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0.75
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0.25
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0.70
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0.46
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0.16
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0.41
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0.42
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0.76
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0.94
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0.88
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0.38
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H
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1
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1
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-9.788
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2.601
-8.385
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5.611
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1.085
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-4.054
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4.451
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5.229
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4.674
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3.381
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3.110
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1.265
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0.748
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2.204
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-7.167
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-4.040
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-2.185
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-4.050
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3.144
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-5.539
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3
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-4.706
1.055
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-4.635
-0.335
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3
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-3.836
-1.004
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-4.027
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3
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-3.184
-6.193
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-3.083
-6.345
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1.590
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-7.950
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3
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-3.554
-6.862
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-2.294
-5.483
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-2.843
-4.322
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3
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-1.386
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-6.860
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3
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-5.216
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3
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-3.862
-2.035
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3
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-3.190
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-2.423
-6.771
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3
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0.527
-5.806
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4
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1.661
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6.534
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4
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0.234
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0.746
-5.178
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4
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3.507
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4
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1.390
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2.205
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4
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1.636
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2.309
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2.486
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4
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1.740
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1.598
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1.994
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0.519
-3.536
1.071
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4
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-2.184
-0.171
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4
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-1.209
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4
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-2.286
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-3.040
-1.114
0.952
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4
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0.22
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-0.436
0.840
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-2.539
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2.190
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-3.326
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3.435
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-1.421
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2.207
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0.219
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3.367
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4
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1.920
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3.824
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4
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1.860
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1.491
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2.546
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3.576
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1.142
-2.354
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4
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2.280
-2.297
1.441
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4
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0.892
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4
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-2.603
-1.041
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4
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-0.416
3.879
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4
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0.77
-4.376
-1.192
3.177
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4
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1
4
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H
0.72
-3.238
-2.149
4.152
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4
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1
4
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-1.070
-2.824
3.152
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4
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-3.414
2.119
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5
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0.31
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-4.189
1.983
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5
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3.419
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0.831
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5
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4.695
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5
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4.282
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-1.514
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5
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2.884
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-1.348
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5
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-1.313
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5.861
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-2.510
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5
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O
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0.626
-1.119
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5
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2.765
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-1.654
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5
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0.451
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5
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0.22
