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1.086
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1
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2.437
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1
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3.395
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1
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1
1
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1
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3.229
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1
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1
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3.107
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1
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1
1
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4.387
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0.390
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1
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2.284
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0.077
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1
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2.958
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1
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1
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2.104
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1
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1
1
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2.353
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1
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1
1
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1
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3.253
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1
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1
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1.583
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1
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1
1
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1
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1
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1
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1
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0.266
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1.080
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2.686
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0.078
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1.115
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-0.439
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-0.541
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-2.943
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1.029
-3.247
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0.830
-5.168
-2.443
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4.729
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1.654
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2
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5.294
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1.181
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2
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3.517
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2.478
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5.825
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2.541
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2.066
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2
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7.751
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2.873
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2
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2.756
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-4.118
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6.654
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4.997
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4.026
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2
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4.870
-2.714
3.917
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2
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3.852
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3.811
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2.688
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3.537
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2.938
-1.762
3.461
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2
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2.061
-0.686
3.141
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1
2
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0.905
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2.725
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2
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2.653
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3.323
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2
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3.966
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3.677
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4.398
1.979
3.858
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3.879
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4.252
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3.759
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7.106
-5.235
1.018
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2
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2.158
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2.414
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4.549
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6.798
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-2.077
4.311
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2
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3.963
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3.950
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2
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2.059
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2
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3.759
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3.767
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2
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1
2
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9.503
-4.115
6.402
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1
3
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10.966
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6.526
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3
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3
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9.014
-5.343
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3
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8.760
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3
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6.421
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3
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8.048
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6.816
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3
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6.697
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6.431
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3
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8.060
-0.002
8.299
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3
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8.414
1.369
8.364
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3
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6.605
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8.739
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3
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5.923
0.167
7.409
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3
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4.537
-0.318
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3
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3.490
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7.096
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3
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3.605
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7.183
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3
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2.272
0.008
6.783
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3
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2.003
-1.343
6.694
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3
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3
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0.884
-1.716
6.355
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3
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3
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3.140
-2.206
6.968
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3
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1
3
1.00
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2.965
-3.713
6.967
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3
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4.351
-1.663
7.239
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3
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8.962
-1.649
5.335
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3
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10.020
-1.257
6.685
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3
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1
3
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0.323
6.096
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3
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8.753
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8.878
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3
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6.477
-1.294
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3
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6.269
0.385
9.584
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1
3
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5.981
1.258
7.212
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1
3
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1.533
0.656
6.516
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1
3
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2.577
-4.026
7.937
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3
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1
3
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2.245
-3.996
6.197
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3
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1
3
1.00
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3.910
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6.776
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3
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1
3
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5.266
-2.225
7.354
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1
3
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8.770
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9.746
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1
4
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10.109
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9.647
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4
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1
4
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8.675
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10.868
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4
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4
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7.676
3.254
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4
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7.701
4.423
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4
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6.453
5.280
9.391
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4
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5.318
4.479
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4
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6.327
5.738
10.860
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4
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6.208
7.145
11.007
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4
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4
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5.064
5.020
11.352
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4
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1
4
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4.332
4.581
10.082
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4
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1
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3.613
3.303
10.285
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4
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1
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4.051
2.182
10.936
