****************************************************************************** 2007src0178 in P2(1)/n Thu Mar 08 2007 at 12:52:11 Sir2004 starts on: 2007src0 Used commands & directives: %data Cell 7.149 18.610 8.865 90.000 113.219 90.000 Space P 1 21/n 1 Content C 32 H 48 N 4 O 6 Si 4 Cl 2 Reflections 2007src0178.hkl Format (3i4,2f8.0) Fosquare %invariants default %phase default %end Files used in Sir2004: Channel Name 5 instruction input file Sir2004.sir 6 printer output file Sir2004.lst 30 direct access structure file 2007src0.bin 31 direct access scratch file 32 sequential scratch file 34 reflection input file 2007src0178.hkl 41 scattering factors file c:\program files\sir2004\sir2004dir\Sir2004.xen ( Release : 05.98 ) Direct access structure file has been initialized ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sir2004 : Data routine Release 01.00 2007src0178 in P2(1)/n ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Direct cell: a = 7.149 b = 18.610 c = 8.865 alpha = 90.000 beta = 113.219 gamma = 90.000 Cell volume = 1083.90 Crystal family : Monoclinic Space group (centrosymmetric) : P 1 21/n 1 Symmetry-operations 1) x , y , z 2) -x+1/2, y+1/2, -z+1/2 3) -x , -y , -z 4) x+1/2, -y+1/2, z+1/2 Seminvariant condition : g g g P-lattice: (0,0,0) Allowed origin translations: ( 0 , 0 , 0 ) (1/2, 0 , 0 ) ( 0 ,1/2, 0 ) ( 0 , 0 ,1/2) ( 0 ,1/2,1/2) (1/2, 0 ,1/2) (1/2,1/2, 0 ) (1/2,1/2,1/2) Space Group Number = 14 Fourier limits : 0.000 < x < 1.000 0.000 < y < 0.250 0.000 < z < 1.000 Patterson limits : 0.000 < x < 0.500 0.000 < y < 0.500 0.000 < z < 1.000 X-ray scattering factors Unit cell contents and scattering factor constants Atom Symbol Number in cell Atomic number Hydrogen H 48 1 Carbon C 32 6 Nitrogen N 4 7 Oxygen O 6 8 Silicon Si 4 14 Chlorine Cl 2 17 Wave Length = 0.7107 f = sum ( a(i) * exp(-b(i)*s2) ) i=1,4 + c a(1) b(1) a(2) b(2) a(3) b(3) a(4) b(4) c H 0.490 20.659 0.262 7.740 0.197 49.552 0.050 2.202 0.001 C 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 0.216 N 12.213 0.006 3.132 9.893 2.013 28.997 1.166 0.583 -11.529 O 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 0.251 Si 6.292 2.439 3.035 32.334 1.989 0.678 1.541 81.694 1.141 Cl 11.460 0.010 7.196 1.166 6.256 18.519 1.646 47.778 -9.557 Number of atoms in asymmetric unit = 12.00 Equivalent number of equal atoms in primitive cell = 30 Volume per atom = 22.58 Syst. absent : 1 0 0 Fobs = 0.000 Sigma(Fobs) = 1.130 Syst. absent : 1 0 0 Fobs = 2.980 Sigma(Fobs) = 1.830 Syst. absent : 1 0 0 Fobs = 0.000 Sigma(Fobs) = 0.660 Syst. absent : 1 0 0 Fobs = 0.000 Sigma(Fobs) = 0.570 Syst. absent : -3 0 0 Fobs = 0.000 Sigma(Fobs) = 3.940 Syst. absent : 3 0 0 Fobs = 10.160 Sigma(Fobs) = 3.570 Syst. absent : -3 0 0 Fobs = 1.890 Sigma(Fobs) = 1.590 Syst. absent : 3 0 0 Fobs = 0.360 Sigma(Fobs) = 1.220 Syst. absent : 3 0 0 Fobs = 14.930 Sigma(Fobs) = 5.030 Syst. absent : 3 0 0 Fobs = 2.390 Sigma(Fobs) = 2.000 .... and so on Space Group Determination Routine Crystal System determination by geometrical analysis of the cell: MONOCLINIC Unique axis b Total number of independent reflections : 16491 Total number of reflections considered: 16491 Total number of reflections greater than 3s: 16487 < fo >Total : 939.3793 < fo/sfo >Total : 16.76492 SYSTEMATIC ABSENCE EXCEPTIONS Note: Symbol # means not equal Refl. Total Condition N.Refl. N.