*** 5m3j modes ***
Output from eigenvector calculation:
STDOUT:
CUTOFF set to default value (CUTOFF=8)
Build Tirion matrix:
Pdbmat> Computes the Hessian matrix, using an Elastic Network Model.
Pdbmat> Version 3.50, Fevrier 2004.
Pdbmat> Options to be read in pdbmat.dat file.
Pdbmat> Coordinate filename = 2610161425241559787.atom
Pdbmat> Distance cutoff = 8.00
Force constant = 10.00
Origin of mass values = CONS
Pdbmat> Levelshift = 1.0E-09
PRINTing level = 2
Pdbmat> Coordinate file 2610161425241559787.atom to be opened.
Openam> File opened: 2610161425241559787.atom
Pdbmat> Coordinate file in PDB format.
Rdatompdb> Reading pdb file.
Rdatompdb> End of file reached.
Rdatompdb> Number of I/O errors: 0
Rdatompdb> Number of residues found = 2215
First residue number = 0
Last residue number = 29
Number of atoms found = 18003
Mean number per residue = 8.1
Pdbmat> Coordinate statistics:
= -70.151413 +/- 20.047073 From: -126.059000 To: -18.134000
= 37.729002 +/- 23.349051 From: -14.993000 To: 94.068000
= -21.432004 +/- 26.804473 From: -91.425000 To: 36.843000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'A ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> residue:'C ' is not a well known amino-acid.
%Pdbmat-W> residue:'U ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 28 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -1.0057 % Filled.
Pdbmat> 6928788 non-zero elements.
Pdbmat> 757980 atom-atom interactions.
Pdbmat> Number per atom= 84.21 +/- 21.45
Maximum number = 136
Minimum number = 8
Pdbmat> Matrix trace = 1.515960E+07
Pdbmat> Larger element = 505.014
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2215 non-zero elements, NRBL set to 12
Diagonalize Tirion matrix using diagrtb
Diagrtb> Diagonalizes a matrix, using the RTB/BNM approximation.
Diagrtb> Version 2.52, November 2004.
Diagrtb> Options to be read in diagrtb.dat file.
Diagrtb> Options taken into account:
MATRix filename = pdbmat.sdijb
COORdinates filename = 2610161425241559787.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 12
Origin of MASS values = CONS
MATRix FORMat = BINA
Temporary files cleaning = ALL
Output PRINting level = 2
Diagrtb> Memory allocation for Blocpdb.
Blocpdb> Entering in.
Openam> file on opening on unit 10:
diagrtb_work.xyzm
Blocpdb> Coordinate file 2610161425241559787.atom to be opened.
Openam> file on opening on unit 11:
2610161425241559787.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 18003 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 12 residue(s) per block.
Blocpdb> 2215 residues.
Blocpdb> 101 atoms in block 1
Block first atom: 1
Blocpdb> 92 atoms in block 2
Block first atom: 102
Blocpdb> 95 atoms in block 3
Block first atom: 194
Blocpdb> 99 atoms in block 4
Block first atom: 289
Blocpdb> 96 atoms in block 5
Block first atom: 388
Blocpdb> 29 atoms in block 6
Block first atom: 484
Blocpdb> 101 atoms in block 7
Block first atom: 513
Blocpdb> 101 atoms in block 8
Block first atom: 614
Blocpdb> 97 atoms in block 9
Block first atom: 715
Blocpdb> 107 atoms in block 10
Block first atom: 812
Blocpdb> 85 atoms in block 11
Block first atom: 919
Blocpdb> 108 atoms in block 12
Block first atom: 1004
Blocpdb> 107 atoms in block 13
Block first atom: 1112
Blocpdb> 87 atoms in block 14
Block first atom: 1219
Blocpdb> 97 atoms in block 15
Block first atom: 1306
Blocpdb> 99 atoms in block 16
Block first atom: 1403
Blocpdb> 94 atoms in block 17