0.474
0.903
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0.625
0.881
-3.160
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1.363
-1.380
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5
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0.24
-0.970
1.435
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17.478
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16.031
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15.246
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9
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-4.813
15.140
-1.628
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14.916
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-1.437
14.955
-2.680
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-0.366
14.628
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15.402
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15.473
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15.735
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14.480
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16.073
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15.295
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17.800
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17.796
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18.257
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15.876
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15.872
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16.125
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16.018
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18.379
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18.768
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19.487
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18.037
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17.399
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17.275
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17.020
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17.214
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17.241
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0.991
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15.199
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1.133
16.531
7.642
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1
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1.284
16.485
6.167
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1
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0.134
16.575
5.351
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1
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-0.986
16.695
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0.298
16.520
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1
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1.506
16.393
3.456
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1
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0.66
1.598
16.351
2.132
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2.688
16.298
4.256
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0.69
2.534
16.355
5.604
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4.127
18.524
9.438
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17.275
10.685
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17.845
10.194
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2.956
15.241
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14.696
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0.794
14.476
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16.815
7.880
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0.750
16.497
1.553
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16.168
1.683
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3.678
16.183
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16.307
6.255
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17.468
8.272
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0.072
14.218
10.843
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2
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-0.757
14.279
12.068
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2
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0.962
13.042
10.710
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2
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14.363
9.437
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2
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13.361
9.234
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2
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-2.951
13.861
8.168
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2
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-2.220
14.201
6.966
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2
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-3.921
12.759
7.779
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2
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-5.260
13.249
8.004
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2
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O
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-3.728
12.462
6.302
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2
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-3.011
13.770
5.851
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2
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-2.094
13.599
4.690
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2
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0.39
-0.772
13.241
4.620
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2
2
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0.39
-0.300
13.272
3.412
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12
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2
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0.31
-1.393
13.664
2.636
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2
2
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0.29
-1.564
13.799
1.250
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2
2
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0.34
-0.574
13.630
0.382
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12
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2
2
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0.25
-2.787
14.111
0.799
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2
2
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0.24
-3.769
14.276
1.677
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2
2
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0.25
-3.739
14.183
2.994
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2
2
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0.27
-2.492
13.871
3.405
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2
2
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0.59
-2.495
13.193
10.179
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2
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0.57
-1.518
12.421
8.925
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2
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-3.505
14.728
8.533
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2
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0.37
-3.733
11.867
8.369
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2
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0.32
-3.098
11.572
6.162
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2
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-4.690
12.298
5.787
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2
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-3.746
14.571
5.596
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2
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-0.176
12.964
5.482
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12
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2
2
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0.34
-0.730
13.802
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12
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H61
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2
2
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0.41
0.354
13.328
0.716
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12
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2
2
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0.28
-4.738
14.520
1.249
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12
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2
2
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0.42
-6.612
12.188
7.840
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P
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3
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0.50
-7.780
12.736
8.569
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3
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0.43
-6.217
10.803
8.187
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3
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0.34
