1_0_fm.mrg Opening scratch file for script: scratch.script Opened formatted file: scratch.script Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: lambda_1_0_fp.mrg INPUT FILE 2> Opened binary file: lambda_1_0_fm.mrg What is the output file to be called > Opened binary file: lambda_1_0_fpfm.scl Please enter overall title for new file > lambda_1_0_fp.mrg (cols 1 to 2) and lambda_1_0_fm.mrg ,cols 1 to 2) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: Scaled derivative data COL 1: F+ from separateano Wavelength # 1 ! a label for this wavelength COL 2: sig of F+ Wavelength # 1 ! a label for this wavelength What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: Scaled derivative data COL 1: F- from separateano Wavelength # 1 ! a label for this wavelength COL 2: sig of F- Wavelength # 1 ! a label for this wavelength What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Total of 12402 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Getting Fbar,sig,delano,sig at lambda 1 GETANOM: Convert from F+,F- to Fbar, DelAno Input name of dorgbn-style file containing F+,sig,F-,sig data> Opened binary file: lambda_1_0_fpfm.scl ...and name of output dorgbn-style file> Opened binary file: lambda_1_0_fbar.scl Overall title for output file: Input data col 0: lambda_1_0_fp.mrg (cols 1 to 2) and lambda_1_0_fm.mrg ,cols 1 to 2) Input data col 1: F+ from separateano Wavelength # 1 ! a label for this wavelength Input data col 2: sig of F+ Wavelength # 1 ! a label for this wavelength Input data col 3: F- from separateano Wavelength # 1 ! a label for this wavelength Input data col 4: sig of F- Wavelength # 1 ! a label for this wavelength Column numbers for F+, sigma of F+ (0 if not present)> Column numbers for F-, sigma of F- (0 if not present)> Column numbers for F+, sigma: 1 2 Column numbers for F-, sigma: 3 4 For acentric reflections, those with either F+ and F- or both will be written out... Resolution range will be from 2.0999999 to 20. Number of records written= 12402 including 0 zeros... Number out of resolution range (not written out): 0 Merging scaled data in F+ at lambda 2 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_2_0_fp.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_2_1_fp.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F+ from separateano set 2 Col: 2 sig of F+ set 2 analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.203030154 This will be applied to all sigmas Summary of data: Reflections read : 42561 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 42561 Rejected : |obs-mean|> 4 Sig: 15 Chisqr > 20 : 0 Unique hkl : 12382 overall r-factor on F: 2.6 % overall r-factor on I: 3.8 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 3015 837 1.8 3.4 0.025 2 4.2 2748 778 1.8 3.2 0.023 3 3.7 2672 766 2.0 3.2 0.023 4 3.1 4880 1378 2.1 3.5 0.023 5 2.9 2887 830 2.5 4.0 0.024 6 2.7 3934 1125 2.7 4.3 0.024 7 2.5 5227 1522 3.1 4.9 0.026 8 2.3 7206 2119 3.6 5.6 0.028 9 2.2 4540 1358 3.9 6.0 0.030 10 2.1 5437 1669 4.4 6.8 0.037 Merging scaled data in F- at lambda 2 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_2_0_fm.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_2_1_fm.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F- from separateano set 2 Col: 2 sig of F- set 2 analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.202274621 This will be applied to all sigmas Summary of data: Reflections read : 35669 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 35669 Rejected : |obs-mean|> 4 Sig: 14 Chisqr > 20 : 0 Unique hkl : 11138 overall r-factor on F: 2.5 % overall r-factor on I: 3.8 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 2342 662 1.7 3.3 0.025 2 4.2 2321 678 1.8 3.4 0.024 3 3.7 2320 682 1.9 3.2 0.024 4 3.1 4132 1229 2.1 3.5 0.024 5 2.9 2514 751 2.3 3.8 0.024 6 2.7 3369 1024 2.6 4.2 0.025 7 2.5 4484 1395 3.0 4.7 0.027 8 2.3 6052 1954 3.3 5.2 0.028 9 2.2 3714 1249 3.6 5.6 0.031 10 2.1 4407 1514 4.0 6.2 0.037 Combining all data in one file with F+,sig,F-,sig at lambda 2 Run_filemerge: files to merge are: lambda_2_0_fp.mrg lambda_2_0_fm.mrg Output file is: lambda_2_0_fpfm.scl Opened binary file: lambda_2_0_fp.mrg Opened binary file: lambda_2_0_fm.mrg Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: lambda_2_0_fp.mrg INPUT FILE 2> Opened binary file: lambda_2_0_fm.mrg What is the output file to be called > Opened binary file: lambda_2_0_fpfm.scl Please enter overall title for new file > lambda_2_0_fp.mrg (cols 1 to 2) and lambda_2_0_fm.mrg ,cols 1 to 2) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: Scaled derivative data COL 1: F+ from separateano set 2 COL 2: sig of F+ set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: Scaled derivative data COL 1: F- from separateano set 2 COL 2: sig of F- set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Total of 12448 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Getting Fbar,sig,delano,sig at lambda 2 GETANOM: Convert from F+,F- to Fbar, DelAno Input name of dorgbn-style file containing F+,sig,F-,sig data> Opened binary file: lambda_2_0_fpfm.scl ...and name of output dorgbn-style file> Opened binary file: lambda_2_0_fbar.scl Overall title for output file: Input data col 0: lambda_2_0_fp.mrg (cols 1 to 2) and lambda_2_0_fm.mrg ,cols 1 to 2) Input data col 1: F+ from separateano set 2 Input data col 2: sig of F+ set 2 Input data col 3: F- from separateano set 2 Input data col 4: sig of F- set 2 Column numbers for F+, sigma of F+ (0 if not present)> Column numbers for F-, sigma of F- (0 if not present)> Column numbers for F+, sigma: 1 2 Column numbers for F-, sigma: 3 4 For acentric reflections, those with either F+ and F- or both will be written out... Resolution range will be from 2.0999999 to 20. Number of records written= 12448 including 0 zeros... Number out of resolution range (not written out): 0 Merging scaled data in F+ at lambda 3 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_3_0_fp.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_3_1_fp.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F+ from separateano set 3 Col: 2 sig of F+ set 3 analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.361788481 This will be applied to all sigmas Summary of data: Reflections read : 22952 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 22952 Rejected : |obs-mean|> 4 Sig: 0 Chisqr > 20 : 0 Unique hkl : 11605 overall r-factor on F: 2.1 % overall r-factor on I: 3.2 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 1520 774 1.6 3.3 0.028 2 4.2 1429 728 1.6 3.1 0.025 3 3.7 1396 719 1.5 2.6 0.026 4 3.1 2625 1288 1.7 2.9 0.025 5 2.9 1528 763 1.9 2.9 0.026 6 2.7 2153 1051 2.0 3.3 0.027 7 2.5 2958 1443 2.4 3.7 0.028 8 2.3 3968 1989 2.9 4.4 0.031 9 2.2 2453 1284 3.3 5.0 0.033 10 2.1 2922 1566 3.4 5.4 0.040 Merging scaled data in F- at lambda 3 from all 1 files . MERGE: Merge data for equivalent reflns. This routine reads in hkl and F and sigma from any number of files, merges equivalent reflections and writes out an asymmetric unit of data. Resolution range will be from 2.0999999 to 20. This program keeps track of the ratio of rms differences among equivalent reflections to the sigmas. Do you want to keep reflections even if chisqr>20? 1=keep anyways, 0 = toss them. (Usually toss them)> Tossing reflections with chisqr > 20 What is OUTPUT file name (not input file!) ? Opened binary file: lambda_3_0_fm.mrg How many input files will there be ? > There will be 1 input files What is file name for first file to be merged? > Opened binary file: lambda_3_1_fm.scltofp Columns 1, 2 assumed to be f,sig. Col: 0 Scaled derivative data Col: 1 F- from separateano set 3 Col: 2 sig of F- set 3 analyzing data... Estimate of multiplicative error error on I: Sig**2(I)=Sig**2(Poisson)* 0.454939842 This will be applied to all sigmas Summary of data: Reflections read : 18534 No data (Sig<0) : 0 Absence/out of res: 0 Data present,F=0 : 0 Data present,F>0 : 18534 Rejected : |obs-mean|> 4 Sig: 6 Chisqr > 20 : 0 Unique hkl : 10859 overall r-factor on F: 2.2 % overall r-factor on I: 3.5 % shell dmin nobs nunique r on F r on I rms(sig)/rms(F) (A) (%) (%) 1 5.2 1228 649 1.5 2.9 0.029 2 4.2 1204 664 1.7 3.3 0.027 3 3.7 1208 668 1.8 3.1 0.027 4 3.1 2137 1205 2.0 3.4 0.027 5 2.9 1253 727 2.2 3.7 0.028 6 2.7 1714 998 2.3 3.7 0.028 7 2.5 2301 1359 2.6 4.2 0.030 8 2.3 3158 1897 2.8 4.5 0.032 9 2.2 1983 1219 3.0 4.8 0.035 10 2.1 2342 1473 3.2 5.1 0.042 Combining all data in one file with F+,sig,F-,sig at lambda 3 Run_filemerge: files to merge are: lambda_3_0_fp.mrg lambda_3_0_fm.mrg Output file is: lambda_3_0_fpfm.scl Opened binary file: lambda_3_0_fp.mrg Opened binary file: lambda_3_0_fm.mrg Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: lambda_3_0_fp.mrg INPUT FILE 2> Opened binary file: lambda_3_0_fm.mrg What is the output file to be called > Opened binary file: lambda_3_0_fpfm.scl Please enter overall title for new file > lambda_3_0_fp.mrg (cols 1 to 2) and lambda_3_0_fm.mrg ,cols 1 to 2) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: Scaled derivative data COL 1: F+ from separateano set 3 COL 2: sig of F+ set 3 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: Scaled derivative data COL 1: F- from separateano set 3 COL 2: sig of F- set 3 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 2 What file do you want to read from (type 0 to end input) > Total of 12202 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Getting Fbar,sig,delano,sig at lambda 3 GETANOM: Convert from F+,F- to Fbar, DelAno Input name of dorgbn-style file containing F+,sig,F-,sig data> Opened binary file: lambda_3_0_fpfm.scl ...and name of output dorgbn-style file> Opened binary file: lambda_3_0_fbar.scl Overall title for output file: Input data col 0: lambda_3_0_fp.mrg (cols 1 to 2) and lambda_3_0_fm.mrg ,cols 1 to 2) Input data col 1: F+ from separateano set 3 Input data col 2: sig of F+ set 3 Input data col 3: F- from separateano set 3 Input data col 4: sig of F- set 3 Column numbers for F+, sigma of F+ (0 if not present)> Column numbers for F-, sigma of F- (0 if not present)> Column numbers for F+, sigma: 1 2 Column numbers for F-, sigma: 3 4 For acentric reflections, those with either F+ and F- or both will be written out... Resolution range will be from 2.0999999 to 20. Number of records written= 12202 including 0 zeros... Number out of resolution range (not written out): 0 *************************************************************************** SOLVE STATUS 30-apr-05 