Block first atom: 1502
Blocpdb> 97 atoms in block 18
Block first atom: 1596
Blocpdb> 86 atoms in block 19
Block first atom: 1693
Blocpdb> 94 atoms in block 20
Block first atom: 1779
Blocpdb> 96 atoms in block 21
Block first atom: 1873
Blocpdb> 99 atoms in block 22
Block first atom: 1969
Blocpdb> 102 atoms in block 23
Block first atom: 2068
Blocpdb> 96 atoms in block 24
Block first atom: 2170
Blocpdb> 87 atoms in block 25
Block first atom: 2266
Blocpdb> 92 atoms in block 26
Block first atom: 2353
Blocpdb> 101 atoms in block 27
Block first atom: 2445
Blocpdb> 95 atoms in block 28
Block first atom: 2546
Blocpdb> 111 atoms in block 29
Block first atom: 2641
Blocpdb> 97 atoms in block 30
Block first atom: 2752
Blocpdb> 91 atoms in block 31
Block first atom: 2849
Blocpdb> 99 atoms in block 32
Block first atom: 2940
Blocpdb> 96 atoms in block 33
Block first atom: 3039
Blocpdb> 97 atoms in block 34
Block first atom: 3135
Blocpdb> 91 atoms in block 35
Block first atom: 3232
Blocpdb> 86 atoms in block 36
Block first atom: 3323
Blocpdb> 106 atoms in block 37
Block first atom: 3409
Blocpdb> 92 atoms in block 38
Block first atom: 3515
Blocpdb> 102 atoms in block 39
Block first atom: 3607
Blocpdb> 91 atoms in block 40
Block first atom: 3709
Blocpdb> 93 atoms in block 41
Block first atom: 3800
Blocpdb> 95 atoms in block 42
Block first atom: 3893
Blocpdb> 89 atoms in block 43
Block first atom: 3988
Blocpdb> 93 atoms in block 44
Block first atom: 4077
Blocpdb> 101 atoms in block 45
Block first atom: 4170
Blocpdb> 96 atoms in block 46
Block first atom: 4271
Blocpdb> 97 atoms in block 47
Block first atom: 4367
Blocpdb> 102 atoms in block 48
Block first atom: 4464
Blocpdb> 96 atoms in block 49
Block first atom: 4566
Blocpdb> 95 atoms in block 50
Block first atom: 4662
Blocpdb> 93 atoms in block 51
Block first atom: 4757
Blocpdb> 87 atoms in block 52
Block first atom: 4850
Blocpdb> 91 atoms in block 53
Block first atom: 4937
Blocpdb> 104 atoms in block 54
Block first atom: 5028
Blocpdb> 84 atoms in block 55
Block first atom: 5132
Blocpdb> 101 atoms in block 56
Block first atom: 5216
Blocpdb> 100 atoms in block 57
Block first atom: 5317
Blocpdb> 91 atoms in block 58
Block first atom: 5417
Blocpdb> 117 atoms in block 59
Block first atom: 5508
Blocpdb> 93 atoms in block 60
Block first atom: 5625
Blocpdb> 30 atoms in block 61
Block first atom: 5718
Blocpdb> 104 atoms in block 62
Block first atom: 5748
Blocpdb> 92 atoms in block 63
Block first atom: 5852
Blocpdb> 82 atoms in block 64
Block first atom: 5944
Blocpdb> 98 atoms in block 65
Block first atom: 6026
Blocpdb> 98 atoms in block 66
Block first atom: 6124
Blocpdb> 80 atoms in block 67
Block first atom: 6222
Blocpdb> 93 atoms in block 68
Block first atom: 6302
Blocpdb> 94 atoms in block 69
Block first atom: 6395
Blocpdb> 92 atoms in block 70
Block first atom: 6489
Blocpdb> 89 atoms in block 71
Block first atom: 6581
Blocpdb> 104 atoms in block 72
Block first atom: 6670
Blocpdb> 86 atoms in block 73
Block first atom: 6774
Blocpdb> 97 atoms in block 74
Block first atom: 6860
Blocpdb> 83 atoms in block 75
Block first atom: 6957
Blocpdb> 96 atoms in block 76
Block first atom: 7040
Blocpdb> 102 atoms in block 77
Block first atom: 7136
Blocpdb> 101 atoms in block 78
Block first atom: 7238
Blocpdb> 97 atoms in block 79
Block first atom: 7339
Blocpdb> 97 atoms in block 80
Block first atom: 7436
Blocpdb> 99 atoms in block 81
