*** 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 = 2607020454031883798.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 2607020454031883798.atom to be opened.
Openam> File opened: 2607020454031883798.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.
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 = 2607020454031883798.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 25
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 2607020454031883798.atom to be opened.
Openam> file on opening on unit 11:
2607020454031883798.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> 25 residue(s) per block.
Blocpdb> 5308 residues.
Blocpdb> 167 atoms in block 1
Block first atom: 1
Blocpdb> 176 atoms in block 2
Block first atom: 168
Blocpdb> 175 atoms in block 3
Block first atom: 344
Blocpdb> 196 atoms in block 4
Block first atom: 519
Blocpdb> 190 atoms in block 5
Block first atom: 715
Blocpdb> 193 atoms in block 6
Block first atom: 905
Blocpdb> 189 atoms in block 7
Block first atom: 1098
Blocpdb> 205 atoms in block 8
Block first atom: 1287
Blocpdb> 189 atoms in block 9
Block first atom: 1492
Blocpdb> 193 atoms in block 10
Block first atom: 1681
Blocpdb> 194 atoms in block 11
Block first atom: 1874
Blocpdb> 194 atoms in block 12
Block first atom: 2068
Blocpdb> 190 atoms in block 13
Block first atom: 2262
Blocpdb> 198 atoms in block 14
Block first atom: 2452
Blocpdb> 189 atoms in block 15
Block first atom: 2650
Blocpdb> 187 atoms in block 16
Block first atom: 2839
Blocpdb> 187 atoms in block 17
Block first atom: 3026
Blocpdb> 189 atoms in block 18
Block first atom: 3213
Blocpdb> 179 atoms in block 19
Block first atom: 3402
Blocpdb> 175 atoms in block 20
Block first atom: 3581
Blocpdb> 188 atoms in block 21
Block first atom: 3756
Blocpdb> 188 atoms in block 22
Block first atom: 3944
Blocpdb> 180 atoms in block 23
Block first atom: 4132
Blocpdb> 177 atoms in block 24
Block first atom: 4312
Blocpdb> 185 atoms in block 25
Block first atom: 4489
Blocpdb> 188 atoms in block 26
Block first atom: 4674
Blocpdb> 193 atoms in block 27
Block first atom: 4862
Blocpdb> 175 atoms in block 28
Block first atom: 5055
Blocpdb> 199 atoms in block 29
Block first atom: 5230
Blocpdb> 211 atoms in block 30
Block first atom: 5429
Blocpdb> 189 atoms in block 31
Block first atom: 5640
Blocpdb> 192 atoms in block 32
Block first atom: 5829
Blocpdb> 175 atoms in block 33
Block first atom: 6021
Blocpdb> 210 atoms in block 34
Block first atom: 6196
Blocpdb> 209 atoms in block 35
Block first atom: 6406
Blocpdb> 206 atoms in block 36
Block first atom: 6615
Blocpdb> 200 atoms in block 37
Block first atom: 6821
Blocpdb> 213 atoms in block 38
Block first atom: 7021
Blocpdb> 168 atoms in block 39
Block first atom: 7234
Blocpdb> 214 atoms in block 40
Block first atom: 7402
Blocpdb> 201 atoms in block 41
Block first atom: 7616
Blocpdb> 195 atoms in block 42
Block first atom: 7817
Blocpdb> 205 atoms in block 43
Block first atom: 8012
Blocpdb> 217 atoms in block 44
Block first atom: 8217
Blocpdb> 199 atoms in block 45
Block first atom: 8434
Blocpdb> 202 atoms in block 46
Block first atom: 8633
Blocpdb> 208 atoms in block 47
Block first atom: 8835
Blocpdb> 210 atoms in block 48
Block first atom: 9043
