****************************************************************************** 2007src0769 in P-1 Wed Jun 27 2007 at 17:36:18 Sir2004 starts on: 2007src0 Used commands & directives: %data Cell 8.897 9.597 9.888 64.918 81.546 68.435 Space P -1 Content C 34 H 70 N 4 O 6 Reflections 2007src0769.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 2007src0769.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 2007src0769 in P-1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Direct cell: a = 8.897 b = 9.597 c = 9.888 alpha = 64.918 beta = 81.546 gamma = 68.435 Cell volume = 711.10 Crystal family : Triclinic Space group (centrosymmetric) : P -1 Symmetry-operations 1) x , y , z 2) -x , -y , -z 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 = 2 Fourier limits : 0.000 < x < 0.500 0.000 < y < 1.000 0.000 < z < 1.000 Patterson limits : 0.000 < x < 0.500 0.000 < y < 1.000 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 70 1 Carbon C 34 6 Nitrogen N 4 7 Oxygen O 6 8 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 Number of atoms in asymmetric unit = 22.00 Equivalent number of equal atoms in primitive cell = 47 Volume per atom = 16.16 11965 input reflections 897 Fo(s) negative set to 0.0 3252 independent input reflections 11 12 12 maximum h,k,l values 0.4248 maximum s**2 = (sin(theta)/lambda)**2 0.7672 Angstrom resolution 46 reflections are not in input data Symmetry equivalent reflections merged: Rsym(F) = 5.18% 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 3 0 3 100 8.0 - 6.0 9 7 2 22 6.0 - 5.0 7 7 0 0 5.0 - 4.0 73 73 0 0 4.0 - 3.0 188 188 0 0 3.0 - 2.5 250 250 0 0 2.5 - 2.0 591 591 0 0 2.0 - 1.8 414 414 0 0 1.8 - 1.6 683 683 0 0 1.6 - 1.4 1034 1034 0 0 1.4 - 1.3 789 789 0 0 1.3 - 1.2 935 935 0 0 1.2 - 1.1 1106 1106 0 0 1.1 - 1.0 1435 1435 0 0 1.0 - 0.9 1696 1691 5 0 0.9 - 0.8 2029 2019 10 0 0.8 - 0.7 769 743 26 3 -1.604 -1.293 -0.982 -0.671 -0.360 -0.049 * * * * * * ********************************************************* * * * * 0.031* *w ** * w * * * w * * * w * * * w * * 0.107* w * ** * w * * * w * * * x * * * w * 0.183* * w ** * * w * * * w ********************************** * * w * y = s**2 * * * w * x = ln / sigfsq * 0.259* * w * ( w ) = wilson * * *w * ( * ) = calc * * w* ********************************** * w * * intercept = 0.01377 * * w * * slope = -3.93291 * 0.335* w * * b(iso) = 1.96646 * * w * * u(iso) = 0.02491 * * w * * scale = 0.98633 * * w* * scale*f(obs.)**2 = f(abs.)**2 * * * w ********************************** 0.411* * w ** * * * * ********************************************************* * * * * * * ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** pseudotranslation section *** 2007src0769 in P-1 *** 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 0.2607 0.3259 Resol. 