------------------------ 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: SOLVE 06-Apr-05 Space group number is: 5 Space group name from file name is: c2 Rescaling standard dataset to put it on approximate absolute scale. NRES = 80; expected = 78400.00 ; observed in lowest resolution shell = 432433.2 ... Scale factor = 0.1812997 -------------------------------------------------- *** 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 6.000 239 237 99.2 2 4.500 317 315 99.4 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 1818 99.8 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 3.975 120 119 99.2 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 1818 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 4.500 317 315 99.4 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 1819 99.8 ** R-factors for F-bar data dispersive differences ** Dispersive differences lambda 2 - lambda 1 (Delta f-prime = 2.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 233 192.039 0.053 0.997 0.00 14.89 0.00 2 4.500 314 182.586 0.060 1.002 6.42 13.09 0.49 3 4.200 118 175.552 0.056 1.003 3.11 12.56 0.25 4 3.975 116 150.026 0.055 1.002 1.03 11.06 0.09 5 3.750 153 151.332 0.059 1.002 4.53 10.98 0.41 6 3.600 111 135.142 0.047 0.999 0.00 9.62 0.00 7 3.450 142 115.315 0.054 1.001 0.00 8.34 0.00 8 3.300 169 113.266 0.056 1.000 0.75 8.54 0.09 9 3.150 189 110.951 0.054 1.001 0.00 7.89 0.00 10 3.000 250 103.016 0.053 1.001 0.00 7.39 0.00 Total: 1795 145.176 0.056 1.001 1.80 10.93 0.15 Recommended resolution cut-off = 3.75 Dispersive differences lambda 3 - lambda 1 (Delta f-prime = 8.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 234 195.008 0.067 0.999 0.00 17.63 0.00 2 4.500 310 179.300 0.070 1.001 6.90 14.46 0.48 3 4.200 120 176.643 0.071 1.003 6.26 14.59 0.43 4 3.975 120 151.557 0.074 1.002 7.56 13.15 0.57 5 3.750 153 152.318 0.060 1.000 0.00 12.80 0.00 6 3.600 111 134.361 0.072 1.000 4.78 11.19 0.43 7 3.450 142 114.752 0.077 1.000 5.92 9.67 0.61 8 3.300 170 114.174 0.070 0.999 3.19 9.92 0.32 9 3.150 190 111.306 0.081 1.000 7.36 9.04 0.81 10 3.000 252 104.085 0.075 1.000 4.87 8.64 0.56 Total: 1802 145.338 0.071 1.000 4.68 12.62 0.42 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 2 (Delta f-prime = 5.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 235 195.883 0.062 1.002 0.00 17.80 0.00 2 4.500 313 181.394 0.061 0.998 0.00 14.87 0.00 3 4.200 118 172.821 0.056 1.000 0.00 14.15 0.00 4 3.975 115 147.979 0.059 1.000 0.00 12.21 0.00 5 3.750 152 151.221 0.060 0.999 0.00 12.46 0.00 6 3.600 112 135.314 0.057 1.001 0.00 10.93 0.00 7 3.450 142 117.095 0.070 1.000 4.25 9.58 0.44 8 3.300 170 114.758 0.062 1.000 0.00 9.94 0.00 9 3.150 190 111.384 0.066 1.001 3.59 8.93 0.40 10 3.000 251 101.874 0.061 0.999 0.00 8.15 0.00 Total: 1798 145.289 0.061 1.000 0.00 12.55 0.08 Recommended resolution cut-off = 3.00 Anomalous differences lambda 1 (f" = 3.