------------------------ 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 02-Apr-2005 / Size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" Dataset title: 5-wavelength 2-ano scatterer MAD dataset ! a title for th Space group number is: 5 Space group name from file name is: c2 Rescaling standard dataset to put it on approximate absolute scale. NRES = 100; expected = 98000.00 ; observed in lowest resolution shell = 441085.0 ... Scale factor = 0.2221794 -------------------------------------------------- *** 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) Wavelength # 1 ! a label for this wavelength Reflections observed: Possible Found % complete shell dmin 1 6.000 239 239 100.0 2 4.500 317 316 99.7 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 155 100.0 6 3.600 112 112 100.0 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1821 99.9 Completeness of dataset 2 ( F > 2.000000 * sigma) set 2 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 238 99.6 2 4.500 317 317 100.0 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 154 99.4 6 3.600 112 112 100.0 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 190 100.0 10 3.000 254 253 99.6 total 1822 1819 99.8 Completeness of dataset 3 ( F > 2.000000 * sigma) set 3 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 238 99.6 2 4.500 317 316 99.7 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 154 99.4 6 3.600 112 112 100.0 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 189 99.5 10 3.000 254 254 100.0 total 1822 1818 99.8 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 (Delta f-prime = 6.900000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 235 218.217 0.038 0.999 2.97 9.85 0.30 2 4.500 315 204.705 0.037 1.001 4.90 8.42 0.58 3 4.200 120 194.749 0.038 1.002 4.74 8.01 0.59 4 3.975 120 172.429 0.041 1.001 5.52 7.15 0.77 5 3.750 153 169.131 0.037 1.001 3.84 6.91 0.56 6 3.600 111 149.405 0.035 0.999 2.29 6.20 0.37 7 3.450 143 129.313 0.041 1.000 3.87 5.35 0.72 8 3.300 170 127.987 0.037 1.000 2.87 5.43 0.53 9 3.150 189 121.589 0.038 1.000 2.51 5.06 0.50 10 3.000 253 115.801 0.042 1.001 3.74 4.76 0.79 Total: 1809 162.970 0.038 1.000 3.87 7.06 0.57 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 1 (Delta f-prime = 8.250000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 235 220.145 0.041 0.999 4.42 9.93 0.45 2 4.500 311 201.222 0.039 1.002 5.91 8.18 0.72 3 4.200 119 192.819 0.037 1.002 4.15 7.86 0.53 4 3.975 120 172.429 0.047 1.001 7.32 7.24 1.01 5 3.750 151 167.018 0.035 1.000 2.91 6.88 0.42 6 3.600 110 147.993 0.042 0.999 4.44 6.20 0.72 7 3.450 142 128.263 0.048 1.000 5.46 5.22 1.05 8 3.300 169 127.759 0.043 0.998 4.38 5.39 0.81 9 3.150 189 121.449 0.045 1.000 4.45 5.02 0.89 10 3.000 254 116.982 0.050 0.999 5.25 4.93 1.07 Total: 1800 162.179 0.042 1.000 5.03 7.02 0.77 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 2 (Delta f-prime = 1.350000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 233 215.942 0.026 1.000 0.00 8.86 0.00 2 4.500 312 202.298 0.027 1.000 0.00 7.64 0.00 3 4.200 119 191.608 0.026 1.000 0.00 7.30 0.00 4 3.975 119 172.941 0.028 