-6.858
12.326
6.136
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3
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13.500
5.648
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3
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0.18
-8.114
13.228
4.239
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2
3
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0.11
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13.191
3.308
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3
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11.864
4.183
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3
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0.24
-10.066
12.027
3.558
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3
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0.19
-7.889
10.963
3.320
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3
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-7.146
12.021
2.471
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3
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-5.806
11.560
2.142
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3
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0.15
-4.889
10.951
2.929
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13
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3
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1
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0.18
-3.784
10.665
2.306
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13
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3
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1
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-4.023
11.121
1.002
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13
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3
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1
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0.23
-3.195
11.051
-0.211
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13
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2
3
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1
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0.28
-2.062
10.583
-0.261
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13
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3
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1
O
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-3.819
11.561
-1.316
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3
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1
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0.23
-5.090
12.081
-1.308
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13
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3
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1
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0.30
-5.567
12.508
-2.462
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13
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3
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-5.856
12.168
-0.215
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13
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3
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-5.258
11.673
0.896
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3
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-6.912
14.359
5.646
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3
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13.718
6.332
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3
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13.997
3.944
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3
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11.456
5.196
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3
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10.395
3.896
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10.274
2.750
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12.295
1.519
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3
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10.682
3.976
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3
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-3.299
11.548
-2.202
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3
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12.497
-3.307
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3
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12.836
-2.524
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3
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10.649
3.206
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4
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-12.479
11.028
3.207
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4
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-10.671
9.516
4.084
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4
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10.354
1.592
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4
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11.491
0.664
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4
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-9.994
11.017
-0.701
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4
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10.844
-0.657
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4
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O
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-10.585
9.664
-1.020
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4
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-11.244
9.748
-2.304
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4
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O
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-9.432
8.656
-1.110
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4
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0.31
-8.240
9.625
-1.346
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4
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C
0.27
-7.012
9.112
-0.744
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2
4
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1
N
0.25
-6.744
8.760
0.548
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14
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2
4
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1
C
0.23
-5.522
8.345
0.716
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14
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N7
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2
4
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1
N
0.24
-4.966
8.425
-0.573
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14
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2
4
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1
C
0.25
-3.718
8.040
-1.094
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14
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2
4
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1
C
0.24
-2.732
7.582
-0.334
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14
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2
4
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1
N
0.27
-3.528
8.160
-2.416
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14
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2
4
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1
N
0.28
-4.513
8.634
-3.163
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14
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2
4
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1
C
0.28
-5.718
9.035
-2.802
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14
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2
4
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1
N
0.26
-5.870
8.897
-1.466
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14
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2
4
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1
C
0.42
-9.815
12.260
1.064
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4
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0.42
-11.483
11.914
0.589
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14
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4
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0.40
-10.268
11.734
-1.477
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14
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DA
2
4
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1
H
0.36
-11.304
9.383
-0.235
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14
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DA
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4
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1
H
0.28
-9.284
8.073
-0.132
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14
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4
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H
0.31
-9.589
7.927
-1.967
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4