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4
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1
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C
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3.273
1.141
10.829
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4
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1
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2.197
1.640
10.105
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4
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1
4
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1
C
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1.004
1.059
9.650
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4
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1
4
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1
C
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0.775
-0.247
9.771
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4
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1
4
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1
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0.076
1.838
9.073
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4
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1
4
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1
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0.331
3.138
8.951
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4
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1
4
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1
C
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1.433
3.800
9.281
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4
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1
4
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2.353
2.976
9.843
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4
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4
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7.727
4.141
8.098
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4
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1
4
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8.593
5.009
9.380
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4
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1
4
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6.513
6.142
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4
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4
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5.441
11.409
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4
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4
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4.264
12.120
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4
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1
4
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4.429
5.707
11.849
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4
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4
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3.625
5.342
9.756
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4
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1
4
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2.190
11.504
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4
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1
4
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-0.055
-0.671
9.376
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4
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1
4
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1.450
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10.274
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4
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1
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3.743
8.508
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4
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12.470
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6.522
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12.345
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13.387
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8.506
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12.298
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13.256
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12.809
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12.037
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12.352
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11.389
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13.184
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11.388
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14.029
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5
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14.377
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13.412
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10.455
13.832
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15.043
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14.256
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13.354
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6
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6
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14.872
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6
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15.888
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6
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16.513
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6
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6
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O
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15.301
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6
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14.218
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6
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6
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6
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6
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13.254
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6
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12.933
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6
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6
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15.200
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6
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6
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O
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17.175
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16.345
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1
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16.662
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14.817
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1
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14.553
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1
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15.486
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1
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15.755
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1
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N
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15.175
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1
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C
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14.352
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1
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O
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15.551
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1
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N
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16.411
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1
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C
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0.329
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16.778
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1
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16.978
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1
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16.615
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1
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18.235
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-6.482
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16.703
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-5.676
14.491
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14.843
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-3.346
13.522
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-1.893
15.106
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1
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0.300
1.740
16.485
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1
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0.464
17.439
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1
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H
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-1.762
17.676
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1
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H
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16.951
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1
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H
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-6.299
17.396
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1
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12.926
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8
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2
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P
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13.364
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2
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O
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12.093
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2
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O
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12.065
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2
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O
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12.550
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2
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11.783
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2
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C
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11.930
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2
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O
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10.273
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2
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2
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O
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2
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C
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10.670
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2
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C
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10.777
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2
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N
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-2.484
10.845
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2
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C
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11.129
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N7
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2
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N
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-3.411
-0.959
11.252
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ATOM
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2
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C
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-2.263
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11.603
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ATOM
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2
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C
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12.010
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ATOM
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2
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O
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11.467
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N1
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ATOM
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N1
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1
2
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N
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-3.678
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11.128
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ATOM
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C2
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1
