*** ***
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 = 2402061808291718695.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 2402061808291718695.atom to be opened.
Openam> File opened: 2402061808291718695.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 = 2622
First residue number = 1
Last residue number = 214
Number of atoms found = 40922
Mean number per residue = 15.6
Pdbmat> Coordinate statistics:
= -162.445864 +/- 32.785051 From: -242.397000 To: -90.969000
= 70.153524 +/- 46.795259 From: -32.229000 To: 178.390000
= -142.734012 +/- 37.853422 From: -234.060000 To: -60.336000
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 -2.7848 % Filled.
Pdbmat> 29354904 non-zero elements.
Pdbmat> 3234933 atom-atom interactions.
Pdbmat> Number per atom= 158.10 +/- 48.37
Maximum number = 256
Minimum number = 20
Pdbmat> Matrix trace = 6.469866E+07
Pdbmat> Larger element = 930.931
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2622 non-zero elements, NRBL set to 14
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 = 2402061808291718695.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 14
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 2402061808291718695.atom to be opened.
Openam> file on opening on unit 11:
2402061808291718695.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 40922 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 14 residue(s) per block.
Blocpdb> 2622 residues.
Blocpdb> 221 atoms in block 1
Block first atom: 1
Blocpdb> 191 atoms in block 2
Block first atom: 222
Blocpdb> 222 atoms in block 3
Block first atom: 413
Blocpdb> 233 atoms in block 4
Block first atom: 635
Blocpdb> 238 atoms in block 5
Block first atom: 868
Blocpdb> 268 atoms in block 6
Block first atom: 1106
Blocpdb> 196 atoms in block 7
Block first atom: 1374
Blocpdb> 266 atoms in block 8
Block first atom: 1570
Blocpdb> 193 atoms in block 9
Block first atom: 1836
Blocpdb> 164 atoms in block 10
Block first atom: 2029
Blocpdb> 234 atoms in block 11
Block first atom: 2193
Blocpdb> 184 atoms in block 12
Block first atom: 2427
Blocpdb> 205 atoms in block 13
Block first atom: 2611
Blocpdb> 198 atoms in block 14
Block first atom: 2816
Blocpdb> 232 atoms in block 15
Block first atom: 3014
Blocpdb> 207 atoms in block 16
Block first atom: 3246
Blocpdb> 196 atoms in block 17
Block first atom: 3453
Blocpdb> 236 atoms in block 18
Block first atom: 3649
Blocpdb> 201 atoms in block 19
Block first atom: 3885
Blocpdb> 228 atoms in block 20
Block first atom: 4086
Blocpdb> 231 atoms in block 21
Block first atom: 4314
Blocpdb> 233 atoms in block 22
Block first atom: 4545
Blocpdb> 239 atoms in block 23
Block first atom: 4778
Blocpdb> 221 atoms in block 24
Block first atom: 5017
Blocpdb> 217 atoms in block 25
Block first atom: 5238
Blocpdb> 227 atoms in block 26
Block first atom: 5455
Blocpdb> 222 atoms in block 27
Block first atom: 5682
Blocpdb> 205 atoms in block 28
Block first atom: 5904
Blocpdb> 220 atoms in block 29
Block first atom: 6109
Blocpdb> 225 atoms in block 30
Block first atom: 6329
Blocpdb> 215 atoms in block 31
Block first atom: 6554
Blocpdb> 137 atoms in block 32
Block first atom: 6769
Blocpdb> 203 atoms in block 33
Block first atom: 6906
Blocpdb> 204 atoms in block 34
Block first atom: 7109
Blocpdb> 322 atoms in block 35
Block first atom: 7313
Blocpdb> 235 atoms in block 36
Block first atom: 7635
Blocpdb> 176 atoms in block 37
Block first atom: 7870
Blocpdb> 202 atoms in block 38
Block first atom: 8046
Blocpdb> 240 atoms in block 39
Block first atom: 8248
Blocpdb> 213 atoms in block 40
Block first atom: 8488
Blocpdb> 224 atoms in block 41
Block first atom: 8701
Blocpdb> 202 atoms in block 42
Block first atom: 8925
Blocpdb> 235 atoms in block 43
Block first atom: 9127
Blocpdb> 188 atoms in block 44
Block first atom: 9362
Blocpdb> 209 atoms in block 45
Block first atom: 9550
Blocpdb> 230 atoms in block 46
Block first atom: 9759
Blocpdb> 207 atoms in block 47
Block first atom: 9989
Blocpdb> 57 atoms in block 48
Block first atom: 10196
Blocpdb> 221 atoms in block 49
Block first atom: 10253
Blocpdb> 191 atoms in block 50
Block first atom: 10474