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0.33
-8.049
9.844
-2.439
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14
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DA
2
4
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1
H
0.25
-7.497
8.802
1.362
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14
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H8
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2
4
1.00
1
H
0.25
-1.812
7.372
-0.755
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H61
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14
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B
H61
DA
2
4
1.00
1
H
0.23
-2.882
7.444
0.676
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H62
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14
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B
H62
DA
2
4
1.00
1
H
0.30
-4.299
8.704
-4.226
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14
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B
H2
DA
2
4
1.00
1
H
0.53
-12.113
8.383
-2.919
B
P
DT
15
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B
P
DT
2
5
1.00
1
P
0.62
-13.322
8.835
-3.649
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15
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B
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2
5
1.00
1
O
0.49
-12.337
7.396
-1.837
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15
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2
5
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1
O
0.55
-10.932
7.772
-4.035
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15
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5
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1
O
0.52
-11.194
7.952
-5.466
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15
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DT
2
5
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1
C
0.50
-10.136
7.208
-6.299
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15
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DT
2
5
1.00
1
C
0.46
-8.858
7.207
-5.596
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15
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DT
2
5
1.00
1
O
0.48
-10.527
5.752
-6.474
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15
ATOM
B
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DT
2
5
1.00
1
C
0.54
-10.350
5.425
-7.874
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15
ATOM
B
O3'
DT
2
5
1.00
1
O
0.40
-9.577
4.923
-5.624
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DT
15
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B
C2'
DT
2
5
1.00
1
C
0.41
-8.334
5.860
-5.638
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DT
15
ATOM
B
C1'
DT
2
5
1.00
1
C
0.36
-7.455
5.678
-4.458
B
N1
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15
ATOM
B
N1
DT
2
5
1.00
1
N
0.36
-6.066
5.556
-4.645
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C2
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15
ATOM
B
C2
DT
2
5
1.00
1
C
0.39
-5.557
5.615
-5.754
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O2
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15
ATOM
B
O2
DT
2
5
1.00
1
O
0.32
-5.306
5.372
-3.516
B
N3
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15
ATOM
B
N3
DT
2
5
1.00
1
N
0.29
-5.773
5.299
-2.226
B
C4
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15
ATOM
B
C4
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2
5
1.00
1
C
0.27
-4.997
5.132
-1.292
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15
ATOM
B
O4
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2
5
1.00
1
O
0.30
-7.216
5.429
-2.102
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15
ATOM
B
C5
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2
5
1.00
1
C
0.28
-7.769
5.359
-0.705
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C7
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15
ATOM
B
C7
DT
2
5
1.00
1
C
0.34
-7.998
5.614
-3.191
B
C6
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15
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C6
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2
5
1.00
1
C
0.55
-11.178
9.018
-5.693
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15
ATOM
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2
5
1.00
1
H
0.50
-12.193
7.576
-5.689
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15
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H5''
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2
5
1.00
1
H
0.55
-10.027
7.677
-7.278
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15
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H4'
DT
2
5
1.00
1
H
0.49
-11.563
5.596
-6.166
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15
ATOM
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H3'
DT
2
5
1.00
1
H
0.38
-9.963
4.804
-4.611
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15
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H2'
DT
2
5
1.00
1
H
0.37
-9.388
3.913
-6.046
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15
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H2''
DT
2
5
1.00
1
H
0.42
-7.710
5.736
-6.577
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15
ATOM
B
H1'
DT
2
5
1.00
1
H
0.32
-4.295
5.256
-3.649
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15
ATOM
B
H3
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2
5
1.00
1
H
0.82
-8.823
5.639
-0.716
B
H71
DT
15
ATOM
B
H71
DT
2
5
1.00
1
H
0.75
-7.670
4.342
-0.325
B
H72
DT
15
ATOM
B
H72
DT
2
5
1.00
1
H
0.68
-7.219
6.041
-0.059
B
H73
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15
ATOM
B
H73
DT
2
5
1.00
1
H
0.35
-9.085
5.687
-3.064
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H6
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15
ATOM
B
H6
DT
2
5
1.00
1
H
0.49
-10.474
3.792
-8.424
B
P
DA
16
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B
P
DA
2
6
1.00
1
P
0.56
-10.850
3.765
-9.856
B
OP1
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16
ATOM
B
OP1
DA
2
6
1.00
1
O
0.47
-11.335
3.009
-7.507
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16
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B
OP2
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2
6
1.00
1
O
0.41
-8.822
3.315
-8.236
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16
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B
O5'
DA
2
6
1.00
1
O
0.48
-7.800
4.137
-8.894
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DA
16
ATOM
B
C5'
DA
2
6
1.00
1
C
0.46
-6.490
3.350
-8.999
B
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DA
16
ATOM
B
C4'
DA
2
6
1.00
1
C
0.39
-5.767
3.487
-7.751
B
O4'
DA
16
ATOM
B
O4'
DA
2
6
1.00
1
O
0.40
-6.772
1.872
-9.190
B
C3'
DA
16
ATOM
B
C3'
DA
2
6
1.00
1
C
0.46
-5.885
1.381
-10.207
B
O3'
DA
16
ATOM
B
O3'
DA
2
6
1.00
1
O
0.32
-6.494
1.178
-7.877
B
C2'
DA
16
ATOM
B
C2'
DA
2
6
1.00
1
C
0.34
-5.433
2.175
-7.260
B
C1'
DA
16
ATOM
B
C1'
DA
2
6
1.00
1
C
0.30
-5.553
2.249
-5.810
B
N9
DA
16
ATOM
B
N9
DA
2
6
1.00
1
N
0.31
-6.633
2.520
-5.045
B
C8
DA
16
ATOM
B
C8
DA
2
6
1.00
1
C
0.32
-6.368
2.545
-3.770
B
N7
DA
16
ATOM
B
N7
DA
2
6
1.00
1
N
0.31
-4.998
2.253
-3.721
B
C5
DA
16
ATOM
B
C5
DA
2
6
1.00
1
C
0.32
-4.111
2.036
-2.654
B
C6
DA
16
ATOM
B
C6
DA
2
6
1.00
1
C
0.35
-4.455
2.203
-1.380
B
N6
DA
16
ATOM
B
N6
DA
2
6
1.00
1
N
0.31
-2.859
1.667
-2.953
B
N1
DA
16
ATOM
B
N1
DA
2
6
1.00
1
N
0.31
-2.518
1.527
-4.226
B
C2
DA
16
ATOM
B
C2
DA
2
6
1.00
1
C
0.32
-3.243
1.706
-5.309
B
N3
DA
16
ATOM
B
N3
DA
2
6
1.00
1
N
0.30
-4.494
2.076
-4.968
B
C4
DA
16
ATOM
B
C4
DA
2
6
1.00
1
C
0.50
-7.651
5.052
-8.310
B
H5'
DA
16
ATOM
B
H5'
DA
2
6
1.00
1
H
0.56
-8.156
4.420
-9.883
B
H5''
DA
16
ATOM
B
H5''
DA
2
6
1.00
1
H
0.56
-5.888
3.719
-9.828
B
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DA
16
ATOM
B
H4'
DA
2
6
1.00
1
H
0.40
-7.815
1.725
-9.481
B
H3'
DA
16
ATOM
B
H3'
DA
2
6
1.00
1
H
0.28
-7.452
1.146
-7.235
B
H2'
DA
16
ATOM
B
H2'
DA
2
6
1.00
1
H
0.33
-6.087
0.100
-8.036
B
H2''
DA
16
ATOM
B
H2''
DA
2
6
1.00
1
H
0.37
-4.349
1.933
-7.523
B
H1'
DA
16
ATOM
B
H1'
DA
2
6
1.00
1
H
0.32
-7.628
2.676
-5.462
B
H8
DA
16
ATOM
B
H8
DA
2
6
1.00
1
H
0.37
-3.744
2.091
-0.636
B
H61
DA
16
ATOM
B
H61
DA
2
6
1.00
1
H
0.37
-5.426
2.452
-1.135
B
H62
DA
16
ATOM
B
H62
DA
2
6
1.00
1
H
0.34
-1.493
1.219
-4.399
B
H2
DA
16
ATOM
B
H2
DA
2
6
1.00
1
H
0.49
-6.196
-0.132
-10.970
B
P
DA
17
ATOM
B
P
DA
2
7
1.00
1
P
0.64
-5.935
-0.036
-12.423
B
OP1
DA
17
ATOM
B
OP1
DA
2
7
1.00
1
O
0.46
-7.532
-0.640
-10.576
B
OP2
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17
ATOM
B
OP2
DA
2
7
1.00
1
O
0.43
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-10.209
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17
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7
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0.57
-3.701
-0.394
-9.891
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7
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1
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0.50
-2.713
-1.417
-9.319
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7