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 229 190.512 0.081 1.001 0.00 21.05 0.00 2 4.500 306 179.141 0.086 1.002 9.16 18.39 0.50 3 4.200 117 171.992 0.083 1.001 7.47 17.65 0.42 4 3.975 114 144.091 0.076 1.001 0.00 15.38 0.00 5 3.750 149 147.864 0.080 1.000 3.10 15.39 0.20 6 3.600 108 130.305 0.073 1.001 0.00 13.49 0.00 7 3.450 137 111.783 0.085 1.000 5.39 11.29 0.48 8 3.300 165 110.242 0.088 1.000 5.20 11.63 0.45 9 3.150 185 109.106 0.091 1.000 6.86 11.22 0.61 10 3.000 245 100.255 0.077 1.000 0.00 10.39 0.00 Total: 1755 142.080 0.083 1.001 5.02 15.34 0.28 Recommended resolution cut-off = 3.00 Anomalous differences lambda 2 (f" = 5.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 222 180.184 0.087 1.004 0.00 21.29 0.00 2 4.500 301 176.235 0.080 1.002 0.00 19.97 0.00 3 4.200 114 167.398 0.071 0.999 0.00 19.13 0.00 4 3.975 118 151.609 0.081 0.999 0.00 17.62 0.00 5 3.750 149 145.763 0.088 0.999 0.00 16.48 0.00 6 3.600 109 133.239 0.094 0.999 5.73 15.18 0.38 7 3.450 138 114.444 0.090 1.000 4.11 12.72 0.32 8 3.300 165 109.644 0.095 1.002 1.58 12.63 0.12 9 3.150 182 107.695 0.083 1.001 0.00 12.12 0.00 10 3.000 247 100.684 0.105 1.002 7.60 11.44 0.66 Total: 1745 140.182 0.087 1.001 0.00 16.45 0.15 Recommended resolution cut-off = 3.00 Anomalous differences lambda 3 (f" = 3.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 226 184.079 0.078 1.002 0.00 21.82 0.00 2 4.500 303 177.051 0.081 1.000 0.00 20.25 0.00 3 4.200 115 168.951 0.087 1.003 0.00 19.20 0.00 4 3.975 113 142.748 0.085 1.000 0.00 16.32 0.00 5 3.750 148 148.788 0.076 1.002 0.00 16.78 0.00 6 3.600 108 130.329 0.086 1.002 0.00 14.82 0.00 7 3.450 134 109.136 0.087 1.001 2.08 12.05 0.17 8 3.300 166 109.848 0.092 1.002 4.87 12.60 0.39 9 3.150 187 110.207 0.092 1.000 6.22 12.32 0.50 10 3.000 246 101.345 0.088 1.001 1.44 11.60 0.12 Total: 1746 140.494 0.084 1.001 0.00 16.53 0.12 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 0.11 -0.06 0.05 4.50 0.15 0.18 0.22 4.20 0.00 0.10 0.08 3.98 0.14 -0.04 0.13 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 0.06 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 = -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 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 = 430408.9 ... Scale factor = 0.1821524 -------------------------------------------------- *** 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 6.000 239 239 100.0 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 3.300 172 171 99.4 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1820 99.9 Completeness of dataset 2 ( F > 2.000000 * sigma) Fe PK Reflections observed: Possible Found % complete shell dmin 1 6.000 239 238 99.6 2 4.500 317 317 100.0 3 4.200 120 119 99.2 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 3.000 254 253 99.6 total 1822 1817 99.7 Completeness of dataset 3 ( F > 2.000000 * sigma) Fe RM 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 3.975 120 119 99.2 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 3.000 254 254 100.0 total 1822 1819 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 6.000 234 195.280 0.042 0.999 0.00 11.82 0.00 2 4.500 313 178.804 0.045 1.002 2.45 10.25 0.24 3 