*** nompcdar12 ***
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 = 2607020356251869765.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 2607020356251869765.atom to be opened.
Openam> File opened: 2607020356251869765.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 = 5308
First residue number = 1
Last residue number = 1327
Number of atoms found = 40840
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= 242.320703 +/- 29.633453 From: 166.439000 To: 323.318000
= 243.037248 +/- 29.789911 From: 160.172000 To: 325.203000
= 279.313377 +/- 49.297280 From: 154.812000 To: 382.338000
Pdbmat> Masses are all set to one.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is 1.3808 % Filled.
Pdbmat> 14680576 non-zero elements.
Pdbmat> 1604229 atom-atom interactions.
Pdbmat> Number per atom= 78.56 +/- 24.78
Maximum number = 132
Minimum number = 8
Pdbmat> Matrix trace = 3.208458E+07
Pdbmat> Larger element = 520.047
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
5308 non-zero elements, NRBL set to 27
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 = 2607020356251869765.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 27
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 2607020356251869765.atom to be opened.
Openam> file on opening on unit 11:
2607020356251869765.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 40840 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 27 residue(s) per block.
Blocpdb> 5308 residues.
Blocpdb> 178 atoms in block 1
Block first atom: 1
Blocpdb> 191 atoms in block 2
Block first atom: 179
Blocpdb> 196 atoms in block 3
Block first atom: 370
Blocpdb> 216 atoms in block 4
Block first atom: 566
Blocpdb> 198 atoms in block 5
Block first atom: 782
Blocpdb> 211 atoms in block 6
Block first atom: 980
Blocpdb> 211 atoms in block 7
Block first atom: 1191
Blocpdb> 207 atoms in block 8
Block first atom: 1402
Blocpdb> 207 atoms in block 9
Block first atom: 1609
Blocpdb> 213 atoms in block 10
Block first atom: 1816
Blocpdb> 206 atoms in block 11
Block first atom: 2029
Blocpdb> 209 atoms in block 12
Block first atom: 2235
Blocpdb> 214 atoms in block 13
Block first atom: 2444
Blocpdb> 202 atoms in block 14
Block first atom: 2658
Blocpdb> 202 atoms in block 15
Block first atom: 2860
Blocpdb> 201 atoms in block 16
Block first atom: 3062
Blocpdb> 206 atoms in block 17
Block first atom: 3263
Blocpdb> 185 atoms in block 18
Block first atom: 3469
Blocpdb> 197 atoms in block 19
Block first atom: 3654
Blocpdb> 206 atoms in block 20
Block first atom: 3851
Blocpdb> 196 atoms in block 21
Block first atom: 4057
Blocpdb> 195 atoms in block 22
Block first atom: 4253
Blocpdb> 198 atoms in block 23
Block first atom: 4448
Blocpdb> 202 atoms in block 24
Block first atom: 4646
Blocpdb> 207 atoms in block 25
Block first atom: 4848
Blocpdb> 191 atoms in block 26
Block first atom: 5055
Blocpdb> 219 atoms in block 27
Block first atom: 5246
Blocpdb> 225 atoms in block 28
Block first atom: 5465
Blocpdb> 204 atoms in block 29
Block first atom: 5690
Blocpdb> 195 atoms in block 30
Block first atom: 5894
Blocpdb> 207 atoms in block 31
Block first atom: 6089
Blocpdb> 232 atoms in block 32
Block first atom: 6296
Blocpdb> 218 atoms in block 33
Block first atom: 6528
Blocpdb> 219 atoms in block 34
Block first atom: 6746
Blocpdb> 225 atoms in block 35
Block first atom: 6965
Blocpdb> 197 atoms in block 36
Block first atom: 7190
Blocpdb> 218 atoms in block 37
Block first atom: 7387
Blocpdb> 220 atoms in block 38
Block first atom: 7605
Blocpdb> 213 atoms in block 39
Block first atom: 7825
Blocpdb> 225 atoms in block 40
Block first atom: 8038
Blocpdb> 223 atoms in block 41
Block first atom: 8263
Blocpdb> 226 atoms in block 42
Block first atom: 8486
Blocpdb> 214 atoms in block 43
Block first atom: 8712
Blocpdb> 219 atoms in block 44
Block first atom: 8926
Blocpdb> 232 atoms in block 45
Block first atom: 9145
Blocpdb> 209 atoms in block 46
Block first atom: 9377
Blocpdb> 203 atoms in block 47
Block first atom: 9586
Blocpdb> 203 atoms in block 48
Block first atom: 9789
Blocpdb> 187 atoms in block 49
Block first atom: 9992
Blocpdb> 32 atoms in block 50
Block first atom: 10179
Blocpdb> 178 atoms in block 51
Block first atom: 10211
Blocpdb> 191 atoms in block 52
Block first atom: 10389
Blocpdb> 196 atoms in block 53