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1
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0.39
-2.722
-1.303
-7.875
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7
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-3.174
-2.813
-9.628
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7
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-2.013
-3.634
-9.854
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7
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-3.905
-3.311
-8.408
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7
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-2.568
-7.312
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7
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0.26
-4.023
-2.248
-6.186
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17
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7
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1
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0.24
-5.351
-1.979
-6.162
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7
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1
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0.22
-5.788
-1.652
-4.981
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17
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7
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1
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0.21
-4.645
-1.734
-4.183
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17
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2
7
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1
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0.23
-4.440
-1.600
-2.807
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1
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0.29
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-1.219
-1.959
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17
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1
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0.22
-3.221
-1.847
-2.344
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17
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2
7
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1
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0.20
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-2.196
-3.185
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17
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1
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0.22
-2.317
-2.351
-4.483
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17
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2
7
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1
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0.22
-3.560
-2.093
-4.919
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7
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0.82
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-9.160
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-3.306
0.067
-10.796
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7
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-1.710
-1.254
-9.716
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7
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-2.811
-10.507
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7
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0.37
-4.934
-3.052
-8.415
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7
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-3.841
-4.346
-8.305
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7
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-2.279
-3.147
-6.940
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7
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-5.992
-2.074
-7.045
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7
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0.33
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-1.076
-0.959
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1
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-6.355
-1.061
-2.299
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1
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-1.297
-2.386
-2.732
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-2.204
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-10.455
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18
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8
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1
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0.49
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-5.471
-11.575
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18
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8
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0.60
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8
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-9.045
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8
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-5.922
-8.543
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8
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-0.198
-6.442
-7.091
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8
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-5.784
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8
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-0.502
-7.926
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8
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0.619
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-6.479
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8
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-1.749
-8.129
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8
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-6.783
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8
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-6.308
-5.064
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8
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0.16
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-6.096
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8
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8
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-5.564
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8
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0.20
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8
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0.19
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8
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-5.833
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8
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0.35
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-6.916
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18
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8
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0.31
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-6.093
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8
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8
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0.364
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8
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8
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-8.294
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8
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8
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-1.570
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8
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-6.829
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8
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8
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0.92
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18
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8
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8
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0.99
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8
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0.39
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-7.109
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8
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0.42
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2
9
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1
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9
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0.41
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9
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0.51
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0.28
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0.38
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0.39
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0.36
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0.29
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19
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B