7.67 3.84 2.56 1.92 1.53 0.0000 1.5568 0.9191 0.8199 0.9057 number 0 23 59 124 201 sinth/lambda 0.3910 0.4562 0.5214 0.5866 0.6517 Resol. 1.28 1.10 0.96 0.85 0.77 0.9138 1.1313 1.1899 0.8586 1.0025 number 296 421 549 728 851 Average values Average Numeric Graphic all data acentric centric hypercentric a. c. h. mod(E) 0.806 0.886 0.798 0.718 * E**2 1.000 1.000 1.000 1.000 E**3 1.587 1.329 1.596 1.916 * E**4 2.980 2.000 3.000 4.500 * E**5 6.327 3.323 6.383 12.260 * E**6 14.722 6.000 15.000 37.500 * mod(E**2-1) 0.952 0.736 0.968 1.145 * (E**2-1)**2 1.980 1.000 2.000 3.500 * (E**2-1)**3 7.782 2.000 8.000 26.000 * (mod(E**2-1))**3 8.442 2.415 8.691 26.903 * n(z) cumulative probability distribution z all data acentric centric hypercentric a. c. h. 0.1 0.220 0.095 0.248 0.368 * 0.2 0.324 0.181 0.345 0.463 * 0.3 0.407 0.259 0.416 0.526 * 0.4 0.468 0.330 0.473 0.574 * 0.5 0.516 0.393 0.520 0.612 * 0.6 0.560 0.451 0.561 0.643 * 0.7 0.595 0.503 0.597 0.670 * 0.8 0.629 0.551 0.629 0.694 * 0.9 0.658 0.593 0.657 0.715 * 1.0 0.685 0.632 0.683 0.733 * 1.2 0.730 0.699 0.727 0.765 * 1.4 0.769 0.753 0.763 0.791 * 1.6 0.803 0.798 0.794 0.813 * 1.8 0.828 0.835 0.820 0.832 * 2.0 0.848 0.865 0.843 0.848 * 2.2 0.870 0.889 0.862 0.863 * 2.4 0.888 0.909 0.879 0.875 * 2.6 0.899 0.926 0.893 0.886 * 2.8 0.907 0.939 0.906 0.896 * 3.0 0.915 0.950 0.917 0.905 * 3.2 0.923 0.959 0.926 0.913 * 3.4 0.933 0.967 0.935 0.920 * 3.6 0.941 0.973 0.942 0.926 * 3.8 0.949 0.978 0.949 0.932 * 4.0 0.954 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 1811 1584 1389 1198 1025 867 737 602 507 411 E 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 number 335 287 243 189 149 115 86 65 51 45 Number and percentage Number and percentage of F's > param * sigma(F) of F's > limit number percentage param number percentage limit 2991 92% 0.50 325 10% 15.57 2791 86% 1.00 650 20% 10.68 2648 81% 1.50 975 30% 8.03 2593 80% 2.00 1300 40% 6.22 2515 77% 2.50 1625 50% 4.87 2451 75% 3.00 1950 60% 3.84 2364 73% 3.50 2275 70% 3.05 2263 70% 4.00 2600 80% 2.27 2180 67% 4.50 2925 90% 1.23 2103 65% 5.00 3250 100% 0.00 299 largest E-values > 1.682 to phase. ( 10 printed ) code h k l E fo/sig. code h k l E fo/sig. 1 6 5 -2 3.297 >6 2 6 3 8 3.284 >6 3 2 -6 4 3.262 >6 4 5 8 7 3.223 >6 5 0 2 -10 3.177 >6 6 2 6 -5 3.164 >6 7 4 8 0 3.116 >6 8 6 1 6 3.090 >6 9 2 2 5 3.089 >6 10 10 9 6 3.065 >6 . . . . . . . . . 664 smallest E-values for psi0 and negative quartets ( 10 printed ) code h k l E fo/sig. code h k l E fo/sig. 3243 0 4 12 0.000 0.00 3244 2 6 -6 0.000 0.00 3245 3 -9 0 0.000 0.00 3246 1 6 12 0.000 0.00 3247 1 -6 6 0.000 0.00 3248 3 11 7 0.000 0.00 3249 3 8 12 0.000 0.00 3250 1 3 -10 0.000 0.00 3251 8 -3 0 0.000 0.00 3252 3 9 -3 0.000 0.00 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sir2004 : Invariants routine Release 01.00 2007src0769 in P-1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2123 strong triplets found among 299 strongest reflections (E-min = 1.682) strengthned by 53 free vectors using P-10 formula Used 7 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. 