CNRS Nantes University US2B US2B
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Should you encounter any unexpected behaviour,
please let us know.
 elNémo has been hacked on november 27th.
It has been moved away and runs again.
**Still some additional cleaning from time to time**
Sorry for the inconvenience.


***  hiv1_closed_cutoff8_ca  ***

Normal Mode Analysis for ID 2604200934113787486

Conformational change expected to be analysed

%Projmod-Wn> Eigenvector 18 Norm= 0.9999 %Projmod-Wn> Eigenvector 39 Norm= 1.0001 %Projmod-Wn> Eigenvector 46 Norm= 0.9999

The following table indicates for every normal mode its frequency (black, normalized relative to the lowest mode frequency) and its collectivity (magenta). If a second structure was submitted, the cummulative overlap between the normal modes and the conformational change is computed (red). The corresponding amplitude (dq) is then also given (green). Click on the mode link to obtain a visualization of the mean square displacement <R2> of the C-alpha atoms associated to each mode.

WARNING: there are 1 low-collectivity modes among your first 5 modes (see below)! The degree of collectivity indicates the fraction of residues that are significantly affected by a given mode. While low-frequency modes are expected to have collective character, computed ones sometimes happen to be localized. In such cases, they correspond to motions of some extended parts of the system, as often observed in crystallographic protein structures for N- and C-termini.

WARNING: Rotation-translation modes have a cumulative overlap of 0.3280 !!! This probably means that the second conformation was not fitted properly onto the first one.

[HELP on collectivity] [HELP on overlap]