Block first atom: 7533
Blocpdb> 87 atoms in block 82
Block first atom: 7632
Blocpdb> 92 atoms in block 83
Block first atom: 7719
Blocpdb> 82 atoms in block 84
Block first atom: 7811
Blocpdb> 89 atoms in block 85
Block first atom: 7893
Blocpdb> 80 atoms in block 86
Block first atom: 7982
Blocpdb> 94 atoms in block 87
Block first atom: 8062
Blocpdb> 101 atoms in block 88
Block first atom: 8156
Blocpdb> 110 atoms in block 89
Block first atom: 8257
Blocpdb> 89 atoms in block 90
Block first atom: 8367
Blocpdb> 90 atoms in block 91
Block first atom: 8456
Blocpdb> 94 atoms in block 92
Block first atom: 8546
Blocpdb> 106 atoms in block 93
Block first atom: 8640
Blocpdb> 104 atoms in block 94
Block first atom: 8746
Blocpdb> 81 atoms in block 95
Block first atom: 8850
Blocpdb> 91 atoms in block 96
Block first atom: 8931
Blocpdb> 78 atoms in block 97
Block first atom: 9022
Blocpdb> 101 atoms in block 98
Block first atom: 9100
Blocpdb> 98 atoms in block 99
Block first atom: 9201
Blocpdb> 99 atoms in block 100
Block first atom: 9299
Blocpdb> 92 atoms in block 101
Block first atom: 9398
Blocpdb> 98 atoms in block 102
Block first atom: 9490
Blocpdb> 103 atoms in block 103
Block first atom: 9588
Blocpdb> 81 atoms in block 104
Block first atom: 9691
Blocpdb> 84 atoms in block 105
Block first atom: 9772
Blocpdb> 88 atoms in block 106
Block first atom: 9856
Blocpdb> 87 atoms in block 107
Block first atom: 9944
Blocpdb> 110 atoms in block 108
Block first atom: 10031
Blocpdb> 97 atoms in block 109
Block first atom: 10141
Blocpdb> 99 atoms in block 110
Block first atom: 10238
Blocpdb> 87 atoms in block 111
Block first atom: 10337
Blocpdb> 105 atoms in block 112
Block first atom: 10424
Blocpdb> 100 atoms in block 113
Block first atom: 10529
Blocpdb> 95 atoms in block 114
Block first atom: 10629
Blocpdb> 90 atoms in block 115
Block first atom: 10724
Blocpdb> 108 atoms in block 116
Block first atom: 10814
Blocpdb> 105 atoms in block 117
Block first atom: 10922
Blocpdb> 92 atoms in block 118
Block first atom: 11027
Blocpdb> 92 atoms in block 119
Block first atom: 11119
Blocpdb> 99 atoms in block 120
Block first atom: 11211
Blocpdb> 97 atoms in block 121
Block first atom: 11310
Blocpdb> 94 atoms in block 122
Block first atom: 11407
Blocpdb> 8 atoms in block 123
Block first atom: 11501
Blocpdb> 96 atoms in block 124
Block first atom: 11509
Blocpdb> 98 atoms in block 125
Block first atom: 11605
Blocpdb> 105 atoms in block 126
Block first atom: 11703
Blocpdb> 98 atoms in block 127
Block first atom: 11808
Blocpdb> 95 atoms in block 128
Block first atom: 11906
Blocpdb> 91 atoms in block 129
Block first atom: 12001
Blocpdb> 97 atoms in block 130
Block first atom: 12092
Blocpdb> 82 atoms in block 131
Block first atom: 12189
Blocpdb> 97 atoms in block 132
Block first atom: 12271
Blocpdb> 104 atoms in block 133
Block first atom: 12368
Blocpdb> 108 atoms in block 134
Block first atom: 12472
Blocpdb> 97 atoms in block 135
Block first atom: 12580
Blocpdb> 99 atoms in block 136
Block first atom: 12677
Blocpdb> 90 atoms in block 137
Block first atom: 12776
Blocpdb> 94 atoms in block 138
Block first atom: 12866
Blocpdb> 113 atoms in block 139
Block first atom: 12960
Blocpdb> 91 atoms in block 140
Block first atom: 13073
Blocpdb> 101 atoms in block 141
Block first atom: 13164
Blocpdb> 87 atoms in block 142
Block first atom: 13265
Blocpdb> 99 atoms in block 143
Block first atom: 13352
