COMMAND FILE FOR SHELXL-97 APPLICATION AFTER THE RIETVELD REFINEMENT
TITL Cimetidine P21/n
CELL 1.52904 10.700 18.820 6.825 90. 111.285 90.
ZERR 4 .001 .001 .001 0 0.001 0
LATT 1
SYMM 0.5-X,0.5+Y,0.5-Z
SFAC S N C H
UNIT 4 24 40 64
L.S. 10
ACTA
WGHT 0.100000
FVAR 0.20089
S1 1 0.98225 0.41503 0.19332 11.00000 0.06166
C6 3 0.14177 0.39598 0.15023 11.00000 0.07330
N4 2 0.45158 0.37269 0.55990 11.00000 0.06746
N1 2 0.13296 0.23003 0.73484 11.00000 0.01762
N5 2 0.60019 0.40636 0.39380 11.00000 0.02201
N3 2 0.36284 0.44256 0.25554 11.00000 0.03143
C8 3 0.46544 0.40529 0.38373 11.00000 0.08578
C3 3 0.03672 0.28399 0.66286 11.00000 0.07166
C1 3 0.23339 0.25847 0.68097 11.00000 0.04662
N2 2 0.20613 0.31654 0.57497 11.00000 0.02112
C5 3 0.00746 0.40654 0.48431 11.00000 0.04670
C7 3 0.23358 0.46350 0.26609 11.00000 0.03099
C4 3 0.90373 0.28652 0.71387 11.00000 0.04716
C2 3 0.09607 0.33236 0.57021 11.00000 0.05999
N6 2 0.66480 0.49081 0.15447 11.00000 0.01508
C10 3 0.62061 0.45236 0.25369 11.00000 0.00413
C9 3 0.55481 0.39157 0.71394 11.00000 0.04022
HKLF 3
RESULTS
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXL-97 - CRYSTAL STRUCTURE REFINEMENT - MSDOS 32-BIT VERSION +
+ Copyright(C) George M. Sheldrick 1993-7 Release 97-1 +
+ cim1 started at 09:47:37 on 25-Jun-1997 +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TITL Cimetidine P21/n
CELL 1.52904 10.700 18.820 6.825 90. 111.285 90.
ZERR 4 .001 .001 .001 0 0.001 0
LATT 1
SYMM 0.5-X,0.5+Y,0.5-Z
SFAC S N C H
UNIT 4 24 40 64
V = 1280.63 F(000) = 536.0 Mu = 2.16 mm-1 Cell Wt = 1009.39 Rho = 1.309
L.S. 10
ACTA
WGHT 0.100000
FVAR 0.20089
S1 1 0.98225 0.41503 0.19332 11.00000 0.06166
C6 3 0.14177 0.39598 0.15023 11.00000 0.07330
N4 2 0.45158 0.37269 0.55990 11.00000 0.06746
N1 2 0.13296 0.23003 0.73484 11.00000 0.01762
N5 2 0.60019 0.40636 0.39380 11.00000 0.02201
N3 2 0.36284 0.44256 0.25554 11.00000 0.03143
C8 3 0.46544 0.40529 0.38373 11.00000 0.08578
C3 3 0.03672 0.28399 0.66286 11.00000 0.07166
C1 3 0.23339 0.25847 0.68097 11.00000 0.04662
N2 2 0.20613 0.31654 0.57497 11.00000 0.02112
C5 3 0.00746 0.40654 0.48431 11.00000 0.04670
C7 3 0.23358 0.46350 0.26609 11.00000 0.03099
C4 3 0.90373 0.28652 0.71387 11.00000 0.04716
C2 3 0.09607 0.33236 0.57021 11.00000 0.05999
N6 2 0.66480 0.49081 0.15447 11.00000 0.01508
C10 3 0.62061 0.45236 0.25369 11.00000 0.00413
C9 3 0.55481 0.39157 0.71394 11.00000 0.04022
HKLF 3
Covalent radii and connectivity table for Cimetidine P21/n
S 1.030
N 0.700
C 0.770
H 0.320
S1 - C6_$2 C5_$2
C6 - C7 S1_$1
N4 - C9 C8
N1 - C1 C3
N5 - C10 C8
N3 - C8 C7
C8 - N3 N4 N5
C3 - C2 N1 C4_$1
C1 - N2 N1 C2
N2 - C2 C1
C5 - C2 S1_$1
C7 - N3 C6
C4 - C3_$2
C2 - N2 C3 C5 C1
N6 - C10
C10 - N6 N5
C9 - N4
Operators for generating equivalent atoms:
$1 x-1, y, z
$2 x+1, y, z
924 Reflections read, of which 0 rejected
0 =< h =< 9, 0 =< k =< 16, -6 =< l =< 5, Max. 2-theta = 84.94
0 Systematic absence violations
0 Inconsistent equivalents
924 Unique reflections, of which 0 suppressed
R(int) = 0.0000 R(sigma) = 0.0950 Friedel opposites merged
Maximum memory for data reduction = 1208 / 9253
** Cell contents from UNIT instruction and atom list do not agree **
Unit-cell contents from UNIT instruction and atom list resp.