1.001 0.00 6.55 0.00 5 3.750 153 168.137 0.028 1.000 0.00 6.29 0.00 6 3.600 110 149.875 0.026 1.000 0.00 5.67 0.00 7 3.450 140 127.560 0.028 1.000 0.00 4.87 0.00 8 3.300 169 127.881 0.029 1.000 0.81 5.01 0.16 9 3.150 185 120.177 0.027 1.000 0.00 4.53 0.00 10 3.000 250 114.023 0.028 0.999 0.00 4.25 0.00 Total: 1790 161.583 0.027 1.000 0.00 6.40 0.02 Recommended resolution cut-off = 3.00 Anomalous differences lambda 1 (f" = 3.400000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 230 212.730 0.045 1.000 0.00 12.88 0.00 2 4.500 309 200.601 0.047 1.000 5.44 11.35 0.48 3 4.200 119 193.694 0.049 0.999 5.41 11.00 0.49 4 3.975 117 167.885 0.045 1.001 3.06 9.73 0.31 5 3.750 153 169.878 0.049 1.000 4.61 9.72 0.47 6 3.600 108 145.102 0.044 1.001 2.66 8.24 0.32 7 3.450 140 125.881 0.054 1.000 5.32 7.07 0.75 8 3.300 168 127.966 0.051 1.000 3.89 7.45 0.52 9 3.150 187 120.508 0.054 1.001 4.84 6.89 0.70 10 3.000 243 110.784 0.045 1.000 0.63 6.23 0.10 Total: 1774 160.003 0.048 1.000 3.93 9.49 0.39 Recommended resolution cut-off = 3.00 Anomalous differences lambda 2 (f" = 4.800000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 228 207.783 0.051 1.002 7.28 12.31 0.59 2 4.500 308 200.322 0.048 1.001 5.25 11.36 0.46 3 4.200 114 185.291 0.045 0.999 1.72 10.61 0.16 4 3.975 118 172.446 0.045 0.999 0.00 9.98 0.00 5 3.750 151 165.460 0.053 0.999 6.49 9.36 0.69 6 3.600 110 149.615 0.056 0.999 6.49 8.52 0.76 7 3.450 136 124.869 0.052 0.999 4.26 7.09 0.60 8 3.300 165 125.230 0.056 1.000 4.71 7.22 0.65 9 3.150 187 120.391 0.052 1.000 3.87 6.89 0.56 10 3.000 252 114.486 0.057 1.000 5.47 6.48 0.84 Total: 1769 158.845 0.051 1.000 5.22 9.36 0.56 Recommended resolution cut-off = 3.00 Anomalous differences lambda 3 (f" = 2.860000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 230 211.880 0.040 1.001 0.00 12.59 0.00 2 4.500 306 198.776 0.041 1.000 0.00 11.32 0.00 3 4.200 116 188.011 0.044 1.000 0.00 10.72 0.00 4 3.975 115 164.981 0.047 1.000 3.75 9.42 0.40 5 3.750 147 163.704 0.043 1.001 0.00 9.26 0.00 6 3.600 109 146.694 0.049 1.000 3.97 8.36 0.48 7 3.450 137 121.796 0.048 1.001 3.34 6.88 0.49 8 3.300 164 123.022 0.047 1.000 3.22 7.06 0.46 9 3.150 184 119.630 0.047 0.999 3.29 6.82 0.48 10 3.000 246 113.607 0.048 1.000 3.17 6.50 0.49 Total: 1754 158.047 0.044 1.000 0.00 9.34 0.26 Recommended resolution cut-off = 3.00 ANALYZE_MAD: Run MADMRG and MADBST on MAD data to get ready for SOLVE 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 0.26 0.01 0.11 4.50 0.12 0.18 0.28 4.20 0.32 0.14 0.13 3.98 0.30 0.05 0.14 3.75 0.38 0.20 0.28 3.60 0.45 0.30 0.34 3.45 0.29 0.24 0.31 3.30 0.44 0.22 0.23 3.15 0.36 0.15 0.31 3.00 0.32 0.24 0.32 ALL 0.28 0.15 0.23 Final refined values of fprime and fdoubleprime Form factors at lambda = 0.9000 f-prime = -1.60 f" = 3.40 Form factors at lambda = 0.9794 f-prime = -8.50 f" = 4.80 Form factors at lambda = 0.9797 f-prime = -9.85 f" = 2.86 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 = 100; expected = 98000.00 ; observed in lowest resolution shell = 431826.0 ... Scale factor = 0.2269433 -------------------------------------------------- *** 