Blocpdb> 222 atoms in block 51
Block first atom: 10665
Blocpdb> 233 atoms in block 52
Block first atom: 10887
Blocpdb> 238 atoms in block 53
Block first atom: 11120
Blocpdb> 268 atoms in block 54
Block first atom: 11358
Blocpdb> 196 atoms in block 55
Block first atom: 11626
Blocpdb> 266 atoms in block 56
Block first atom: 11822
Blocpdb> 193 atoms in block 57
Block first atom: 12088
Blocpdb> 164 atoms in block 58
Block first atom: 12281
Blocpdb> 234 atoms in block 59
Block first atom: 12445
Blocpdb> 184 atoms in block 60
Block first atom: 12679
Blocpdb> 205 atoms in block 61
Block first atom: 12863
Blocpdb> 198 atoms in block 62
Block first atom: 13068
Blocpdb> 232 atoms in block 63
Block first atom: 13266
Blocpdb> 207 atoms in block 64
Block first atom: 13498
Blocpdb> 196 atoms in block 65
Block first atom: 13705
Blocpdb> 236 atoms in block 66
Block first atom: 13901
Blocpdb> 201 atoms in block 67
Block first atom: 14137
Blocpdb> 228 atoms in block 68
Block first atom: 14338
Blocpdb> 231 atoms in block 69
Block first atom: 14566
Blocpdb> 233 atoms in block 70
Block first atom: 14797
Blocpdb> 239 atoms in block 71
Block first atom: 15030
Blocpdb> 221 atoms in block 72
Block first atom: 15269
Blocpdb> 217 atoms in block 73
Block first atom: 15490
Blocpdb> 227 atoms in block 74
Block first atom: 15707
Blocpdb> 222 atoms in block 75
Block first atom: 15934
Blocpdb> 205 atoms in block 76
Block first atom: 16156
Blocpdb> 220 atoms in block 77
Block first atom: 16361
Blocpdb> 225 atoms in block 78
Block first atom: 16581
Blocpdb> 216 atoms in block 79
Block first atom: 16806
Blocpdb> 94 atoms in block 80
Block first atom: 17022
Blocpdb> 203 atoms in block 81
Block first atom: 17116
Blocpdb> 204 atoms in block 82
Block first atom: 17319
Blocpdb> 322 atoms in block 83
Block first atom: 17523
Blocpdb> 235 atoms in block 84
Block first atom: 17845
Blocpdb> 176 atoms in block 85
Block first atom: 18080
Blocpdb> 202 atoms in block 86
Block first atom: 18256
Blocpdb> 240 atoms in block 87
Block first atom: 18458
Blocpdb> 213 atoms in block 88
Block first atom: 18698
Blocpdb> 224 atoms in block 89
Block first atom: 18911
Blocpdb> 202 atoms in block 90
Block first atom: 19135
Blocpdb> 235 atoms in block 91
Block first atom: 19337
Blocpdb> 188 atoms in block 92
Block first atom: 19572
Blocpdb> 209 atoms in block 93
Block first atom: 19760
Blocpdb> 229 atoms in block 94
Block first atom: 19969
Blocpdb> 207 atoms in block 95
Block first atom: 20198
Blocpdb> 57 atoms in block 96
Block first atom: 20405
Blocpdb> 221 atoms in block 97
Block first atom: 20462
Blocpdb> 191 atoms in block 98
Block first atom: 20683
Blocpdb> 222 atoms in block 99
Block first atom: 20874
Blocpdb> 233 atoms in block 100
Block first atom: 21096
Blocpdb> 238 atoms in block 101
Block first atom: 21329
Blocpdb> 268 atoms in block 102
Block first atom: 21567
Blocpdb> 196 atoms in block 103
Block first atom: 21835
Blocpdb> 266 atoms in block 104
Block first atom: 22031
Blocpdb> 193 atoms in block 105
Block first atom: 22297
Blocpdb> 164 atoms in block 106
Block first atom: 22490
Blocpdb> 234 atoms in block 107
Block first atom: 22654
Blocpdb> 184 atoms in block 108
Block first atom: 22888
Blocpdb> 205 atoms in block 109
Block first atom: 23072
Blocpdb> 198 atoms in block 110
Block first atom: 23277
Blocpdb> 232 atoms in block 111
Block first atom: 23475
Blocpdb> 207 atoms in block 112
Block first atom: 23707
Blocpdb> 196 atoms in block 113
Block first atom: 23914
Blocpdb> 236 atoms in block 114
Block first atom: 24110
Blocpdb> 201 atoms in block 115
Block first atom: 24346
Blocpdb> 228 atoms in block 116
Block first atom: 24547
Blocpdb> 231 atoms in block 117
Block first atom: 24775
Blocpdb> 233 atoms in block 118
Block first atom: 25006
Blocpdb> 239 atoms in block 119
Block first atom: 25239
Blocpdb> 221 atoms in block 120
Block first atom: 25478
Blocpdb> 217 atoms in block 121
Block first atom: 25699
Blocpdb> 227 atoms in block 122
Block first atom: 25916
Blocpdb> 222 atoms in block 123
Block first atom: 26143
Blocpdb> 205 atoms in block 124
Block first atom: 26365
Blocpdb> 220 atoms in block 125
Block first atom: 26570