S 4.00 4.00
N 24.00 24.00
C 40.00 40.00
H 64.00 0.00
Least-squares cycle 1 Maximum vector length = 511 Memory required = 1379 / 96066
wR2 = 0.9272 before cycle 1 for 924 data and 69 / 69 parameters
GooF = S = 9.651; Restrained GooF = 9.651 for 0 restraints
Weight = 1 / [ sigma^2(Fo^2) + ( 0.1000 * P )^2 + 0.00 * P ] where P = ( Max ( Fo^2, 0 ) + 2 * Fc^2 ) / 3
N value esd shift/esd parameter
1 0.36237 0.02650 6.093 OSF
8 0.07711 0.01805 -4.051 z C6
17 0.09755 0.01902 4.202 U11 N1
21 0.13123 0.02261 4.830 U11 N5
22 0.38894 0.00738 3.538 x N3
25 0.11712 0.02243 3.820 U11 N3
37 0.14221 0.02598 3.679 U11 C1
41 0.12475 0.02211 4.686 U11 N2
49 0.14922 0.02668 4.431 U11 C7
50 0.87114 0.00895 -3.640 x C4
55 0.35000 0.00541 3.260 y C2
61 0.13760 0.02111 5.805 U11 N6
65 0.11381 0.02144 5.115 U11 C10
69 0.25039 0.02593 8.106 U11 C9
Mean shift/esd = 1.826 Maximum = 8.106 for U11 C9
Max. shift = 0.469 A for C6 Max. dU = 0.210 for C9
Least-squares cycle 10 Maximum vector length = 511 Memory required = 1379 / 96066
wR2 = 0.2128 before cycle 10 for 924 data and 69 / 69 parameters
GooF = S = 1.205; Restrained GooF = 1.205 for 0 restraints
Weight = 1 / [ sigma^2(Fo^2) + ( 0.1000 * P )^2 + 0.00 * P ] where P = ( Max ( Fo^2, 0 ) + 2 * Fc^2 ) / 3
N value esd shift/esd parameter
1 0.50420 0.00376 0.037 OSF
Mean shift/esd = 0.188 Maximum = -0.606 for z C6
Max. shift = 0.002 A for C6 Max. dU = 0.000 for C4
Largest correlation matrix elements
0.838 U11 S1 / OSF 0.720 U11 C7 / U11 S1 0.701 U11 C5 / U11 S1
0.808 U11 N1 / U11 S1 0.719 U11 N2 / U11 S1 0.700 U11 C4 / U11 N5
0.787 U11 C4 / U11 S1 0.717 U11 C9 / U11 S1 0.698 U11 C10 / U11 S1
0.759 U11 C2 / U11 S1 0.717 U11 C2 / U11 N1 0.695 U11 C4 / U11 C6
0.750 U11 C3 / U11 S1 0.713 U11 C6 / U11 S1 0.691 U11 C2 / OSF
0.743 U11 N4 / U11 S1 0.711 U11 C1 / U11 S1 0.690 U11 C4 / U11 N4
0.727 U11 N3 / U11 S1 0.710 U11 N6 / U11 S1 0.683 U11 C2 / U11 N4
0.725 U11 N1 / OSF 0.707 U11 C4 / OSF 0.682 U11 C3 / U11 N1
Cimetidine P21/n
ATOM x y z sof U11 U22 U33 U23 U13 U12 Ueq
S1 0.98468 0.41389 0.19880 1.00000 0.04633
0.00223 0.00010 0.00005 0.00019 0.00000 0.00096
C6 0.14412 0.39432 0.14410 1.00000 0.03522
0.00698 0.00034 0.00020 0.00054 0.00000 0.00120
N4 0.45193 0.37313 0.55985 1.00000 0.04469
0.00585 0.00028 0.00014 0.00046 0.00000 0.00113
N1 0.12804 0.23565 0.72779 1.00000 0.03509
0.00569 0.00029 0.00013 0.00039 0.00000 0.00112
N5 0.59391 0.40922 0.39058 1.00000 0.05532
0.00665 0.00036 0.00012 0.00052 0.00000 0.00132
N3 0.36866 0.44607 0.24637 1.00000 0.05525
0.00686 0.00037 0.00016 0.00050 0.00000 0.00128
