The date today is 12-apr-01. Your license expires on 15-jul-07. ------------------------ 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 2.00 of 12-Apr-2001 / Size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" Space group number is: 5 Space group name from file name is: c2 The fft containing the asymmetric unit of the map runs from: 0 to 95 in x, where the cell translation is 96 0 to 17 in y, where the cell translation is 36 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 95 96 0 17 36 0 24 48 The EZD map file containing the output map runs from: 0 to 95 in x, where the cell translation is 96 0 to 17 in y, where the cell translation is 36 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 95 0 17 0 24 The patterson containing the asymmetric unit of the map runs from: 0 to 95 in x, where the cell translation is 96 0 to 18 in y, where the cell translation is 36 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 95 96 0 18 36 0 24 48 Rescaling standard dataset to put it on approximate absolute scale. NRES = 80; expected = 78400.00 ; observed in lowest resolution shell = 432677.4 ... Scale factor = 0.1811973 -------------------------------------------------- *** Analysis of this scaled MAD data set *** Fbar,sigma,Delano,sigma for 3 wavelengths written to: mad_fbar.scl F+,sigma,F-,sigma for 3 wavelengths written to: mad_fpfm.scl ** Completeness of Fbar data at each wavelength: ** Completeness of dataset 1 ( F > 2.000000 * sigma) set 1 with 2 se atoms, lambda 1 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 233 97.5 2 4.500 317 312 98.4 3 4.200 120 119 99.2 4 3.975 120 118 98.3 5 3.750 155 155 100.0 6 3.600 112 109 97.3 7 3.450 143 138 96.5 8 3.300 172 167 97.1 9 3.150 190 188 98.9 10 3.000 254 250 98.4 total 1822 1789 98.2 Completeness of dataset 2 ( F > 2.000000 * sigma) set 2 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 233 97.5 2 4.500 317 308 97.2 3 4.200 120 116 96.7 4 3.975 120 118 98.3 5 3.750 155 151 97.4 6 3.600 112 110 98.2 7 3.450 143 139 97.2 8 3.300 172 167 97.1 9 3.150 190 186 97.9 10 3.000 254 248 97.6 total 1822 1776 97.5 Completeness of dataset 3 ( F > 2.000000 * sigma) set 3 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 235 98.3 2 4.500 317 309 97.5 3 4.200 120 117 97.5 4 3.975 120 117 97.5 5 3.750 155 152 98.1 6 3.600 112 108 96.4 7 3.450 143 137 95.8 8 3.300 172 166 96.5 9 3.150 190 188 98.9 10 3.000 254 248 97.6 total 1822 1777 97.5 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 224 182.668 9.777 0.054 1.000 0.973 1.024 2 4.500 301 176.331 10.523 0.060 1.002 0.980 1.031 3 4.200 113 169.880 9.280 0.055 1.002 0.984 1.023 4 3.975 113 146.034 8.023 0.055 1.002 0.984 1.021 5 3.750 150 147.399 8.904 0.060 1.001 0.980 1.023 6 3.600 106 130.646 6.117 0.047 0.999 0.979 1.017 7 3.450 133 108.657 5.728 0.053 1.000 0.982 1.019 8 3.300 160 105.862 5.940 0.056 0.999 0.979 1.018 9 3.150 183 107.665 5.953 0.055 1.000 0.975 1.019 10 3.000 241 98.444 5.271 0.054 1.000 0.969 1.022 Total: 1724 139.482 7.754 0.056 1.000 Dispersive differences lambda 3 - lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 228 188.230 12.980 0.069 1.000 0.974 1.022 2 4.500 304 176.736 12.264 0.069 1.001 0.977 1.027 3 4.200 116 173.593 12.418 0.072 1.003 0.980 1.020 4 3.975 114 141.613 10.761 0.076 1.002 0.979 1.030 5 3.750 149 149.181 8.836 0.059 1.000 0.972 1.021 6 3.600 103 125.755 9.280 0.074 1.000 0.973 1.032 7 3.450 134 107.882 8.707 0.081 1.000 0.965 1.029 8 3.300 159 104.566 7.113 0.068 0.998 0.970 1.021 9 3.150 186 109.499 9.062 0.083 1.000 0.963 1.039 10 3.000 245 101.060 7.604 0.075 1.000 0.971 1.033 Total: 1738 140.572 10.054 0.072 1.000 Dispersive differences lambda 3 - lambda 2 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 228 187.306 12.019 0.064 1.001 0.972 