*** 5a0u ***
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 = 250201203548774964.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 250201203548774964.atom to be opened.
Openam> File opened: 250201203548774964.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 = 6345
First residue number = 337
Last residue number = 1128
Number of atoms found = 50095
Mean number per residue = 7.9
Pdbmat> Coordinate statistics:
= -23.637665 +/- 19.409043 From: -79.348000 To: 31.166000
= 11.117574 +/- 31.634110 From: -74.643000 To: 70.393000
= -141.001304 +/- 77.920552 From: -300.362000 To: 17.059000
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 3.7595 % Filled.
Pdbmat> 20882237 non-zero elements.
Pdbmat> 2287203 atom-atom interactions.
Pdbmat> Number per atom= 91.31 +/- 20.73
Maximum number = 133
Minimum number = 14
Pdbmat> Matrix trace = 4.574406E+07
Pdbmat> Larger element = 519.251
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
6345 non-zero elements, NRBL set to 32
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 = 250201203548774964.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 32
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 250201203548774964.atom to be opened.
Openam> file on opening on unit 11:
250201203548774964.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 50095 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 32 residue(s) per block.
Blocpdb> 6345 residues.
Blocpdb> 266 atoms in block 1
Block first atom: 1
Blocpdb> 243 atoms in block 2
Block first atom: 267
Blocpdb> 254 atoms in block 3
Block first atom: 510
Blocpdb> 266 atoms in block 4
Block first atom: 764
Blocpdb> 251 atoms in block 5
Block first atom: 1030
Blocpdb> 230 atoms in block 6
Block first atom: 1281
Blocpdb> 263 atoms in block 7
Block first atom: 1511
Blocpdb> 246 atoms in block 8
Block first atom: 1774
Blocpdb> 255 atoms in block 9
Block first atom: 2020
Blocpdb> 264 atoms in block 10
Block first atom: 2275
Blocpdb> 251 atoms in block 11
Block first atom: 2539
Blocpdb> 249 atoms in block 12
Block first atom: 2790
Blocpdb> 252 atoms in block 13
Block first atom: 3039
Blocpdb> 267 atoms in block 14
Block first atom: 3291
Blocpdb> 256 atoms in block 15
Block first atom: 3558
Blocpdb> 254 atoms in block 16
Block first atom: 3814
Blocpdb> 230 atoms in block 17
Block first atom: 4068
Blocpdb> 242 atoms in block 18
Block first atom: 4298
Blocpdb> 262 atoms in block 19
Block first atom: 4540
Blocpdb> 275 atoms in block 20
Block first atom: 4802
Blocpdb> 233 atoms in block 21
Block first atom: 5077
Blocpdb> 230 atoms in block 22
Block first atom: 5310
Blocpdb> 246 atoms in block 23
Block first atom: 5540
Blocpdb> 270 atoms in block 24
Block first atom: 5786
Blocpdb> 199 atoms in block 25
Block first atom: 6056
Blocpdb> 264 atoms in block 26
Block first atom: 6255
Blocpdb> 244 atoms in block 27
Block first atom: 6519
Blocpdb> 254 atoms in block 28
Block first atom: 6763
Blocpdb> 266 atoms in block 29
Block first atom: 7017
Blocpdb> 255 atoms in block 30
Block first atom: 7283
Blocpdb> 226 atoms in block 31
Block first atom: 7538
Blocpdb> 261 atoms in block 32
Block first atom: 7764
Blocpdb> 249 atoms in block 33
Block first atom: 8025
Blocpdb> 254 atoms in block 34
Block first atom: 8274
Blocpdb> 266 atoms in block 35
Block first atom: 8528
Blocpdb> 251 atoms in block 36