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) Wavelength # 1 ! a label for this wavelength Reflections observed: Possible Found % complete shell dmin 1 6.000 239 239 100.0 2 4.500 317 317 100.0 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 155 100.0 6 3.600 112 112 100.0 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 189 99.5 10 3.000 254 254 100.0 total 1822 1821 99.9 Completeness of dataset 2 ( F > 2.000000 * sigma) set 2 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 239 100.0 2 4.500 317 317 100.0 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 155 100.0 6 3.600 112 112 100.0 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1822 100.0 Completeness of dataset 3 ( F > 2.000000 * sigma) set 3 Reflections observed: Possible Found % complete shell dmin 1 6.000 239 237 99.2 2 4.500 317 317 100.0 3 4.200 120 120 100.0 4 3.975 120 120 100.0 5 3.750 155 154 99.4 6 3.600 112 111 99.1 7 3.450 143 143 100.0 8 3.300 172 172 100.0 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1818 99.8 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 (Delta f-prime = 4.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 234 220.477 0.031 1.000 0.00 9.60 0.00 2 4.500 314 204.955 0.031 1.000 1.05 8.26 0.13 3 4.200 119 194.771 0.032 1.000 2.08 7.70 0.27 4 3.975 119 171.543 0.031 1.000 0.00 7.11 0.00 5 3.750 152 170.614 0.031 0.999 0.00 6.91 0.00 6 3.600 111 150.925 0.026 1.000 0.00 5.94 0.00 7 3.450 142 128.418 0.033 1.000 1.50 5.09 0.29 8 3.300 170 130.293 0.035 1.000 2.33 5.40 0.43 9 3.150 186 122.859 0.030 0.999 0.00 4.89 0.00 10 3.000 249 115.635 0.032 1.000 0.00 4.72 0.00 Total: 1796 163.839 0.031 1.000 0.00 6.91 0.10 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 1 (Delta f-prime = 9.300000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 236 219.981 0.059 1.001 12.72 9.57 1.33 2 4.500 315 206.125 0.050 1.003 9.92 8.44 1.17 3 4.200 120 196.780 0.047 1.002 8.56 8.09 1.06 4 3.975 120 172.916 0.058 1.000 9.97 7.38 1.35 5 3.750 153 173.204 0.053 0.999 8.83 7.17 1.23 6 3.600 111 150.631 0.059 0.999 9.10 6.12 1.49 7 3.450 142 128.418 0.059 0.999 7.86 5.22 1.50 8 3.300 171 130.508 0.067 0.999 9.17 5.45 1.68 9 3.150 189 123.416 0.058 0.999 7.69 5.06 1.52 10 3.000 253 117.220 0.063 1.000 7.91 4.86 1.63 Total: 1810 164.621 0.056 1.000 9.44 7.06 1.40 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 2 (Delta f-prime = 5.300000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 234 215.887 0.055 1.000 11.13 9.44 1.18 2 4.500 315 205.942 0.046 1.002 8.80 8.50 1.04 3 4.200 120 196.269 0.046 1.001 7.76 8.03 0.97 4 3.975 120 173.187 0.047 1.000 6.60 7.57 0.87 5 3.750 153 172.408 0.045 1.000 6.52 7.09 0.92 6 3.600 110 148.865 0.052 0.999 7.72 6.00 1.29 7 3.450 143 129.807 0.055 1.000 6.87 5.23 1.31 8 3.300 171 130.712 0.054 1.000 6.54 5.55 1.18 9 3.150 188 121.800 0.050 1.000 5.63 5.03 1.12 10 3.000 252 117.205 0.053 1.000 5.95 4.84 1.23 Total: 1806 163.802 0.050 1.001 7.73 7.05 1.12 Recommended resolution cut-off = 3.00 Anomalous differences lambda 1 (f" = 2.