Block first atom: 10580
Blocpdb> 216 atoms in block 54
Block first atom: 10776
Blocpdb> 198 atoms in block 55
Block first atom: 10992
Blocpdb> 211 atoms in block 56
Block first atom: 11190
Blocpdb> 211 atoms in block 57
Block first atom: 11401
Blocpdb> 207 atoms in block 58
Block first atom: 11612
Blocpdb> 207 atoms in block 59
Block first atom: 11819
Blocpdb> 213 atoms in block 60
Block first atom: 12026
Blocpdb> 206 atoms in block 61
Block first atom: 12239
Blocpdb> 209 atoms in block 62
Block first atom: 12445
Blocpdb> 214 atoms in block 63
Block first atom: 12654
Blocpdb> 202 atoms in block 64
Block first atom: 12868
Blocpdb> 202 atoms in block 65
Block first atom: 13070
Blocpdb> 201 atoms in block 66
Block first atom: 13272
Blocpdb> 206 atoms in block 67
Block first atom: 13473
Blocpdb> 185 atoms in block 68
Block first atom: 13679
Blocpdb> 197 atoms in block 69
Block first atom: 13864
Blocpdb> 206 atoms in block 70
Block first atom: 14061
Blocpdb> 196 atoms in block 71
Block first atom: 14267
Blocpdb> 195 atoms in block 72
Block first atom: 14463
Blocpdb> 198 atoms in block 73
Block first atom: 14658
Blocpdb> 202 atoms in block 74
Block first atom: 14856
Blocpdb> 207 atoms in block 75
Block first atom: 15058
Blocpdb> 191 atoms in block 76
Block first atom: 15265
Blocpdb> 219 atoms in block 77
Block first atom: 15456
Blocpdb> 225 atoms in block 78
Block first atom: 15675
Blocpdb> 204 atoms in block 79
Block first atom: 15900
Blocpdb> 195 atoms in block 80
Block first atom: 16104
Blocpdb> 207 atoms in block 81
Block first atom: 16299
Blocpdb> 232 atoms in block 82
Block first atom: 16506
Blocpdb> 218 atoms in block 83
Block first atom: 16738
Blocpdb> 219 atoms in block 84
Block first atom: 16956
Blocpdb> 225 atoms in block 85
Block first atom: 17175
Blocpdb> 197 atoms in block 86
Block first atom: 17400
Blocpdb> 218 atoms in block 87
Block first atom: 17597
Blocpdb> 220 atoms in block 88
Block first atom: 17815
Blocpdb> 213 atoms in block 89
Block first atom: 18035
Blocpdb> 225 atoms in block 90
Block first atom: 18248
Blocpdb> 223 atoms in block 91
Block first atom: 18473
Blocpdb> 226 atoms in block 92
Block first atom: 18696
Blocpdb> 214 atoms in block 93
Block first atom: 18922
Blocpdb> 219 atoms in block 94
Block first atom: 19136
Blocpdb> 232 atoms in block 95
Block first atom: 19355
Blocpdb> 209 atoms in block 96
Block first atom: 19587
Blocpdb> 203 atoms in block 97
Block first atom: 19796
Blocpdb> 203 atoms in block 98
Block first atom: 19999
Blocpdb> 187 atoms in block 99
Block first atom: 20202
Blocpdb> 32 atoms in block 100
Block first atom: 20389
Blocpdb> 178 atoms in block 101
Block first atom: 20421
Blocpdb> 191 atoms in block 102
Block first atom: 20599
Blocpdb> 196 atoms in block 103
Block first atom: 20790
Blocpdb> 216 atoms in block 104
Block first atom: 20986
Blocpdb> 198 atoms in block 105
Block first atom: 21202
Blocpdb> 211 atoms in block 106
Block first atom: 21400
Blocpdb> 211 atoms in block 107
Block first atom: 21611
Blocpdb> 207 atoms in block 108
Block first atom: 21822
Blocpdb> 207 atoms in block 109
Block first atom: 22029
Blocpdb> 213 atoms in block 110
Block first atom: 22236
Blocpdb> 206 atoms in block 111
Block first atom: 22449
Blocpdb> 209 atoms in block 112
Block first atom: 22655
Blocpdb> 214 atoms in block 113
Block first atom: 22864
Blocpdb> 202 atoms in block 114
Block first atom: 23078
Blocpdb> 202 atoms in block 115
Block first atom: 23280
Blocpdb> 201 atoms in block 116
Block first atom: 23482
Blocpdb> 206 atoms in block 117
Block first atom: 23683
Blocpdb> 185 atoms in block 118
Block first atom: 23889
Blocpdb> 197 atoms in block 119
Block first atom: 24074
Blocpdb> 206 atoms in block 120
Block first atom: 24271
Blocpdb> 196 atoms in block 121
Block first atom: 24477
Blocpdb> 195 atoms in block 122
Block first atom: 24673
Blocpdb> 198 atoms in block 123
Block first atom: 24868
Blocpdb> 202 atoms in block 124
Block first atom: 25066
Blocpdb> 207 atoms in block 125
Block first atom: 25268
Blocpdb> 191 atoms in block 126
Block first atom: 25475
Blocpdb> 219 atoms in block 127
Block first atom: 25666
Blocpdb> 225 atoms in block 128
Block first atom: 25885
Blocpdb> 204 atoms in block 129
Block first atom: 26110
Blocpdb> 195 atoms in block 130