(>3s) Sym. Op. Type Number 0 0 l 29 l#2n 14 14 1.7 0.1 ______ 0 k 0 82 k#2n 39 39 3.5 0.3 _ 21 _ h 0 0 34 h#2n 17 17 2.5 0.3 ______ 0 k l 1497 k#2n 760 760 392.7 2.9 ______ l#2n 741 741 560.2 3.1 ______ k#2n,l#2n 1125 1125 505.9 2.9 ______ k+l#2n 749 749 567.0 2.9 ______ h 0 l 426 h#2n 210 210 317.1 1.5 ______ l#2n 210 210 316.9 1.5 ______ h#2n,l#2n 318 318 210.4 1.0 ______ h+l#2n 216 216 3.0 0.2 _ n _ h k 0 1316 h#2n 663 663 516.4 3.0 ______ k#2n 657 657 652.6 3.0 ______ h#2n,k#2n 990 990 571.4 3.0 ______ h+k#2n 660 660 545.7 2.9 ______ h k l 16487 h+k#2n 8256 8256 453.6 2.8 ______ k+l#2n 8258 8258 471.8 2.8 ______ h+l#2n 8220 8220 474.4 2.8 ______ h+k+l#2n 8232 8232 462.7 2.8 ______ Extinction Group Fig.Mer P 1 21/n 1 0.514 P 1 n 1 0.190 P 1 21 1 0.143 P 1 21/c 1 0.066 P 1 21/a 1 0.066 I 1 _ 1 0.057 P 1 _ 1 0.053 P 1 a 1 0.024 P 1 c 1 0.024 C 1 _ 1 0.007 A 1 _ 1 0.007 A 1 n 1 0.007 C 1 c 1 0.007 I 1 a 1 0.007 Systematically absent reflections analisys Number and percentage of F's > param * sigma(F) Number percentage param 146 57% 0.00 107 42% 0.50 67 26% 1.00 38 15% 1.50 23 9% 2.00 14 5% 2.50 6 2% 3.00 3 1% 3.50 0 0% 4.00 0 0% 4.50 0 0% 5.00 16491 input reflections 648 Fo(s) negative set to 0.0 2484 independent input reflections 257 systematically absent reflections rejected 9 24 11 maximum h,k,l values 0.4245 maximum s**2 = (sin(theta)/lambda)**2 0.7674 Angstrom resolution 36 reflections are not in input data Symmetry equivalent reflections merged: Rsym(F) = 4.05% Distribution of reflections Angstrom No. of No. of No. of % of resolution expected observed missing missing up to 10.0 0 0 0 0 10.0 - 8.0 1 0 1 100 8.0 - 6.0 7 5 2 29 6.0 - 5.0 9 9 0 0 5.0 - 4.0 49 49 0 0 4.0 - 3.0 195 193 2 1 3.0 - 2.5 259 259 0 0 2.5 - 2.0 615 615 0 0 2.0 - 1.8 394 394 0 0 1.8 - 1.6 811 811 0 0 1.6 - 1.4 1187 1187 0 0 1.4 - 1.3 879 879 0 0 1.3 - 1.2 1226 1226 0 0 1.2 - 1.1 1694 1694 0 0 1.1 - 1.0 2374 2374 0 0 1.0 - 0.9 2812 2812 0 0 0.9 - 0.8 2843 2843 0 0 0.8 - 0.7 915 884 31 3 -0.893 -0.654 -0.416 -0.177 0.061 0.300 * * * * * * ********************************************************* * * * * 0.033* w * ** * w * * * w * * * w * * * * w * 0.109* * w ** * *w * * x * * * w * * * w * 0.184* * w ** * * w * * * w ********************************** * *w * y = s**2 * * x * x = ln / sigfsq * 0.259* w* * ( w ) = wilson * * w * * ( * ) = calc * * w * ********************************** * w * * intercept = 0.40171 * * w * * slope = -3.04604 * 0.334* x * b(iso) = 1.52302 * * * w * u(iso) = 0.01929 * * * w * scale = 0.66917 * * *w * scale*f(obs.)**2 = f(abs.)**2 * * w* ********************************** 0.410* w* ** * * * * ********************************************************* * * * * * * ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** pseudotranslation section *** 2007src0178 in P2(1)/n *** program searched for pseudo-translational symmetry *** *** no pseudo-translational symmetry has been found *** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** Final statistics section *** Distribution of with sin(th)/lambda and Resol. (Ang.) sinth/lambda 0.0652 0.1303 0.1955 0.2606 0.3258 Resol. 