1.033 2 4.500 299 176.400 10.572 0.060 0.998 0.974 1.024 3 4.200 111 167.533 9.612 0.057 1.000 0.981 1.019 4 3.975 112 144.029 8.492 0.059 1.000 0.976 1.025 5 3.750 146 144.819 8.962 0.062 0.999 0.975 1.023 6 3.600 107 130.722 7.590 0.058 1.001 0.984 1.022 7 3.450 133 108.546 7.647 0.070 1.000 0.976 1.030 8 3.300 162 106.804 6.703 0.063 1.000 0.970 1.025 9 3.150 184 108.211 7.011 0.065 1.001 0.975 1.024 10 3.000 243 99.332 6.261 0.063 1.000 0.976 1.023 Total: 1725 139.765 8.669 0.062 1.000 anomalous differences lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 229 190.362 15.476 0.081 1.003 0.971 1.037 2 4.500 306 179.052 15.464 0.086 1.003 0.969 1.029 3 4.200 117 171.908 14.250 0.083 1.001 0.964 1.034 4 3.975 114 144.008 10.826 0.075 1.001 0.976 1.027 5 3.750 149 147.797 11.831 0.080 1.000 0.973 1.026 6 3.600 108 130.278 9.561 0.073 1.001 0.962 1.031 7 3.450 137 111.763 9.470 0.085 0.999 0.968 1.027 8 3.300 165 110.219 9.737 0.088 0.999 0.963 1.034 9 3.150 185 109.083 9.975 0.091 0.999 0.973 1.033 10 3.000 245 100.246 7.755 0.077 0.999 0.970 1.023 Total: 1755 142.019 11.750 0.083 1.001 anomalous differences lambda 2 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 222 180.228 15.746 0.087 1.003 0.967 1.041 2 4.500 301 176.263 14.092 0.080 1.002 0.968 1.033 3 4.200 114 167.430 11.851 0.071 0.999 0.967 1.025 4 3.975 118 151.613 12.246 0.081 0.999 0.974 1.032 5 3.750 149 145.772 12.892 0.088 0.999 0.967 1.024 6 3.600 109 133.238 12.536 0.094 0.999 0.968 1.033 7 3.450 138 114.431 10.293 0.090 1.000 0.969 1.027 8 3.300 165 109.631 10.383 0.095 1.002 0.963 1.037 9 3.150 182 107.689 8.903 0.083 1.001 0.967 1.039 10 3.000 247 100.668 10.615 0.105 1.002 0.963 1.037 Total: 1745 140.190 12.147 0.087 1.001 anomalous differences lambda 3 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 226 184.123 14.309 0.078 1.003 0.968 1.051 2 4.500 303 177.049 14.386 0.081 1.000 0.968 1.039 3 4.200 115 168.936 14.651 0.087 1.003 0.974 1.043 4 3.975 113 142.745 12.078 0.085 1.000 0.976 1.031 5 3.750 148 148.767 11.380 0.076 1.002 0.973 1.039 6 3.600 108 130.307 11.278 0.087 1.002 0.969 1.040 7 3.450 134 109.122 9.487 0.087 1.001 0.972 1.029 8 3.300 166 109.825 10.166 0.093 1.002 0.972 1.041 9 3.150 187 110.183 10.186 0.092 1.000 0.976 1.030 10 3.000 246 101.326 8.951 0.088 1.001 0.959 1.030 Total: 1746 140.487 11.804 0.084 1.001 ANALYZE_MAD: Run MADMRG and MADBST on MAD data to get ready for SOLVE Form factors at lambda = 0.9782 f-prime = -10.00 f" = 3.00 Form factors at lambda = 0.9779 f-prime = -7.50 f" = 5.00 Form factors at lambda = 0.8856 f-prime = -2.00 f" = 3.50 Correlation of anomalous differences at different wavelengths. (You should probably cut your data off at the resolution where this drops below about 0.3. A good dataset has correlation between peak and remote of at least 0.7 overall. Data with correlations below about 0.5 probably are not contributing much.) CORRELATION FOR WAVELENGTH PAIRS DMIN 1 VS 2 1 VS 3 2 VS 3 6.00 0.10 -0.06 0.05 4.50 0.15 0.18 0.22 4.20 0.00 0.09 0.08 3.98 0.13 -0.04 0.12 3.75 0.14 0.04 0.12 3.60 0.20 0.08 0.19 3.45 0.14 0.22 0.17 3.30 0.23 0.09 0.04 3.15 0.17 0.05 0.31 3.00 0.25 0.08 0.19 ALL 0.14 0.08 0.15 Final refined values of fprime and fdoubleprime Form factors at lambda = 0.9782 f-prime = -9.35 f" = 3.38 Form factors at lambda = 0.9779 f-prime = -7.30 f" = 5.56 Form factors at lambda = 0.8856 f-prime = -2.83 f" = 4.03 Fa Patterson from MADBST to be written to: patterson.patt Script file suitable for running SOLVE written to: solve_mad.script Datafile for SOLVE with MADMRG-compressed dataset ("Fnat",sig,"Fder",sig,"Delano",sig,iso diffs, ano diffs, , from MADBST) is: solve.data ----------NEW DATASET BEGINS HERE--------------- Rescaling standard dataset to put it on approximate absolute