2123 2113 2106 2100 2097 2087 2065 2046 2030 1979 g 2.0 2.5 3.0 3.5 4.0 5.0 6.0 7.0 9.0 10.0 no. 1911 1831 1717 1577 1423 1107 814 570 272 178 7206 Psi-zero triplets found among 299 strongest reflections and the 664 weakest reflections Quartets statistic 4798 negative quartets found ( 4000 stored ) among 7206 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 3856 3789 3707 3645 3547 3360 3135 2860 2320 g 2.0 2.5 3.0 3.5 4.0 5.0 6.0 7.0 9.0 10.0 no. 1765 1261 879 595 380 181 84 38 8 1 number of relationships calculated stored positive estimated triplets 2064 2064 negative estimated triplets 56 56 psi-zero triplets 7206 7206 negative estimated quartets 3550 3550 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sir2004 : Phase routine Release 01.00 2007src0769 in P-1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Number of Pos. Est. Triplets = 2064 with G > 0.17 Number of Neg. Est. Triplets = 46 with |G| > 0.60 Number of Neg. Est. Quartets = 1000 with |G| > 0.20 Number of refl. to phase = 299 Number of random phases = 99 Number of reflexions in LSQ = 2274 ( 70% of total, F's > 3.051 ) Number of atoms to locate = 22.00 Number of atoms used in LSQ = 26.00 Observations / Parameters = 21.87 Resolution & grid step (Ang) = 0.77 0.33 Fourier map grid points = 27 30 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 Cell: 8.90 9.60 9.89 0.50 0.00 0.00 Cheshire cell: 4.45 4.80 4.94 Transf. Matrix 0.00 0.50 0.00 Grid: 0.07 0.07 0.07 0.00 0.00 0.50 Grid points: 14 15 15 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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 ( 10) 4.035 6 2 ( 56) 3.676 8 3 ( 47) 3.583 27 4 ( 5) 3.182 16 5 ( 37) 3.116 17 6 ( 45) 2.916 52 7 ( 38) 2.822 29 8 ( 18) 2.739 22 9 ( 74) 2.711 18 10 ( 82) 2.697 16 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Extending phases for Block # 1 Set 1 Trial 10 eFom = 4.035 UnDet 2% Trial 10 End of DSR - Final FOM = 6.111 R% = 33.99 29.44 25.49 26.08 28.76 34.71 20.36 17.15 14.85 17.29 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** Final interpretation *** 2007src0769 in P-1 Assumed atomic parameters and limits for interatomic bonds and angles (interspecies and intraspecies) distances angles atomic type radius minimum maximum minimum maximum number O 0.730 0.88 1.80 80.00 155.00 8 N 0.750 0.89 1.82 80.00 155.00 7 C 0.770 0.90 1.85 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 3 O O 80. - 155. 2 2 N N 80. - 155. 