2
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C
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-3.735
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10.992
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N2
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ATOM
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N2
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1
2
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N
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10.897
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2
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N
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-4.592
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10.971
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8
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2
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C
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13.608
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8
ATOM
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2
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H
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12.431
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8
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1
2
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H
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-1.518
12.258
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8
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2
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H
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-3.366
10.064
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8
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2
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H
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-7.047
-2.935
9.433
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8
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2
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H
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-7.658
-1.634
8.691
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8
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1
2
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H
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-7.327
-0.086
10.417
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ATOM
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1
2
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H
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-5.237
-3.472
10.672
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1
2
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H
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-1.677
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11.708
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8
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1
2
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-2.899
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11.107
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2
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10.693
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2
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H
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8.274
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9
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3
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8.165
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9
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3
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O
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7.569
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9
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-9.279
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7.705
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9
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3
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O
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1.070
8.334
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9
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3
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-7.911
1.889
7.972
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9
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3
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-6.644
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8.347
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9
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3
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O
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6.505
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9
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3
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-7.735
3.775
6.490
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3
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O
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-6.463
1.738
6.052
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3
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-5.700
1.876
7.390
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9
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3
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1.010
7.473
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9
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3
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-3.254
1.556
7.702
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9
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3
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7.658
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9
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3
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O
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0.655
7.989
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9
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3
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8.030
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3
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8.348
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9
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3
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O
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-3.715
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7.734
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9
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3
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C
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-3.979
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7.684
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9
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3
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C
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7.490
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9
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3
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0.941
9.417
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3
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1.663
8.085
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2.675
8.717
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3
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0.691
5.713
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2.254
5.224
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2.930
7.623
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3
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1.055
8.273
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3
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7.864
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9
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3
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6.702
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3
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8.440
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3
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7.363
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3
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H
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4.629
5.137
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4
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5.606
5.265
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4
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O
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3.722
3.982
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4
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O
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5.420
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4
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O
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5.801
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4
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5.584
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4
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5.883
5.870
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4
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O
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7.437
4.130
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4
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8.755
4.028
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10
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4
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O
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6.403
3.608
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4
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C
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-2.893
5.729
4.859
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4
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C
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4.306
4.609
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10
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N9
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4
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N
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-3.311
3.381
3.923
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10
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4
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C
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2.158
3.991
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10
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4
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N
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-1.695
2.301
4.725
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10
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4
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C
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1.386
5.153
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10
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1
4
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C
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-0.876
0.075
4.986
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10
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4
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N
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0.389
1.845
5.751
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10
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4
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N
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0.518
3.159
5.920
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10
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C
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-0.346
4.120
5.618
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10
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4
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N
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-1.461
3.615
5.034
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10
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4
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C
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-6.279
6.221
6.845
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10
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4
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H
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-6.852
7.345
5.597
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4
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H
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7.806
6.300
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4
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H
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-5.406
7.429
3.576
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4