11:29:03 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS Combining all data in one file with F+,sig,F-,sig at each wavelength: mad_fpfm.scl Run_filemerge: files to merge are: lambda_1_0_fpfm.scl lambda_2_0_fpfm.scl Output file is: scratch_2.dat Opened binary file: lambda_1_0_fpfm.scl Opened binary file: lambda_2_0_fpfm.scl Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: lambda_1_0_fpfm.scl INPUT FILE 2> Opened binary file: lambda_2_0_fpfm.scl What is the output file to be called > Opened binary file: scratch_2.dat Please enter overall title for new file > lambda_1_0_fpfm.scl (cols 1 to 4) and lambda_2_0_fpfm.scl ,cols 1 to 4) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: lambda_1_0_fp.mrg (cols 1 to 2) and lambda_1_0_fm.mrg ,cols 1 to 2) COL 1: F+ from separateano Wavelength # 1 ! a label for this wavelength COL 2: sig of F+ Wavelength # 1 ! a label for this wavelength COL 3: F- from separateano Wavelength # 1 ! a label for this wavelength COL 4: sig of F- Wavelength # 1 ! a label for this wavelength What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: lambda_2_0_fp.mrg (cols 1 to 2) and lambda_2_0_fm.mrg ,cols 1 to 2) COL 1: F+ from separateano set 2 COL 2: sig of F+ set 2 COL 3: F- from separateano set 2 COL 4: sig of F- set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Total of 12478 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Run_filemerge: files to merge are: scratch_2.dat lambda_3_0_fpfm.scl Output file is: mad_fpfm.scl Opened binary file: scratch_2.dat Opened binary file: lambda_3_0_fpfm.scl Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: scratch_2.dat INPUT FILE 2> Opened binary file: lambda_3_0_fpfm.scl What is the output file to be called > Opened binary file: mad_fpfm.scl Please enter overall title for new file > mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: lambda_1_0_fpfm.scl (cols 1 to 4) and lambda_2_0_fpfm.scl ,cols 1 to 4) COL 1: F+ from separateano Wavelength # 1 ! a label for this wavelength COL 2: sig of F+ Wavelength # 1 ! a label for this wavelength COL 3: F- from separateano Wavelength # 1 ! a label for this wavelength COL 4: sig of F- Wavelength # 1 ! a label for this wavelength COL 5: F+ from separateano set 2 COL 6: sig of F+ set 2 COL 7: F- from separateano set 2 COL 8: sig of F- set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 8 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: lambda_3_0_fp.mrg (cols 1 to 2) and lambda_3_0_fm.mrg ,cols 1 to 2) COL 1: F+ from separateano set 3 COL 2: sig of F+ set 3 COL 3: F- from separateano set 3 COL 4: sig of F- set 3 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Total of 12490 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Combining all data in one file with Fbar,sig,delano,sig at each wavelength: mad_fbar.scl Run_filemerge: files to merge are: lambda_1_0_fbar.scl lambda_2_0_fbar.scl Output file is: scratch_2.dat Opened binary file: lambda_1_0_fbar.scl Opened binary file: lambda_2_0_fbar.scl Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: lambda_1_0_fbar.scl INPUT FILE 2> Opened binary file: lambda_2_0_fbar.scl What is the output file to be called > Opened binary file: scratch_2.dat Overwriting this file. Please enter overall title for new file > lambda_1_0_fbar.scl (cols 1 to 4) and lambda_2_0_fbar.scl ,cols 1 to 4) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: Fbar,sigFbar,delano,sigano COL 1: Fbar Wavelength # 1 ! a label for this wavelength COL 2: Sig of Fbar Wavelength # 1 ! a label for this wavelength COL 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength COL 4: sig of Del Ano Wavelength # 1 ! a label for this wavelength What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: Fbar,sigFbar,delano,sigano COL 1: Fbar set 2 COL 2: Sig of Fbar set 2 COL 3: Del Ano (F+ - F-) set 2 COL 4: sig of Del Ano set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Total of 12478 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Run_filemerge: files to merge are: scratch_2.dat lambda_3_0_fbar.scl Output file is: mad_fbar.scl Opened binary file: scratch_2.dat Opened binary file: lambda_3_0_fbar.scl Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: scratch_2.dat INPUT FILE 2> Opened binary file: lambda_3_0_fbar.scl What is the output file to be called > Opened binary file: mad_fbar.scl Please enter overall title for new file > mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: lambda_1_0_fbar.scl (cols 1 to 4) and lambda_2_0_fbar.scl ,cols 1 to 4) COL 1: Fbar Wavelength # 1 ! a label for this wavelength COL 2: Sig of Fbar Wavelength # 1 ! a label for this wavelength COL 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength COL 4: sig of Del Ano Wavelength # 1 ! a label for this wavelength COL 5: Fbar set 2 COL 6: Sig of Fbar set 2 COL 7: Del Ano (F+ - F-) set 2 COL 8: sig of Del Ano set 2 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 8 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: Fbar,sigFbar,delano,sigano COL 1: Fbar set 3 COL 2: Sig of Fbar set 3 COL 3: Del Ano (F+ - F-) set 3 COL 4: sig of Del Ano set 3 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 4 What file do you want to read from (type 0 to end input) > Total of 12490 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script *************************************************************************** SOLVE STATUS 30-apr-05 11:29:05 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS Resolution range will be from 2.0999999 to 20. Please enter input dorgbn-style file> Opened binary file: mad_fpfm.scl This file has 12 columns of data. They are: Col: 0:mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1:F+ from separateano Wavelength # 1 ! a label for th Col: 2:sig of F+ Wavelength # 1 ! a label for th Col: 3:F- from separateano Wavelength # 1 ! a label for th Col: 4:sig of F- Wavelength # 1 ! a label for th Col: 5:F+ from separateano set 2 Col: 6:sig of F+ set 2 Col: 7:F- from separateano set 2 Col: 8:sig of F- set 2 Col: 9:F+ from separateano set 3 Col: 10:sig of F+ set 3 Col: 11:F- from separateano set 3 Col: 12:sig of F- set 3 How many records would you like to see? (if you type "-1" you can enter a particular reflection to look at) > 20records will be listed. H K L Resol Col1 Col2 Col3 Col4 Col5 (etc) 0 0 4 8.12 -1.00 -1.00 761.83 19.68 -1.00 -1.00 700.66 17.52 652.05 15.07 713.16 20.05 0 0 8 4.06 423.89 9.91 492.69 12.25 447.46 7.43 490.13 8.28 465.67 10.63 499.57 13.24 0 0 12 2.71 724.80 17.74 -1.00 -1.00 715.17 12.52 -1.00 -1.00 717.74 16.11 -1.00 -1.00 1 0 3 10.78 296.84 3.82 271.02 4.66 302.62 2.92 280.18 3.03 311.42 3.70 296.59 3.95 1 0 5 6.48 297.73 3.68 296.80 4.95 307.90 3.08 304.59 7.88 318.47 4.90 319.19 4.20 1 0 7 4.64 303.05 4.16 306.33 4.50 296.05 3.41 299.65 3.01 283.65 3.22 284.89 4.82 1 0 9 3.61 219.91 7.96 193.93 8.53 205.70 4.19 191.43 9.29 208.10 6.87 194.48 3.92 1 0 11 2.95 275.46 4.04 296.43 7.45 276.65 2.68 300.81 5.29 271.81 3.29 279.35 5.10 1 0 13 2.50 69.10 4.41 -1.00 -1.00 79.54 5.99 -1.00 -1.00 61.36 5.49 -1.00 -1.00 1 0 15 2.16 194.40 4.01 -1.00 -1.00 192.92 4.12 -1.00 -1.00 202.23 3.58 -1.00 -1.00 1 1 2 15.92 181.17 6.78 168.61 14.92 190.25 2.32 175.54 2.30 190.92 2.66 182.28 3.59 1 1 4 8.08 237.52 7.37 242.37 9.74 237.66 2.69 246.69 4.24 254.61 2.94 257.44 3.38 1 1 6 5.40 189.65 2.32 218.04 8.57 188.24 3.60 207.64 2.56 184.91 2.17 199.97 7.25 1 1 8 4.05 315.84 10.49 352.54 4.85 327.30 4.06 350.41 5.57 335.21 5.38 347.82 5.10 1 1 10 3.24 53.28 8.65 55.75 9.43 51.94 10.30 -1.00 -1.00 57.78 6.72 51.35 5.05 1 1 12 2.70 86.93 15.80 85.89 6.31 79.51 5.16 76.80 3.88 65.63 4.76 81.88 7.28 1 1 14 2.32 61.26 6.99 -1.00 -1.00 52.86 6.06 -1.00 -1.00 65.78 7.04 -1.00 -1.00 2 -1 3 10.59 725.37 10.42 687.84 12.38 704.25 13.31 661.07 11.23 713.28 8.71 679.25 13.55 2 -1 5 6.44 685.82 8.25 655.29 9.47 689.32 6.35 665.75 6.69 680.69 7.75 672.81 10.08 2 -1 7 4.62 749.24 10.05 751.56 10.43 755.29 7.19 756.50 9.47 754.52 8.40 756.47 13.26 Opened binary file: mad_fpfm.scl Opened formatted file: solve_1.sca 12490 RECORDS WRITTEN Opened binary file: mad_fpfm.scl Opened formatted file: solve_2.sca 12490 RECORDS WRITTEN Opened binary file: mad_fpfm.scl Opened formatted file: solve_3.sca 12490 RECORDS WRITTEN Resolution range will be from 2.0999999 to 20. Please enter input dorgbn-style file> Opened binary file: mad_fbar.scl This file has 12 columns of data. They are: Col: 0:mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1:Fbar Wavelength # 1 ! a label for th Col: 2:Sig of Fbar Wavelength # 1 ! a label for th Col: 3:Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4:sig of Del Ano Wavelength # 1 ! a label for th Col: 5:Fbar set 2 Col: 6:Sig of Fbar set 2 Col: 7:Del Ano (F+ - F-) set 2 Col: 8:sig of Del Ano set 2 Col: 9:Fbar set 3 Col: 10:Sig of Fbar set 3 Col: 11:Del Ano (F+ - F-) set 3 Col: 12:sig of Del Ano set 3 How many records would you like to see? (if you type "-1" you can enter a particular reflection to look at) > 20records will be listed. H K L Resol Col1 Col2 Col3 Col4 Col5 (etc) 0 0 4 8.12 761.83 19.68 0.00 0.00 700.66 17.52 0.00 0.00 682.61 12.54 -61.10 25.08 0 0 8 4.06 458.29 7.88 -68.80 15.76 468.80 5.56 -42.68 11.12 482.62 8.49 -33.90 16.98 0 0 12 2.71 724.80 17.74 0.00 0.00 715.17 12.52 0.00 0.00 717.74 16.11 0.00 0.00 1 0 3 10.78 283.93 3.01 25.82 6.03 291.40 2.10 22.44 4.21 304.00 2.71 14.83 5.41 1 0 5 6.48 297.27 3.09 0.93 6.17 306.25 4.23 3.31 8.46 318.83 3.23 -0.72 6.46 1 0 7 4.64 304.69 3.07 -3.28 6.13 297.85 2.27 -3.60 4.55 284.27 2.90 -1.24 5.80 1 0 9 3.61 206.92 5.84 25.98 11.67 198.56 5.10 14.27 10.19 201.29 3.96 13.62 7.91 1 0 11 2.95 285.95 4.24 -20.97 8.48 288.73 2.97 -24.16 5.93 275.58 3.03 -7.54 6.07 1 0 13 2.50 69.10 4.41 0.00 0.00 79.54 5.99 0.00 0.00 61.36 5.49 0.00 0.00 1 0 15 2.16 194.40 4.01 0.00 0.00 192.92 4.12 0.00 0.00 202.23 3.58 0.00 0.00 1 1 2 15.92 174.89 8.19 12.56 16.39 182.89 1.63 14.72 3.27 186.60 2.24 8.64 4.47 1 1 4 8.08 239.95 6.11 -4.85 12.22 242.17 2.51 -9.03 5.02 256.02 2.24 -2.83 4.48 1 1 6 5.40 203.85 4.44 -28.39 8.88 197.94 2.21 -19.41 4.42 192.44 3.78 -15.06 7.57 1 1 8 4.05 334.19 5.78 -36.70 11.56 338.86 3.44 -23.11 6.89 341.51 3.71 -12.61 7.41 1 1 10 3.24 54.51 6.40 -2.47 12.80 51.94 10.30 0.00 0.00 54.56 4.20 6.43 8.41 1 1 12 2.70 86.41 8.51 1.03 17.02 78.16 3.23 2.71 6.45 73.75 4.35 -16.25 8.70 1 1 14 2.32 61.26 6.99 0.00 0.00 52.86 6.06 0.00 0.00 65.78 7.04 0.00 0.00 2 -1 3 10.59 706.61 8.09 37.52 16.18 682.66 8.71 43.18 17.41 696.27 8.05 34.03 16.11 2 -1 5 6.44 670.55 6.28 30.53 12.56 677.53 4.61 23.57 9.22 676.75 6.36 7.88 12.71 2 -1 7 4.62 750.40 7.24 -2.32 14.48 755.90 5.95 -1.21 11.89 755.49 7.85 -1.95 15.69 *************************************************************************** SOLVE STATUS 30-apr-05 11:29:06 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS -------------------------------------------------- *** Analysis of this scaled MAD data set *** ** Completeness of Fbar data at each wavelength: ** Completeness of dataset 1 ( F > 2. * sigma) Wavelength # 1 ! a label for this wavelength COMPLETE: Analyzes completeness of a dataset. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with data to be examined.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for F and Sigma. Use "0" if missing> F from column: 1: Fbar Wavelength # 1 Sig of F from col: 2: Sig of Fbar Wavelength # 1 What is minimum ratio of F/sig to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Total of 12402 unique reflections for native were found in the resolution range out of 12490 in the file **** Acentric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1345 1343 99.9 2 3.150 1927 1926 99.9 3 2.940 757 757 100.0 4 2.783 767 766 99.9 5 2.625 935 931 99.6 6 2.520 753 750 99.6 7 2.415 901 897 99.6 8 2.310 1097 1088 99.2 9 2.205 1285 1268 98.7 10 2.100 1592 1566 98.4 total 11359 11292 99.4 **** Centric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 276 276 100.0 2 3.150 227 223 98.2 3 2.940 75 74 98.7 4 2.783 64 62 96.9 5 2.625 87 84 96.6 6 2.520 60 57 95.0 7 2.415 75 71 94.7 8 2.310 76 74 97.4 9 2.205 97 89 91.8 10 2.100 110 100 90.9 total 1147 1110 96.8 **** All reflections ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1621 1619 99.9 2 3.150 2154 2149 99.8 3 2.940 832 831 99.9 4 2.783 831 828 99.6 5 2.625 1022 1015 99.3 6 2.520 813 807 99.3 7 2.415 976 968 99.2 8 2.310 1173 1162 99.1 9 2.205 1382 1357 98.2 10 2.100 1702 1666 97.9 total 12506 12402 99.2 Completeness of dataset 2 ( F > 2. * sigma) set 2 COMPLETE: Analyzes completeness of a dataset. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with data to be examined.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for F and Sigma. Use "0" if missing> F from column: 5: Fbar set 2 Sig of F from col: 6: Sig of Fbar set 2 What is minimum ratio of F/sig to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Total of 12448 unique reflections for native were found in the resolution range out of 12490 in the file **** Acentric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1345 1343 99.9 2 3.150 1927 1925 99.9 3 2.940 757 756 99.9 4 2.783 767 764 99.6 5 2.625 935 933 99.8 6 2.520 753 752 99.9 7 2.415 901 900 99.9 8 2.310 1097 1088 99.2 9 2.205 1285 1281 99.7 10 2.100 1592 1581 99.3 total 11359 11323 99.7 **** Centric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 276 274 99.3 2 3.150 227 224 98.7 3 2.940 75 74 98.7 4 2.783 64 64 100.0 5 2.625 87 86 98.9 6 2.520 60 58 96.7 7 2.415 75 73 97.3 8 2.310 76 74 97.4 9 2.205 97 94 96.9 10 2.100 110 104 94.5 total 1147 1125 98.1 **** All reflections ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1621 1617 99.8 2 3.150 2154 2149 99.8 3 2.940 832 830 99.8 4 2.783 831 828 99.6 5 2.625 1022 1019 99.7 6 2.520 813 810 99.6 7 2.415 976 973 99.7 8 2.310 1173 1162 99.1 9 2.205 1382 1375 99.5 10 2.100 1702 1685 99.0 total 12506 12448 99.5 Completeness of dataset 3 ( F > 2. * sigma) set 3 COMPLETE: Analyzes completeness of a dataset. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with data to be examined.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for F and Sigma. Use "0" if missing> F from column: 9: Fbar set 3 Sig of F from col: 10: Sig of Fbar set 3 What is minimum ratio of F/sig to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Total of 12202 unique reflections for native were found in the resolution range out of 12490 in the file **** Acentric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1345 1331 99.0 2 3.150 1927 1911 99.2 3 2.940 757 752 99.3 4 2.783 767 763 99.5 5 2.625 935 926 99.0 6 2.520 753 747 99.2 7 2.415 901 890 98.8 8 2.310 1097 1085 98.9 9 2.205 1285 1277 99.4 10 2.100 1592 1572 98.7 total 11359 11254 99.1 **** Centric reflections only ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 276 220 79.7 2 3.150 227 200 88.1 3 2.940 75 62 82.7 4 2.783 64 53 82.8 5 2.625 87 74 85.1 6 2.520 60 51 85.0 7 2.415 75 62 82.7 8 2.310 76 62 81.6 9 2.205 97 79 81.4 10 2.100 110 85 77.3 total 1147 948 82.7 **** All reflections ****** Reflections observed: Possible Found % complete shell dmin 1 4.200 1621 1551 95.7 2 3.150 2154 2111 98.0 3 2.940 832 814 97.8 4 2.783 831 816 98.2 5 2.625 1022 1000 97.8 6 2.520 813 798 98.2 7 2.415 976 952 97.5 8 2.310 1173 1147 97.8 9 2.205 1382 1356 98.1 10 2.100 1702 1657 97.4 total 12506 12202 97.6 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 (Delta f-prime = 0.520000458 ) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: Fbar Wavelength # 1 Sig of Nat F from col: 2: Sig of Fbar Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 5: Fbar set 2 Sig of Der F from col: 6: Sig of Fbar set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12402 unique reflections for native Summary of data for derivative : A total of 12449 unique derivative data were found Total of 12402 native F, 12448 deriv F observed Additionally, 88 native and 42 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1619 1617 1617 1603 2 3.150 2154 2149 2149 2146 2130 3 2.940 832 831 830 830 821 4 2.783 831 828 828 825 815 5 2.625 1022 1015 1019 1012 1007 6 2.520 813 807 810 806 801 7 2.415 976 968 973 967 958 8 2.310 1173 1162 1162 1157 1144 9 2.205 1382 1357 1375 1354 1350 10 2.100 1702 1666 1685 1658 1641 total 12506 12402 12448 12372 12270 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A total of 95 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 1.001 0.000 -0.017 0.000 Overall average scale factor = 1.00003529 for n = 12270 Note that there were 76 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 12343 records written. Of these, 12343 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 12267 had F for native Number of reflns rejected >3sig: 105 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1601 522.961 0.019 1.000 5.71 11.48 0.50 2 3.150 2126 463.429 0.018 1.000 0.00 10.85 0.00 3 2.940 825 320.324 0.022 1.000 2.38 8.68 0.27 4 2.783 815 281.046 0.021 1.000 0.00 7.81 0.00 5 2.625 1007 235.866 0.026 0.999 2.53 7.29 0.35 6 2.520 800 205.602 0.030 1.000 3.29 6.92 0.48 7 2.415 957 195.348 0.030 1.000 1.96 7.15 0.27 8 2.310 1144 193.785 0.031 1.000 1.68 7.45 0.23 9 2.205 1351 182.081 0.035 1.001 2.64 7.54 0.35 10 2.100 1641 163.756 0.038 1.001 1.47 7.81 0.19 Total: 12267 296.827 0.024 1.000 2.37 8.82 0.25 Recommended resolution cut-off = 3.15 Dispersive differences lambda 3 - lambda 1 (Delta f-prime = 5.36000061 ) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: Fbar Wavelength # 1 Sig of Nat F from col: 2: Sig of Fbar Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 9: Fbar set 3 Sig of Der F from col:10: Sig of Fbar set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12402 unique reflections for native Summary of data for derivative : A total of 12203 unique derivative data were found Total of 12402 native F, 12202 deriv F observed Additionally, 88 native and 288 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1619 1551 1551 1543 2 3.150 2154 2149 2111 2110 2090 3 2.940 832 831 814 813 808 4 2.783 831 828 816 813 808 5 2.625 1022 1015 1000 996 995 6 2.520 813 807 798 795 793 7 2.415 976 968 952 947 941 8 2.310 1173 1162 1147 1140 1134 9 2.205 1382 1357 1356 1338 1332 10 2.100 1702 1666 1657 1635 1630 total 12506 12402 12202 12138 12074 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 1.00 A total of 61 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 1.002 0.000 -0.055 0.000 Overall average scale factor = 0.99998641 for n = 12074 Note that there were 64 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 12127 records written. Of these, 12127 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 12063 had F for native Number of reflns rejected >3sig: 75 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1540 523.093 0.040 1.001 22.24 14.65 1.52 2 3.150 2085 464.284 0.035 0.999 15.70 13.08 1.20 3 2.940 806 319.717 0.042 0.999 14.10 10.04 1.40 4 2.783 809 277.701 0.042 1.000 12.37 8.72 1.42 5 2.625 994 236.945 0.047 1.000 11.40 8.07 1.41 6 2.520 793 205.893 0.052 1.001 11.07 7.53 1.47 7 2.415 941 196.474 0.051 1.001 10.10 7.68 1.31 8 2.310 1133 192.521 0.052 1.001 10.05 7.92 1.27 9 2.205 1332 181.693 0.053 1.001 9.02 7.95 1.13 10 2.100 1630 163.599 0.057 1.001 8.34 8.34 1.00 Total: 12063 295.651 0.043 1.000 13.56 10.24 1.29 Recommended resolution cut-off = 2.10 Dispersive differences lambda 3 - lambda 2 (Delta f-prime = 4.84000015 ) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 5: Fbar set 2 Sig of Nat F from col: 6: Sig of Fbar set 2 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fbar.scl Col: 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col: 1: Fbar Wavelength # 1 ! a label for th Col: 2: Sig of Fbar Wavelength # 1 ! a label for th Col: 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for th Col: 4: sig of Del Ano Wavelength # 1 ! a label for th Col: 5: Fbar set 2 Col: 6: Sig of Fbar set 2 Col: 7: Del Ano (F+ - F-) set 2 Col: 8: sig of Del Ano set 2 Col: 9: Fbar set 3 Col: 10: Sig of Fbar set 3 Col: 11: Del Ano (F+ - F-) set 3 Col: 12: sig of Del Ano set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 9: Fbar set 3 Sig of Der F from col:10: Sig of Fbar set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12448 unique reflections for native Summary of data for derivative : A total of 12203 unique derivative data were found Total of 12448 native F, 12202 deriv F observed Additionally, 42 native and 288 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1617 1551 1550 1537 2 3.150 2154 2149 2111 2110 2087 3 2.940 832 830 814 812 806 4 2.783 831 828 816 813 805 5 2.625 1022 1019 1000 998 990 6 2.520 813 810 798 795 790 7 2.415 976 973 952 951 943 8 2.310 1173 1162 1147 1142 1135 9 2.205 1382 1375 1356 1352 1341 10 2.100 1702 1685 1657 1647 1638 total 12506 12448 12202 12170 12072 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A total of 97 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 1.001 0.000 -0.036 0.000 Overall average scale factor = 1.00001574 for n = 12072 Note that there were 32 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 12086 records written. Of these, 12086 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 12054 had F for native Number of reflns rejected >3sig: 116 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1540 523.328 0.027 1.001 11.04 14.07 0.79 2 3.150 2081 463.827 0.024 1.000 6.56 12.46 0.53 3 2.940 805 317.553 0.030 1.000 7.87 9.27 0.85 4 2.783 803 277.132 0.029 1.000 6.73 8.21 0.82 5 2.625 990 236.264 0.032 1.000 5.78 7.48 0.77 6 2.520 787 205.189 0.036 1.000 6.12 6.97 0.88 7 2.415 941 195.450 0.036 1.001 5.29 7.08 0.75 8 2.310 1132 192.327 0.038 1.001 5.56 7.28 0.76 9 2.205 1339 180.046 0.038 1.000 4.61 7.31 0.63 10 2.100 1636 162.600 0.043 1.000 4.61 7.56 0.61 Total: 12054 294.793 0.030 1.000 6.76 9.63 0.71 Recommended resolution cut-off = 2.10 ** R-factors for anomalous differences ** Anomalous differences lambda 1 (f" = 2.83999991) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 1: F+ from separateano Wavelength # 1 Sig of Nat F from col: 2: sig of F+ Wavelength # 1 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 3: F- from separateano Wavelength # 1 Sig of Der F from col: 4: sig of F- Wavelength # 1 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12319 unique reflections for native Summary of data for derivative : A total of 10968 unique derivative data were found Total of 12319 native F, 10967 deriv F observed Additionally, 171 native and 1523 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1613 1336 1330 1329 2 3.150 2154 2139 1909 1899 1891 3 2.940 832 828 740 737 735 4 2.783 831 828 754 754 753 5 2.625 1022 1010 911 906 903 6 2.520 813 799 732 724 721 7 2.415 976 963 865 860 857 8 2.310 1173 1153 1042 1033 1030 9 2.205 1382 1344 1216 1203 1200 10 2.100 1702 1642 1462 1438 1432 total 12506 12319 10967 10884 10851 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.01 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A total of 27 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 0.999 0.000 0.066 0.000 Overall average scale factor = 0.999774218 for n = 10851 Note that there were 83 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 10931 records written. Of these, 10931 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 10848 had F for native Number of reflns rejected >3sig: 36 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1328 538.790 0.073 0.999 46.84 16.18 2.89 2 3.150 1890 470.288 0.064 1.000 34.22 14.92 2.29 3 2.940 734 320.741 0.081 1.002 29.96 11.83 2.53 4 2.783 752 276.589 0.083 1.001 26.44 10.66 2.48 5 2.625 902 235.654 0.091 1.000 24.84 10.08 2.46 6 2.520 722 208.964 0.093 1.000 22.65 9.83 2.31 7 2.415 858 198.018 0.100 1.000 22.44 10.11 2.22 8 2.310 1027 195.721 0.096 0.998 20.96 10.42 2.01 9 2.205 1201 182.567 0.097 0.997 19.31 10.64 1.82 10 2.100 1434 167.318 0.102 0.999 18.39 11.06 1.66 Total: 10848 298.793 0.081 0.999 28.89 12.25 2.24 Recommended resolution cut-off = 2.10 Opened formatted file: solve_1.sn Anomalous differences lambda 2 (f" = 4.) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 5: F+ from separateano set 2 Sig of Nat F from col: 6: sig of F+ set 2 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 7: F- from separateano set 2 Sig of Der F from col: 8: sig of F- set 2 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 12382 unique reflections for native Summary of data for derivative : A total of 11139 unique derivative data were found Total of 12382 native F, 11138 deriv F observed Additionally, 108 native and 1352 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1615 1340 1338 1333 2 3.150 2154 2144 1911 1906 1898 3 2.940 832 830 751 751 748 4 2.783 831 828 756 756 755 5 2.625 1022 1014 922 917 914 6 2.520 813 805 741 736 734 7 2.415 976 967 887 881 880 8 2.310 1173 1152 1067 1057 1053 9 2.205 1382 1358 1249 1232 1229 10 2.100 1702 1669 1514 1498 1492 total 12506 12382 11138 11072 11036 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A total of 29 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 1.001 0.000 0.015 0.000 Overall average scale factor = 0.999859691 for n = 11036 Note that there were 66 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 11103 records written. Of these, 11103 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 11037 had F for native Number of reflns rejected >3sig: 35 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1334 539.391 0.063 0.999 40.40 14.03 2.88 2 3.150 1897 471.634 0.055 0.999 29.57 12.91 2.29 3 2.940 748 316.300 0.070 1.000 26.20 9.88 2.65 4 2.783 755 276.402 0.070 1.001 22.22 9.05 2.45 5 2.625 915 234.303 0.077 1.002 21.06 8.30 2.54 6 2.520 733 206.662 0.083 1.002 19.99 8.43 2.37 7 2.415 879 195.399 0.085 1.000 19.40 8.40 2.31 8 2.310 1053 193.394 0.081 0.999 17.64 8.72 2.02 9 2.205 1229 180.128 0.083 0.998 16.41 9.01 1.82 10 2.100 1494 164.148 0.086 0.998 15.06 9.26 1.63 Total: 11037 296.041 0.069 1.000 24.73 10.42 2.26 Recommended resolution cut-off = 2.10 Opened formatted file: solve_2.sn Anomalous differences lambda 3 (f" = 3.69000006) LOCALSCALE: Space-group general scaling. In this program the Native data is mapped to the asymmetric unit, then expanded to the entire sphere. The Derivative data is scaled without mapping to the asymmetric unit. Both native and derivative must be in dorgbn-style files. If anomalous differences are present in the derivative file, they will be scaled and written out. Resolution range will be from 2.0999999 to 20. Please enter name of dorgbn-style input file with "native" data to be used as a reference in scaling a "derivative" dataset.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Native F and Sigma. Use "0" if missing> Native F from column: 9: F+ from separateano set 3 Sig of Nat F from col: 10: sig of F+ set 3 What is minimum ratio of F/sig to for F native or F Deriv to be read in at all? > For measurements with F/sigma of F < 2.00 the F will be ignored Now enter name of "derivative" dataset to be scaled.> Opened binary file: mad_fpfm.scl Col: 0: mad_fpfm.scl Fnat,sig,(F+,sig,F-,sig)n Col: 1: F+ from separateano Wavelength # 1 ! a label for th Col: 2: sig of F+ Wavelength # 1 ! a label for th Col: 3: F- from separateano Wavelength # 1 ! a label for th Col: 4: sig of F- Wavelength # 1 ! a label for th Col: 5: F+ from separateano set 2 Col: 6: sig of F+ set 2 Col: 7: F- from separateano set 2 Col: 8: sig of F- set 2 Col: 9: F+ from separateano set 3 Col: 10: sig of F+ set 3 Col: 11: F- from separateano set 3 Col: 12: sig of F- set 3 Please enter column numbers for Deriv F and Sigma and for DelAno and Sig if present. Use "0" if missing> Assuming you have no del Ano measurements Deriv F from column: 11: F- from separateano set 3 Sig of Der F from col:12: sig of F- set 3 Each of these columns will be scaled and written to the output file. The output file will have 2 columns of data. Enter name of output file to be written with scaled derivative data > Opened binary file: scratch3 Overwriting this file. Enter overall title for scaled output data > Are we to keep reflections with especially large differences (1), or toss them just before writing out data (0)? > Reflections with large differences will be tossed. What is the minimum number of reflections surrounding a reflection to be scaled to use in scaling (30) > Minimum number of reflections used in scaling will be 30 Total of 11605 unique reflections for native Summary of data for derivative : A total of 10860 unique derivative data were found Total of 11605 native F, 10859 deriv F observed Additionally, 885 native and 1631 der were not observed. Duplicate measurements (averaged) of nat = 0, of der = 0 Reflections observed for derivative: Possible Unique All All shell dmin Unique nat der both both > 3sig 1 4.200 1621 1502 1313 1264 1259 2 3.150 2154 2007 1873 1769 1754 3 2.940 832 763 727 676 675 4 2.783 831 773 739 696 694 5 2.625 1022 961 896 857 855 6 2.520 813 760 722 684 679 7 2.415 976 903 859 810 805 8 2.310 1173 1086 1038 977 970 9 2.205 1382 1284 1219 1147 1142 10 2.100 1702 1566 1473 1382 1377 total 12506 11605 10859 10262 10210 Mean value of Nat/Der for 10 resol ranges: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A total of 48 reflections were not used in determining scale factors because del fs or sigmas were too large. Wilson scaling of data: Derivative A Sig of A B Sig of B 1 0.999 0.000 0.028 0.000 Overall average scale factor = 0.999886453 for n = 10210 Note that there were 597 reflections for which only derivative data was present but which were scaled and written out. For this set of native + 1 derivative, there were a total of 10808 records written. Of these, 10808 had Fbar for the deriv and 0 had delf ano for the deriv. A total of 10211 had F for native Number of reflns rejected >3sig: 51 Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 4.200 1259 538.200 0.047 0.999 24.67 20.59 1.20 2 3.150 1754 468.243 0.042 1.000 16.59 17.87 0.93 3 2.940 675 317.664 0.052 1.001 16.46 13.05 1.26 4 2.783 693 275.912 0.052 1.001 13.72 11.52 1.19 5 2.625 854 231.905 0.059 1.001 13.46 10.21 1.32 6 2.520 681 205.422 0.060 1.000 11.73 9.95 1.18 7 2.415 805 195.961 0.065 0.999 12.57 9.75 1.29 8 2.310 969 191.574 0.065 0.998 11.99 9.98 1.20 9 2.205 1143 181.018 0.066 0.998 11.27 9.96 1.13 10 2.100 1378 164.197 0.071 0.999 10.06 10.28 0.98 Total: 10211 295.663 0.053 0.999 15.21 13.60 1.13 Recommended resolution cut-off = 2.10 Opened formatted file: solve_3.sn Deleting scratch files... *************************************************************************** SOLVE STATUS 30-apr-05 11:29:20 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SCALE_MAD STEP TIME: 2 MIN STATUS Enter "HELP", commands, or keywords > >ANALYZE_MAD ! run MADMRG and MADBST and analyze all the Patterson Resolution range will be from 2.0999999 to 20. *************************************************************************** SOLVE STATUS 30-apr-05 11:29:20 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 2 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 0 SEC STATUS Output summary will be written to solve.prt ANALYZE_MAD: Run MADMRG and MADBST on MAD data to get ready for SOLVE Opened binary file: mad_fbar.scl MADMRG: program to merge MAD data and convert it to pseudo-SIR+ano data and to map all data to the asymmetric unit of the space group. Scattering form factors read for 3 wavelengths for anomalously scattering atoms and for nitrogen (used for protein) 