4.200 116 171.340 0.040 1.003 0.00 9.75 0.00 4 3.975 120 154.011 0.043 1.001 0.00 8.93 0.00 5 3.750 152 147.529 0.041 1.001 0.00 8.40 0.00 6 3.600 110 133.788 0.036 1.000 0.00 7.60 0.00 7 3.450 143 111.995 0.043 1.001 0.00 6.60 0.00 8 3.300 168 113.456 0.043 1.000 0.00 6.65 0.00 9 3.150 189 109.306 0.040 1.000 0.00 6.25 0.00 10 3.000 250 100.592 0.043 1.001 0.00 5.69 0.00 Total: 1795 143.756 0.042 1.001 0.00 8.59 0.04 Recommended resolution cut-off = 3.30 Dispersive differences lambda 3 - lambda 1 (Delta f-prime = 10.00000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 237 201.844 0.054 1.000 4.94 12.74 0.39 2 4.500 313 178.453 0.059 1.001 8.32 10.37 0.80 3 4.200 119 175.136 0.051 1.003 4.76 10.19 0.47 4 3.975 119 153.114 0.061 1.000 8.17 8.98 0.91 5 3.750 153 148.150 0.050 0.999 3.13 8.64 0.36 6 3.600 110 133.631 0.054 1.000 4.43 7.81 0.57 7 3.450 143 111.995 0.064 1.001 5.77 6.83 0.84 8 3.300 170 115.066 0.056 1.000 3.84 7.02 0.55 9 3.150 190 109.527 0.064 1.001 6.26 6.35 0.98 10 3.000 253 102.825 0.061 1.001 4.96 6.22 0.80 Total: 1807 145.281 0.057 1.001 5.89 8.95 0.68 Recommended resolution cut-off = 3.00 Dispersive differences lambda 3 - lambda 2 (Delta f-prime = 6.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 235 198.772 0.046 1.001 0.00 12.64 0.00 2 4.500 312 178.411 0.045 0.999 0.00 10.48 0.00 3 4.200 119 173.257 0.045 1.000 2.03 10.06 0.20 4 3.975 119 154.540 0.049 1.000 4.02 8.99 0.45 5 3.750 152 146.118 0.044 0.999 0.00 8.56 0.00 6 3.600 110 134.072 0.042 1.000 0.00 7.77 0.00 7 3.450 141 111.854 0.046 1.000 0.00 6.70 0.00 8 3.300 170 115.147 0.046 1.001 0.00 7.15 0.00 9 3.150 188 108.397 0.049 1.002 2.43 6.35 0.38 10 3.000 251 100.247 0.046 1.001 1.26 5.79 0.22 Total: 1797 144.256 0.046 1.000 0.00 8.90 0.11 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 6.000 229 193.187 0.057 1.000 0.00 15.56 0.00 2 4.500 305 175.425 0.060 1.000 6.43 13.43 0.48 3 4.200 117 172.210 0.060 0.999 4.23 13.12 0.32 4 3.975 115 148.059 0.054 1.002 0.00 11.63 0.00 5 3.750 153 148.036 0.061 1.000 4.25 11.52 0.37 6 3.600 107 130.528 0.055 1.001 0.00 10.01 0.00 7 3.450 136 107.254 0.060 1.000 2.16 8.11 0.27 8 3.300 167 113.203 0.059 1.000 0.00 8.80 0.00 9 3.150 186 107.628 0.061 1.001 2.70 8.28 0.33 10 3.000 244 97.237 0.058 1.000 0.00 7.37 0.00 Total: 1759 141.428 0.059 1.000 2.50 11.31 0.19 Recommended resolution cut-off = 3.98 Anomalous differences lambda 2 (f" = 4.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 227 188.885 0.067 1.001 5.37 15.67 0.34 2 4.500 301 172.899 0.057 1.001 0.00 13.87 0.00 3 4.200 114 167.698 0.052 1.000 0.00 13.54 0.00 4 3.975 117 152.365 0.059 1.000 0.00 12.45 0.00 5 3.750 150 142.807 0.066 1.000 3.65 11.50 0.32 6 3.600 109 132.978 0.057 1.000 0.00 10.63 0.00 7 3.450 139 109.253 0.067 1.000 4.39 8.69 0.51 8 3.300 162 110.604 0.059 1.001 0.00 8.94 0.00 9 3.150 184 106.070 0.061 1.000 0.00 8.53 0.00 10 3.000 244 97.956 0.067 1.001 3.01 7.86 0.38 Total: 1747 139.841 0.061 1.001 0.00 11.64 0.17 Recommended resolution cut-off = 3.75 Anomalous differences