Blocpdb> 199 atoms in block 49
Block first atom: 9253
Blocpdb> 193 atoms in block 50
Block first atom: 9452
Blocpdb> 193 atoms in block 51
Block first atom: 9645
Blocpdb> 179 atoms in block 52
Block first atom: 9838
Blocpdb> 177 atoms in block 53
Block first atom: 10017
Blocpdb> 17 atoms in block 54
Block first atom: 10194
Blocpdb> 167 atoms in block 55
Block first atom: 10211
Blocpdb> 176 atoms in block 56
Block first atom: 10378
Blocpdb> 175 atoms in block 57
Block first atom: 10554
Blocpdb> 196 atoms in block 58
Block first atom: 10729
Blocpdb> 190 atoms in block 59
Block first atom: 10925
Blocpdb> 193 atoms in block 60
Block first atom: 11115
Blocpdb> 189 atoms in block 61
Block first atom: 11308
Blocpdb> 205 atoms in block 62
Block first atom: 11497
Blocpdb> 189 atoms in block 63
Block first atom: 11702
Blocpdb> 193 atoms in block 64
Block first atom: 11891
Blocpdb> 194 atoms in block 65
Block first atom: 12084
Blocpdb> 194 atoms in block 66
Block first atom: 12278
Blocpdb> 190 atoms in block 67
Block first atom: 12472
Blocpdb> 198 atoms in block 68
Block first atom: 12662
Blocpdb> 189 atoms in block 69
Block first atom: 12860
Blocpdb> 187 atoms in block 70
Block first atom: 13049
Blocpdb> 187 atoms in block 71
Block first atom: 13236
Blocpdb> 189 atoms in block 72
Block first atom: 13423
Blocpdb> 179 atoms in block 73
Block first atom: 13612
Blocpdb> 175 atoms in block 74
Block first atom: 13791
Blocpdb> 188 atoms in block 75
Block first atom: 13966
Blocpdb> 188 atoms in block 76
Block first atom: 14154
Blocpdb> 180 atoms in block 77
Block first atom: 14342
Blocpdb> 177 atoms in block 78
Block first atom: 14522
Blocpdb> 185 atoms in block 79
Block first atom: 14699
Blocpdb> 188 atoms in block 80
Block first atom: 14884
Blocpdb> 193 atoms in block 81
Block first atom: 15072
Blocpdb> 175 atoms in block 82
Block first atom: 15265
Blocpdb> 199 atoms in block 83
Block first atom: 15440
Blocpdb> 211 atoms in block 84
Block first atom: 15639
Blocpdb> 189 atoms in block 85
Block first atom: 15850
Blocpdb> 192 atoms in block 86
Block first atom: 16039
Blocpdb> 175 atoms in block 87
Block first atom: 16231
Blocpdb> 210 atoms in block 88
Block first atom: 16406
Blocpdb> 209 atoms in block 89
Block first atom: 16616
Blocpdb> 206 atoms in block 90
Block first atom: 16825
Blocpdb> 200 atoms in block 91
Block first atom: 17031
Blocpdb> 213 atoms in block 92
Block first atom: 17231
Blocpdb> 168 atoms in block 93
Block first atom: 17444
Blocpdb> 214 atoms in block 94
Block first atom: 17612
Blocpdb> 201 atoms in block 95
Block first atom: 17826
Blocpdb> 195 atoms in block 96
Block first atom: 18027
Blocpdb> 205 atoms in block 97
Block first atom: 18222
Blocpdb> 217 atoms in block 98
Block first atom: 18427
Blocpdb> 199 atoms in block 99
Block first atom: 18644
Blocpdb> 202 atoms in block 100
Block first atom: 18843
Blocpdb> 208 atoms in block 101
Block first atom: 19045
Blocpdb> 210 atoms in block 102
Block first atom: 19253
Blocpdb> 199 atoms in block 103
Block first atom: 19463
Blocpdb> 193 atoms in block 104
Block first atom: 19662
Blocpdb> 193 atoms in block 105
Block first atom: 19855
Blocpdb> 179 atoms in block 106
Block first atom: 20048
Blocpdb> 177 atoms in block 107