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2
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1
C
0.24
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19
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B
N1
DC
2
9
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1
N
0.21
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19
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B
C2
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2
9
1.00
1
C
0.25
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19
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B
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2
9
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1
O
0.17
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-9.187
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19
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B
N3
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2
9
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1
N
0.13
-5.482
-8.762
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19
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B
C4
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2
9
1.00
1
C
0.10
-6.428
-7.888
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19
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B
N4
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2
9
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1
N
0.17
-4.536
-9.208
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19
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B
C5
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2
9
1.00
1
C
0.22
-3.553
-10.062
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19
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B
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2
9
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1
C
0.40
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-9.564
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9
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0.36
1.552
-11.210
-3.824
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B
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9
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0.34
0.659
-11.068
-1.433
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9
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0.41
0.009
-12.933
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19
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9
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1
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0.37
-2.254
-12.534
-3.649
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19
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0.39
-2.338
-13.443
-2.215
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0.31
-2.480
-11.366
-0.702
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19
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B
H1'
DC
2
9
1.00
1
H
0.12
-7.063
-7.489
-2.807
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H41
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19
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B
H41
DC
2
9
1.00
1
H
0.11
-6.518
-7.608
-4.495
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H42
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19
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B
H42
DC
2
9
1.00
1
H
0.18
-4.596
-8.898
-5.157
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19
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B
H5
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2
9
1.00
1
H
0.27
-2.811
-10.440
-4.384
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19
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B
H6
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2
9
1.00
1
H
0.41
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-14.197
-1.498
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20
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B
P
DA
2
10
1.00
1
P
0.42
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-13.817
-0.371
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20
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B
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DA
2
10
1.00
1
O
0.42
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-2.858
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20
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B
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2
10
1.00
1
O
0.40
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20
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B
O5'
DA
2
10
1.00
1
O
0.44
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-16.210
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20
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B
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DA
2
10
1.00
1
C
0.43
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20
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B
C4'
DA
2
10
1.00
1
C
0.39
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-0.446
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20
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B
O4'
DA
2
10
1.00
1
O
0.42
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20
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B
C3'
DA
2
10
1.00
1
C
0.44
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-19.463
-0.235
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20
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B
O3'
DA
2
10
1.00
1
O
0.41
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B
C2'
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20
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B
C2'
DA
2
10
1.00
1
C
0.40
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-1.655
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20
ATOM
B
C1'
DA
2
10
1.00
1
C
0.39
-2.653
-16.138
-2.574
B
N9
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20
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B
N9
DA
2
10
1.00
1
N
0.41
-2.454
-15.848
-3.913
B
C8
DA
20
ATOM
B
C8
DA
2
10
1.00
1
C
0.40
-3.248
-14.941
-4.363
B
N7
DA
20
ATOM
B
N7
DA
2
10
1.00
1
N
0.38
-4.017
-14.583
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B
C5
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20
ATOM
B
C5
DA
2
10
1.00
1
C
0.38
-5.114
-13.701
-3.125
B
C6
DA
20
ATOM
B
C6
DA
2
10
1.00
1
C
0.40
-5.638
-12.983
-4.130
B
N6
DA
20
ATOM
B
N6
DA
2
10
1.00
1
N
0.38
-5.700
-13.625
-1.924
B
N1
DA
20
ATOM
B
N1
DA
2
10
1.00
1
N
0.36
-5.250
-14.371
-0.931
B
C2
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20
ATOM
B
C2
DA
2
10
1.00
1
C
0.36
-4.249
-15.232
-0.919
B
N3
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20
ATOM
B
N3
DA
2
10
1.00
1
N
0.37
-3.662
-15.284
-2.157
B
C4
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20
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B
C4
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2
10
1.00
1
C
0.43
0.394
-15.332
0.743
B
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20
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B
H5'
DA
2
10
1.00
1
H
0.51
1.484
-16.702
0.515
B
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20
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B
H5''
DA
2
10
1.00
1
H
0.46
-0.774
-17.494
1.158
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20
ATOM
B
H4'
DA
2
10
1.00
1
H
0.43
0.930
-18.453
-0.684
B
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DA
20
ATOM
B
H3'
DA
2
10
1.00
1
H
0.38
-0.642
-19.507
0.915
B
HO3'
DA
20
ATOM
B
HO3'
DA
2
10
1.00
1
H
0.41
-0.220
-17.309
-2.750
B
H2'
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20
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B
H2'
DA
2
10
1.00
1
H
0.43
-1.032
-18.832
-2.734
B
H2''
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20
ATOM
B
H2''
DA
2
10
1.00
1
H
0.42
-2.940
-17.908
-1.412
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20
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B
H1'
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2
10
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1
H
0.43
-1.673
-16.226
-4.482
B
H8
DA
20
ATOM
B
H8
DA
2
10
1.00
1
H
0.41
-6.409
-12.307
-3.929
B
H61
DA
20
ATOM
B
H61
DA
2
10
1.00
1
H
0.40
-5.291
-13.099
-5.105
B
H62
DA
20
ATOM
B
H62
DA
2
10
1.00
1
H
0.36
-5.763
-14.238
0.029
B
H2
DA
20
ATOM
B
H2
DA
2
10
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
Kumar, S.
Reed, M.W.
Gamper Junior, H.B.
Gorn, V.V.
Lukhtanov, E.A.
Foti, M.
West, J.
Meyer Junior, R.B.
Schweitzer, B.I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C50 H53 N10 O12 P
1016.989
PHOSPHONIC ACID 6-({6-[6-(6-CARBAMOYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CA RBONYL]-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)-HEXYL ESTER 5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL ESTER
CDPI3
DNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
26
831
838
10.1093/nar/26.3.831
9443977
Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.