C8 0.46100 0.40386 0.40125 1.00000 0.03615
0.00712 0.00035 0.00014 0.00060 0.00000 0.00133
C3 0.02816 0.28808 0.66757 1.00000 0.02883
0.00691 0.00033 0.00017 0.00054 0.00000 0.00119
C1 0.23103 0.25175 0.67590 1.00000 0.05184
0.00724 0.00034 0.00021 0.00056 0.00000 0.00131
N2 0.21052 0.31729 0.56755 1.00000 0.04183
0.00543 0.00026 0.00012 0.00042 0.00000 0.00121
C5 0.02485 0.41153 0.49316 1.00000 0.02554
0.00626 0.00032 0.00015 0.00051 0.00000 0.00129
C7 0.23588 0.46336 0.27745 1.00000 0.02866
0.00718 0.00032 0.00021 0.00048 0.00000 0.00118
C4 0.89656 0.28138 0.70832 1.00000 0.01420
0.00602 0.00028 0.00014 0.00049 0.00000 0.00112
C2 0.08661 0.33688 0.57698 1.00000 0.01462
0.00555 0.00024 0.00014 0.00041 0.00000 0.00116
N6 0.66679 0.48744 0.15076 1.00000 0.05794
0.00627 0.00030 0.00016 0.00057 0.00000 0.00127
C10 0.62397 0.44966 0.25845 1.00000 0.02596
0.00779 0.00037 0.00016 0.00058 0.00000 0.00125
C9 0.56400 0.34167 0.72801 1.00000 0.03313
0.00637 0.00029 0.00020 0.00046 0.00000 0.00124
Final Structure Factor Calculation for Cimetidine P21/n
Total number of l.s. parameters = 69 Maximum vector length = 511 Memory required = 1310 / 22995
wR2 = 0.2092 before cycle 11 for 924 data and 0 / 69 parameters
GooF = S = 1.182; Restrained GooF = 1.182 for 0 restraints
Weight = 1 / [ sigma^2(Fo^2) + ( 0.1000 * P )^2 + 0.00 * P ] where P = ( Max ( Fo^2, 0 ) + 2 * Fc^2 ) / 3
R1 = 0.0753 for 849 Fo > 4sig(Fo) and 0.0789 for all 924 data
wR2 = 0.2092, GooF = S = 1.182, Restrained GooF = 1.182 for all data
Occupancy sum of asymmetric unit = 17.00 for non-hydrogen and 0.00 for hydrogen atoms
Analysis of variance for reflections employed in refinement K = Mean[Fo^2] / Mean[Fc^2] for group
Fc/Fc(max) 0.000 0.012 0.025 0.040 0.056 0.070 0.093 0.117 0.156 0.211 1.000
Number in group 94. 94. 89. 94. 92. 92. 92. 96. 89. 92.
GooF 1.517 1.346 1.071 0.945 0.993 1.216 1.219 1.153 1.151 1.062
K 2.115 1.331 1.169 1.209 1.131 1.083 1.112 1.120 1.017 1.016
Resolution(A) 1.13 1.17 1.22 1.28 1.34 1.43 1.54 1.68 1.94 2.45 inf
Number in group 95. 91. 94. 90. 94. 92. 91. 94. 91. 92.
GooF 0.985 1.075 0.989 0.985 0.887 1.139 1.324 1.222 1.382 1.621
K 1.161 1.179 1.062 0.970 1.027 1.083 1.000 1.016 1.083 1.018
R1 0.107 0.102 0.082 0.078 0.084 0.092 0.083 0.075 0.076 0.054
Recommended weighting scheme: WGHT 0.1073 0.0920
Note that in most cases convergence will be faster if fixed weights (e.g. the
default WGHT 0.1) are retained until the refinement is virtually complete, and
only then should the above recommended values be used.