Blocpdb> 225 atoms in block 126
Block first atom: 26790
Blocpdb> 215 atoms in block 127
Block first atom: 27015
Blocpdb> 137 atoms in block 128
Block first atom: 27230
Blocpdb> 203 atoms in block 129
Block first atom: 27367
Blocpdb> 204 atoms in block 130
Block first atom: 27570
Blocpdb> 322 atoms in block 131
Block first atom: 27774
Blocpdb> 235 atoms in block 132
Block first atom: 28096
Blocpdb> 176 atoms in block 133
Block first atom: 28331
Blocpdb> 202 atoms in block 134
Block first atom: 28507
Blocpdb> 240 atoms in block 135
Block first atom: 28709
Blocpdb> 213 atoms in block 136
Block first atom: 28949
Blocpdb> 224 atoms in block 137
Block first atom: 29162
Blocpdb> 202 atoms in block 138
Block first atom: 29386
Blocpdb> 235 atoms in block 139
Block first atom: 29588
Blocpdb> 188 atoms in block 140
Block first atom: 29823
Blocpdb> 209 atoms in block 141
Block first atom: 30011
Blocpdb> 230 atoms in block 142
Block first atom: 30220
Blocpdb> 207 atoms in block 143
Block first atom: 30450
Blocpdb> 57 atoms in block 144
Block first atom: 30657
Blocpdb> 221 atoms in block 145
Block first atom: 30714
Blocpdb> 191 atoms in block 146
Block first atom: 30935
Blocpdb> 222 atoms in block 147
Block first atom: 31126
Blocpdb> 233 atoms in block 148
Block first atom: 31348
Blocpdb> 238 atoms in block 149
Block first atom: 31581
Blocpdb> 268 atoms in block 150
Block first atom: 31819
Blocpdb> 196 atoms in block 151
Block first atom: 32087
Blocpdb> 266 atoms in block 152
Block first atom: 32283
Blocpdb> 193 atoms in block 153
Block first atom: 32549
Blocpdb> 164 atoms in block 154
Block first atom: 32742
Blocpdb> 234 atoms in block 155
Block first atom: 32906
Blocpdb> 184 atoms in block 156
Block first atom: 33140
Blocpdb> 205 atoms in block 157
Block first atom: 33324
Blocpdb> 198 atoms in block 158
Block first atom: 33529
Blocpdb> 232 atoms in block 159
Block first atom: 33727
Blocpdb> 207 atoms in block 160
Block first atom: 33959
Blocpdb> 196 atoms in block 161
Block first atom: 34166
Blocpdb> 236 atoms in block 162
Block first atom: 34362
Blocpdb> 201 atoms in block 163
Block first atom: 34598
Blocpdb> 228 atoms in block 164
Block first atom: 34799
Blocpdb> 231 atoms in block 165
Block first atom: 35027
Blocpdb> 233 atoms in block 166
Block first atom: 35258
Blocpdb> 239 atoms in block 167
Block first atom: 35491
Blocpdb> 221 atoms in block 168
Block first atom: 35730
Blocpdb> 217 atoms in block 169
Block first atom: 35951
Blocpdb> 227 atoms in block 170
Block first atom: 36168
Blocpdb> 222 atoms in block 171
Block first atom: 36395
Blocpdb> 205 atoms in block 172
Block first atom: 36617
Blocpdb> 220 atoms in block 173
Block first atom: 36822
Blocpdb> 225 atoms in block 174
Block first atom: 37042
Blocpdb> 216 atoms in block 175
Block first atom: 37267
Blocpdb> 94 atoms in block 176
Block first atom: 37483
Blocpdb> 203 atoms in block 177
Block first atom: 37577
Blocpdb> 204 atoms in block 178
Block first atom: 37780
Blocpdb> 322 atoms in block 179
Block first atom: 37984
Blocpdb> 235 atoms in block 180
Block first atom: 38306
Blocpdb> 176 atoms in block 181
Block first atom: 38541
Blocpdb> 202 atoms in block 182
Block first atom: 38717
Blocpdb> 240 atoms in block 183
Block first atom: 38919
Blocpdb> 213 atoms in block 184
Block first atom: 39159
Blocpdb> 224 atoms in block 185
Block first atom: 39372
Blocpdb> 202 atoms in block 186
Block first atom: 39596
Blocpdb> 235 atoms in block 187
Block first atom: 39798
Blocpdb> 188 atoms in block 188
Block first atom: 40033
Blocpdb> 209 atoms in block 189
Block first atom: 40221
Blocpdb> 229 atoms in block 190
Block first atom: 40430
Blocpdb> 207 atoms in block 191
Block first atom: 40659
Blocpdb> 57 atoms in block 192
Block first atom: 40865
Blocpdb> 192 blocks.
Blocpdb> At most, 322 atoms in each of them.
Blocpdb> At least, 57 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: 119525113 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 0m0.212s
user 0m0.204s
sys 0m0.008s
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).
Last modification: April 25th, 2023.
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