lambda 3 (f" = 1.500000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 227 189.070 0.053 1.003 0.00 15.23 0.00 2 4.500 305 174.238 0.055 1.000 0.00 13.75 0.00 3 4.200 118 171.259 0.059 1.001 2.52 13.40 0.19 4 3.975 116 149.421 0.062 0.999 4.09 11.80 0.35 5 3.750 145 140.756 0.050 1.001 0.00 11.07 0.00 6 3.600 108 130.392 0.054 1.000 0.00 10.23 0.00 7 3.450 134 103.646 0.056 1.001 0.00 8.02 0.00 8 3.300 163 111.202 0.055 1.002 0.00 8.78 0.00 9 3.150 181 104.837 0.054 1.000 0.00 8.20 0.00 10 3.000 247 99.023 0.058 1.002 0.00 7.76 0.00 Total: 1744 139.646 0.055 1.001 0.00 11.36 0.04 Recommended resolution cut-off = 3.15 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 = 0.9780 f-prime = 1.00 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: 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 0.2271466 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 6.4755760E-02 +/- 3.4622770E-02 For this map the correlation of r.m.s. density in neighboring boxes is 0.1684203 The correlation coefficient is used here in scoring. Skew of the map is: 0.1915549 ****** 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 68.084 2 0.229 0.458 0.167 62.690 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 7757.40 9270.82 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 7339.48 4268.16 1 2 -0.667 0.292 -0.552 7571.71 4268.16 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 6151.03 7860.00 2 Overall quality of this Patterson soln = 8017.65 Overall quality of the fit to patterson = 2.26086 Avg normalized peak height = 3585.60 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 0.439 0.160 0.382 0.522 26.244 13.94 2 0.229 0.452 0.167 0.296 9.188 12.59 ----------------------------------------------- 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 89.156 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 15897.5 15897.5 2 Overall quality of this Patterson soln = 5620.60 Overall quality of the fit to patterson = 0.690534E-06 Avg normalized peak height = 3974.37 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 0.491 27.986 18.82 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 3.22 2.25 8.40 2.30 Cross-validation Fourier: 11.9 0.500 34.4 45.0 NatFourier CCx100: 6.48 3.46 16.8 2.99 Mean figure of meritx100: 0.000E+00 10.7 60.3 5.64 Correction for Z-scores: -23.0 Overall Z-score value: 32.9 ****** Overall analysis of phasing for solution 1************ HEAVY: Refine heavy atom parameters File title: SOLVE 06-Apr-05 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 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 = 1784 NUMBER OF F IN RES. LIMITS = 1784 NUMBER OF F .GT. MIN = 1780 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 92 128 164 125 147 173 161 190 209 394 FIGURE OF MERIT WITH RESOLUTION DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 N: 1783 102 147 197 216 244 273 290 314 MEAN FIG MERIT: 0.60 0.59 0.64 0.58 0.55 0.58 0.63 0.61 0.63 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 3.10 CENTRIC REFLNS: 256. 32. 33. 31. 30. 36. 