1: lambda = 0.9790 ATOM a1 a2 a3 a4 b1 b2 b3 b4 c f' f" ANO 17.001 5.820 3.973 4.354 2.410 0.273 15.237 43.816 2.841 -8.520 2.840 2: lambda = 0.9788 ATOM a1 a2 a3 a4 b1 b2 b3 b4 c f' f" ANO 17.001 5.820 3.973 4.354 2.410 0.273 15.237 43.816 2.841 -8.000 4.000 3: lambda = 0.9600 ATOM a1 a2 a3 a4 b1 b2 b3 b4 c f' f" ANO 17.001 5.820 3.973 4.354 2.410 0.273 15.237 43.816 2.841 -3.160 3.690 Resolution range will be from 2.0999999 to 20. Enter name of .drg file containing reflection data> Opened binary file: mad_fbar.scl col 0 : mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n col 1 : Fbar Wavelength # 1 ! a label for this wavelength col 2 : Sig of Fbar Wavelength # 1 ! a label for this wavelength col 3 : Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength col 4 : sig of Del Ano Wavelength # 1 ! a label for this wavelength col 5 : Fbar set 2 col 6 : Sig of Fbar set 2 col 7 : Del Ano (F+ - F-) set 2 col 8 : sig of Del Ano set 2 col 9 : Fbar set 3 col 10 : Sig of Fbar set 3 col 11 : Del Ano (F+ - F-) set 3 col 12 : sig of Del Ano set 3 ENTER NAME OF OUTPUT FILE (.drg format): Opened binary file: madmrg.out col 0 : madmrg output: col 1 : madmrg: MOCK FNAT col 2 : madmrg: MOCK sig FNAT col 3 : madmrg: MOCK FDER col 4 : madmrg: MOCK sig FDER col 5 : madmrg: MOCK DEL ANO col 6 : madmrg: MOCK sig DEL ANO col 7 : madmrg: Del iso for Patterson col 8 : madmrg: Sigma of del iso for Patterson Enter number of protein residues per a.u.: Enter #of anomalously scattering atoms in the a.u. How many wavelengths (up to 6) are in this input file? > Expecting 3 wavelengths in this file. Set # 1 label: Wavelength # 1 ! a label for this wavelength Set # 2 label: set 2 Set # 3 label: set 3 Set: 1 2 3 Lambda : 0.9790 0.9788 0.9600 N protein : 147 147 147 # anom atoms: 3 3 3 Col for Fbar: 1 5 9 Col for Sig : 2 6 10 Col DelfAno : 3 7 11 Col for sig : 4 8 12 Which of the 3 wavelengths is to be defined as the "standard" at which all values of Fa will be calculated? > Chose wavelength 2 as standard based on its value of f-doubleprime Wavelength # 2 with lambda=0.9788, corresponding to data set 2 will be used as the standard wavelength. 12490 REFLECTIONS READ FROM THIS FILE *** Warning -- f" values for lambda 1 and 2 as input were: lambda 1 f"= 2.83999991 lambda 2 f"= 4. After refinement, these have switched: lambda 1 f"= 4.55928755 lambda 2 f"= 4.0365324 You may wish to use FIXSCATTFACTORS so as not to refine them. Defining new atom type "LAM1" with the values of fprime, f" ready for using MADMRG output data in HEAVY at lambda 1 New itypemad = 212 NEWATOMTYPE LAM1 AVAL 17.00060 5.81960 3.97310 4.35430 BVAL 2.40980 0.27260 15.23720 43.81630 CVAL 2.84090 FPRIMV -8.43941 FPRPRV 4.55929 Defining new atom type "LAM2" with the values of fprime, f" ready for using MADMRG output data in HEAVY at lambda 2 New itypemad = 213 NEWATOMTYPE LAM2 AVAL 17.00060 5.81960 3.97310 4.35430 BVAL 2.40980 0.27260 15.23720 43.81630 CVAL 2.84090 FPRIMV -8.09081 FPRPRV 4.03653 Defining new atom type "LAM3" with the values of fprime, f" ready for using MADMRG output data in HEAVY at lambda 3 New itypemad = 214 NEWATOMTYPE LAM3 AVAL 17.00060 5.81960 3.97310 4.35430 BVAL 2.40980 0.27260 15.23720 43.81630 CVAL 2.84090 FPRIMV -4.14946 FPRPRV 2.84570 Summary of averaging results. Total of 12170 reflections written out Type Mean Chi Naveraged Iso 1.0000 12170 Ano 1.0000 11239 Fbar 1.0000 12170 Acentric reflections: Summary of merging statistics by shell: Note: all data are written out, only data with >1 observation used in this analysis shell Nobs Mult RMS value sig Norm value sig 1 4.200 Iso : 1337. 2.9 269.206 187.295 0.392 0.272 Ano: 1341. 2.9 43.683 9.501 0.064 0.014 Fbar : 1337. 2.9 687.606 187.535 1.000 0.273 2 3.150 Iso : 1909. 2.8 203.375 185.320 0.362 0.330 Ano: 1922. 2.9 33.459 8.806 0.060 0.016 Fbar : 1909. 2.8 561.991 185.476 1.000 0.330 3 2.940 Iso : 746. 2.8 190.044 161.707 0.464 0.395 Ano: 753. 2.9 28.415 6.688 0.069 0.016 Fbar : 746. 2.8 409.745 161.834 1.000 0.395 4 2.783 Iso : 756. 2.8 173.043 130.707 0.487 0.368 Ano: 763. 2.9 24.668 6.323 0.069 0.018 Fbar : 756. 2.8 355.472 130.844 1.000 0.368 5 2.625 Iso : 915. 2.8 116.447 107.870 0.410 0.379 Ano: 927. 2.9 23.188 5.833 0.082 0.021 Fbar : 915. 2.8 284.306 108.031 1.000 0.380 6 2.520 Iso : 738. 2.8 146.939 115.973 0.539 0.425 Ano: 748. 2.9 21.723 5.853 0.080 0.021 Fbar : 738. 2.8 272.655 116.109 1.000 0.426 7 2.415 Iso : 879. 2.8 119.676 108.171 0.486 0.439 Ano: 890. 2.9 21.507 5.852 0.087 0.024 Fbar : 879. 2.8 246.327 108.301 1.000 0.440 8 2.310 Iso : 1054. 2.8 130.005 110.280 0.534 0.453 Ano: 1081. 2.8 20.763 6.314 0.085 0.026 Fbar : 1054. 2.8 243.591 110.417 1.000 0.453 9 2.205 Iso : 1230. 2.8 128.439 113.803 0.540 0.478 Ano: 1267. 2.8 19.295 6.826 0.081 0.029 Fbar : 1230. 2.8 237.887 113.957 1.000 0.479 10 2.100 Iso : 1491. 2.7 131.959 114.142 0.588 0.509 Ano: 1547. 2.8 18.530 7.272 0.083 0.032 Fbar : 1491. 2.7 224.467 114.285 1.000 0.509 All Iso : 11055. 2.8 172.887 142.320 0.423 0.348 Ano: 11239. 2.9 27.525 7.342 0.067 0.018 Fbar : 11055. 2.8 408.555 142.476 1.000 0.349 Centric reflections: Summary of merging statistics by shell: Note: all data are written out, only data with >1 observation used in this analysis shell Nobs Mult RMS value sig Norm value sig 1 4.200 Iso : 275. 2.6 800.344 480.488 0.773 0.464 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 275. 2.6 1036.002 480.645 1.000 0.464 2 3.150 Iso : 223. 2.8 364.133 420.970 0.539 0.623 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 223. 2.8 675.274 421.143 1.000 0.624 3 2.940 Iso : 74. 2.6 361.445 288.536 0.620 0.495 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 74. 2.6 582.911 288.685 1.000 0.495 4 2.783 Iso : 64. 2.6 312.882 403.040 0.559 0.720 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 64. 2.6 560.161 403.131 1.000 0.720 5 2.625 Iso : 85. 2.7 262.337 254.959 0.667 0.649 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 85. 2.7 393.087 255.133 1.000 0.649 6 2.520 Iso : 57. 2.7 179.286 142.505 0.571 0.454 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 57. 2.7 313.915 142.641 1.000 0.454 7 2.415 Iso : 71. 2.7 198.382 205.045 0.566 0.585 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 71. 2.7 350.682 205.214 1.000 0.585 8 2.310 Iso : 73. 2.7 254.402 191.650 0.694 0.523 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 73. 2.7 366.647 191.798 1.000 0.523 9 2.205 Iso : 91. 2.7 182.987 267.727 0.550 0.805 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 91. 2.7 332.421 267.796 1.000 0.806 10 2.100 Iso : 102. 2.6 228.733 220.577 0.713 0.688 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 102. 2.6 320.585 220.706 1.000 0.688 All Iso : 1115. 2.7 468.981 358.622 0.700 0.536 Ano: 0. 0.0 0.000 0.000 0.000 0.000 Fbar : 1115. 2.7 669.586 358.763 1.000 0.536 All reflections: Summary of merging statistics by shell: Note: all data are written out, only data with >1 observation used in this analysis shell Nobs Mult RMS value sig Norm value sig 1 4.200 Iso : 1612. 2.8 411.562 261.687 0.543 0.345 Ano: 1341. 2.9 43.683 9.501 0.058 0.013 Fbar : 1612. 2.8 758.449 261.879 1.000 0.345 2 3.150 Iso : 2132. 2.8 225.619 222.008 0.392 0.386 Ano: 1922. 2.9 33.459 8.806 0.058 0.015 Fbar : 2132. 2.8 574.886 222.158 1.000 0.386 3 2.940 Iso : 820. 2.8 211.298 176.925 0.493 0.413 Ano: 753. 2.9 28.415 6.688 0.066 0.016 Fbar : 820. 2.8 428.256 177.053 1.000 0.413 4 2.783 Iso : 820. 2.8 187.743 168.610 0.500 0.449 Ano: 763. 2.9 24.668 6.323 0.066 0.017 Fbar : 820. 2.8 375.484 168.725 1.000 0.449 5 2.625 Iso : 1000. 2.8 135.118 127.170 0.458 0.431 Ano: 927. 2.9 23.188 5.833 0.079 0.020 Fbar : 1000. 2.8 295.116 127.325 1.000 0.431 6 2.520 Iso : 795. 2.8 149.491 118.074 0.542 0.428 Ano: 748. 2.9 21.723 5.853 0.079 0.021 Fbar : 795. 2.8 275.819 118.209 1.000 0.429 7 2.415 Iso : 950. 2.8 127.252 118.189 0.498 0.462 Ano: 890. 2.9 21.507 5.852 0.084 0.023 Fbar : 950. 2.8 255.604 118.321 1.000 0.463 8 2.310 Iso : 1127. 2.8 141.416 117.274 0.558 0.463 Ano: 1081. 2.8 20.763 6.314 0.082 0.025 Fbar : 1127. 2.8 253.379 117.409 1.000 0.463 9 2.205 Iso : 1321. 2.8 132.917 130.371 0.541 0.531 Ano: 1267. 2.8 19.295 6.826 0.079 0.028 Fbar : 1321. 2.8 245.569 130.506 1.000 0.531 10 2.100 Iso : 1593. 2.7 140.172 123.731 0.605 0.534 Ano: 1547. 2.8 18.530 7.272 0.080 0.031 Fbar : 1593. 2.7 231.819 123.870 1.000 0.534 All Iso : 12170. 2.8 217.491 173.730 0.495 0.396 Ano: 11239. 2.9 27.525 7.342 0.063 0.017 Fbar : 12170. 2.8 438.977 173.873 1.000 0.396 Bayesian weighting: rms sigmas are nearly as large as rms deltas. Sigmas not used. Total # of reflections written out = 12170 Final refined values of fprime and fdoubleprime Form factors at lambda = 0.9790 f-prime = -8.44 f" = 4.56 Form factors at lambda = 0.9788 f-prime = -8.09 f" = 4.04 Form factors at lambda = 0.9600 f-prime = -4.15 f" = 2.85 Resolution range will be from 2.0999999 to 20. *************************************************************************** SOLVE STATUS 30-apr-05 11:32:03 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 3 MIN STATUS Resolution range will be from 2.10017443 to 20. Setting up arrays...this may take some time for large unit cells.... SETGRID: set fft and patterson grids (This can take some time for big unit cells) Setting fft grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:32:04 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 0 SEC STATUS The fft containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of map requires 221232 of 1825201 points in unit cell. The fft containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 190 192 0 96 192 0 23 48 The EZD map file containing the output map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 190 0 96 0 23 Setting patt grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:32:08 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 4 SEC STATUS The patterson containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of Patterson map requires 230450 of 1825201 points in unit cell. The patterson containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: PATTGRID 0 190 192 0 96 192 0 24 48 *************************************************************************** SOLVE STATUS 30-apr-05 11:32:10 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 6 SEC STATUS This unit cell is not chiral Opened binary file: mad_fbar.scl Opened binary file: madbst.out Opened formatted file: FA.sca *************************************************************************** SOLVE