scale. NRES = 80; expected = 78400.00 ; observed in lowest resolution shell = 430653.5 ... Scale factor = 0.1820489 -------------------------------------------------- *** Analysis of this scaled MAD data set *** Fbar,sigma,Delano,sigma for 3 wavelengths written to: mad_fbar.scl_2 F+,sigma,F-,sigma for 3 wavelengths written to: mad_fpfm.scl ** Completeness of Fbar data at each wavelength: ** Completeness of dataset 1 ( F > 2.000000 * sigma) set 1 with 1 fe atoms, lambda 1 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 234 97.9 2 4.500 317 311 98.1 3 4.200 120 118 98.3 4 3.975 120 118 98.3 5 3.750 155 155 100.0 6 3.600 112 109 97.3 7 3.450 143 139 97.2 8 3.300 172 169 98.3 9 3.150 190 188 98.9 10 3.000 254 247 97.2 total 1822 1788 98.1 Completeness of dataset 2 ( F > 2.000000 * sigma) Fe PK Reflections observed: Possible Found % complete shell dmin 1 6.000 239 234 97.9 2 4.500 317 307 96.8 3 4.200 120 117 97.5 4 3.975 120 117 97.5 5 3.750 155 153 98.7 6 3.600 112 109 97.3 7 3.450 143 139 97.2 8 3.300 172 165 95.9 9 3.150 190 185 97.4 10 3.000 254 250 98.4 total 1822 1776 97.5 Completeness of dataset 3 ( F > 2.000000 * sigma) Fe RM Reflections observed: Possible Found % complete shell dmin 1 6.000 239 234 97.9 2 4.500 317 310 97.8 3 4.200 120 120 100.0 4 3.975 120 119 99.2 5 3.750 155 150 96.8 6 3.600 112 109 97.3 7 3.450 143 138 96.5 8 3.300 172 165 95.9 9 3.150 190 187 98.4 10 3.000 254 247 97.2 total 1822 1779 97.6 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 226 186.980 7.890 0.042 0.999 0.981 1.015 2 4.500 298 171.904 7.666 0.045 1.002 0.986 1.021 3 4.200 113 168.554 6.842 0.041 1.003 0.990 1.018 4 3.975 115 149.580 6.480 0.043 1.002 0.988 1.015 5 3.750 151 146.152 6.077 0.042 1.001 0.986 1.021 6 3.600 105 129.190 4.631 0.036 1.000 0.982 1.013 7 3.450 135 104.701 4.365 0.042 1.001 0.987 1.019 8 3.300 162 108.223 4.809 0.044 1.000 0.987 1.018 9 3.150 183 105.616 4.317 0.041 1.000 0.983 1.021 10 3.000 241 96.472 4.151 0.043 1.001 0.976 1.017 Total: 1729 138.584 5.869 0.042 1.001 Dispersive differences lambda 3 - lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 228 192.144 10.622 0.055 1.000 0.982 1.016 2 4.500 303 173.246 10.240 0.059 1.002 0.976 1.023 3 4.200 117 173.681 8.925 0.051 1.004 0.986 1.020 4 3.975 117 150.813 9.159 0.061 1.001 0.984 1.018 5 3.750 149 144.998 7.176 0.049 0.999 0.980 1.021 6 3.600 105 127.537 7.258 0.057 1.000 0.977 1.021 7 3.450 136 105.449 6.805 0.065 1.001 0.975 1.024 8 3.300 162 108.387 6.217 0.057 0.999 0.977 1.018 9 3.150 185 106.433 7.087 0.067 1.001 0.976 1.029 10 3.000 242 97.735 6.195 0.063 1.001 0.980 1.022 Total: 1744 140.198 8.151 0.058 1.001 Dispersive differences lambda 3 - lambda 2 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 228 190.889 8.846 0.046 1.000 0.979 1.016 2 4.500 297 171.729 7.728 0.045 1.000 0.981 1.020 3 4.200 117 171.188 7.712 0.045 1.001 0.988 1.019 4 3.975 116 152.208 7.426 0.049 1.000 0.976 1.017 5 3.750 147 141.639 6.211 0.044 0.999 0.982 1.016 6 3.600 106 129.874 5.458 0.042 1.001 0.985 1.017 7 3.450 134 104.011 5.086 0.049 1.000 0.978 1.019 8 3.300 158 105.403 5.071 0.048 1.000 0.977 1.017 9 3.150 181 104.543 5.269 0.050 1.001 0.984 1.021 10 3.000 243 97.354 4.530 0.047 1.001 0.982 1.014 Total: 1727 138.952 6.430 0.046 1.000 anomalous differences lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 229 193.110 10.986 0.057 1.000 0.981 1.028 2 4.500 305 175.370 10.586 0.060 0.999 0.979 1.019 3 4.200 117 172.185 10.352 0.060 0.999 0.977 1.017 4 3.975 115 148.056 8.029 0.054 1.002 0.989 1.019 5 3.750 153 148.038 9.034 0.061 1.000 0.982 1.018 6 3.600 107 130.561 7.154 0.055 1.001 0.983 1.026 7 3.450 136 107.292 6.492 0.061 1.000 0.975 1.019 8 3.300 167 113.262 6.666 0.059 1.000 0.977 1.028 9 3.150 186 107.710 6.517 0.061 