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 232 220.771 0.038 0.999 0.00 13.44 0.00 2 4.500 306 199.647 0.043 1.000 0.00 11.31 0.00 3 4.200 117 193.773 0.041 0.999 0.00 11.01 0.00 4 3.975 117 167.285 0.038 1.000 0.00 9.64 0.00 5 3.750 152 168.847 0.046 1.001 3.65 9.66 0.38 6 3.600 110 149.197 0.047 0.999 2.37 8.43 0.28 7 3.450 140 126.492 0.043 1.000 0.00 7.21 0.00 8 3.300 168 128.786 0.047 1.000 2.10 7.50 0.28 9 3.150 183 119.213 0.042 1.000 0.00 6.76 0.00 10 3.000 247 113.788 0.045 0.999 1.46 6.46 0.23 Total: 1772 161.342 0.042 1.000 0.00 9.61 0.11 Recommended resolution cut-off = 3.00 Anomalous differences lambda 2 (f" = 4.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 227 209.192 0.048 1.000 4.27 12.50 0.34 2 4.500 308 200.604 0.047 0.999 5.27 11.34 0.46 3 4.200 117 193.828 0.046 0.999 0.00 11.06 0.00 4 3.975 114 163.635 0.045 1.000 0.00 9.43 0.00 5 3.750 150 168.890 0.051 1.001 5.46 9.65 0.57 6 3.600 112 151.295 0.059 1.000 7.47 8.60 0.87 7 3.450 142 129.488 0.059 1.000 5.65 7.36 0.77 8 3.300 167 126.610 0.058 1.001 5.84 7.33 0.80 9 3.150 184 119.911 0.054 1.001 5.29 6.84 0.77 10 3.000 247 113.895 0.058 1.000 5.33 6.48 0.82 Total: 1768 159.847 0.051 1.000 5.03 9.44 0.56 Recommended resolution cut-off = 3.00 Anomalous differences lambda 3 (f" = 1.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 229 208.844 0.042 1.003 0.00 12.25 0.00 2 4.500 307 201.327 0.041 1.001 0.00 11.49 0.00 3 4.200 115 188.831 0.044 1.001 0.00 10.80 0.00 4 3.975 115 165.530 0.049 0.999 4.91 9.45 0.52 5 3.750 148 168.501 0.043 1.000 0.00 9.59 0.00 6 3.600 109 147.208 0.050 0.999 4.42 8.40 0.53 7 3.450 139 125.412 0.049 1.000 3.96 7.14 0.55 8 3.300 168 127.829 0.049 1.000 4.32 7.38 0.59 9 3.150 183 120.334 0.046 0.999 2.60 6.88 0.38 10 3.000 248 114.963 0.048 0.999 3.02 6.58 0.46 Total: 1761 159.459 0.045 1.000 1.09 9.40 0.27 Recommended resolution cut-off = 3.00 ANALYZE_MAD: Run MADMRG and MADBST on MAD data to get ready for SOLVE Final refined values of fprime and fdoubleprime 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 = 0.9797 f-prime = 0.30 f" = 1.50 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: 1 (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 1 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 Derivative 2: Site X Y Z Derivative 3: Site X Y Z 1 0.150 0.330 0.400 ********************************************************** 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 0.2356218 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 9.0876520E-02 +/- 3.9091922E-02 For this map the correlation of r.m.s. density in neighboring boxes is 0.1658869 The correlation coefficient is used here in scoring. Skew of the map is: 0.1755039 ****** 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 0.443 0.167 0.375 96.025 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 -0.885 0.000 -0.750 18441.7 18441.6 2 Overall quality of this Patterson soln = 6520.13 Overall quality of the fit to patterson = 0.621481E-04 Avg normalized peak height = 4610.43 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 0.380 0.486 18.353 17.48 ----------------------------------------------- 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 