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H
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-3.816
5.748
2.815
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10
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4
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H
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-2.652
6.894
3.131
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10
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4
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H
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-1.998
6.242
5.207
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10
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DA
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4
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H
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3.669
3.360
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10
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1
4
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H
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-0.204
-0.583
5.360
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10
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1
4
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H
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-1.679
-0.245
4.468
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10
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1
4
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1
H
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1.430
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6.378
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10
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1
4
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1
H
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-3.702
9.452
2.589
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11
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P
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1
5
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P
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-3.630
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2.763
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11
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1
5
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O
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-4.775
9.049
1.654
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11
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1
5
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O
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-2.285
8.926
2.038
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11
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DC
1
5
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O
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-1.096
9.368
2.659
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11
ATOM
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DC
1
5
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C
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0.036
8.328
2.741
B
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11
ATOM
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DC
1
5
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C
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-0.168
7.037
3.238
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11
ATOM
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DC
1
5
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O
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1.237
8.379
1.789
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11
ATOM
B
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DC
1
5
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C
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2.250
9.248
2.268
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11
ATOM
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DC
1
5
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O
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1.662
6.893
1.697
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11
ATOM
B
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DC
1
5
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C
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0.997
6.283
2.940
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DC
11
ATOM
B
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DC
1
5
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C
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0.546
4.933
2.579
B
N1
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11
ATOM
B
N1
DC
1
5
1.00
1
N
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1.330
3.831
2.877
B
C2
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11
ATOM
B
C2
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1
5
1.00
1
C
10.00
2.372
3.936
3.518
B
O2
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11
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B
O2
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1
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1.00
1
O
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0.924
2.609
2.440
B
N3
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11
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N3
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1
5
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N
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-0.155
2.497
1.659
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11
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C4
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1
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1.00
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C
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-0.549
1.276
1.328
B
N4
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11
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N4
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1
5
1.00
1
N
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-0.907
3.641
1.238
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11
ATOM
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C5
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1
5
1.00
1
C
10.00
-0.529
4.837
1.749
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C6
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11
ATOM
B
C6
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1
5
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1
C
10.00
-1.334
9.657
3.686
B
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11
ATOM
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DC
1
5
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H
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-0.736
10.261
2.146
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11
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1
5
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H
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0.417
8.622
3.678
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11
ATOM
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DC
1
5
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H
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0.785
8.762
0.869
B
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11
ATOM
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DC
1
5
1.00
1
H
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1.219
6.505
0.780
B
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11
ATOM
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DC
1
5
1.00
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H
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2.737
6.597
1.714
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11
ATOM
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DC
1
5
1.00
1
H
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1.673
6.312
3.797
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11
ATOM
B
H1'
DC
1
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1.00
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H
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-0.033
0.493
1.712
B
H41
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11
ATOM
B
H41
DC
1
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1.00
1
H
10.00
-1.364
1.132
0.756
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H42
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11
ATOM
B
H42
DC
1
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1.00
1
H
10.00
-1.685
3.588
0.495
B
H5
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11
ATOM
B
H5
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1
5
1.00
1
H
10.00
-1.009
5.794
1.538
B
H6
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11
ATOM
B
H6
DC
1
5
1.00
1
H
10.00
3.114
10.178
1.275
B
P
DG
12
ATOM
B
P
DG
1
6
1.00
1
P
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3.520
11.398
2.006
B
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12
ATOM
B
OP1
DG
1
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1.00
1
O
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2.319
10.496
0.069
B
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12
ATOM
B
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1
6
1.00
1
O
10.00
4.434
9.390
0.835
B
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12
ATOM
B
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DG
1
6
1.00
1
O
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5.514
9.273
1.740
B
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12
ATOM
B
C5'
DG
1
6
1.00
1
C
10.00
6.534
8.235
1.268
B
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12
ATOM
B
C4'
DG
1
6
1.00
1
C
10.00
5.841
7.045
0.969
B
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12
ATOM
B
O4'
DG
1
6
1.00
1
O
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7.319
8.633
0.001
B
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12
ATOM
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C3'
DG
1
6
1.00
1
C
10.00
8.701
8.440
0.219
B
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12
ATOM
B
O3'
DG
1
6
1.00
1
O
10.00
6.842
7.712
-1.141
B
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12
ATOM
B
C2'
DG
1
6
1.00
1
C
10.00
6.121
6.596
-0.345
B
C1'
DG
12
ATOM
B
C1'
DG
1
6
1.00
1
C
10.00
4.808
6.174
-0.899
B
N9
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12
ATOM
B
N9
DG
1
6
1.00
1
N
10.00
3.810
6.908
-1.511
B
C8
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12
ATOM
B
C8
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1
6
1.00
1
C
10.00
2.706
6.235
-1.699
B
N7
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12
ATOM
B
N7
DG
1
6
1.00
1
N
10.00
2.968
4.981
-1.154
B
C5
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12
ATOM
B
C5
DG
1
6
1.00
1
C
10.00
2.139
3.823
-1.024
B
C6
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12
ATOM
B
C6
DG
1
6
1.00
1
C
10.00
0.965
3.681
-1.362
B
O6
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12
ATOM
B
O6
DG
1
6
1.00
1
O
10.00
2.796
2.752
-0.436
B
N1
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12
ATOM
B
N1
DG
1
6
1.00
1
N
10.00
4.074
2.813
0.061
B
C2
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12
ATOM
B
C2
DG
1
6
1.00
1
C
10.00
4.587
1.726
0.625
B
N2
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12
ATOM
B
N2
DG
1
6
1.00
1
N
10.00
4.849
3.895
-0.032
B
N3
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12
ATOM
B
N3
DG
1
6
1.00
1
N
10.00
4.246
4.941
-0.658
B
C4
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12
ATOM
B
C4
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1
6
1.00
1
C
10.00
5.129
8.940
2.706
B
H5'
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12
ATOM
B
H5'
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1
6
1.00
1
H
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6.002
10.239
1.874
B
H5''
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12
ATOM
B
H5''
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1
6
1.00
1
H
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7.191
8.045
2.136
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12
ATOM
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H4'
DG
1
6
1.00
1
H
10.00
7.133
9.686
-0.230
B
H3'
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12
ATOM
B
H3'
DG
1
6
1.00
1
H
10.00
8.978
9.007
0.943
B
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12
ATOM
B
HO3'
DG
1
6
1.00
1
H
10.00
6.332
8.204
-2.004
B
H2'
DG
12
ATOM
B
H2'
DG
1
6
1.00
1
H
10.00
7.721
7.241
-1.587
B
H2''
DG
12
ATOM
B
H2''
DG
1
6
1.00
1
H
10.00
6.790
5.730
-0.203
B
H1'
DG
12
ATOM
B
H1'
DG
1
6
1.00
1
H
10.00
3.887
7.947
-1.829
B
H8
DG
12
ATOM
B
H8
DG
1
6
1.00
1
H
10.00
2.303
1.858
-0.434
B
H1
DG
12
ATOM
B
H1
DG
1
6
1.00
1
H
10.00
4.068
0.858
0.660
B
H21
DG
12
ATOM
B
H21
DG
1
6
1.00
1
H
10.00
5.513
1.778
1.019
B
H22
DG
12
ATOM
B
H22
DG
1
6
1.00
1
H
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lam, S.L.
Ip, L.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
US
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
19
907
917
11922844
Low temperature solution structures and base pair stacking of double helical d(CGTACG)(2).