7.67 3.84 2.56 1.92 1.53 0.0000 0.5358 0.7969 0.7757 1.0751 number 0 30 87 178 297 sinth/lambda 0.3909 0.4561 0.5212 0.5864 0.6515 Resol. 1.28 1.10 0.96 0.85 0.77 0.9935 1.1423 1.0176 0.9416 1.0090 number 445 626 841 1085 1294 Average values Average Numeric Graphic all data acentric centric hypercentric a. c. h. mod(E) 0.810 0.886 0.798 0.718 * E**2 1.000 1.000 1.000 1.000 E**3 1.583 1.329 1.596 1.916 * E**4 2.969 2.000 3.000 4.500 * E**5 6.352 3.323 6.383 12.260 * E**6 15.181 6.000 15.000 37.500 * mod(E**2-1) 0.954 0.736 0.968 1.145 * (E**2-1)**2 1.969 1.000 2.000 3.500 * (E**2-1)**3 8.274 2.000 8.000 26.000 * (mod(E**2-1))**3 8.932 2.415 8.691 26.903 * n(z) cumulative probability distribution z all data acentric centric hypercentric a. c. h. 0.1 0.232 0.095 0.248 0.368 * 0.2 0.335 0.181 0.345 0.463 * 0.3 0.413 0.259 0.416 0.526 * 0.4 0.465 0.330 0.473 0.574 * 0.5 0.511 0.393 0.520 0.612 * 0.6 0.557 0.451 0.561 0.643 * 0.7 0.596 0.503 0.597 0.670 * 0.8 0.633 0.551 0.629 0.694 * 0.9 0.666 0.593 0.657 0.715 * 1.0 0.693 0.632 0.683 0.733 * 1.2 0.734 0.699 0.727 0.765 * 1.4 0.769 0.753 0.763 0.791 * 1.6 0.797 0.798 0.794 0.813 * 1.8 0.821 0.835 0.820 0.832 * 2.0 0.842 0.865 0.843 0.848 * 2.2 0.859 0.889 0.862 0.863 * 2.4 0.877 0.909 0.879 0.875 * 2.6 0.889 0.926 0.893 0.886 * 2.8 0.904 0.939 0.906 0.896 * 3.0 0.918 0.950 0.917 0.905 * 3.2 0.927 0.959 0.926 0.913 * 3.4 0.938 0.967 0.935 0.920 * 3.6 0.944 0.973 0.942 0.926 * 3.8 0.950 0.978 0.949 0.932 * 4.0 0.958 0.982 0.954 0.938 * Distribution of E - number of E's .gt. limit E 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 number 1380 1228 1061 904 762 651 556 475 401 340 E 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 number 281 225 177 138 104 84 64 51 40 24 Number and percentage Number and percentage of F's > param * sigma(F) of F's > limit number percentage param number percentage limit 2398 97% 0.50 248 10% 32.96 2296 92% 1.00 496 20% 23.73 2259 91% 1.50 744 30% 18.35 2242 90% 2.00 992 40% 14.47 2209 89% 2.50 1240 50% 11.48 2179 88% 3.00 1488 60% 8.93 2145 86% 3.50 1736 70% 6.44 2106 85% 4.00 1984 80% 4.50 2065 83% 4.50 2232 90% 3.04 2016 81% 5.00 2480 100% 0.00 204 largest E-values > 1.729 to phase. ( 10 printed ) code h k l E fo/sig. code h k l E fo/sig. 1 6 3 -5 4.169 >6 2 1 3 -10 3.278 >6 3 1 5 -7 3.176 >6 4 5 19 -3 3.092 >6 5 5 8 2 3.066 >6 6 5 2 2 3.059 >6 7 1 9 2 2.993 >6 8 5 3 -10 2.948 >6 9 1 1 -7 2.946 >6 10 2 3 9 2.934 >6 . . . . . . . . . 534 smallest E-values for psi0 and negative quartets ( 10 printed ) code h k l E fo/sig. code h k l E fo/sig. 2475 6 2 5 0.000 0.00 2476 6 4 4 0.000 0.00 2477 1 14 7 0.000 0.00 2478 1 4 -10 0.000 0.00 2479 1 10 8 0.000 0.00 2480 1 19 -5 0.000 0.00 2481 1 0 -1 0.000 0.00 2482 7 5 3 0.000 0.00 2483 7 0 -9 0.000 0.00 2484 7 12 -8 0.000 0.00 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sir2004 : Invariants routine Release 01.00 2007src0178 in P2(1)/n ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2193 