0.151 0.333 0.396 75.507 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 -0.302 0.000 -0.792 11402.6 11402.6 2 Overall quality of this Patterson soln = 4031.42 Overall quality of the fit to patterson = 0.690534E-06 Avg normalized peak height = 2850.65 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 0.150 0.333 0.400 0.433 18.475 22.08 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 1.86 1.44 6.22 3.03 Cross-validation Fourier: 0.000E+00 0.500 33.0 65.9 NatFourier CCx100: 9.09 3.91 16.6 1.92 Mean figure of meritx100: 0.000E+00 12.1 66.3 5.49 Correction for Z-scores: -32.7 Overall Z-score value: 43.7 ****** Overall analysis of phasing for solution 1************ HEAVY: Refine heavy atom parameters File title: 5-wavelength 2-ano scatterer MAD dataset ! a title for this d 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 1 INPUT data FILE WITH 20 COLUMNS IS: combine.scl_1_2 COLUMN 0 : solve.data (cols 1 to 10) and solve.data_2 ,cols 1 to 1 COLUMN 1 : madmrg: MOCK FNAT COLUMN 2 : madmrg: MOCK sig FNAT COLUMN 3 : madmrg: MOCK FDER COLUMN 4 : madmrg: MOCK sig FDER COLUMN 5 : madmrg: MOCK DEL ANO COLUMN 6 : madmrg: MOCK sig DEL ANO COLUMN 7 : madmrg: Del iso for Patterson COLUMN 8 : madmrg: Sigma of del iso for Patterson COLUMN 9 : = Fa component along Fo weighted by fom COLUMN 10 : = weighted Fa component perpendicular to Fo COLUMN 11 : madmrg: MOCK FNAT COLUMN 12 : madmrg: MOCK sig FNAT COLUMN 13 : madmrg: MOCK FDER COLUMN 14 : madmrg: MOCK sig FDER COLUMN 15 : madmrg: MOCK DEL ANO COLUMN 16 : madmrg: MOCK sig DEL ANO COLUMN 17 : madmrg: Del iso for Patterson COLUMN 18 : madmrg: Sigma of del iso for Patterson COLUMN 19 : = Fa component along Fo weighted by fom COLUMN 20 : = weighted Fa component perpendicular to Fo 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 Wavelength # 1 ! a label for this wavelength 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 set 3 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 = 1813 NUMBER OF F IN RES. LIMITS = 1813 NUMBER OF F .GT. MIN = 1810 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 96 110 111 114 123 162 202 357 456 FIGURE OF MERIT WITH RESOLUTION DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 N: 1812 105 150 200 218 246 277 297 319 MEAN FIG MERIT: 0.66 0.64 0.67 0.64 0.60 0.64 0.68 0.69 0.70 COMPOUND 1 Wavelength # 1 ! a label for this wavelength DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 CENTRIC REFLNS: 260. 33. 35. 31. 30. 36. 33. 33. 29. RMS HA F: 24.5 33.6 27.9 28.3 21.5 24.3 20.7 16.7 17.2 RMS RESIDUAL: 19.9 32.7 18.2 22.2 19.8 19.4 13.7 13.7 10.1 RMS(FH)/RMS(E): 1.23 1.03 1.54 1.27 1.09 1.25 1.51 1.22 1.70 CENTRIC R FACT: 0.46 0.48 0.44 0.42 0.52 0.54 0.51 0.42 0.32 ACENTRIC REFLN: 1540. 72. 115. 169. 187. 210. 239. 260. 288. RMS DERIV FPH: 192.1 319.2 221.8 232.5 228.4 199.3 158.0 146.6 132.2 RMS SIGMA FPH: 23.4 30.0 44.2 20.4 23.7 22.5 19.7 17.9 18.1 RMS SIGMA FP: 23.7 30.6 44.4 21.0 24.1 22.9 20.0 18.2 18.3 RMS HA F: 22.6 32.5 28.1 27.9 24.1 22.2 20.9 18.7 16.8 RMS RESIDUAL: 21.1 26.5 43.9 23.2 20.4 19.6 15.0 13.5 14.5 RMS(FH)/RMS(E): 1.07 1.23 0.64 1.20 1.18 1.13 1.39 1.39 1.15 ANOM DIFFS: 1540. 