3 21 C C 80. - 155. range of bond distances used to build fragments group group 1 group 2 group 3 1 (0.88-1.75) (0.89-1.78) (0.90-1.80) 2 (0.90-1.80) (0.91-1.82) 3 (0.92-1.85) ------------------------------------------------------------------------------ interpeak distances up to 2.40 1) 11( 1) 1.26 2) 18( 1) 1.40 21( 1) 1.62 3) 8( 1) 1.47 14( 1) 1.49 15( 1) 1.48 22( 1) 1.74 4) 11( 1) 1.32 5) 12( 1) 1.45 13( 1) 1.48 16( 1) 1.47 6) 9( 1) 1.20 7) 9( 1) 1.35 8) 3( 1) 1.47 13( 1) 1.54 20( 1) 1.22 9) 6( 1) 1.20 7( 1) 1.35 10( 1) 1.53 10) 9( 1) 1.53 12( 1) 1.53 11) 1( 1) 1.26 4( 1) 1.32 17( 1) 1.56 12) 5( 1) 1.45 10( 1) 1.53 23( 1) 1.04 24( 1) 0.98 13) 5( 1) 1.48 8( 1) 1.54 14) 3( 1) 1.49 17( 1) 1.50 22( 1) 1.83 15) 3( 1) 1.48 16( -1) 1.53 22( 1) 1.14 26( 1) 1.70 16) 5( 1) 1.47 15( -1) 1.53 26( -1) 1.77 17) 11( 1) 1.56 14( 1) 1.50 19( 1) 1.00 18) 2( 1) 1.40 19) 17( 1) 1.00 20) 8( 1) 1.22 21) 2( 1) 1.62 22) 3( 1) 1.74 14( 1) 1.83 15( 1) 1.14 25( 1) 1.58 23) 12( 1) 1.04 24( 1) 1.55 24) 12( 1) 0.98 23( 1) 1.55 25) 22( 1) 1.58 26) 15( 1) 1.70 16( -1) 1.77 accepted distances in this interpretation 1) 11( 1) 1.26 2) 18( 1) 1.40 21( 1) 1.62 3) 8( 1) 1.47 14( 1) 1.49 15( 1) 1.48 22( 1) 1.74 4) 11( 1) 1.32 5) 12( 1) 1.45 13( 1) 1.48 16( 1) 1.47 6) 9( 1) 1.20 7) 9( 1) 1.35 8) 3( 1) 1.47 13( 1) 1.54 20( 1) 1.22 9) 6( 1) 1.20 7( 1) 1.35 10( 1) 1.53 10) 9( 1) 1.53 12( 1) 1.53 11) 1( 1) 1.26 4( 1) 1.32 17( 1) 1.56 12) 5( 1) 1.45 10( 1) 1.53 23( 1) 1.04 24( 1) 0.98 13) 5( 1) 1.48 8( 1) 1.54 14) 3( 1) 1.49 17( 1) 1.50 22( 1) 1.83 15) 3( 1) 1.48 16( -1) 1.53 22( 1) 1.14 26( 1) 1.70 16) 5( 1) 1.47 15( -1) 1.53 26( -1) 1.77 17) 11( 1) 1.56 14( 1) 1.50 19( 1) 1.00 18) 2( 1) 1.40 19) 17( 1) 1.00 20) 8( 1) 1.22 21) 2( 1) 1.62 22) 3( 1) 1.74 14( 1) 1.83 15( 1) 1.14 25( 1) 1.58 23) 12( 1) 1.04 24( 1) 1.55 24) 12( 1) 0.98 23( 1) 1.55 25) 22( 1) 1.58 26) 15( 1) 1.70 16( -1) 1.77 bond angles in this interpretation ( 18( 1) - 2 - 21( 1)) 33.0 ( 8( 1) - 3 - 14( 1)) 110.5 ( 8( 1) - 3 - 15( 1)) 109.8 ( 8( 1) - 3 - 22( 1)) 122.6 ( 14( 1) - 3 - 15( 1)) 109.1 ( 14( 1) - 3 - 22( 1)) 68.6 ( 15( 1) - 3 - 22( 1)) 40.7 ( 12( 1) - 5 - 13( 1)) 111.5 ( 12( 1) - 5 - 16( 1)) 110.9 ( 13( 1) - 5 - 16( 1)) 109.9 ( 3( 1) - 8 - 13( 1)) 111.5 ( 3( 1) - 8 - 20( 1)) 95.9 ( 13( 1) - 8 - 20( 1)) 95.2 ( 6( 1) - 9 - 7( 1)) 123.9 ( 6( 1) - 9 - 10( 1)) 120.8 ( 7( 1) - 9 - 10( 1)) 115.3 ( 9( 1) - 10 - 12( 1)) 111.0 ( 1( 1) - 11 - 4( 1)) 123.3 ( 1( 1) - 11 - 17( 1)) 119.5 ( 4( 1) - 11 - 17( 1)) 117.2 ( 5( 1) - 12 - 10( 1)) 113.3 ( 5( 1) - 12 - 23( 1)) 110.1 ( 5( 1) - 12 - 24( 1)) 110.6 ( 10( 1) - 12 - 23( 1)) 112.5 ( 10( 1) - 12 - 24( 1)) 109.8 ( 23( 1) - 12 - 24( 1)) 99.8 ( 5( 1) - 13 - 8( 1)) 110.3 ( 3( 1) - 14 - 17( 1)) 110.9 ( 3( 1) - 14 - 22( 1)) 62.1 ( 17( 1) - 14 - 22( 1)) 94.5 ( 3( 1) - 15 - 16( -1)) 114.2 ( 3( 1) - 15 - 22( 1)) 81.8 ( 3( 1) - 15 - 26( 1)) 175.7 ( 16( -1) - 15 - 22( 1)) 153.4 ( 