2002
10.2210/pdb1k2k/pdb
pdb_00001k2k
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
1809.217
5'-D(*CP*GP*TP*AP*CP*G)-3'
2
syn
polymer
no
no
(DC)(DG)(DT)(DA)(DC)(DG)
CGTACG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
-35.676
1
19
A
1
B
12
-0.501
A_DC1:DG12_B
1
8.759
0.214
0.629
-0.010
-1.326
1
19
A
2
B
11
-2.184
A_DG2:DC11_B
2
-24.276
-0.448
0.369
-0.280
-9.612
1
20
A
3
B
10
-4.308
A_DT3:DA10_B
3
-12.647
0.002
0.695
-0.193
9.698
1
20
A
4
B
9
-4.385
A_DA4:DT9_B
4
-12.679
0.000
0.698
-0.193
1.356
1
19
A
5
B
8
-2.221
A_DC5:DG8_B
5
-24.311
0.448
0.374
-0.281
35.801
1
19
A
6
B
7
-0.438
A_DG6:DC7_B
6
9.343
-0.218
0.629
-0.010
2.780
43.523
A
A
1
2
-6.381
B
B
12
11
2.854
-4.709
-1.321
2.001
AA_DC1DG2:DC11DG12_BB
1
-5.924
8.026
42.891
3.093
1.286
3.469
31.621
A
A
2
3
-4.144
B
B
11
10
3.419
-2.251
-0.394
-0.511
AA_DG2DT3:DA10DC11_BB
2
-3.768
6.936
31.323
-0.497
-0.015
2.577
46.882
A
A
3
4
-14.873
B
B
10
9
2.767
-11.721
-0.005
0.474
AA_DT3DA4:DT9DA10_BB
3
-0.026
0.033
45.474
1.402
0.005
3.470
31.612
A
A
4
5
-4.103
B
B
9
8
3.420
-2.229
0.393
-0.511
AA_DA4DC5:DG8DT9_BB
4
3.746
-6.897
31.317
-0.501
0.013
2.766
43.405
A
A
5
6
-6.694
B
B
8
7
2.859
-4.928
1.316
2.033
AA_DC5DG6:DC7DG8_BB
5
5.773
-7.842
42.768
3.163
-1.294
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-04-10
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
1K2J contains the same nucleic acid structure.
RCSB
Y
RCSB
2001-09-28
REL
REL
from solid-phase DNA synthesizer
sample
1
7.0
288
K
using AMBER 4.0
restrained molecular dynamics and energy minimization
3.1 mM (total strand concentration) 5'-d(CGTACG)2 in 10 mM sodium phosphate pH 7.0
D2O
Bruker
processing
XwinNMR
2.1
James et al.
data analysis
MARDIGRAS
3.5
Kollman et al.
refinement
Amber
4.0
500
Bruker
ARX
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
7
B
G
8
n
2
DG
8
B
T
9
n
3
DT
9
B
A
10
n
4
DA
10
B
C
11
n
5
DC
11
B
G
12
n
6
DG
12
B
author_defined_assembly
2
dimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
DG
2
0.112
SIDE CHAIN
1
A
DT
3
0.070
SIDE CHAIN
1
A
DA
4
0.097
SIDE CHAIN
1
B
DG
8
0.112
SIDE CHAIN
1
B
DT
9
0.070
SIDE CHAIN
1
B
DA
10
0.096
SIDE CHAIN
1
4.65
0.30
108.30
112.95
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
9.09
1.10
109.80
118.89
A
A
A
C5'
C4'
O4'
DT
DT
DT
3
3
3
N
1
3.67
0.30
108.30
111.97
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
5.46
0.60
106.00
111.46
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
12.56
1.10
109.80
122.36
A
A
A
C5'
C4'
O4'
DC
DC
DC
5
5
5
N
1
3.20
0.50
106.80
110.00
A
A
A
O4'
C1'
C2'
DG
DG
DG
6
6
6
N
1
4.42
0.30
108.30
112.72
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
9.11
1.10
109.80
118.91
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
1
3.74
0.30
108.30
112.04
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
5.45
0.60
106.00
111.45
B
B
B
O4'
C4'
C3'
DC
DC
DC
11
11
11
N
1
12.57
1.10
109.80
122.37
B
B
B
C5'
C4'
O4'
DC
DC
DC
11
11
11
N
1
3.10
0.50
106.80
109.90
B
B
B
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
NMR MINIMIZED AVERAGE STRUCTURE OF d(CGTACG)2
1
N
N
1
N
N
hydrog
DC-DC MISPAIR
A
DC
1
A
N3
DC
1
1_555
B
DC
11
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
11
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
10
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
10
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
9
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
9
B
O4
DT
3
1_555
hydrog
DC-DC MISPAIR
A
DC
5
A
N4
DC
5
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
7
B
N4
DC
1
1_555
DNA
self-complementary DNA, DNA
1K2K
PDB
1
1K2K
1
6
1K2K
1
6
1K2K
A
1
1
6
7
12
1K2K
7
12
1K2K
B
1
1
6