72. 115. 169. 187. 210. 239. 260. 288. RMS OBS DIFF: 9.4 12.5 11.6 11.0 10.4 9.6 8.8 7.8 7.2 RMS CALC DIFF: 6.8 8.8 7.8 8.2 6.9 6.9 6.7 6.1 5.5 RMS RESIDUAL: 7.3 10.5 8.7 8.9 8.7 7.1 6.2 5.6 5.6 RATIO ISO/ANO: 4.64 5.15 4.99 4.82 4.67 4.54 4.42 4.30 4.19 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 2.8 0.0 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 319.2 221.8 232.5 228.4 199.3 158.0 146.6 132.2 RMS FH : 32.5 28.1 27.9 24.1 22.2 20.9 18.7 16.8 RMS SIGMA: 42.9 62.6 29.2 33.8 32.1 28.1 25.6 25.8 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 3.10 CENTRIC REFLNS: 245. 31. 32. 31. 27. 34. 32. 31. 27. RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 55.7 85.0 59.7 69.4 51.5 47.0 41.8 39.4 28.5 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: 1530. 71. 114. 167. 188. 206. 241. 256. 287. RMS DERIV FPH: 196.5 327.9 222.3 243.9 232.5 192.3 163.7 154.6 138.3 RMS SIGMA FPH: 14.7 30.0 17.4 18.4 16.9 13.7 11.3 10.3 9.4 RMS SIGMA FP: 23.7 30.2 44.6 21.1 24.0 22.5 20.1 18.4 18.4 RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 44.7 70.2 69.3 54.0 43.9 43.6 36.3 33.2 33.3 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: 75.1 53.3 23.9 44.8 40.8 37.9 37.0 26.1 RMS FPH : 327.9 222.3 243.9 232.5 192.3 163.7 154.6 138.3 RMS FH : 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS SIGMA: 42.6 47.8 28.0 29.4 26.4 23.1 21.1 20.7 COMPOUND 3 set 3 DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 CENTRIC REFLNS: 257. 32. 34. 31. 29. 36. 33. 33. 29. RMS HA F: 18.0 23.9 21.7 20.7 17.0 15.9 15.5 12.6 12.8 RMS RESIDUAL: 39.0 59.6 41.4 47.4 37.6 32.4 31.6 28.4 18.5 RMS(FH)/RMS(E): 0.46 0.40 0.52 0.44 0.45 0.49 0.49 0.44 0.69 CENTRIC R FACT: 0.66 0.73 0.53 0.67 0.65 0.75 0.68 0.65 0.56 ACENTRIC REFLN: 1544. 71. 115. 169. 188. 206. 244. 261. 290. RMS DERIV FPH: 193.1 317.8 223.0 234.6 230.9 194.7 161.5 150.0 135.6 RMS SIGMA FPH: 14.5 29.8 16.9 18.1 16.7 13.6 11.1 10.0 9.2 RMS SIGMA FP: 23.6 30.2 44.4 21.0 24.0 22.5 20.0 18.2 18.3 RMS HA F: 16.4 24.1 21.2 19.6 17.3 16.4 14.5 13.7 12.3 RMS RESIDUAL: 30.5 44.5 52.5 36.0 29.4 28.9 24.2 22.4 23.1 RMS(FH)/RMS(E): 0.54 0.54 0.40 0.54 0.59 0.57 0.60 0.61 0.53 ANOM DIFFS: 1544. 71. 115. 169. 188. 206. 244. 261. 290. RMS OBS DIFF: 10.4 17.4 12.0 12.4 11.3 9.8 9.0 9.1 8.1 RMS CALC DIFF: 5.8 7.5 6.9 6.8 6.0 5.9 5.4 5.2 4.9 RMS RESIDUAL: 8.8 15.7 10.4 10.7 9.7 8.4 7.5 7.2 6.4 RATIO ISO/ANO: 4.03 4.50 4.34 4.19 4.05 3.93 3.83 3.73 3.64 ESTIMATES OF LACK-OF-CLOSURE RESIDUALS LESS AVERAGE VALUE OF SIGMAS IN data (AS INPUT TO NEXT CYCLE) CENTRIC LOC: 45.0 32.5 0.0 28.6 23.3 26.5 25.2 15.0 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 317.8 223.0 234.6 230.9 194.7 161.5 150.0 135.6 RMS FH : 24.1 21.2 19.6 17.3 16.4 14.5 13.7 12.3 RMS SIGMA: 42.5 47.5 27.7 29.3 26.3 22.8 20.8 20.5 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 Set 2 contains derivatives 2 3 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 3.10 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: 1.0 0.0 0.0 0.0 0.0 0.0 0.0 2.8 0.0 Correlation of errors with other derivs: DERIV 2: 