34. 32. 28. RMS HA F: 30.9 43.2 35.4 36.5 26.4 31.2 25.1 19.1 21.6 RMS RESIDUAL: 34.0 50.5 42.4 28.1 40.3 33.5 21.5 25.5 14.2 RMS(FH)/RMS(E): 0.91 0.86 0.84 1.30 0.66 0.93 1.17 0.75 1.52 CENTRIC R FACT: 0.55 0.50 0.60 0.46 0.65 0.55 0.53 0.58 0.46 ACENTRIC REFLN: 1522. 70. 114. 165. 185. 208. 238. 256. 286. RMS DERIV FPH: 171.5 282.5 199.4 206.4 208.7 174.5 141.6 129.3 120.7 RMS SIGMA FPH: 39.5 81.3 41.6 45.1 46.5 39.6 34.3 27.8 24.6 RMS SIGMA FP: 39.7 81.8 42.1 45.7 45.6 40.0 34.6 28.1 24.9 RMS HA F: 27.8 41.0 35.8 33.7 29.9 27.3 25.7 22.6 20.3 RMS RESIDUAL: 39.1 57.1 48.3 54.3 42.9 39.1 31.0 29.8 28.2 RMS(FH)/RMS(E): 0.71 0.72 0.74 0.62 0.70 0.70 0.83 0.76 0.72 ANOM DIFFS: 1522. 70. 114. 165. 185. 208. 238. 256. 286. RMS OBS DIFF: 14.1 19.6 17.9 17.4 16.6 13.0 12.4 11.5 10.9 RMS CALC DIFF: 8.4 11.2 9.9 9.8 8.7 8.4 8.3 7.5 6.6 RMS RESIDUAL: 12.3 17.9 15.3 15.2 15.4 11.4 10.1 9.4 9.2 RATIO ISO/ANO: 4.65 5.15 4.99 4.83 4.68 4.56 4.44 4.33 4.23 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 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 282.5 199.4 206.4 208.7 174.5 141.6 129.3 120.7 RMS FH : 41.0 35.8 33.7 29.9 27.3 25.7 22.6 20.3 RMS SIGMA: 115.4 59.2 64.2 65.1 56.3 48.8 39.5 35.0 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: 251. 32. 33. 31. 28. 36. 34. 30. 27. RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 24.3 43.0 23.3 19.8 21.7 28.9 15.6 13.8 8.2 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 0.99 ACENTRIC REFLN: 1518. 69. 114. 164. 186. 208. 237. 256. 284. RMS DERIV FPH: 172.3 282.3 198.4 215.1 207.7 175.2 141.7 129.9 118.7 RMS SIGMA FPH: 16.6 32.1 20.0 21.3 18.3 15.7 13.7 12.3 10.0 RMS SIGMA FP: 39.5 80.1 42.1 45.9 45.5 40.0 34.6 27.7 24.6 RMS HA F: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS RESIDUAL: 22.3 28.6 23.4 30.1 25.6 22.3 18.9 18.5 17.7 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 : 282.3 198.4 215.1 207.7 175.2 141.7 129.9 118.7 RMS FH : 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS SIGMA: 86.3 46.6 50.6 49.1 43.0 37.2 30.3 26.6 COMPOUND 3 Fe RM DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 CENTRIC REFLNS: 256. 32. 33. 31. 30. 36. 34. 32. 28. RMS HA F: 18.2 26.3 22.7 19.4 18.4 15.6 13.2 13.3 11.0 RMS RESIDUAL: 32.9 47.1 36.7 32.3 38.7 35.2 19.9 25.2 14.7 RMS(FH)/RMS(E): 0.55 0.56 0.62 0.60 0.48 0.44 0.66 0.53 0.75 CENTRIC R FACT: 0.63 0.55 0.71 0.60 0.71 0.62 0.62 0.65 0.59 ACENTRIC REFLN: 1521. 69. 114. 165. 186. 208. 238. 256. 285. RMS DERIV FPH: 170.1 275.9 201.1 206.1 207.5 174.1 140.4 129.5 116.5 RMS SIGMA FPH: 16.3 31.8 19.8 21.0 18.0 15.5 13.5 12.1 9.8 RMS SIGMA FP: 39.4 80.1 42.1 45.8 45.5 40.0 34.6 27.7 24.6 RMS HA F: 16.4 25.6 23.5 20.6 17.6 16.0 13.7 12.6 10.9 RMS RESIDUAL: 35.9 50.1 44.1 50.6 39.1 35.5 28.3 27.5 27.4 RMS(FH)/RMS(E): 0.46 0.51 0.53 0.41 0.45 0.45 0.49 0.46 0.40 ANOM DIFFS: 1521. 69. 114. 165. 186. 208. 238. 256. 