Block first atom: 26314
Blocpdb> 207 atoms in block 131
Block first atom: 26509
Blocpdb> 232 atoms in block 132
Block first atom: 26716
Blocpdb> 218 atoms in block 133
Block first atom: 26948
Blocpdb> 219 atoms in block 134
Block first atom: 27166
Blocpdb> 225 atoms in block 135
Block first atom: 27385
Blocpdb> 197 atoms in block 136
Block first atom: 27610
Blocpdb> 218 atoms in block 137
Block first atom: 27807
Blocpdb> 220 atoms in block 138
Block first atom: 28025
Blocpdb> 213 atoms in block 139
Block first atom: 28245
Blocpdb> 225 atoms in block 140
Block first atom: 28458
Blocpdb> 223 atoms in block 141
Block first atom: 28683
Blocpdb> 226 atoms in block 142
Block first atom: 28906
Blocpdb> 214 atoms in block 143
Block first atom: 29132
Blocpdb> 219 atoms in block 144
Block first atom: 29346
Blocpdb> 232 atoms in block 145
Block first atom: 29565
Blocpdb> 209 atoms in block 146
Block first atom: 29797
Blocpdb> 203 atoms in block 147
Block first atom: 30006
Blocpdb> 203 atoms in block 148
Block first atom: 30209
Blocpdb> 187 atoms in block 149
Block first atom: 30412
Blocpdb> 32 atoms in block 150
Block first atom: 30599
Blocpdb> 178 atoms in block 151
Block first atom: 30631
Blocpdb> 191 atoms in block 152
Block first atom: 30809
Blocpdb> 196 atoms in block 153
Block first atom: 31000
Blocpdb> 216 atoms in block 154
Block first atom: 31196
Blocpdb> 198 atoms in block 155
Block first atom: 31412
Blocpdb> 211 atoms in block 156
Block first atom: 31610
Blocpdb> 211 atoms in block 157
Block first atom: 31821
Blocpdb> 207 atoms in block 158
Block first atom: 32032
Blocpdb> 207 atoms in block 159
Block first atom: 32239
Blocpdb> 213 atoms in block 160
Block first atom: 32446
Blocpdb> 206 atoms in block 161
Block first atom: 32659
Blocpdb> 209 atoms in block 162
Block first atom: 32865
Blocpdb> 214 atoms in block 163
Block first atom: 33074
Blocpdb> 202 atoms in block 164
Block first atom: 33288
Blocpdb> 202 atoms in block 165
Block first atom: 33490
Blocpdb> 201 atoms in block 166
Block first atom: 33692
Blocpdb> 206 atoms in block 167
Block first atom: 33893
Blocpdb> 185 atoms in block 168
Block first atom: 34099
Blocpdb> 197 atoms in block 169
Block first atom: 34284
Blocpdb> 206 atoms in block 170
Block first atom: 34481
Blocpdb> 196 atoms in block 171
Block first atom: 34687
Blocpdb> 195 atoms in block 172
Block first atom: 34883
Blocpdb> 198 atoms in block 173
Block first atom: 35078
Blocpdb> 202 atoms in block 174
Block first atom: 35276
Blocpdb> 207 atoms in block 175
Block first atom: 35478
Blocpdb> 191 atoms in block 176
Block first atom: 35685
Blocpdb> 219 atoms in block 177
Block first atom: 35876
Blocpdb> 225 atoms in block 178
Block first atom: 36095
Blocpdb> 204 atoms in block 179
Block first atom: 36320
Blocpdb> 195 atoms in block 180
Block first atom: 36524
Blocpdb> 207 atoms in block 181
Block first atom: 36719
Blocpdb> 232 atoms in block 182
Block first atom: 36926
Blocpdb> 218 atoms in block 183
Block first atom: 37158
Blocpdb> 219 atoms in block 184
Block first atom: 37376
Blocpdb> 225 atoms in block 185
Block first atom: 37595
Blocpdb> 197 atoms in block 186
Block first atom: 37820
Blocpdb> 218 atoms in block 187
Block first atom: 38017
Blocpdb> 220 atoms in block 188
Block first atom: 38235
Blocpdb> 213 atoms in block 189
Block first atom: 38455
Blocpdb> 225 atoms in block 190
Block first atom: 38668
Blocpdb> 223 atoms in block 191
Block first atom: 38893
Blocpdb> 226 atoms in block 192
Block first atom: 39116
Blocpdb> 214 atoms in block 193
Block first atom: 39342
Blocpdb> 219 atoms in block 194
Block first atom: 39556
Blocpdb> 232 atoms in block 195
Block first atom: 39775
Blocpdb> 209 atoms in block 196
Block first atom: 40007
Blocpdb> 203 atoms in block 197
Block first atom: 40216
Blocpdb> 203 atoms in block 198
Block first atom: 40419
Blocpdb> 187 atoms in block 199
Block first atom: 40622
Blocpdb> 32 atoms in block 200
Block first atom: 40808
Blocpdb> 200 blocks.
Blocpdb> At most, 232 atoms in each of them.
Blocpdb> At least, 32 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: 85758337 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 0m0.209s
user 0m0.193s
sys 0m0.016s
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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