0.20 0.44 0.28 0.09 0.34 0.20 0.03 0.41 0.19 DERIV 3: 0.21 0.47 0.27 0.08 0.37 0.26 0.16 0.37 0.19 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 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 2: 0.36 0.30 0.51 0.47 0.33 0.33 0.25 0.23 0.29 DERIV 3: 0.39 0.33 0.58 0.49 0.35 0.35 0.26 0.22 0.32 DERIVATIVE: 2 CENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 RMS errors correlated and uncorrelated with others in group: Correlated: 34.7 60.1 41.4 0.0 34.9 31.6 29.0 28.5 18.7 Uncorrelated: 29.0 45.1 33.6 23.9 28.2 25.9 24.4 23.5 18.3 Correlation of errors with other derivs: DERIV 1: 0.20 0.44 0.28 0.09 0.34 0.20 0.03 0.41 0.19 DERIV 3: 0.81 0.91 0.83 0.67 0.82 0.86 0.80 0.81 0.81 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 Errors correlated and uncorrelated with others in group: Correlated: 36.4 59.7 52.8 50.8 33.6 35.1 28.0 25.0 26.7 Uncorrelated: 33.4 51.4 47.3 40.9 31.6 34.2 28.2 26.4 25.4 Correlation of errors with other derivs: DERIV 1: 0.36 0.30 0.51 0.47 0.33 0.33 0.25 0.23 0.29 DERIV 3: 0.90 0.87 0.93 0.89 0.89 0.90 0.91 0.87 0.91 DERIVATIVE: 3 CENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 RMS errors correlated and uncorrelated with others in group: Correlated: 34.9 60.3 41.6 0.0 35.2 31.8 29.1 28.6 18.8 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: 0.21 0.47 0.27 0.08 0.37 0.26 0.16 0.37 0.19 DERIV 2: 0.81 0.91 0.83 0.67 0.82 0.86 0.80 0.81 0.81 ACENTRIC REFLECTIONS: DMIN: ALL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 Errors correlated and uncorrelated with others in group: Correlated: 36.5 59.7 53.2 50.9 33.6 35.1 28.2 25.2 26.8 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: 0.39 0.33 0.58 0.49 0.35 0.35 0.26 0.22 0.32 DERIV 2: 0.90 0.87 0.93 0.89 0.89 0.90 0.91 0.87 0.91 PARAMETER SHIFTS FOR DERIV 1 : Wavelength # 1 ! a label for this wavelength SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 Fe 0.4865 0.4405 0.1600 0.3801 18.3530 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 Fe 0.0100 0.0000 0.0000 0.0000 0.0000 PARAMETER SHIFTS FOR DERIV 3 : set 3 SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 Fe 0.4329 0.1499 0.3331 0.4001 18.4753 ************************************************************* ************************************************************* *** Summary of solutions and their relationships to each other and to check solution *** ---------------------------------------------------------- solution # 1 with overall quality = 43.69228 Derivative 1 with 1 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.4404781 0.1600000 0.3801189 0.4864987 18.35298 Derivative 3 with 1 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.1498983 0.3331375 0.4001377 0.4328635 18.47534 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 0.380 1 0.440 0.160 0.380 0.04 Derivative 3 1 0.150 0.333 0.400 1 0.150 0.330 0.400 0.09 Comparison of this solution with check solution: Number of sites in this solution matching check= 2 ... and number not matching = 0 by derivative, this is... Deriv nsame ndifferent 1 1 0 2 0 0 3 1 0 All sites in this solution are contained in check soln