Bond lengths and angles
S1 - Distance Angles
C6_$2 1.9100 (0.0034)
C5_$2 1.8963 (0.0036) 109.12 (0.14)
S1 - C6_$2
C6 - Distance Angles
C7 1.6828 (0.0054)
S1_$1 1.9100 (0.0034) 97.62 (0.20)
C6 - C7
N4 - Distance Angles
C9 1.4513 (0.0036)
C8 1.2617 (0.0044) 124.51 (0.30)
N4 - C9
N1 - Distance Angles
C1 1.3096 (0.0036)
C3 1.4022 (0.0039) 112.61 (0.25)
N1 - C1
N5 - Distance Angles
C10 1.3063 (0.0040)
C8 1.4537 (0.0041) 124.44 (0.30)
N5 - C10
N3 - Distance Angles
C8 1.4023 (0.0047)
C7 1.5453 (0.0049) 116.56 (0.26)
N3 - C8
C8 - Distance Angles
N3 1.4023 (0.0047)
N4 1.2617 (0.0044) 130.83 (0.32)
N5 1.4537 (0.0041) 110.93 (0.24) 117.14 (0.31)
C8 - N3 N4
C3 - Distance Angles
C2 1.3775 (0.0041)
N1 1.4022 (0.0039) 100.30 (0.20)
C4_$1 1.5363 (0.0042) 136.99 (0.25) 122.71 (0.24)
C3 - C2 N1
C1 - Distance Angles
N2 1.4137 (0.0043)
N1 1.3096 (0.0036) 110.94 (0.28)
C2 2.1570 (0.0043) 39.71 (0.15) 71.28 (0.19)
C1 - N2 N1
N2 - Distance Angles
C2 1.3999 (0.0033)
C1 1.4137 (0.0043) 100.10 (0.23)
N2 - C2
C5 - Distance Angles
C2 1.5695 (0.0040)
S1_$1 1.8963 (0.0036) 108.10 (0.19)
C5 - C2
C7 - Distance Angles
N3 1.5453 (0.0049)
C6 1.6828 (0.0054) 98.52 (0.26)
C7 - N3
C4 - Distance Angles
C3_$2 1.5363 (0.0042)
C4 -
C2 - Distance Angles
N2 1.3999 (0.0033)
C3 1.3775 (0.0041) 115.91 (0.24)
C5 1.5695 (0.0040) 119.96 (0.21) 124.10 (0.21)
C1 2.1570 (0.0043) 40.18 (0.15) 75.81 (0.19) 159.71 (0.19)
C2 - N2 C3 C5
N6 - Distance Angles
C10 1.2249 (0.0040)
N6 -
C10 - Distance Angles
N6 1.2249 (0.0040)
N5 1.3063 (0.0040) 172.72 (0.42)
C10 - N6
C9 - Distance Angles
N4 1.4513 (0.0036)
C9 -
FMAP and GRID set by program
FMAP 2 3 9
GRID -4.167 -2 -2 4.167 2 2
R1 = 0.0789 for 924 unique reflections after merging for Fourier
Electron density synthesis with coefficients Fo-Fc
Highest peak 0.33 at 0.9824 0.4192 0.1996 [ 0.10 A from S1 ]
Deepest hole -0.26 at 0.0932 0.9013 0.0959 [ 0.59 A from C8 ]
Mean = 0.00, Rms deviation from mean = 0.07 e/A^3, Highest memory used = 1556 / 12978
Fourier peaks appended to .res file
x y z sof U Peak Distances to nearest atoms (including symmetry equivalents)
Q1 1 0.2560 0.4634 0.4553 1.00000 0.05 0.29 1.15 C7 2.20 N3 2.41 C6 2.51 C10
Q2 1 0.9202 0.3055 0.7833 1.00000 0.05 0.26 0.66 C4 1.65 C3 2.71 C2 2.73 N1
Q3 1 0.6063 0.3841 0.8373 1.00000 0.05 0.25 1.07 C9 2.02 N4 2.79 N6 2.84 C8
Q4 1 -0.1067 0.4246 0.4678 1.00000 0.05 0.24 1.38 C5 2.38 S1 2.54 C2 2.75 C10
Q5 1 0.8774 0.2480 0.5984 1.00000 0.05 0.23 0.94 C4 1.69 C3 2.51 N1 2.74 C1
Q6 1 0.1070 0.2047 0.6554 1.00000 0.05 0.23 0.74 N1 1.56 C1 1.80 C3 2.54 C2
Q7 1 0.8997 0.2208 0.6690 1.00000 0.05 0.23 1.17 C4 1.87 C3 2.34 N1 2.77 C8
Q8 1 0.1206 0.3712 -0.0458 1.00000 0.05 0.23 1.30 C6 2.42 C3 2.55 C2 2.70 S1
Q9 1 0.8360 0.3398 0.6694 1.00000 0.05 0.21 1.25 C4 2.28 C3 2.91 N5 2.97 C2