1.001 0.983 1.023 10 3.000 243 96.904 5.628 0.058 1.000 0.975 1.024 Total: 1758 141.405 8.306 0.059 1.000 anomalous differences lambda 2 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 227 188.805 12.599 0.067 1.001 0.972 1.027 2 4.500 301 172.844 9.921 0.057 1.001 0.977 1.022 3 4.200 114 167.674 8.799 0.052 1.000 0.976 1.026 4 3.975 117 152.353 8.917 0.059 1.000 0.982 1.031 5 3.750 150 142.800 9.425 0.066 1.000 0.982 1.025 6 3.600 109 132.976 7.579 0.057 1.000 0.973 1.021 7 3.450 139 109.263 7.341 0.067 1.000 0.977 1.020 8 3.300 162 110.620 6.492 0.059 1.001 0.978 1.030 9 3.150 184 106.085 6.501 0.061 1.000 0.981 1.028 10 3.000 244 97.981 6.534 0.067 1.001 0.979 1.026 Total: 1747 139.825 8.583 0.061 1.001 anomalous differences lambda 3 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 226 188.736 9.996 0.053 1.003 0.982 1.029 2 4.500 305 174.171 9.496 0.055 1.000 0.973 1.032 3 4.200 118 171.230 10.099 0.059 1.002 0.981 1.030 4 3.975 116 149.405 9.244 0.062 0.999 0.976 1.026 5 3.750 145 140.749 7.055 0.050 1.001 0.980 1.037 6 3.600 108 130.388 7.045 0.054 1.000 0.976 1.026 7 3.450 134 103.653 5.795 0.056 1.001 0.973 1.030 8 3.300 163 111.220 6.074 0.055 1.002 0.977 1.025 9 3.150 181 104.860 5.683 0.054 1.000 0.980 1.019 10 3.000 247 99.071 5.735 0.058 1.002 0.979 1.025 Total: 1743 139.571 7.697 0.055 1.001 ANALYZE_MAD: Run MADMRG and MADBST on MAD data to get ready for SOLVE Form factors at lambda = 1.7400 f-prime = -9.00 f" = 2.50 Form factors at lambda = 1.7365 f-prime = -5.00 f" = 4.50 Form factors at lambda = 0.9780 f-prime = 1.00 f" = 1.50 Final refined values of fprime and fdoubleprime Form factors at lambda = 1.7400 f-prime = -8.92 f" = 4.19 Form factors at lambda = 1.7365 f-prime = -5.64 f" = 6.30 Form factors at lambda = 0.9780 f-prime = -1.31 f" = 2.81 Fa Patterson from MADBST to be written to: patterson.patt_2 Script file suitable for running SOLVE written to: solve_mad.script Datafile for SOLVE with MADMRG-compressed dataset ("Fnat",sig,"Fder",sig,"Delano",sig,iso diffs, ano diffs, , from MADBST) is: solve.data_2 ------------------------------------------------ Combining a total of 0 MIR and 2 MAD datasets to form a composite dataset ----------NEW DATASET BEGINS HERE--------------- **** SOLVE: Solutions to MIR or SIR datasets ****** Derivatives considered: 3 (NSET) Cross-vectors tested in HASSP: 6 (ICRMAX, DEFAULT=20) HASSP solutions saved per deriv: 30 (NTOPHASSP, DEFAULT=30) Fourier peaks saved per map: 30 (NTOPFOUR, DEFAULT=10) Sites per derivative: 2 (NSOLSITE, DEFAULT=20) Derivative solutions per seed: 5 (NTOPDERIV, DEFAULT=5) Seeds per derivative tested: 3 (NSEEDTEST,DEFAULT=10) Sorted seeds to use 5 (NSEEDSOLVE, DEFAULT=5) Number of final solutions saved: 5 (NTOPSOLVE, DEFAULT=5) Sites per derivative vary with derivative. Derivative Max sites 1 2 2 -1 3 1 Solutions obtained will be compared to input solution (ICHECKSOLVE) Correlated phasing used (CORRELPHASE) Patterson map for derivative 1 will be read directly from: patterson.patt Patterson map for derivative 3 will be read directly from: patterson.patt_2 For derivative 1 the heavy atom structure factor components parallel to and perpendicular to the native structure factor will be read from columns 9 and 10 Standard difference fouriers will be calculated for derivative 2 For derivative 3 the heavy atom structure factor components parallel to and perpendicular to the native structure factor will be read from columns 19 and 20 For derivative 3 the corresponding native data will be read from columns 11 and 12 For derivative 3 the corresponding native dataset is "derivative" 2 Datafile with 20 columns of data: Title:solve.data (cols 1 to 10) and solve.data_2 Data: madmrg: MOCK FNAT Data: madmrg: MOCK sig FNAT Data: madmrg: MOCK FDER Data: madmrg: MOCK sig FDER Data: madmrg: MOCK DEL ANO Data: madmrg: MOCK sig DEL ANO Data: madmrg: Del iso for Patterson Data: madmrg: Sigma of del iso for Patterson Data: = Fa component along Fo weighted by fom Data: = weighted Fa component perpendicular to Fo Data: madmrg: MOCK FNAT Data: madmrg: MOCK sig FNAT Data: madmrg: MOCK FDER Data: madmrg: MOCK sig FDER Data: madmrg: MOCK DEL ANO Data: madmrg: MOCK sig DEL ANO Data: madmrg: Del iso for Patterson Data: madmrg: Sigma of del iso for Patterson Data: = Fa component along Fo weighted by fom Data: = weighted Fa component perpendicular to Fo Fnat,sigma taken from columns 1 2 Fder,sig,Delano,sig deriv 1 from cols: 3 4 5 6 Fder,sig,Delano,sig deriv 2 from cols: 11 12 0 0 Fder,sig,Delano,sig deriv 3 from cols: 13 14 15 16 Check solution to be compared to all solutions found: Derivative 1: Site X Y Z 1 0.440 0.160 0.380 2 0.230 0.450 0.165 Derivative 2: Site X Y Z Derivative 3: Site X Y Z 1 0.180 0.530 0.770 ********************************************************** ANALYZE_SOLVE: analysis of top 1 solutions ************************************************************* Solution 1 *********************** Analysis of this solution ************* ****** Analysis of non-randomness of native Fourier map ****** A. Maps with distinct solvent regions havea high standard deviation of local r.m.s. electron density. For this map the SD of this local r.m.s. is 0.2207377 B. Maps with distinct solvent regions also have a high correlation of local r.m.s. electron density with density at neighboring locations. Typical values for poor maps in this structure solution are 7.7645741E-02 +/- 1.8577987E-02 For this map the correlation of r.m.s. density in neighboring boxes is 0.1696443 The correlation coefficient is used here in scoring. ****** Analysis of derivative solutions with the difference Patterson ****** and with cross-validation difference Fouriers ----------------------------------------------- Derivative # 1 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.438 0.167 0.385 66.538 2 0.229 0.458 0.167 62.618 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 -0.875 0.000 -0.771 7368.51 8854.54 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.208 0.292 -0.219 7441.43 4166.44 1 2 -0.667 0.292 -0.552 7427.92 4166.44 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.458 0.000 -0.333 6086.11 7841.97 2 Overall quality of this Patterson soln = 7832.43 Overall quality of the fit to patterson = 2.30886 Avg normalized peak height = 3502.77 Cross-validation fouriers calculated with all heavy atoms in all derivs except the site being evaluated and any sites equivalent to it. Site x y z occ B -- PEAK HEIGHT -- 1 0.440 0.160 0.384 0.566 25.013 12.21 2 0.229 0.453 0.168 0.397 19.917 11.80 ----------------------------------------------- Derivative # 2 Cross-validation fouriers calculated with all heavy atoms in all derivs except the site being evaluated and any sites equivalent to it. Site x y z occ B -- PEAK HEIGHT -- ----------------------------------------------- Derivative # 3 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.318 0.000 0.229 88.346 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 -0.635 0.000 -0.458 15610.1 15610.0 2 Overall quality of this Patterson soln = 5518.99 Overall quality of the fit to patterson = 0.283119E-04 Avg normalized peak height = 3902.52 Cross-validation fouriers calculated with all heavy atoms in all derivs except the site being evaluated and any sites equivalent to it. Site x y z occ B -- PEAK HEIGHT -- 1 0.320 0.000 0.229 0.545 27.744 17.70 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 4.37 1.66 8.22 2.32 Cross-validation Fourier: 11.1 0.500 31.6 40.9 NatFourier CCx100: 7.76 1.86 17.0 4.95 Mean figure of meritx100: 0.000E+00 5.00 