1998
10.2210/pdb1aul/pdb
pdb_00001aul
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER
3744.794
DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3')
1
syn
polymer
TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER
3037.032
DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')
1
syn
polymer
no
yes
(THX)(DG)(DA)(DT)(DT)(DA)(DT)(DC)(DT)(DG)
NGATTATCTG
A
polydeoxyribonucleotide
no
no
(DC)(DA)(DG)(DA)(DT)(DA)(DA)(DT)(DC)(DA)
CAGATAATCA
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
0.709
1
A
2
B
19
26.294
A_DG2:DC19_B
1
7.219
0.840
0.941
0.149
3.244
1
20
A
3
B
18
14.693
A_DA3:DT18_B
2
-20.653
-1.088
0.744
-0.539
-24.666
1
20
A
4
B
17
14.899
A_DT4:DA17_B
3
-11.516
0.144
1.258
-0.460
-9.415
1
20
A
5
B
16
4.457
A_DT5:DA16_B
4
-1.416
-0.283
0.534
-0.212
-1.083
1
20
A
6
B
15
-6.322
A_DA6:DT15_B
5
-6.569
0.467
-0.465
-0.077
16.877
1
20
A
7
B
14
1.194
A_DT7:DA14_B
6
-14.113
-0.175
-0.590
-0.122
7.590
1
19
A
8
B
13
3.882
A_DC8:DG13_B
7
-8.338
0.684
-0.424
-0.242
9.588
1
20
A
9
B
12
-5.710
A_DT9:DA12_B
8
-7.991
0.400
0.176
-0.259
6.923
1
19
A
10
B
11
-3.536
A_DG10:DC11_B
9
1.045
-0.616
0.206
-0.342
2.674
28.852
A
A
2
3
14.748
B
B
19
18
3.171
7.125
0.023
-0.895
AA_DG2DA3:DT18DC19_BB
1
9.932
-20.557
26.185
-3.287
2.032
4.196
42.791
A
A
3
4
13.320
B
B
18
17
4.347
9.642
0.458
-0.197
AA_DA3DT4:DA17DT18_BB
2
-0.655
0.905
41.736
-1.545
-0.715
2.913
29.589
A
A
4
5
7.458
B
B
17
16
3.031
3.791
-0.064
-0.560
AA_DT4DT5:DA16DA17_BB
3
3.245
-6.383
29.174
-1.830
0.755
2.273
35.981
A
A
5
6
9.916
B
B
16
15
2.762
6.010
-0.531
-1.104
AA_DT5DA6:DT15DA16_BB
4
10.725
-17.696
33.881
-2.467
2.074
2.672
34.716
A
A
6
7
10.360
B
B
15
14
2.782
6.151
0.506
-0.384
AA_DA6DT7:DA14DT15_BB
5
-0.186
0.313
34.183
-1.435
-0.871
3.115
38.710
A
A
7
8
17.651
B
B
14
13
3.388
11.535
-0.478
-0.453
AA_DT7DC8:DG13DA14_BB
6
0.019
-0.029
37.015
-2.124
0.723
3.586
37.505
A
A
8
9
-9.038
B
B
13
12
3.505
-5.778
-0.102
-0.869
AA_DC8DT9:DA12DG13_BB
7
-4.169
6.521
36.846
-0.524
-0.439
2.824
30.325
A
A
9
10
4.864
B
B
12
11
2.927
2.490
-0.705
-1.955
AA_DT9DG10:DC11DA12_BB
8
-10.600
20.704
28.346
-4.194
-0.595
chem_comp
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Structure summary
1
0
1997-12-24
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
Y
BNL
1997-08-29
REL
CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER
sample
CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER
sample
LEAST RESTRAINT VIOLATION
6
1
NOESY
DQF-COSY
HETEROTOCSY
TOCSY
6.0
293.15
K
CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED HERE.
RESTRAINED MOLECULAR DYNAMICS/RELAXATION MATRIX REFINEMENT
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
3.1
600
Varian
UNITYPLUS
THX
1
n
1
THX
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
C
8
n
8
DC
8
A
T
9
n
9
DT
9
A
G
10
n
10
DG
10
A
C
11
n
1
DC
11
B
A
12
n
2
DA
12
B
G
13
n
3
DG
13
B
A
14
n
4
DA
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
A
17
n
7
DA
17
B
T
18
n
8
DT
18
B
C
19
n
9
DC
19
B
A
20
n
10
DA
20
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
B
O4
H61
THX
DA
1
20
1.39
1
A
B
H3
N1
THX
DA
1
20
1.57
1
B
DC
19
0.072