STATUS 30-apr-05 11:32:10 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 3 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:32:38 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 5 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 3 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:33:07 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 6 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 4 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:33:36 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 6 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 4 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:34:03 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 7 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 5 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:34:29 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 7 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 5 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:34:53 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 8 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 6 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:34:53 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 8 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 6 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:35:23 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 8 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 6 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:35:52 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 9 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 7 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:36:20 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 9 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 7 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:36:46 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 7 MIN STATUS *************************************************************************** SOLVE STATUS 30-apr-05 11:37:11 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 8 MIN STATUS Opened formatted file: solve_0.sn *************************************************************************** SOLVE STATUS 30-apr-05 11:37:11 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 8 MIN STATUS Fa Patterson from MADBST to be written to: patt_Fa.ezd MAPS. Generates Patterson or Fourier maps from .drg files. Enter "0" for Patterson, "-1" for origin-removed Patterson, or "1" for Fourier > Patterson will be calculated Enter name of .drg file with data > Opened binary file: madbst.out Col 0:mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Col 1:Fbar Wavelength # 1 ! a label for this wavelength Col 2:Sig of Fbar Wavelength # 1 ! a label for this wavelength Col 3:Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength Col 4:sig of Del Ano Wavelength # 1 ! a label for this wavelength Col 5:Fbar set 2 Col 6:Sig of Fbar set 2 Col 7:Del Ano (F+ - F-) set 2 Col 8:sig of Del Ano set 2 Col 9:Fbar set 3 Col 10:Sig of Fbar set 3 Col 11:Del Ano (F+ - F-) set 3 Col 12:sig of Del Ano set 3 Col 13: = Fa component along Fo weighted by fom Col 14: = weighted Fa component perpendicular to Fo Col 15: = best estimate of Fa Col 16:sigma of Col 17:sqrt = sqrt of best estimate of Fa**2 Col 18:sigma of sqrt Enter column numbers for f**2 OR F and for sigma of F**2 or F> F**2 or F and sigma from columns: 17 0 Is this f**2 (0) or F (1)> Opened binary scratch file: /var/tmp/scratch.dat_0 Resolution range will be from 2.10017443 to 20. Please enter maximum value of |F|, |delF|, or |DelAno| to include, or "0" to include everything > No cutoff for |F|, |delF|, or |DelAno| will be used Total of 12377 records read and 12377 records written. There were 0 records without phase and 0 without data and 0 with |F| or |delF| that was too large. and 0 out of resolution range Fast Fourier Transform Overall title from file: Patterson data |F|. Col: 1: Patterson data |F|. Columns for A, B are: 1 0 ORDERING: A HORIZONTAL B VERTICAL C SECTIONS Opened binary scratch file: /var/tmp/scratch.dat_0 REFLECTIONS read, EXPANDED, FOURIER coeff 12377 49508 12813 MAXIMUM HKL 54 38 15 MAXIMUM P 54 The output fft containing an asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 Please enter name of output FFT file > Opened binary file: patterson.patt SCALE AND F000... 1.00 0.00 WHOLE MAP XBAR, SIG... 7667.4 0.38771E+07 FFTtoEZD: Convert from an asymmetric unit of FFT to any grid and output the file in EZD format. The fft containing an asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 What is the output ezd file name > Opened formatted file: patt_Fa.ezd The EZD-format fft containing the desired region of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 This output map is contained within the input map. for 463175. points in input map, mean 7667.222, rms= 3876572.2 Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: madmrg.out INPUT FILE 2> Opened binary file: madbst.out What is the output file to be called > Opened binary file: solve.data Please enter overall title for new file > MADMRG output (cols 1 to 8) and MADBST fh cos,sin theta (cols13 and 14) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: madmrg output: COL 1: madmrg: MOCK FNAT COL 2: madmrg: MOCK sig FNAT COL 3: madmrg: MOCK FDER COL 4: madmrg: MOCK sig FDER COL 5: madmrg: MOCK DEL ANO COL 6: madmrg: MOCK sig DEL ANO COL 7: madmrg: Del iso for Patterson COL 8: madmrg: Sigma of del iso for Patterson What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 8 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n COL 1: Fbar Wavelength # 1 ! a label for this wavelength COL 2: Sig of Fbar Wavelength # 1 ! a label for this wavelength COL 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength COL 4: sig of Del Ano Wavelength # 1 ! a label for this wavelength COL 5: Fbar set 2 COL 6: Sig of Fbar set 2 COL 7: Del Ano (F+ - F-) set 2 COL 8: sig of Del Ano set 2 COL 9: Fbar set 3 COL 10: Sig of Fbar set 3 COL 11: Del Ano (F+ - F-) set 3 COL 12: sig of Del Ano set 3 COL 13: = Fa component along Fo weighted by fom COL 14: = weighted Fa component perpendicular to Fo COL 15: = best estimate of Fa COL 16: sigma of COL 17: sqrt = sqrt of best estimate of Fa**2 COL 18: sigma of sqrt What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 13 to 14 What file do you want to read from (type 0 to end input) > Total of 12377 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Resolution range will be from 2.0999999 to 20. Setting up arrays...this may take some time for large unit cells.... SETGRID: set fft and patterson grids (This can take some time for big unit cells) Setting fft grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:37:21 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 0 SEC STATUS The fft containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of map requires 221232 of 1825201 points in unit cell. The fft containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 190 192 0 96 192 0 23 48 The EZD map file containing the output map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 190 0 96 0 23 Setting patt grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:37:24 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 3 SEC STATUS The patterson containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of Patterson map requires 230450 of 1825201 points in unit cell. The patterson containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: PATTGRID 0 190 192 0 96 192 0 24 48 *************************************************************************** SOLVE STATUS 30-apr-05 11:37:26 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 5 SEC STATUS This unit cell is not chiral Opening scratch file for script: scratch.script Opened formatted file: scratch.script Overwriting this file. Opened formatted file: scratch.script FILE MERGING How many files do you want to open for reading in data > Opening 2 files for reading in data: INPUT FILE 1> Opened binary file: madmrg.out INPUT FILE 2> Opened binary file: mad_fbar.scl What is the output file to be called > Opened binary file: mad_all.drg Please enter overall title for new file > MADMRG output (cols 1 to 6) and MAD_FBAR.SCL (cols 1 and 12) This program copies columns of data from the input files to the output file. The columns to copy (and their order) are specified by a series of commands of the form: File #, then on the next line: ColA,ColB, This command causes columns ColA through ColB from this file to be copied to the output file. Note: The tiles of columns usually are just copied to the output file. To change the titles, type the new title for ColA at the end of the command line. The program will prompt for titles for the other columns. What file do you want to read from (type 0 to end input) > Reading from file 1 COL 0: madmrg output: COL 1: madmrg: MOCK FNAT COL 2: madmrg: MOCK sig FNAT COL 3: madmrg: MOCK FDER COL 4: madmrg: MOCK sig FDER COL 5: madmrg: MOCK DEL ANO COL 6: madmrg: MOCK sig DEL ANO COL 7: madmrg: Del iso for Patterson COL 8: madmrg: Sigma of del iso for Patterson What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 6 What file do you want to read from (type 0 to end input) > Reading from file 2 COL 0: mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n COL 1: Fbar Wavelength # 1 ! a label for this wavelength COL 2: Sig of Fbar Wavelength # 1 ! a label for this wavelength COL 3: Del Ano (F+ - F-) Wavelength # 1 ! a label for this wavelength COL 4: sig of Del Ano Wavelength # 1 ! a label for this wavelength COL 5: Fbar set 2 COL 6: Sig of Fbar set 2 COL 7: Del Ano (F+ - F-) set 2 COL 8: sig of Del Ano set 2 COL 9: Fbar set 3 COL 10: Sig of Fbar set 3 COL 11: Del Ano (F+ - F-) set 3 COL 12: sig of Del Ano set 3 What is the range of columns to copy ? ColA, ColB, (optional new title for ColA)> Range of columns is: 1 to 12 What file do you want to read from (type 0 to end input) > Total of 12490 records written out. All done with file merging... you might wish to view your new file with VIEW now to check it... Closed command file: scratch.script Opening scratch file for script: solve_mad.script Opened formatted file: solve_mad.script Opened formatted file: solve_combine.script Setting max # of sites ("NSOLSITE") to 3 based on value of "NANOMALOUS" as nsolsite is not set Opened formatted file: solve_mad.script Closed command file: solve_mad.script ------- setting