61.0 12.2 Correction for Z-scores: -24.2 Overall Z-score value: 36.1 ****** Overall analysis of phasing for solution 1************ HEAVY: Refine heavy atom parameters File title: CRYSTALLOGRAPHIC PARAMETERS A = 76.00 B = 28.00 C = 42.00 alpha = 90.00 beta = 103.00 gamma = 90.00 PHASES CALCULATED EVERY 5 DEGREES RESIDUALS CALCULATED ON EXTRA ZEROTH CYCLE ONLY SIGMAS FROM data FILE WILL BE USED STATISTICS WILL BE PRINTED ON ZEROTH CYCLE, SHIFTS ON LAST PHASING WILL BE DONE TAKING INTO ACCOUNT THE CORRELATIONS AMONG DERIVATIVES THE GROUPS OF DERIVATIVES WITH CORRELATIONS WILL BE UPDATED THE BETA VALUES FOR EACH DERIV WILL BE SET TO 1.0 PHASE-AVERAGED RESIDUALS WILL BE USED FOR PHASING TYPE OF REFINEMENT SELECTED: UNPHASED ORIGIN-REMOVED PATTERSON REFINEMENT ONLY Bayesian Correlated Phasing will be used RESOLUTION LIMITS IN ANGSTROMS: 3.000 20.000 MINIMUM RATIO OF FDER TO RMS LACK-OF-CLOSURE FOR INCLUSION IN REFINEMENT OR PHASING= 0.000 MINIMUM NATIVE F: 0.000 MINIMUM FIGURE OF MERIT FOR PHASED REFINEMENT: 0.000 MINIMUM ALLOWED ISOTROPIC B: 0.000 PARAMETER SHIFTS GREATER THAN 0.0000 TIMES SIGMA WILL BE SCALED BY 0.5000 MINIMUM RATIO OF FNAT/SIGMA OR FDER/SIGMA TO INCLUDE: 1.000 NUMBER OF REFINEMENT CYCLES IS 2 DERIVATIVES REFINED DURING THESE CYCLES ARE : 0 0 TYPE OF OUTPUT SELECTED IS: +10 COLUMNS OF HENDRICKSON-LATTMAN COEFFICIENTS data COLUMNS FOR NATIVE F AND SIGMA: 1 2 data COLUMNS FOR BEST AND MOST PROB PHASES AND FIGURE OF MERIT: 0 0 0 OVERALL SCALE FACTOR FOR ALL data = 1.000 SCALE FACTOR FOR NATIVE SIGMAS = 1.000 DERIVATIVE INFORMATION FOR 3 COMPOUNDS COMPOUND 1 set 1 with 1 fe atoms, lambda 1 COLUMNS FOR F, SIGMA, AND ANOM DIFF and sig (=F+ - F-) 3 4 5 6 THIS DERIVATIVE WILL BE USED IN PHASING ANOMALOUS DIFFERENCES WILL BE USED IN PHASING FOR THIS DERIVATIVE AFTER OVERALL SCALING OBSERVED STRUCTURE FACTORS AND SIGMAS WILL BE DIVIDED BY : 1.000*EXP( 0.000*(SIN theta/LAMBDA)**2 ) THEN SIGMAS WILL BE MULTIPLIED BY 1.000 COMPOUND 2 Native from dataset # 2 (a MAD set) used as a deriv. COLUMNS FOR F, SIGMA, AND ANOM DIFF and sig (=F+ - F-) 11 12 0 0 THIS DERIVATIVE WILL BE USED IN PHASING OVERALL SCALING FOR THIS DERIVATIVE WILL BE REFINED AFTER OVERALL SCALING OBSERVED STRUCTURE FACTORS AND SIGMAS WILL BE DIVIDED BY : 1.000*EXP( 0.000*(SIN theta/LAMBDA)**2 ) THEN SIGMAS WILL BE MULTIPLIED BY 1.000 COMPOUND 3 Fe RM COLUMNS FOR F, SIGMA, AND ANOM DIFF and sig (=F+ - F-) 13 14 15 16 THIS DERIVATIVE WILL BE USED IN PHASING ANOMALOUS DIFFERENCES WILL BE USED IN PHASING FOR THIS DERIVATIVE AFTER OVERALL SCALING OBSERVED STRUCTURE FACTORS AND SIGMAS WILL BE DIVIDED BY : 1.000*EXP( 0.000*(SIN theta/LAMBDA)**2 ) THEN SIGMAS WILL BE MULTIPLIED BY 1.000 CARRYING OUT STANDARD REFINEMENT Total of 2 cycles will be done Derivs refined will be 0 0 SUMMARY OF RESULTS ON FINAL CYCLE: NUMBER OF REFLECTIONS READ = 1822 NUMBER OF F .GT. FMIN = 1768 NUMBER OF F IN RES. LIMITS = 1768 NUMBER OF F .GT. MIN = 1766 NUMBER OF F USED TO REFINE = 0 FIGURE OF MERIT < 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 # OF REFLECTIONS 81 129 131 133 145 173 187 204 222 363 FIGURE OF MERIT WITH RESOLUTION DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 N: 1768 102 145 195 214 244 272 287 309 MEAN FIG MERIT: 0.61 0.58 0.64 0.59 0.55 0.59 0.63 0.61 0.65 COMPOUND 1 set 1 with 1 fe atoms, lambda 1 DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 CENTRIC REFLNS: 248. 32. 32. 30. 30. 35. 33. 30. 26. RMS HA F: 34.7 50.2 38.8 41.1 30.0 34.9 28.4 19.5 21.8 RMS RESIDUAL: 43.2 62.9 53.3 34.3 50.0 41.8 29.0 35.5 18.6 RMS(FH)/RMS(E): 0.80 0.80 0.73 1.20 0.60 0.83 0.98 0.55 1.17 CENTRIC R FACT: 0.57 0.49 0.62 0.48 0.66 0.55 0.58 0.65 0.48 ACENTRIC REFLN: 1515. 70. 113. 164. 183. 209. 238. 255. 