Block first atom: 20227
Blocpdb> 17 atoms in block 108
Block first atom: 20404
Blocpdb> 167 atoms in block 109
Block first atom: 20421
Blocpdb> 176 atoms in block 110
Block first atom: 20588
Blocpdb> 175 atoms in block 111
Block first atom: 20764
Blocpdb> 196 atoms in block 112
Block first atom: 20939
Blocpdb> 190 atoms in block 113
Block first atom: 21135
Blocpdb> 193 atoms in block 114
Block first atom: 21325
Blocpdb> 189 atoms in block 115
Block first atom: 21518
Blocpdb> 205 atoms in block 116
Block first atom: 21707
Blocpdb> 189 atoms in block 117
Block first atom: 21912
Blocpdb> 193 atoms in block 118
Block first atom: 22101
Blocpdb> 194 atoms in block 119
Block first atom: 22294
Blocpdb> 194 atoms in block 120
Block first atom: 22488
Blocpdb> 190 atoms in block 121
Block first atom: 22682
Blocpdb> 198 atoms in block 122
Block first atom: 22872
Blocpdb> 189 atoms in block 123
Block first atom: 23070
Blocpdb> 187 atoms in block 124
Block first atom: 23259
Blocpdb> 187 atoms in block 125
Block first atom: 23446
Blocpdb> 189 atoms in block 126
Block first atom: 23633
Blocpdb> 179 atoms in block 127
Block first atom: 23822
Blocpdb> 175 atoms in block 128
Block first atom: 24001
Blocpdb> 188 atoms in block 129
Block first atom: 24176
Blocpdb> 188 atoms in block 130
Block first atom: 24364
Blocpdb> 180 atoms in block 131
Block first atom: 24552
Blocpdb> 177 atoms in block 132
Block first atom: 24732
Blocpdb> 185 atoms in block 133
Block first atom: 24909
Blocpdb> 188 atoms in block 134
Block first atom: 25094
Blocpdb> 193 atoms in block 135
Block first atom: 25282
Blocpdb> 175 atoms in block 136
Block first atom: 25475
Blocpdb> 199 atoms in block 137
Block first atom: 25650
Blocpdb> 211 atoms in block 138
Block first atom: 25849
Blocpdb> 189 atoms in block 139
Block first atom: 26060
Blocpdb> 192 atoms in block 140
Block first atom: 26249
Blocpdb> 175 atoms in block 141
Block first atom: 26441
Blocpdb> 210 atoms in block 142
Block first atom: 26616
Blocpdb> 209 atoms in block 143
Block first atom: 26826
Blocpdb> 206 atoms in block 144
Block first atom: 27035
Blocpdb> 200 atoms in block 145
Block first atom: 27241
Blocpdb> 213 atoms in block 146
Block first atom: 27441
Blocpdb> 168 atoms in block 147
Block first atom: 27654
Blocpdb> 214 atoms in block 148
Block first atom: 27822
Blocpdb> 201 atoms in block 149
Block first atom: 28036
Blocpdb> 195 atoms in block 150
Block first atom: 28237
Blocpdb> 205 atoms in block 151
Block first atom: 28432
Blocpdb> 217 atoms in block 152
Block first atom: 28637
Blocpdb> 199 atoms in block 153
Block first atom: 28854
Blocpdb> 202 atoms in block 154
Block first atom: 29053
Blocpdb> 208 atoms in block 155
Block first atom: 29255
Blocpdb> 210 atoms in block 156
Block first atom: 29463
Blocpdb> 199 atoms in block 157
Block first atom: 29673
Blocpdb> 193 atoms in block 158
Block first atom: 29872
Blocpdb> 193 atoms in block 159
Block first atom: 30065
Blocpdb> 179 atoms in block 160
Block first atom: 30258
Blocpdb> 177 atoms in block 161
Block first atom: 30437
Blocpdb> 17 atoms in block 162
Block first atom: 30614
Blocpdb> 167 atoms in block 163
Block first atom: 30631
Blocpdb> 176 atoms in block 164
Block first atom: 30798
