Should you encounter any unexpected behaviour,
please let us know.

* Lyzozyme_1aki_clean_H *

Normal Mode Analysis for ID 250228134049613773

Conformational change expected to be analysed

%Projmod-Wn> Atom 11 has name HB1 in a file and HB2 in the other. %Projmod-Wn> Atom 12 has name HB2 in a file and HB3 in the other. %Projmod-Wn> Atom 13 has name HG1 in a file and HG2 in the other. %Projmod-Wn> Atom 14 has name HG2 in a file and HG3 in the other. %Projmod-Wn> ... %Projmod-Wn> 829 atoms have different names in the two pdb files. %Projmod-Wn> Eigenvector 15 Norm= 0.9999 %Projmod-Wn> Eigenvector 23 Norm= 0.9999 %Projmod-Wn> Eigenvector 56 Norm= 1.0001 %Projmod-Wn> Eigenvector 59 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: Rotation-translation modes have a cumulative overlap of 0.9960 !!! 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 0.3983 0.000 -13.0970

mode 8 1.14 0.2581 0.000 13.7331

mode 9 1.20 0.1009 0.000 8.2547

mode 10 1.47 0.4152 0.000 -5.8037

mode 11 1.76 0.1006 0.000 -16.4800

mode 12 1.96 0.3240 0.000 -7.5953

mode 13 2.06 0.5117 0.000 -3.2452

mode 14 2.20 0.4438 0.997 -20.9602

mode 15 2.27 0.2773 0.997 -18.8909

mode 16 2.33 0.2336 0.997 1.9483

mode 17 2.44 0.1333 0.997 2.3289

mode 18 2.49 0.3764 0.997 -6.6424

mode 19 2.57 0.4001 0.997 0.4507

mode 20 2.61 0.3693 0.997 -7.3378

mode 21 2.79 0.4258 0.997 -1.9417

mode 22 2.80 0.6164 0.997 0.4448

mode 23 2.91 0.2789 0.997 -9.0777

mode 24 2.92 0.3822 0.997 -0.5176

mode 25 3.00 0.4680 0.997 -1.3785

mode 26 3.05 0.3375 0.997 6.4138

mode 27 3.09 0.4341 0.997 0.2994

mode 28 3.14 0.2783 0.997 1.1974

mode 29 3.21 0.4757 0.997 -1.7774

mode 30 3.23 0.5023 0.997 0.1178

mode 31 3.25 0.3394 0.997 -6.1343

mode 32 3.28 0.1820 0.997 1.6479

mode 33 3.32 0.2863 0.997 8.9660

mode 34 3.35 0.3928 0.997 5.5718

mode 35 3.41 0.4467 0.997 -6.2924

mode 36 3.43 0.3279 0.997 1.8434

mode 37 3.50 0.2823 0.997 -2.9987

mode 38 3.52 0.4904 0.997 2.4915

mode 39 3.56 0.2930 0.997 -2.1366

mode 40 3.61 0.3340 0.997 -0.1031

mode 41 3.71 0.3345 0.997 1.9076

mode 42 3.73 0.5250 0.997 -1.4578

mode 43 3.75 0.3827 0.997 4.4410

mode 44 3.78 0.3605 0.997 3.9708

mode 45 3.81 0.4111 0.997 -2.7899

mode 46 3.82 0.3026 0.997 10.1323

mode 47 3.84 0.2248 0.997 2.5270

mode 48 3.93 0.2373 0.997 -3.8464

mode 49 3.95 0.1053 0.997 8.3930

mode 50 3.98 0.2980 0.997 -8.2434

mode 51 4.01 0.2457 0.997 0.0303

mode 52 4.03 0.2883 0.997 -4.7477

mode 53 4.10 0.3959 0.997 -4.3213

mode 54 4.12 0.4903 0.997 -0.9825

mode 55 4.14 0.3868 0.997 -2.1605

mode 56 4.19 0.3112 0.997 3.7838

mode 57 4.21 0.3643 0.997 -0.3936

mode 58 4.22 0.4569 0.997 -1.0817

mode 59 4.29 0.2871 0.997 1.8860

mode 60 4.32 0.2917 0.997 -0.0860

mode 61 4.34 0.3350 0.997 1.5953

mode 62 4.35 0.4568 0.997 5.8664

mode 63 4.38 0.3596 0.997 -2.7314

mode 64 4.38 0.2829 0.997 -10.8481

mode 65 4.41 0.3687 0.997 -3.7506

mode 66 4.44 0.0289 0.997 -4.0483

mode 67 4.45 0.2657 0.997 -1.0641

mode 68 4.48 0.3550 0.997 4.1157

mode 69 4.50 0.4511 0.997 7.3864

mode 70 4.54 0.3476 0.997 6.6173

mode 71 4.57 0.3343 0.997 4.1523

mode 72 4.58 0.3693 0.997 -1.5043

mode 73 4.60 0.4185 0.997 -0.0802

mode 74 4.61 0.4982 0.997 -6.3704

mode 75 4.65 0.4604 0.997 1.5140

mode 76 4.65 0.4628 0.997 -0.0685

mode 77 4.67 0.3430 0.997 2.3734

mode 78 4.72 0.4791 0.997 -3.7902

mode 79 4.72 0.4726 0.997 -3.5424

mode 80 4.77 0.4846 0.997 -5.9192

mode 81 4.78 0.4917 0.997 -4.8058

mode 82 4.80 0.3169 0.997 4.8516

mode 83 4.82 0.4233 0.997 0.5385

mode 84 4.88 0.1072 0.997 -4.0793

mode 85 4.89 0.0746 0.997 -1.6115

mode 86 4.92 0.3887 0.997 -1.7060

mode 87 4.94 0.2278 0.997 1.3458

mode 88 4.94 0.2538 0.997 5.0821

mode 89 4.96 0.3413 0.997 1.0224

mode 90 5.02 0.4930 0.997 1.3523

mode 91 5.03 0.2653 0.997 -0.7584

mode 92 5.05 0.3602 0.997 7.5128

mode 93 5.08 0.3825 0.997 7.7567

mode 94 5.08 0.3515 0.997 -2.9595

mode 95 5.11 0.5194 0.997 -1.0652

mode 96 5.13 0.4552 0.997 8.4950

mode 97 5.15 0.4750 0.997 1.6711

mode 98 5.17 0.3459 0.997 -0.5185

mode 99 5.18 0.4687 0.997 0.4437

mode 100 5.19 0.3954 0.997 0.4645

mode 101 5.21 0.4301 0.997 2.4684

mode 102 5.23 0.4745 0.997 3.9426

mode 103 5.23 0.3571 0.997 -1.8836

mode 104 5.26 0.2670 0.997 -1.2667

mode 105 5.28 0.3861 0.997 3.1993

mode 106 5.29 0.3178 0.997 -1.7048

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

K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004.
K. Suhre & Y.H. Sanejouand, On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004 © International Union of Crystallography.

elNémo is maintained by Yves-Henri Sanejouand.
It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: April 8th, 2025.

Should you encounter any unexpected behaviour, please let us know.

*** Lyzozyme_1aki_clean_H ***

Normal Mode Analysis for ID 250228134049613773

Conformational change expected to be analysed

Should you encounter any unexpected behaviour,
please let us know.

* Lyzozyme_1aki_clean_H *