283. RMS DERIV FPH: 171.2 277.3 200.0 206.8 209.6 173.8 140.7 129.6 121.0 RMS SIGMA FPH: 48.2 97.4 51.7 55.8 57.7 47.5 40.5 34.4 30.5 RMS SIGMA FP: 48.0 97.9 52.2 56.3 56.4 45.9 40.8 34.7 30.7 RMS HA F: 31.4 47.8 41.3 38.5 33.6 30.6 28.6 25.1 22.1 RMS RESIDUAL: 47.8 61.9 60.0 66.9 53.4 49.2 37.7 37.1 34.8 RMS(FH)/RMS(E): 0.66 0.77 0.69 0.58 0.63 0.62 0.76 0.68 0.63 ANOM DIFFS: 1515. 70. 113. 164. 183. 209. 238. 255. 283. RMS OBS DIFF: 14.0 18.9 17.7 17.2 16.4 12.8 12.3 11.4 10.8 RMS CALC DIFF: 10.1 13.2 12.2 12.1 10.5 10.2 9.7 9.0 7.7 RMS RESIDUAL: 12.1 17.4 15.1 15.0 15.3 11.3 10.0 9.2 9.0 RATIO ISO/ANO: 4.22 4.67 4.53 4.38 4.25 4.14 4.03 3.93 3.84 ESTIMATES OF LACK-OF-CLOSURE RESIDUALS LESS AVERAGE VALUE OF SIGMAS IN data (AS INPUT TO NEXT CYCLE) CENTRIC LOC: 0.0 0.0 0.0 0.0 0.0 0.0 6.1 0.0 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 277.3 200.0 206.8 209.6 173.8 140.7 129.6 121.0 RMS FH : 47.8 41.3 38.5 33.6 30.6 28.6 25.1 22.1 RMS SIGMA: 138.1 73.5 79.3 80.7 66.1 57.5 48.8 43.3 COMPOUND 2 Native from dataset # 2 (a MAD set) used as a deriv. DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 CENTRIC REFLNS: 244. 32. 32. 30. 28. 35. 33. 29. 25. RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 27.5 43.9 31.4 21.5 25.2 31.8 19.6 18.0 10.6 RMS(FH)/RMS(E): 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CENTRIC R FACT: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ACENTRIC REFLN: 1512. 70. 113. 163. 184. 208. 237. 255. 282. RMS DERIV FPH: 173.3 282.3 199.1 218.3 209.5 174.7 141.7 130.7 119.5 RMS SIGMA FPH: 20.9 40.3 25.9 26.6 23.3 20.2 16.9 15.2 12.7 RMS SIGMA FP: 48.0 97.9 52.2 56.6 56.4 46.0 40.8 34.2 30.3 RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 27.3 37.0 29.0 36.0 31.4 27.2 22.9 22.7 21.7 RMS(FH)/RMS(E): 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ESTIMATES OF LACK-OF-CLOSURE RESIDUALS LESS AVERAGE VALUE OF SIGMAS IN data (AS INPUT TO NEXT CYCLE) CENTRIC LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 282.3 199.1 218.3 209.5 174.7 141.7 130.7 119.5 RMS FH : 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS SIGMA: 105.8 58.2 62.5 61.0 50.2 44.2 37.4 32.9 COMPOUND 3 Fe RM DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 CENTRIC REFLNS: 248. 32. 32. 30. 30. 35. 33. 30. 26. RMS HA F: 19.6 28.2 24.4 21.2 19.7 16.6 13.9 14.2 11.7 RMS RESIDUAL: 41.3 59.2 47.4 38.4 48.1 41.1 26.1 33.8 18.7 RMS(FH)/RMS(E): 0.47 0.48 0.51 0.55 0.41 0.40 0.53 0.42 0.62 CENTRIC R FACT: 0.68 0.67 0.77 0.60 0.75 0.69 0.61 0.71 0.61 ACENTRIC REFLN: 1515. 70. 113. 164. 184. 209. 238. 255. 282. RMS DERIV FPH: 170.3 273.8 201.8 206.4 208.5 173.5 139.6 130.0 116.8 RMS SIGMA FPH: 20.7 40.0 25.7 26.3 23.1 20.0 16.8 15.0 12.6 RMS SIGMA FP: 47.9 97.9 52.2 56.4 56.4 45.9 40.7 34.2 30.3 RMS HA F: 17.6 27.4 25.1 22.1 18.9 17.2 14.7 13.5 11.6 RMS RESIDUAL: 44.3 61.3 55.1 61.8 48.6 44.3 34.4 34.0 33.7 RMS(FH)/RMS(E): 0.40 0.45 0.45 0.36 0.39 0.39 0.43 0.40 0.34 ANOM DIFFS: 1515. 70. 113. 164. 184. 209. 238. 255. 282. RMS OBS DIFF: 10.4 13.6 13.4 13.8 12.6 9.8 8.7 7.7 7.5 RMS CALC DIFF: 8.3 11.9 10.8 10.0 9.0 8.3 7.2 6.7 6.2 RMS RESIDUAL: 9.6 12.4 12.4 13.2 11.9 8.9 7.7 7.2 6.7 RATIO ISO/ANO: 2.77 3.11 3.00 2.89 2.79 2.71 2.63 2.56 2.50 ESTIMATES OF LACK-OF-CLOSURE RESIDUALS LESS AVERAGE VALUE OF SIGMAS IN data (AS INPUT TO NEXT CYCLE) CENTRIC LOC: 0.0 0.0 0.0 0.0 0.0 0.0 20.2 0.0 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 273.8 201.8 206.4 208.5 173.5 139.6 130.0 116.8 RMS FH : 27.4 25.1 22.1 18.9 17.2 14.7 13.5 11.6 RMS SIGMA: 105.7 58.2 62.2 60.9 50.1 44.1 37.3 32.9 Analysis of correlated modeling and non-isomorphism errors obtained using phased residuals. The derivatives were grouped into 2 sets where the members of a set had some mutual correlation. Set 1 contains derivatives 1 3 Set 2 contains derivatives 2 SUMMARY OF CORRELATED