up for combine-------- *************************************************************************** SOLVE STATUS 30-apr-05 11:37:27 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:ANALYZE_MAD STEP TIME: 8 MIN STATUS Enter "HELP", commands, or keywords > >SOLVE ! Solve the structure Resolution range will be from 2.0999999 to 20. *************************************************************************** SOLVE STATUS 30-apr-05 11:37:27 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 0 SEC STATUS SOLVE: Solve MIR or SIR datasets for heavy atoms Log file for "solve" is mad.logfile Output summary will be written to solve.prt Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /usr/local/lib/solve/syminfo.lib Dataset name:Solve_mtz Using Bayesian MAD phasing at end of SOLVE *************************************************************************** SOLVE STATUS 30-apr-05 11:37:27 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 0 SEC STATUS Datafile with 10 columns of data: Setting up arrays...this may take some time for large unit cells.... SETGRID: set fft and patterson grids (This can take some time for big unit cells) Setting fft grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:37:29 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 0 SEC STATUS The fft containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of map requires 221232 of 1825201 points in unit cell. The fft containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 190 192 0 96 192 0 23 48 The EZD map file containing the output map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 23 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 190 0 96 0 23 Setting patt grid... *************************************************************************** SOLVE STATUS 30-apr-05 11:37:33 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 4 SEC STATUS The patterson containing the whole map runs from: 0 to 192 in x, where the cell translation is 192 0 to 192 in y, where the cell translation is 192 0 to 48 in z, where the cell translation is 48 Asymmetric unit of Patterson map requires 230450 of 1825201 points in unit cell. The patterson containing the asymmetric unit of the map runs from: 0 to 190 in x, where the cell translation is 192 0 to 96 in y, where the cell translation is 192 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: PATTGRID 0 190 192 0 96 192 0 24 48 *************************************************************************** SOLVE STATUS 30-apr-05 11:37:34 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SETTING GRIDS STEP TIME: 5 SEC STATUS This unit cell is not chiral INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 0.22174E+07, SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.737 0.185 0.000 88.046 2 0.164 0.294 0.062 74.517 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -1.474 -0.370 0.000 9461.46 15504.2 2 2 -0.922 0.552 0.000 20729.1 15504.2 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.573 0.109 0.062 6372.70 6560.92 1 2 -0.901 -0.479 0.062 7416.29 6560.92 1 3 -1.031 -0.021 0.062 8456.16 6560.92 1 4 -0.443 -0.349 0.062 8164.81 6560.92 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.328 -0.589 0.000 6075.37 11105.5 2 2 -0.458 -0.130 0.000 14988.3 11105.5 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 15524.6 Overall quality of the fit to patterson = 3.17839 Avg normalized peak height = 4680.86 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.112 0.180 0.000 88.315 2 0.794 0.336 0.104 74.196 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.224 -0.359 0.000 8059.00 15599.1 2 2 -0.292 -0.068 0.000 22419.2 15599.1 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 0.682 0.156 0.104 6240.80 6552.64 1 2 -0.906 -0.516 0.104 7241.70 6552.64 1 3 -0.448 0.615 0.104 7773.51 6552.64 1 4 0.224 -0.974 0.104 8339.89 6552.64 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -1.589 -0.672 0.000 6075.37 11010.2 2 2 -1.130 0.458 0.000 14988.3 11010.2 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 15226.4 Overall quality of the fit to patterson = 3.67795 Avg normalized peak height = 4590.94 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.000 78.729 2 0.112 0.180 0.000 79.294 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.46 12396.6 2 2 -0.552 0.078 0.000 20729.1 12396.6 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.203 -0.057 0.000 9192.76 12485.6 2 2 -0.427 -0.417 0.000 10826.8 12485.6 2 3 -0.495 -0.125 0.000 9284.21 12485.6 2 4 -0.135 -0.349 0.000 10064.2 12485.6 2 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.224 -0.359 0.000 8059.00 12575.2 2 2 -0.292 -0.068 0.000 22419.2 12575.2 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 12886.3 Overall quality of the fit to patterson = 4.52318 Avg normalized peak height = 3885.36 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.000 86.840 Evaluation of this test soln with 1 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.46 15082.5 2 2 -0.552 0.078 0.000 20729.1 15082.5 2 Total of 1 of 4 patterson peaks used more than once. Overall quality of this Patterson soln = 6502.16 Overall quality of the fit to patterson = 3.98371 Avg normalized peak height = 3251.08 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.388 0.320 0.000 87.224 Evaluation of this test soln with 1 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.776 -0.641 0.000 8059.00 15216.2 2 2 -0.708 0.068 0.000 22419.2 15216.2 2 Total of 1 of 4 patterson peaks used more than once. Overall quality of this Patterson soln = 6223.87 Overall quality of the fit to patterson = 5.07711 Avg normalized peak height = 3111.93 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.164 0.294 0.000 68.585 2 0.279 0.461 0.062 61.004 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.328 -0.589 0.000 6075.37 9407.76 2 2 -0.458 -0.130 0.000 14988.3 9407.76 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 0.115 0.167 0.062 1664.86 4183.95 1 2 -0.443 -0.755 0.062 2291.62 4183.95 1 3 -0.625 -0.016 0.062 1192.79 4183.95 1 4 0.297 -0.573 0.062 1274.49 4183.95 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.557 -0.922 0.000 16522.0 7442.98 2 2 -0.740 -0.182 0.000 1295.33 7442.98 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 6080.72 Overall quality of the fit to patterson = 4.15394 Avg normalized peak height = 1833.40 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.000 86.712 2 0.018 0.195 0.125 18.722 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.46 15037.9 2 2 -0.552 0.078 0.000 20729.1 15037.9 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.297 -0.042 0.125 788.279 1623.40 1 2 -0.333 -0.432 0.125 1108.80 1623.40 1 3 -0.510 -0.219 0.125 1826.59 1623.40 1 4 -0.120 -0.255 0.125 922.576 1623.40 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.036 -0.391 0.000 2010.06 701.009 2 2 -0.214 -0.177 0.000 1587.10 701.009 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 5816.16 Overall quality of the fit to patterson = 2.47679 Avg normalized peak height = 1753.64 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.112 0.180 0.000 87.074 2 0.018 0.195 0.083 19.812 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.224 -0.359 0.000 8059.00 15163.7 2 2 -0.292 -0.068 0.000 22419.2 15163.7 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.094 0.016 0.083 1246.05 1725.07 1 2 -0.130 -0.375 0.083 599.987 1725.07 1 3 -0.307 -0.161 0.083 1177.80 1725.07 1 4 0.083 -0.198 0.083 2042.28 1725.07 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.036 -0.391 0.000 2010.06 784.997 2 2 -0.214 -0.177 0.000 1587.10 784.997 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 5785.27 Overall quality of the fit to patterson = 3.12116 Avg normalized peak height = 1744.32 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.000 86.589 2 0.133 0.146 0.219 19.585 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.46 14995.1 2 2 -0.552 0.078 0.000 20729.1 14995.1 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.182 -0.091 0.219 831.168 1695.81 1 2 -0.448 -0.383 0.219 1292.59 1695.81 1 3 -0.461 -0.104 0.219 1607.23 1695.81 1 4 -0.169 -0.370 0.219 678.329 1695.81 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.266 -0.292 0.000 2184.93 767.120 2 2 -0.279 -0.013 0.000 2249.59 767.120 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 5784.93 Overall quality of the fit to patterson = 2.51650 Avg normalized peak height = 1744.22 *************************************************************************** SOLVE STATUS 30-apr-05 11:37:40 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 10 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 13 SEC STATUS Skew of the map is: 0.0285138357 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 999.98 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.479 87.105 2 0.167 0.294 0.052 67.087 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.61 15174.6 2 2 -0.552 0.078 0.000 20729.4 15174.6 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.148 0.057 -0.427 7334.30 5843.59 1 2 -0.482 -0.531 -0.427 6652.62 5843.59 1 3 -0.609 -0.070 -0.427 4552.90 5843.59 1 4 -0.021 -0.404 -0.427 5678.01 5843.59 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.333 -0.589 0.000 5383.68 9001.25 2 2 -0.461 -0.128 0.000 12311.1 9001.25 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 13456.5 Overall quality of the fit to patterson = 2.89367 Avg normalized peak height = 4057.27 Skew of the map is: 0.22128135 Skew of the map is: 0.0246571451 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.388 0.320 0.010 88.200 2 0.167 0.294 0.104 68.316 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.776 -0.641 0.000 8059.13 15558.4 2 2 -0.708 0.068 0.000 22419.5 15558.4 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.221 -0.026 0.094 7727.86 6025.49 1 2 -0.555 -0.615 0.094 7105.84 6025.49 1 3 -0.682 -0.154 0.094 6007.67 6025.49 1 4 -0.094 -0.487 0.094 6671.42 6025.49 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.333 -0.589 0.000 5383.67 9334.27 2 2 -0.461 -0.128 0.000 12311.1 9334.27 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 14282.0 Overall quality of the fit to patterson = 3.46759 Avg normalized peak height = 4306.18 Skew of the map is: 0.247676983 Skew of the map is: 0.183744028 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.479 78.913 2 0.112 0.180 0.479 79.267 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.61 12454.6 2 2 -0.552 0.078 0.000 20729.4 12454.6 