16( -1) - 15 - 26( 1)) 66.3 ( 22( 1) - 15 - 26( 1)) 96.1 ( 5( 1) - 16 - 15( -1)) 114.6 ( 5( 1) - 16 - 26( -1)) 109.6 ( 15( -1) - 16 - 26( -1)) 61.3 ( 11( 1) - 17 - 14( 1)) 109.9 ( 11( 1) - 17 - 19( 1)) 105.7 ( 14( 1) - 17 - 19( 1)) 117.7 ( 3( 1) - 22 - 14( 1)) 49.3 ( 3( 1) - 22 - 15( 1)) 57.5 ( 3( 1) - 22 - 25( 1)) 71.5 ( 14( 1) - 22 - 15( 1)) 106.8 ( 14( 1) - 22 - 25( 1)) 27.6 ( 15( 1) - 22 - 25( 1)) 127.0 ( 12( 1) - 23 - 24( 1)) 38.6 ( 12( 1) - 24 - 23( 1)) 41.7 ( 15( 1) - 26 - 16( -1)) 52.3 ------------------------------------------------------------------------------ --------------------- overall plot of the structure ------------------------- ------------ projection on l.s.q. plane ---- scale : 2.30 cms/a ------------ 26 15 * 22 16 8 ** * * * * *20 3 * * * 25 5 * * 13 * * 14 * 19 * * * 7 17* 12 * ** * * 1 23 * * * ** 9 11 * * ** 6 10 * * 4 2 * * 18 21 ---------------------------------------------------------------------------- fragment number 1 , 19 peaks included peak 1 3 4 5 6 7 8 9 10 11 12 13 14 linked to 11 8 11 12 9 9 3 6 9 1 5 5 3 14 13 13 7 12 4 10 8 17 15 16 20 10 17 23 peak 15 16 17 19 20 23 linked to 3 5 11 17 8 12 14 19 ---------------------------------------------------------------------------- fragments with less than five peaks peak 2 18 linked to 18 2 fragment 2 2 ------------------------------------------------------------------------------ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** Output section *** 2007src0769 in P-1 Final residual value = 14.85% Serial Atom Label Height*10 x y z Occ. B[iso] Frag 1) O O1 108 0.605 0.458 0.843 1.000 1.79 0 2) O O2 96 0.117 0.322 0.904 1.000 2.65 0 3) C C1 94 0.538 0.131 0.654 1.000 3.80 0 4) O O3 93 0.367 0.425 0.942 1.000 3.80 0 5) C C2 91 0.288 -0.014 0.617 1.000 3.80 0 6) N N1 88 0.004 0.411 0.344 1.000 3.80 0 7) N N2 87 0.246 0.372 0.426 1.000 3.80 0 8) C C3 78 0.541 -0.039 0.716 1.000 1.61 0 9) C C4 75 0.101 0.350 0.443 1.000 1.55 0 10) C C5 75 0.065 0.242 0.602 1.000 1.63 0 11) C C6 75 0.482 0.423 0.842 1.000 1.47 0 12) C C7 74 0.115 0.064 0.622 1.000 1.59 0 13) C C8 74 0.369 -0.048 0.753 1.000 1.66 0 14) C C9 74 0.531 0.185 0.776 1.000 1.71 0 15) C C10 73 0.686 0.143 0.565 1.000 1.63 0 16) C C11 72 0.327 -0.167 0.596 1.000 1.46 0 17) C C12 70 0.465 0.368 0.719 1.000 1.74 0 18) C C13 45 0.013 0.254 1.011 1.000 3.70 0 19) C C14 12 0.515 0.432 0.627 1.000 3.80 0 20) C C15 12 0.574 -0.071 0.844 1.000 3.80 0 21) Q Q1 11 -0.056 0.295 0.937 1.000 4.08 0 22) C C16 11 0.707 0.180 0.655 1.000 3.80 0 23) C C17 10 0.068 -0.006 0.719 1.000 3.80 0 24) C C18 10 0.060 0.058 0.547 1.000 3.80 0 25) C C19 9 0.625 0.149 0.812 1.000 3.80 0 26) C C20 9 0.849 0.173 0.461 1.000 3.80 0 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Final R value is 14.85% (Block 1, Set 1, # of LSQ Refinement 1)