Blocpdb> 175 atoms in block 165
Block first atom: 30974
Blocpdb> 196 atoms in block 166
Block first atom: 31149
Blocpdb> 190 atoms in block 167
Block first atom: 31345
Blocpdb> 193 atoms in block 168
Block first atom: 31535
Blocpdb> 189 atoms in block 169
Block first atom: 31728
Blocpdb> 205 atoms in block 170
Block first atom: 31917
Blocpdb> 189 atoms in block 171
Block first atom: 32122
Blocpdb> 193 atoms in block 172
Block first atom: 32311
Blocpdb> 194 atoms in block 173
Block first atom: 32504
Blocpdb> 194 atoms in block 174
Block first atom: 32698
Blocpdb> 190 atoms in block 175
Block first atom: 32892
Blocpdb> 198 atoms in block 176
Block first atom: 33082
Blocpdb> 189 atoms in block 177
Block first atom: 33280
Blocpdb> 187 atoms in block 178
Block first atom: 33469
Blocpdb> 187 atoms in block 179
Block first atom: 33656
Blocpdb> 189 atoms in block 180
Block first atom: 33843
Blocpdb> 179 atoms in block 181
Block first atom: 34032
Blocpdb> 175 atoms in block 182
Block first atom: 34211
Blocpdb> 188 atoms in block 183
Block first atom: 34386
Blocpdb> 188 atoms in block 184
Block first atom: 34574
Blocpdb> 180 atoms in block 185
Block first atom: 34762
Blocpdb> 177 atoms in block 186
Block first atom: 34942
Blocpdb> 185 atoms in block 187
Block first atom: 35119
Blocpdb> 188 atoms in block 188
Block first atom: 35304
Blocpdb> 193 atoms in block 189
Block first atom: 35492
Blocpdb> 175 atoms in block 190
Block first atom: 35685
Blocpdb> 199 atoms in block 191
Block first atom: 35860
Blocpdb> 211 atoms in block 192
Block first atom: 36059
Blocpdb> 189 atoms in block 193
Block first atom: 36270
Blocpdb> 192 atoms in block 194
Block first atom: 36459
Blocpdb> 175 atoms in block 195
Block first atom: 36651
Blocpdb> 210 atoms in block 196
Block first atom: 36826
Blocpdb> 209 atoms in block 197
Block first atom: 37036
Blocpdb> 206 atoms in block 198
Block first atom: 37245
Blocpdb> 200 atoms in block 199
Block first atom: 37451
Blocpdb> 213 atoms in block 200
Block first atom: 37651
Blocpdb> 168 atoms in block 201
Block first atom: 37864
Blocpdb> 214 atoms in block 202
Block first atom: 38032
Blocpdb> 201 atoms in block 203
Block first atom: 38246
Blocpdb> 195 atoms in block 204
Block first atom: 38447
Blocpdb> 205 atoms in block 205
Block first atom: 38642
Blocpdb> 217 atoms in block 206
Block first atom: 38847
Blocpdb> 199 atoms in block 207
Block first atom: 39064
Blocpdb> 202 atoms in block 208
Block first atom: 39263
Blocpdb> 208 atoms in block 209
Block first atom: 39465
Blocpdb> 210 atoms in block 210
Block first atom: 39673
Blocpdb> 199 atoms in block 211
Block first atom: 39883
Blocpdb> 193 atoms in block 212
Block first atom: 40082
Blocpdb> 193 atoms in block 213
Block first atom: 40275
Blocpdb> 179 atoms in block 214
Block first atom: 40468
Blocpdb> 177 atoms in block 215
Block first atom: 40647
Blocpdb> 17 atoms in block 216
Block first atom: 40823
Blocpdb> 216 blocks.
Blocpdb> At most, 217 atoms in each of them.
Blocpdb> At least, 17 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: 80184322 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 0m0.193s
user 0m0.183s
sys 0m0.010s
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.
|