strong triplets found among 204 strongest reflections (E-min = 1.729) strengthned by 37 free vectors using P-10 formula Used 11 triplets per reflection. Gmin = 0.15 Triplets statistic distribution of g - number of |g|'s .gt. limit g 0.0 0.2 0.3 0.4 0.5 0.6 0.8 1.0 1.2 1.6 no. 2193 2191 2191 2191 2190 2188 2188 2188 2185 2178 g 2.0 2.5 3.0 3.5 4.0 5.0 6.0 7.0 9.0 10.0 no. 2174 2165 2152 2137 2108 2030 1916 1748 1304 1067 5111 Psi-zero triplets found among 204 strongest reflections and the 534 weakest reflections Quartets statistic 4889 negative quartets found ( 4000 stored ) among 5111 psi-zero relationships distribution of g - number of |g|'s .gt. limit g 0.0 0.2 0.3 0.4 0.5 0.6 0.8 1.0 1.2 1.6 no. 4000 3881 3828 3741 3666 3559 3290 3006 2713 2105 g 2.0 2.5 3.0 3.5 4.0 5.0 6.0 7.0 9.0 10.0 no. 1512 1036 685 473 318 144 72 38 13 5 number of relationships calculated stored positive estimated triplets 2185 2185 negative estimated triplets 7 7 psi-zero triplets 5111 5111 negative estimated quartets 3345 3345 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sir2004 : Phase routine Release 01.00 2007src0178 in P2(1)/n ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Number of Pos. Est. Triplets = 2185 with G > 0.43 Number of Neg. Est. Triplets = 6 with |G| > 0.60 Number of Neg. Est. Quartets = 1000 with |G| > 0.20 Number of refl. to phase = 204 Number of random phases = 68 Number of reflexions in LSQ = 1735 ( 70% of total, F's > 6.436 ) Number of atoms to locate = 12.00 Number of atoms used in LSQ = 14.00 Observations / Parameters = 30.98 Resolution & grid step (Ang) = 0.77 0.33 Fourier map grid points = 24 60 30 Threshold on R % = 25.00 Total number of trials = 300 Solve strategy: small-size structure ( 6-80 atoms in a.u. ) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Space Group: P 1 21/n 1 Cell: 7.15 18.61 8.87 0.50 0.00 0.00 Cheshire cell: 3.57 9.31 4.43 Transf. Matrix 0.00 0.50 0.00 Grid: 0.09 0.04 0.08 0.00 0.00 0.50 Grid points: 11 28 14 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Number of blocks to be used: 3 Block Trials to explore Procedure 1 100 10 Tangent 2 100 20 Tangent 3 100 30 Tangent Summary for Block # 1/ 3 from trial 1 to trial 100 +++++++++++++ Figures of merit ++++++++++++ Set (Trial) eFom undetermined Set (Trial) eFom undetermined 1 ( 84) 4.488 0 2 ( 35) 4.471 0 3 ( 38) 4.471 0 4 ( 80) 4.471 0 5 ( 94) 4.467 0 6 ( 7) 4.437 0 7 ( 66) 4.428 0 8 ( 91) 4.415 0 9 ( 98) 4.415 0 10 ( 32) 4.405 0 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Extending phases for Block # 1 Set 1 Trial 84 eFom = 4.488 UnDet 0 Trial 84 End of DSR - Final FOM = 7.519 R% = 31.22 40.79 26.21 37.96 29.60 40.57 23.00 24.88 19.80 25.16 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** Final interpretation *** 2007src0178 in P2(1)/n Assumed atomic parameters and limits for interatomic bonds and angles (interspecies and intraspecies) distances angles atomic type radius minimum maximum minimum maximum number Si 1.110 1.10 2.66 80.00 155.00 14 O 0.730 0.88 2.21 80.00 155.00 8 N 0.750 0.89 2.23 80.00 155.00 7 C 0.770 0.90 2.26 80.00 155.00 6 Tentative of peak labelling in terms of atomic species group peaks possible species range of number included chemical species assigned bond angles 1 1 Si Si 80. - 155. 