ERRORS AMONG DERIVATIVES DERIVATIVE: 1 CENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 RMS errors correlated and uncorrelated with others in group: Correlated: 9.7 0.0 11.4 0.0 11.7 0.0 0.0 22.2 0.0 Uncorrelated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 2: 0.24 0.18 0.43 0.09 0.34 0.27 0.22 0.60 0.22 DERIV 3: 0.41 0.31 0.69 0.19 0.69 0.37 0.37 0.92 0.50 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 Errors correlated and uncorrelated with others in group: Correlated: 9.4 0.0 14.3 19.4 0.0 0.0 0.0 0.0 13.0 Uncorrelated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 2: 0.31 0.13 0.35 0.41 0.28 0.34 0.27 0.37 0.47 DERIV 3: 0.51 0.22 0.67 0.69 0.45 0.57 0.43 0.60 0.71 DERIVATIVE: 2 CENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 RMS errors correlated and uncorrelated with others in group: Correlated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Uncorrelated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 1: 0.24 0.18 0.43 0.09 0.34 0.27 0.22 0.60 0.22 DERIV 3: 0.33 0.26 0.53 0.17 0.43 0.45 0.26 0.60 0.30 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 Errors correlated and uncorrelated with others in group: Correlated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Uncorrelated: 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 1: 0.31 0.13 0.35 0.41 0.28 0.34 0.27 0.37 0.47 DERIV 3: 0.39 0.18 0.42 0.53 0.35 0.42 0.33 0.49 0.61 DERIVATIVE: 3 CENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 RMS errors correlated and uncorrelated with others in group: Correlated: 9.7 0.0 11.4 0.0 11.7 0.0 0.0 22.2 0.0 Uncorrelated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 1: 0.41 0.31 0.69 0.19 0.69 0.37 0.37 0.92 0.50 DERIV 2: 0.33 0.26 0.53 0.17 0.43 0.45 0.26 0.60 0.30 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 Errors correlated and uncorrelated with others in group: Correlated: 9.7 0.0 14.3 18.9 0.0 0.0 0.0 0.0 14.8 Uncorrelated: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 1: 0.51 0.22 0.67 0.69 0.45 0.57 0.43 0.60 0.71 DERIV 2: 0.39 0.18 0.42 0.53 0.35 0.42 0.33 0.49 0.61 PARAMETER SHIFTS FOR DERIV 1 : set 1 with 1 fe atoms, lambda 1 SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 LAM2 0.5658 0.4398 0.1600 0.3840 25.0127 CURRENT VALUES: 2 LAM2 0.3965 0.2293 0.4527 0.1675 19.9171 PARAMETER SHIFTS FOR DERIV 2 : Native from dataset # 2 (a MAD set) used as a deriv. SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 NATV 0.0100 0.0000 0.0000 0.0000 0.0000 PARAMETER SHIFTS FOR DERIV 3 : Fe RM SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 LAM5 0.5450 0.3197 0.0000 0.2292 27.7438 ************************************************************* ************************************************************* *** Summary of solutions and their relationships to each other and to check solution *** ---------------------------------------------------------- solution # 1 with overall quality = 36.14938 Derivative 1 with 2 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.4397677 0.1600000 0.3840296 0.5657703 25.01274 0.2292830 0.4526818 0.1675112 0.3965251 19.91712 Derivative 3 with 1 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.3197263 0.0000000E+00 0.2291557 0.5450062 27.74378 Best match of solution 1 -> solution 2: -------- solution 1 -------- -------------solution 2 ------ site x y z site x y z DIST (A) Derivative 1 1 0.440 0.160 0.384 1 0.440 0.160 0.380 0.17 2 0.229 0.453 0.168 2 0.230 0.450 0.165 0.15 Derivative 3 1 0.320 0.000 0.229 1 0.320 0.030 0.230 0.84 Comparison of this solution with check solution: Number of sites in this solution matching check= 3 ... and number not matching = 0 by derivative, this is... Deriv nsame ndifferent 1 2 0 2 0 0 3 1 0 All sites in this solution are contained in check soln