Blocpdb> 104 atoms in block 144
Block first atom: 13451
Blocpdb> 90 atoms in block 145
Block first atom: 13555
Blocpdb> 96 atoms in block 146
Block first atom: 13645
Blocpdb> 91 atoms in block 147
Block first atom: 13741
Blocpdb> 90 atoms in block 148
Block first atom: 13832
Blocpdb> 76 atoms in block 149
Block first atom: 13922
Blocpdb> 97 atoms in block 150
Block first atom: 13998
Blocpdb> 105 atoms in block 151
Block first atom: 14095
Blocpdb> 97 atoms in block 152
Block first atom: 14200
Blocpdb> 91 atoms in block 153
Block first atom: 14297
Blocpdb> 95 atoms in block 154
Block first atom: 14388
Blocpdb> 98 atoms in block 155
Block first atom: 14483
Blocpdb> 95 atoms in block 156
Block first atom: 14581
Blocpdb> 98 atoms in block 157
Block first atom: 14676
Blocpdb> 97 atoms in block 158
Block first atom: 14774
Blocpdb> 93 atoms in block 159
Block first atom: 14871
Blocpdb> 113 atoms in block 160
Block first atom: 14964
Blocpdb> 106 atoms in block 161
Block first atom: 15077
Blocpdb> 89 atoms in block 162
Block first atom: 15183
Blocpdb> 89 atoms in block 163
Block first atom: 15272
Blocpdb> 40 atoms in block 164
Block first atom: 15361
Blocpdb> 93 atoms in block 165
Block first atom: 15401
Blocpdb> 86 atoms in block 166
Block first atom: 15494
Blocpdb> 92 atoms in block 167
Block first atom: 15580
Blocpdb> 100 atoms in block 168
Block first atom: 15672
Blocpdb> 107 atoms in block 169
Block first atom: 15772
Blocpdb> 97 atoms in block 170
Block first atom: 15879
Blocpdb> 105 atoms in block 171
Block first atom: 15976
Blocpdb> 89 atoms in block 172
Block first atom: 16081
Blocpdb> 96 atoms in block 173
Block first atom: 16170
Blocpdb> 104 atoms in block 174
Block first atom: 16266
Blocpdb> 97 atoms in block 175
Block first atom: 16370
Blocpdb> 102 atoms in block 176
Block first atom: 16467
Blocpdb> 89 atoms in block 177
Block first atom: 16569
Blocpdb> 96 atoms in block 178
Block first atom: 16658
Blocpdb> 92 atoms in block 179
Block first atom: 16754
Blocpdb> 98 atoms in block 180
Block first atom: 16846
Blocpdb> 85 atoms in block 181
Block first atom: 16944
Blocpdb> 92 atoms in block 182
Block first atom: 17029
Blocpdb> 96 atoms in block 183
Block first atom: 17121
Blocpdb> 96 atoms in block 184
Block first atom: 17217
Blocpdb> 39 atoms in block 185
Block first atom: 17313
Blocpdb> 242 atoms in block 186
Block first atom: 17352
Blocpdb> 40 atoms in block 187
Block first atom: 17594
Blocpdb> 262 atoms in block 188
Block first atom: 17634
Blocpdb> 45 atoms in block 189
Block first atom: 17896
Blocpdb> 38 atoms in block 190
Block first atom: 17941
Blocpdb> 25 atoms in block 191
Block first atom: 17978
Blocpdb> 191 blocks.
Blocpdb> At most, 262 atoms in each of them.
Blocpdb> At least, 8 atoms in each of them.
Blocpdb> Normal end of Blocpdb.
Diagrtb> Memory allocation for Prepmat.
Diagrtb> Memory allocation for RTB.
Diagrtb> Memory allocation for Diagstd.
Diagrtb> Memory allocation for RTB_to_modes.
%Diagrtb-Er> IRWKMX up to: 43068871 Maximum allowed is LRWORK= 32000000
%Diagrtb-Er> Not enough memory allowed for working arrays. Sorry.
Lower the number of blocks, the sizes of the largest ones...
Or recompile DIAGRTB with larger WORKing arrays.
STDERR:
STOP *Working arrays allocation error*
real 0m0.092s
user 0m0.084s
sys 0m0.007s
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: april 24th, 2026.
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