2 1 O O 80. - 155. 3 1 N N 80. - 155. 4 11 C C 80. - 155. range of bond distances used to build fragments group group 1 group 2 group 3 group 4 1 (1.33-2.66) (1.10-2.21) (1.12-2.23) (1.13-2.26) 2 (0.88-1.75) (0.89-1.78) (0.90-1.80) 3 (0.90-1.80) (0.91-1.82) 4 (0.92-1.85) ------------------------------------------------------------------------------ interpeak distances up to 2.63 2) 7( 1) 1.62 3) 8( 1) 1.30 4) 5( 1) 1.35 6( 1) 1.51 8( 1) 1.35 5) 4( 1) 1.35 9( 1) 1.37 6) 4( 1) 1.51 7) 2( 1) 1.62 2( -1) 1.62 8) 3( 1) 1.30 4( 1) 1.35 11( 1) 1.42 9) 5( 1) 1.37 10( 1) 1.40 10) 9( 1) 1.40 11( 1) 1.41 11) 8( 1) 1.42 10( 1) 1.41 accepted distances in this interpretation 2) 7( 1) 1.62 3) 8( 1) 1.30 4) 5( 1) 1.35 6( 1) 1.51 8( 1) 1.35 5) 4( 1) 1.35 9( 1) 1.37 6) 4( 1) 1.51 7) 2( 1) 1.62 2( -1) 1.62 8) 3( 1) 1.30 4( 1) 1.35 11( 1) 1.42 9) 5( 1) 1.37 10( 1) 1.40 10) 9( 1) 1.40 11( 1) 1.41 11) 8( 1) 1.42 10( 1) 1.41 bond angles in this interpretation ( 5( 1) - 4 - 6( 1)) 118.4 ( 5( 1) - 4 - 8( 1)) 122.0 ( 6( 1) - 4 - 8( 1)) 119.6 ( 4( 1) - 5 - 9( 1)) 120.9 ( 2( 1) - 7 - 2( -1)) 180.0 ( 2( -1) - 7 - 2( 1)) 180.0 ( 3( 1) - 8 - 4( 1)) 117.2 ( 3( 1) - 8 - 11( 1)) 122.8 ( 4( 1) - 8 - 11( 1)) 120.0 ( 5( 1) - 9 - 10( 1)) 119.3 ( 9( 1) - 10 - 11( 1)) 120.4 ( 8( 1) - 11 - 10( 1)) 117.3 ------------------------------------------------------------------------------ --------------------- overall plot of the structure ------------------------- ------------ projection on l.s.q. plane ---- scale : 2.50 cms/a ------------ 13 12 9 * *10 * * 7 * * * 5 * * 11 2 * * * 4 ** * 8 * * * 6 3 1 14 ---------------------------------------------------------------------------- fragment number 2 , 8 peaks included peak 3 4 5 6 8 9 10 11 linked to 8 5 4 4 3 5 9 8 6 9 4 10 11 10 8 11 ---------------------------------------------------------------------------- fragments with less than five peaks peak 2 7 linked to 7 2 2' fragment 1 1 ------------------------------------------------------------------------------ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** Output section *** 2007src0178 in P2(1)/n Final residual value = 19.80% Serial Atom Label Height*10 x y z Occ. B[iso] Frag 1) Si Si1 228 0.361 0.329 0.532 1.000 1.41 0 2) O O1 200 0.345 0.039 0.335 1.000 0.10 0 3) N N1 72 0.592 0.150 0.695 1.000 1.15 0 4) C C1 67 0.263 0.154 0.512 1.000 0.95 0 5) C C2 60 0.062 0.165 0.471 1.000 2.22 0 6) C C3 56 0.336 0.140 0.376 1.000 1.93 0 7) C C4 56 0.500 0.000 0.500 0.500 1.98 0 8) C C5 52 0.401 0.158 0.669 1.000 1.91 0 9) C C6 51 -0.012 0.179 0.589 1.000 2.56 0 10) C C7 50 0.123 0.183 0.754 1.000 2.36 0 11) C C8 49 0.334 0.171 0.798 1.000 2.35 0 12) C C9 44 0.086 0.001 0.272 1.000 3.48 0 13) C C10 40 0.567 -0.036 0.838 1.000 2.57 0 14) C C11 22 0.641 0.249 0.475 1.000 1.98 0 Restrictions on Serial Label L.Sq. shifts & Thermal Parameters Site 7) C4 0 0 0 11 22 33 23 13 12 -1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Final R value is 19.80% (Block 1, Set 1, # of LSQ Refinement 1)