Q10 1 0.8054 0.1961 0.7363 1.00000 0.05 0.21 1.92 C4 2.34 C6 2.49 C8 2.55 N4
Q11 1 0.1763 0.4986 0.0811 1.00000 0.05 0.20 1.42 C7 2.06 C6 2.19 N3 2.63 S1
Q12 1 0.5734 0.3104 0.6272 1.00000 0.05 0.20 0.94 C9 1.69 N4 2.36 C8 2.52 N5
Q13 1 0.5362 0.2890 0.8192 1.00000 0.05 0.20 1.26 C9 2.30 N4 2.64 N1 2.68 C1
Q14 1 0.3090 0.3207 0.9584 1.00000 0.05 0.19 2.22 C1 2.49 N2 2.51 C4 2.56 N1
Q15 1 0.0243 0.2960 0.4534 1.00000 0.05 0.19 1.16 C2 1.45 C3 1.90 N2 2.13 N1
Q16 1 0.6817 0.4060 0.6353 1.00000 0.05 0.19 1.59 N5 2.01 C9 2.32 C8 2.40 N4
Q17 1 0.3525 0.1792 0.7121 1.00000 0.05 0.18 1.84 C1 2.27 S1 2.66 N1 2.72 C5
Q18 1 1.0267 0.2630 1.0398 1.00000 0.05 0.18 2.21 C4 2.31 C9 2.59 C3 2.70 N4
Q19 1 0.1512 0.3589 0.2245 1.00000 0.05 0.18 0.85 C6 2.01 S1 2.14 C7 2.33 N2
Q20 1 0.0372 0.3979 0.4168 1.00000 0.05 0.18 0.64 C5 1.42 S1 1.54 C2 2.33 N2
Shortest distances between peaks (including symmetry equivalents)
5 7 0.68 2 9 1.15 7 10 1.33 12 18 1.52 12 13 1.55 2 5 1.60 7 14 1.61
5 14 1.62 5 10 1.72 2 7 1.75 8 19 1.77 4 20 1.77 13 15 1.87 3 16 1.88
2 18 1.88 5 9 1.89 10 19 1.92 3 13 1.93 3 12 1.93 10 14 1.94 15 20 1.95
9 16 2.01 15 17 2.03 13 18 2.11 12 16 2.13 6 13 2.14 6 15 2.18 19 20 2.22
8 14 2.22 6 7 2.27 18 19 2.32 5 15 2.32 4 9 2.33 7 9 2.34 2 10 2.36
2 8 2.38 8 18 2.43 17 20 2.44 1 11 2.47 5 6 2.48 1 19 2.52 7 18 2.53
8 10 2.54 8 11 2.54 4 17 2.55 6 17 2.56 1 20 2.57 11 16 2.67 1 16 2.68
15 19 2.69 7 15 2.71 3 6 2.74 13 17 2.76 17 18 2.76 9 12 2.77 9 10 2.78
1 4 2.81 10 18 2.81 4 15 2.82 11 19 2.85 2 15 2.86 5 18 2.87 10 18 2.89
5 17 2.90 15 18 2.90 4 16 2.90 13 14 2.97 14 19 2.98 9 18 2.98
Time profile in seconds
-----------------------
0.33: Read and process instructions
0.00: Fit rigid groups
0.00: Interpret restraints etc.
0.00: Generate connectivity array
0.05: Analyse DFIX/DANG restraints
0.00: Analyse SAME/SADI restraints
0.00: Generate CHIV restraints
0.00: Check if bonds in residues restrained
0.00: Generate DELU restraints
0.00: Generate SIMU restraints
0.00: Generate ISOR restraints
0.00: Generate NCSY restraints
0.00: Analyse other restraints etc.
0.44: Read intensity data, sort/merge etc.
0.00: Set up constraints
0.00: OSF, H-atoms from difference map
0.30: Set up l.s. refinement
0.06: Generate idealized H-atoms
5.45: Structure factors and derivatives
2.63: Sum l.s. matrices
0.00: Generate and apply antibumping restraints
0.05: Apply other restraints
0.48: Solve l.s. equations
0.00: Generate HTAB table
0.20: Other dependent quantities, CIF, tables
0.83: Analysis of variance
0.33: Merge reflections for Fourier and .fcf
0.17: Fourier summations
0.33: Peaksearch
0.05: Analyse peaklist
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ cim1 finished at 09:47:48 Total elapsed time: 11.8 secs +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++