CNRS Nantes University US2B US2B
home |  start a new run |  job status |  references&downloads |  examples |  help  

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_open_cutoff10_ca  ***

Normal Mode Analysis for ID 2604200934113787484

Conformational change expected to be analysed

%Projmod-Wn> Eigenvector 8 Norm= 0.9999 %Projmod-Wn> Eigenvector 46 Norm= 1.0001 %Projmod-Wn> Eigenvector 61 Norm= 1.0001

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 0.8680 !!! 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 0.0159 0.010 1.9191
mode 8 3.70 0.1142 0.031 -3.1769
mode 9 3.87 0.1896 0.041 2.7100
mode 10 4.29 0.1252 0.072 -4.0850
mode 11 4.99 0.2181 0.072 -0.2638
mode 12 5.83 0.1645 0.072 0.0075
mode 13 7.34 0.3142 0.082 -1.4392
mode 14 8.19 0.2747 0.082 0.3881
mode 15 9.32 0.1664 0.082 0.2918
mode 16 9.75 0.2394 0.092 -2.8922
mode 17 9.96 0.5120 0.092 -0.9511
mode 18 11.06 0.2548 0.102 1.0027
mode 19 12.49 0.2745 0.123 -3.4037
mode 20 13.08 0.4614 0.123 -0.2964
mode 21 13.19 0.3416 0.123 0.2706
mode 22 13.90 0.3707 0.123 -1.4884
mode 23 14.20 0.2374 0.143 3.3799
mode 24 14.51 0.3186 0.154 -1.6978
mode 25 14.75 0.5897 0.164 2.0204
mode 26 15.44 0.3802 0.164 1.7841
mode 27 15.69 0.3888 0.194 -4.0812
mode 28 16.67 0.5381 0.297 7.2163
mode 29 16.95 0.2434 0.327 3.6642
mode 30 17.32 0.5163 0.358 4.1056
mode 31 18.04 0.4427 0.368 1.6074
mode 32 18.16 0.4671 0.379 2.3431
mode 33 18.83 0.5009 0.430 -5.1496
mode 34 18.93 0.2692 0.430 -0.9134
mode 35 19.32 0.5621 0.450 -3.3967
mode 36 19.63 0.7105 0.481 3.6484
mode 37 20.22 0.3262 0.481 1.3517
mode 38 20.32 0.3271 0.491 1.9625
mode 39 21.17 0.4701 0.522 4.2465
mode 40 21.73 0.2409 0.522 -1.0268
mode 41 22.23 0.3921 0.542 2.7536
mode 42 22.41 0.3634 0.553 -1.9599
mode 43 22.59 0.3242 0.553 0.1384
mode 44 22.85 0.2113 0.573 -3.2795
mode 45 23.40 0.4227 0.604 -4.1078
mode 46 23.99 0.3643 0.604 -1.4746
mode 47 24.25 0.3411 0.624 -3.3109
mode 48 24.48 0.4862 0.635 1.3944
mode 49 24.68 0.1867 0.665 -3.9686
mode 50 24.77 0.4487 0.665 -0.6658
mode 51 25.58 0.4667 0.665 -0.2426
mode 52 25.71 0.6187 0.665 0.4200
mode 53 26.00 0.1538 0.665 -0.5842
mode 54 26.51 0.5659 0.675 2.1463
mode 55 26.64 0.2738 0.675 -0.4311
mode 56 26.95 0.4157 0.675 -0.2313
mode 57 27.49 0.2717 0.686 -2.2062
mode 58 27.99 0.2202 0.686 -1.2926
mode 59 28.28 0.2599 0.686 -0.5824
mode 60 28.62 0.4591 0.696 -2.5418
mode 61 28.77 0.5002 0.706 -2.1275
mode 62 29.46 0.5415 0.716 -1.3924
mode 63 29.64 0.3266 0.716 0.2140
mode 64 30.15 0.5472 0.727 2.0829
mode 65 30.55 0.3572 0.747 3.6628
mode 66 30.91 0.4807 0.747 -1.2180
mode 67 31.54 0.4470 0.747 0.1149
mode 68 31.74 0.4599 0.747 -0.0194
mode 69 32.14 0.4445 0.747 -0.1515
mode 70 32.65 0.4839 0.757 1.5112
mode 71 32.87 0.5189 0.768 2.7267
mode 72 33.00 0.5000 0.768 -0.0417
mode 73 33.44 0.3915 0.788 2.9879
mode 74 33.54 0.4576 0.788 0.0885
mode 75 33.71 0.2960 0.788 1.5540
mode 76 33.90 0.4939 0.798 -2.1303
mode 77 34.05 0.4482 0.808 2.1832
mode 78 34.20 0.4013 0.808 0.3801
mode 79 34.46 0.5505 0.819 -1.7118
mode 80 34.67 0.5220 0.819 0.3468
mode 81 34.77 0.5406 0.819 -0.8806
mode 82 35.13 0.4322 0.819 -0.9919
mode 83 35.39 0.3937 0.829 1.6524
mode 84 35.57 0.3974 0.829 -1.0762
mode 85 35.72 0.3974 0.829 -1.2781
mode 86 36.07 0.5896 0.839 1.3198
mode 87 36.29 0.4334 0.839 1.8275
mode 88 36.60 0.3633 0.839 1.0939
mode 89 36.79 0.4836 0.849 0.8191
mode 90 36.96 0.4921 0.870 3.2522
mode 91 37.24 0.4259 0.870 -1.4630
mode 92 37.39 0.6110 0.870 -0.1276
mode 93 37.57 0.5057 0.870 0.8116
mode 94 37.78 0.5285 0.890 2.7617
mode 95 38.07 0.4109 0.890 -1.1080
mode 96 38.28 0.5124 0.890 1.2583
mode 97 38.36 0.4712 0.901 1.7240
mode 98 38.69 0.4852 0.901 -0.3192
mode 99 38.85 0.2192 0.901 1.3091
mode 100 38.96 0.5471 0.911 2.4636
mode 101 39.27 0.4942 0.911 -0.2160
mode 102 39.34 0.3633 0.921 -1.2953
mode 103 39.54 0.4508 0.942 3.5430
mode 104 39.90 0.5176 0.962 2.9067
mode 105 40.02 0.5320 0.962 -0.9747
mode 106 40.30 0.4895 0.962 1.7997

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.