<R2> frequency collectivity cumulative overlap amplitude (dq)
mode 7 1.00 0.1644 0.000 -0.2286
mode 8 1.00 0.0464 0.030 10.3324
mode 9 1.00 0.7023 0.178 22.6553
mode 10 1.00 0.6979 0.206 -9.8720
mode 11 1.00 0.5702 0.774 -44.4529
mode 12 1.03 0.0276 0.774 0.2150
mode 13 5063.85 0.1815 0.797 -8.6389
mode 14 5748.09 0.1551 0.807 -6.2865
mode 15 6769.50 0.2286 0.810 2.7695
mode 16 8591.18 0.0639 0.810 -1.8590
mode 17 10249.82 0.0643 0.812 1.8701
mode 18 10731.12 0.2280 0.819 4.9556
mode 19 11734.50 0.1302 0.821 -2.3880
mode 20 12402.18 0.4174 0.821 0.5337
mode 21 15226.41 0.4075 0.821 -0.6047
mode 22 16143.32 0.2437 0.822 -2.3499
mode 23 17073.74 0.2614 0.822 -0.3986
mode 24 19972.91 0.2505 0.822 -0.1769
mode 25 20940.24 0.2387 0.827 3.9076
mode 26 23134.15 0.5100 0.828 1.9881
mode 27 24167.03 0.4277 0.828 0.5512
mode 28 25309.15 0.2211 0.831 -3.1777
mode 29 26571.35 0.4973 0.831 1.5131
mode 30 28301.88 0.3659 0.831 -0.2334
mode 31 29176.74 0.3619 0.836 -3.6150
mode 32 31485.35 0.5193 0.837 -2.6206
mode 33 33159.44 0.4501 0.837 -1.5539
mode 34 34069.74 0.5620 0.845 -5.0882
mode 35 35664.06 0.5624 0.846 2.0809
mode 36 37667.03 0.5422 0.846 0.4808
mode 37 38164.71 0.3685 0.848 1.2725
mode 38 39232.18 0.3303 0.848 0.3730
mode 39 40674.59 0.2789 0.849 2.7689
mode 40 40799.76 0.4179 0.865 7.2696
mode 41 42188.62 0.4138 0.865 -0.4365
mode 42 42895.91 0.4923 0.865 -0.1619
mode 43 44449.06 0.3981 0.865 -1.3424
mode 44 47445.91 0.3371 0.871 -4.4789
mode 45 48750.12 0.3796 0.875 -3.6156
mode 46 49549.09 0.4675 0.877 2.6003
mode 47 51694.97 0.3390 0.877 -1.3155
mode 48 53029.32 0.4130 0.878 0.7605
mode 49 53173.38 0.3413 0.889 -6.3617
mode 50 55445.88 0.3427 0.892 -2.5324
mode 51 56710.00 0.4294 0.893 -2.7462
mode 52 56862.68 0.4481 0.893 1.3216
mode 53 58854.76 0.3108 0.895 -2.3231
mode 54 61049.47 0.1997 0.895 -0.4768
mode 55 61887.47 0.3832 0.896 -1.4509
mode 56 63674.62 0.4008 0.899 3.0278
mode 57 65280.26 0.4738 0.905 4.8436
mode 58 67045.44 0.6280 0.910 3.8962
mode 59 68757.91 0.4958 0.910 0.1578
mode 60 68920.88 0.4701 0.910 -0.4831
mode 61 69466.29 0.4194 0.911 -1.8826
mode 62 70145.76 0.4401 0.911 1.8021
mode 63 72025.44 0.2114 0.914 3.0744
mode 64 74885.91 0.2562 0.914 -1.0756
mode 65 75718.94 0.4319 0.916 1.9250
mode 66 77166.68 0.6098 0.916 -0.3124
mode 67 79497.50 0.4207 0.916 -0.1656
mode 68 79868.71 0.4999 0.917 -1.8757
mode 69 80530.06 0.2781 0.917 1.0044
mode 70 82110.44 0.4415 0.917 0.3160
mode 71 83233.21 0.4826 0.917 0.9385
mode 72 83868.00 0.4612 0.917 -0.4058
mode 73 85785.88 0.3783 0.917 -0.7528
mode 74 86790.65 0.6532 0.919 1.8353
mode 75 87783.91 0.4520 0.919 0.4603
mode 76 88651.09 0.5300 0.926 -4.9524
mode 77 90049.50 0.6798 0.926 1.4847
mode 78 90732.18 0.2219 0.926 -0.8557
mode 79 91732.82 0.6360 0.926 0.4953
mode 80 92220.76 0.5755 0.926 -0.8558
mode 81 92887.50 0.4571 0.926 0.0302
mode 82 94558.03 0.4941 0.926 0.6093
mode 83 94961.68 0.4788 0.928 -2.1987
mode 84 95934.15 0.4358 0.929 -2.0729
mode 85 97317.00 0.4327 0.929 0.3404
mode 86 97594.35 0.5128 0.934 -3.8639
mode 87 98530.47 0.4305 0.935 -2.0814
mode 88 99739.41 0.5725 0.935 -0.5066
mode 89 102398.65 0.5096 0.938 -3.0591
mode 90 102845.94 0.3370 0.947 5.6928
mode 91 103439.26 0.5352 0.947 1.3523
mode 92 105053.71 0.4488 0.950 -3.0098
mode 93 105779.38 0.3111 0.953 -3.4268
mode 94 107073.24 0.5642 0.953 1.0730
mode 95 109475.44 0.4518 0.958 3.8518
mode 96 109893.88 0.4935 0.959 1.1729
mode 97 110726.09 0.5270 0.959 0.7785
mode 98 112053.85 0.4576 0.959 1.6718
mode 99 113366.03 0.4648 0.959 0.5857
mode 100 114351.47 0.4845 0.959 -1.0100
mode 101 114529.74 0.0873 0.961 -1.1925
mode 102 116033.85 0.4799 0.962 -2.8628
mode 103 117083.94 0.5582 0.964 -1.3339
mode 104 117475.32 0.5810 0.964 -2.0855
mode 105 117865.38 0.6206 0.973 -5.4506
mode 106 118555.68 0.6120 0.976 3.4179

If you find results from this site helpful for your research, please cite one of our papers:

elNémo is maintained by Yves-Henri Sanejouand.
It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Between 2015 and 2025, it was hosted by US2B (Nantes).
Last modification: december 26th, 2025.