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.203 -0.057 0.000 9192.91 12510.3 2 2 -0.427 -0.417 0.000 10827.0 12510.3 2 3 -0.495 -0.125 0.000 9284.36 12510.3 2 4 -0.135 -0.349 0.000 10064.4 12510.3 2 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.224 -0.359 0.000 8059.13 12566.4 2 2 -0.292 -0.068 0.000 22419.5 12566.4 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 12893.1 Overall quality of the fit to patterson = 4.52326 Avg normalized peak height = 3887.41 Skew of the map is: 0.0731901526 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.315 0.237 0.479 86.843 Evaluation of this test soln with 1 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.61 15083.5 2 2 -0.552 0.078 0.000 20729.4 15083.5 2 Total of 1 of 4 patterson peaks used more than once. Overall quality of this Patterson soln = 6502.42 Overall quality of the fit to patterson = 3.98377 Avg normalized peak height = 3251.21 Skew of the map is: 0.0840970874 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.388 0.320 0.010 87.450 Evaluation of this test soln with 1 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.776 -0.641 0.000 8059.13 15295.2 2 2 -0.708 0.068 0.000 22419.5 15295.2 2 Total of 1 of 4 patterson peaks used more than once. Overall quality of this Patterson soln = 6241.68 Overall quality of the fit to patterson = 5.07732 Avg normalized peak height = 3120.84 Skew of the map is: -0.0126505895 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.00 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.333 0.206 0.417 66.413 2 0.216 0.029 0.490 4.578 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.667 -0.411 0.000 5383.67 8821.46 2 2 -0.539 0.128 0.000 12311.1 8821.46 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.117 -0.177 0.073 786.511 304.014 1 2 -0.549 -0.234 0.073 973.962 304.014 1 3 -0.362 0.010 0.073 769.352 304.014 1 4 -0.305 -0.422 0.073 -198.474 304.014 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.432 -0.057 0.000 -1108.79 41.9088 2 2 -0.245 0.188 0.000 -2598.64 41.9088 2 Total of 2 of 11 patterson peaks used more than once. Overall quality of this Patterson soln = 2473.80 Overall quality of the fit to patterson = 1.74365 Avg normalized peak height = 745.880 Skew of the map is: 0.00456976192 *************************************************************************** SOLVE STATUS 30-apr-05 11:41:26 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 14 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 4 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.53; score = 6.77) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.100 19.9 13.9 STATUS 2 0.334 0.206 0.417 1.144 32.8 13.0 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 14 MIN STATUS --------------------------------------------------------------------------- INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 Skew of the map is: 0.597609937 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.388 0.320 0.010 88.917 2 0.333 0.206 0.417 70.149 3 0.315 0.237 0.479 88.841 Evaluation of this test soln with 3 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.776 -0.641 0.000 8059.13 15812.5 2 2 -0.708 0.068 0.000 22419.5 15812.5 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.055 -0.115 0.406 7105.83 6237.47 1 2 -0.721 -0.526 0.406 7727.86 6237.47 1 3 -0.594 0.013 0.406 6671.41 6237.47 1 4 -0.182 -0.654 0.406 6007.66 6237.47 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.667 -0.411 0.000 5383.67 9841.84 2 2 -0.539 0.128 0.000 12311.1 9841.84 2 Cross-vectors for sites 3 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.073 -0.083 0.469 9392.11 7899.48 1 2 -0.703 -0.557 0.469 8054.42 7899.48 1 3 -0.625 -0.005 0.469 7932.37 7899.48 1 4 -0.151 -0.635 0.469 8783.02 7899.48 1 Cross-vectors for sites 3 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.018 0.031 0.062 7146.45 6232.13 1 2 -0.648 -0.443 0.062 8478.72 6232.13 1 3 -0.570 0.109 0.062 6035.57 6232.13 1 4 -0.096 -0.521 0.062 6891.26 6232.13 1 Cross-vectors for sites 3 and 3 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.61 15785.4 2 2 -0.552 0.078 0.000 20729.4 15785.4 2 Total of 3 of 22 patterson peaks used more than once. Overall quality of this Patterson soln = 26105.0 Overall quality of the fit to patterson = 3.06579 Avg normalized peak height = 5565.60 *************************************************************************** SOLVE STATUS 30-apr-05 11:42:08 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 15 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 5 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- Skew of the map is: 0.0100357495 *************************************************************************** SOLVE STATUS 30-apr-05 11:42:21 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 15 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 5 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- *************************************************************************** SOLVE STATUS 30-apr-05 11:42:27 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 15 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 5 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- Skew of the map is: 0.597609937 INPUT PATTERSON MAP HAS 463175 ELEMENTS AND AN RMS VALUE OF 1000.0 , SCALED TO 1000.0 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.388 0.320 0.010 88.917 2 0.333 0.206 0.417 70.149 3 0.315 0.237 0.479 88.841 Evaluation of this test soln with 3 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.776 -0.641 0.000 8059.13 15812.5 2 2 -0.708 0.068 0.000 22419.5 15812.5 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.055 -0.115 0.406 7105.83 6237.47 1 2 -0.721 -0.526 0.406 7727.86 6237.47 1 3 -0.594 0.013 0.406 6671.41 6237.47 1 4 -0.182 -0.654 0.406 6007.66 6237.47 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.667 -0.411 0.000 5383.67 9841.84 2 2 -0.539 0.128 0.000 12311.1 9841.84 2 Cross-vectors for sites 3 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.073 -0.083 0.469 9392.11 7899.48 1 2 -0.703 -0.557 0.469 8054.42 7899.48 1 3 -0.625 -0.005 0.469 7932.37 7899.48 1 4 -0.151 -0.635 0.469 8783.02 7899.48 1 Cross-vectors for sites 3 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.018 0.031 0.062 7146.45 6232.13 1 2 -0.648 -0.443 0.062 8478.72 6232.13 1 3 -0.570 0.109 0.062 6035.57 6232.13 1 4 -0.096 -0.521 0.062 6891.26 6232.13 1 Cross-vectors for sites 3 and 3 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.630 -0.474 0.000 9461.61 15785.4 2 2 -0.552 0.078 0.000 20729.4 15785.4 2 Total of 3 of 22 patterson peaks used more than once. Overall quality of this Patterson soln = 26105.0 Overall quality of the fit to patterson = 3.06579 Avg normalized peak height = 5565.60 *************************************************************************** SOLVE STATUS 30-apr-05 11:42:51 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 16 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 5 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- Total of 12490 data read from file Total of 12490 data read from file **** Expanding heavy atom parameters for Bayesian MAD phasing **** (Shifting for this phasing step only from the MADMRG-compressed dataset in mad_fbar.scl with wavelength 2 as the standard, to the full F+,sigma, F-,sigma at 3 wavelengths in mad_fpfm.scl ) *************************************************************************** SOLVE STATUS 30-apr-05 11:43:05 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 16 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 0 SEC STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- Opened formatted file: phases-hl.export Opened formatted file: phases-hl.script Opened binary file: mad_fpfm.scl Resolution range will be from 2.10017443 to 20. Opened binary file: phases-hl.drg Total of 12490 data read from file PARAMETER SHIFTS FOR DERIV 2 : set 2 SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 Se 1.1321 0.3871 0.3200 0.0117 20.4011 CURRENT VALUES: 2 Se 1.1228 0.3340 0.2059 0.4184 29.9320 CURRENT VALUES: 3 Se 1.1756 0.3147 0.2370 0.4840 23.3759 HA_PDB: writing out current heavy atom sites in PDB format File = ha.pdb Also writing fractional coords to solve.xyz Also writing fractional coords of inverse to solve_inverse.xyz Opened formatted file: ha.pdb Opened formatted file: solve.xyz Opened formatted file: solve_inverse.xyz WRITTEN OUTPUT MTZ FILE Logical Name: solve.mtz Filename: solve.mtz * Title: 3-wavelength MAD dataset ! a title for this dataset * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 Solve_mtz Solve_mtz Solve_mtz 113.9490 113.9490 32.4740 90.0000 90.0000 90.0000 0.97880 * Number of Columns = 11 * Number of Reflections = 12490 * Missing value set to NaN in input mtz file * Column Labels : H K L FP SIGFP PHIB FOM HLA HLB HLC HLD * Column Types : H H H F Q P W A A A A * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - use crystal cells) 113.9490 113.9490 32.4740 90.0000 90.0000 90.0000 * Resolution Range : 0.00262 0.22672 ( 19.542 - 2.100 A ) * Sort Order : 0 0 0 0 0 * Space group = 'I 4' (number 79) Writing final maps to solve.ezd and solve.ccp4_map Opening output file solve.ccp4_map Logical Name: solve.ccp4_map Filename: solve.ccp4_map File name for output map file on unit 1 : solve.ccp4_map logical name solve.ccp4_map *************************************************************************** SOLVE STATUS 30-apr-05 11:50:01 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 23 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE STEP TIME: 7 MIN STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS --------------------------------------------------------------------------- Deleting scratch files... Enter "HELP", commands, or keywords > > Ending this session. *************************************************************************** SOLVE STATUS 30-apr-05 11:50:01 DATASET TITLE: 3-wavelength MAD dataset ! a title for this dataset STATUS TIME ELAPSED: 23 MIN STATUS --------------------------------------------------------------------------- CURRENT STEP:SOLVE MAIN PROGRAM STATUS --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE ( = 0.69; score = 15.65) --- STATUS X Y Z OCCUP B HEIGHT/SIGMA STATUS 2 0.387 0.320 0.012 1.132 20.4 20.4 STATUS 2 0.334 0.206 0.418 1.123 29.9 20.9 STATUS 2 0.315 0.237 0.484 1.176 23.4 18.8 STATUS TIME REQUIRED TO OBTAIN THIS SOLUTION: 15 MIN STATUS ---------------------------------------------------------------------------