285. RMS OBS DIFF: 11.4 15.2 14.5 15.3 13.9 10.7 9.3 8.4 8.1 RMS CALC DIFF: 5.7 8.2 7.7 6.7 6.2 5.7 5.0 4.6 4.2 RMS RESIDUAL: 10.5 13.7 13.2 14.8 13.1 9.7 8.2 7.7 7.3 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: 0.0 0.0 0.0 0.0 0.0 0.0 13.6 0.0 ANOMALOUS LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS FPH : 275.9 201.1 206.1 207.5 174.1 140.4 129.5 116.5 RMS FH : 25.6 23.5 20.6 17.6 16.0 13.7 12.6 10.9 RMS SIGMA: 86.2 46.5 50.4 49.0 42.9 37.1 30.2 26.5 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 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 3.10 RMS errors correlated and uncorrelated with others in group: Correlated: 5.7 0.0 0.0 0.0 7.6 0.0 0.0 14.5 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 0.39 0.10 0.36 0.31 0.17 0.55 0.23 DERIV 3: 0.40 0.30 0.64 0.20 0.68 0.41 0.31 0.85 0.49 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: 6.4 0.0 4.2 15.0 0.0 0.0 0.0 0.0 8.9 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: 0.29 0.12 0.35 0.41 0.28 0.29 0.25 0.35 0.46 DERIV 3: 0.48 0.21 0.65 0.68 0.44 0.48 0.39 0.58 0.69 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: 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 0.39 0.10 0.36 0.31 0.17 0.55 0.23 DERIV 3: 0.36 0.28 0.47 0.21 0.48 0.57 0.22 0.61 0.34 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 0.1 0.0 0.0 0.0 0.0 0.0 Correlation of errors with other derivs: DERIV 1: 0.29 0.12 0.35 0.41 0.28 0.29 0.25 0.35 0.46 DERIV 3: 0.39 0.18 0.43 0.55 0.36 0.38 0.32 0.49 0.62 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: 5.7 0.0 0.0 0.0 7.6 0.0 0.0 14.5 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: 0.40 0.30 0.64 0.20 0.68 0.41 0.31 0.85 0.49 DERIV 2: 0.36 0.28 0.47 0.21 0.48 0.57 0.22 0.61 0.34 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: 6.7 0.0 4.2 14.2 0.0 0.0 0.0 0.0 10.6 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: 0.48 0.21 0.65 0.68 0.44 0.48 0.39 0.58 0.69 DERIV 2: 0.39 0.18 0.43 0.55 0.36 0.38 0.32 0.49 0.62 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 Fe 0.5222 0.4391 0.1600 0.3825 26.2440 CURRENT VALUES: 2 Fe 0.2956 0.2289 0.4525 0.1668 9.1885 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 : Fe RM SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 Fe 0.4912 0.3196 0.0000 0.2287 27.9862 ************************************************************* ************************************************************* *** Summary of solutions and their relationships to each other and to check solution *** ---------------------------------------------------------- solution # 1 with overall quality = 32.89179 Derivative 1 with 2 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.4391191 0.1600000 0.3824790 0.5222168 26.24403 0.2288599 0.4524674 0.1667664 0.2956249 9.188481 Derivative 3 with 1 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.3196436 0.0000000E+00 0.2286830 0.4911909 27.98615 Best match of solution 1 -> solution 2: -------- solution 1 -------- -------------solution 2 ------ site x y z site x y z DIST (A) Derivative 1 1 0.439 0.160 0.382 1 0.440 0.160 0.380 0.14 2 0.229 0.452 0.167 2 0.230 0.450 0.165 0.14 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