SIDE CHAIN
1
B
DA
20
0.059
SIDE CHAIN
1
B
B
O3'
P
DT
DC
18
19
1.75
1
-3.72
0.60
128.60
124.88
A
A
A
C5
C6
O6
DG
DG
DG
10
10
10
N
1
-3.72
0.60
128.60
124.88
B
B
B
C5
C6
O6
DG
DG
DG
13
13
13
N
1
A
A
O3'
P
THX
DG
1
2
0.127
0.012
1.607
1.734
Y
1
A
A
P
O5'
DG
DG
2
2
0.149
0.010
1.593
1.742
N
1
A
A
O3'
P
DG
DA
2
3
0.123
0.012
1.607
1.730
Y
1
A
A
P
O5'
DA
DA
3
3
0.133
0.010
1.593
1.726
N
1
A
A
N9
C4
DA
DA
3
3
-0.042
0.006
1.374
1.332
N
1
A
A
O3'
P
DA
DT
3
4
0.124
0.012
1.607
1.731
Y
1
A
A
P
O5'
DT
DT
4
4
0.140
0.010
1.593
1.733
N
1
A
A
O3'
P
DT
DT
4
5
0.118
0.012
1.607
1.725
Y
1
A
A
P
O5'
DT
DT
5
5
0.123
0.010
1.593
1.716
N
1
A
A
O3'
P
DT
DA
5
6
0.115
0.012
1.607
1.722
Y
1
A
A
P
O5'
DA
DA
6
6
0.134
0.010
1.593
1.727
N
1
A
A
C3'
C2'
DA
DA
6
6
0.134
0.012
1.518
1.652
N
1
A
A
O3'
P
DA
DT
6
7
0.122
0.012
1.607
1.729
Y
1
A
A
P
O5'
DT
DT
7
7
0.137
0.010
1.593
1.730
N
1
A
A
O3'
P
DT
DC
7
8
0.127
0.012
1.607
1.734
Y
1
A
A
P
O5'
DC
DC
8
8
0.140
0.010
1.593
1.733
N
1
A
A
O3'
P
DC
DT
8
9
0.123
0.012
1.607
1.730
Y
1
A
A
P
O5'
DT
DT
9
9
0.133
0.010
1.593
1.726
N
1
A
A
C2'
C1'
DT
DT
9
9
0.070
0.010
1.519
1.589
N
1
A
A
O3'
P
DT
DG
9
10
0.125
0.012
1.607
1.732
Y
1
A
A
P
O5'
DG
DG
10
10
0.139
0.010
1.593
1.732
N
1
B
B
C2'
C1'
DC
DC
11
11
0.065
0.010
1.519
1.584
N
1
B
B
O3'
P
DC
DA
11
12
0.130
0.012
1.607
1.737
Y
1
B
B
P
O5'
DA
DA
12
12
0.140
0.010
1.593
1.733
N
1
B
B
O3'
P
DA
DG
12
13
0.119
0.012
1.607
1.726
Y
1
B
B
P
O5'
DG
DG
13
13
0.134
0.010
1.593
1.727
N
1
B
B
O3'
P
DG
DA
13
14
0.121
0.012
1.607
1.728
Y
1
B
B
P
O5'
DA
DA
14
14
0.133
0.010
1.593
1.726
N
1
B
B
O3'
P
DA
DT
14
15
0.124
0.012
1.607
1.731
Y
1
B
B
P
O5'
DT
DT
15
15
0.143
0.010
1.593
1.736
N
1
B
B
O3'
P
DT
DA
15
16
0.121
0.012
1.607
1.728
Y
1
B
B
P
O5'
DA
DA
16
16
0.137
0.010
1.593
1.730
N
1
B
B
C2'
C1'
DA
DA
16
16
0.062
0.010
1.519
1.581
N
1
B
B
O3'
P
DA
DA
16
17
0.116
0.012
1.607
1.723
Y
1
B
B
P
O5'
DA
DA
17
17
0.125
0.010
1.593
1.718
N
1
B
B
O3'
P
DA
DT
17
18
0.117
0.012
1.607
1.724
Y
1
B
B
P
O5'
DT
DT
18
18
0.151
0.010
1.593
1.744
N
1
B
B
O3'
P
DT
DC
18
19
0.145
0.012
1.607
1.752
Y
1
B
B
P
O5'
DC
DC
19
19
0.145
0.010
1.593
1.738
N
1
B
B
C2'
C1'
DC
DC
19
19
0.082
0.010
1.519
1.601
N
1
B
B
O3'
P
DC
DA
19
20
0.129
0.012
1.607
1.736
Y
1
B
B
P
O5'
DA
DA
20
20
0.133
0.010
1.593
1.726
N
1
B
B
C3'
C2'
DA
DA
20
20
0.075
0.012
1.518
1.593
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.734
one
A
THX
1
A
O3'
THX
1
1_555
A
DG
2
A
P
DG
2
1_555
hydrog
DG-DC PAIR
A
DG
2
A
N1
DG
2
1_555
B
DC
19
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
DT-DA PAIR
A
DT
4
A
O4
DT
4
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
16
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
14
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
12
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
12
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
11
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
11
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
11
B
N4
DC
1
1_555
DNA
DEOXYRIBONUCLEIC ACID, CDPI3, DNA
1AUL
PDB
1
1AUL
1AUL
PDB
2
1AUL
1
10
1AUL
1
10
1AUL
A
1
1
10
11
20
1AUL
11
20
1AUL
B
2
1
10
1
P 1