Block first atom: 8794
Blocpdb> 247 atoms in block 37
Block first atom: 9045
Blocpdb> 252 atoms in block 38
Block first atom: 9292
Blocpdb> 268 atoms in block 39
Block first atom: 9544
Blocpdb> 259 atoms in block 40
Block first atom: 9812
Blocpdb> 250 atoms in block 41
Block first atom: 10071
Blocpdb> 234 atoms in block 42
Block first atom: 10321
Blocpdb> 237 atoms in block 43
Block first atom: 10555
Blocpdb> 267 atoms in block 44
Block first atom: 10792
Blocpdb> 273 atoms in block 45
Block first atom: 11059
Blocpdb> 235 atoms in block 46
Block first atom: 11332
Blocpdb> 227 atoms in block 47
Block first atom: 11567
Blocpdb> 249 atoms in block 48
Block first atom: 11794
Blocpdb> 262 atoms in block 49
Block first atom: 12043
Blocpdb> 211 atoms in block 50
Block first atom: 12305
Blocpdb> 264 atoms in block 51
Block first atom: 12516
Blocpdb> 244 atoms in block 52
Block first atom: 12780
Blocpdb> 254 atoms in block 53
Block first atom: 13024
Blocpdb> 266 atoms in block 54
Block first atom: 13278
Blocpdb> 255 atoms in block 55
Block first atom: 13544
Blocpdb> 226 atoms in block 56
Block first atom: 13799
Blocpdb> 261 atoms in block 57
Block first atom: 14025
Blocpdb> 249 atoms in block 58
Block first atom: 14286
Blocpdb> 254 atoms in block 59
Block first atom: 14535
Blocpdb> 266 atoms in block 60
Block first atom: 14789
Blocpdb> 251 atoms in block 61
Block first atom: 15055
Blocpdb> 247 atoms in block 62
Block first atom: 15306
Blocpdb> 252 atoms in block 63
Block first atom: 15553
Blocpdb> 268 atoms in block 64
Block first atom: 15805
Blocpdb> 259 atoms in block 65
Block first atom: 16073
Blocpdb> 250 atoms in block 66
Block first atom: 16332
Blocpdb> 234 atoms in block 67
Block first atom: 16582
Blocpdb> 237 atoms in block 68
Block first atom: 16816
Blocpdb> 267 atoms in block 69
Block first atom: 17053
Blocpdb> 273 atoms in block 70
Block first atom: 17320
Blocpdb> 235 atoms in block 71
Block first atom: 17593
Blocpdb> 227 atoms in block 72
Block first atom: 17828
Blocpdb> 249 atoms in block 73
Block first atom: 18055
Blocpdb> 262 atoms in block 74
Block first atom: 18304
Blocpdb> 211 atoms in block 75
Block first atom: 18566
Blocpdb> 264 atoms in block 76
Block first atom: 18777
Blocpdb> 244 atoms in block 77
Block first atom: 19041
Blocpdb> 254 atoms in block 78
Block first atom: 19285
Blocpdb> 266 atoms in block 79
Block first atom: 19539
Blocpdb> 255 atoms in block 80
Block first atom: 19805
Blocpdb> 226 atoms in block 81
Block first atom: 20060
Blocpdb> 261 atoms in block 82
Block first atom: 20286
Blocpdb> 249 atoms in block 83
Block first atom: 20547
Blocpdb> 254 atoms in block 84
Block first atom: 20796
Blocpdb> 266 atoms in block 85
Block first atom: 21050
Blocpdb> 251 atoms in block 86
Block first atom: 21316
Blocpdb> 247 atoms in block 87
Block first atom: 21567
Blocpdb> 252 atoms in block 88
Block first atom: 21814
Blocpdb> 268 atoms in block 89
Block first atom: 22066
Blocpdb> 259 atoms in block 90
Block first atom: 22334
Blocpdb> 250 atoms in block 91
Block first atom: 22593
Blocpdb> 234 atoms in block 92
Block first atom: 22843
Blocpdb> 237 atoms in block 93
Block first atom: 23077
Blocpdb> 267 atoms in block 94
Block first atom: 23314
Blocpdb> 273 atoms in block 95
Block first atom: 23581
Blocpdb> 235 atoms in block 96
Block first atom: 23854
Blocpdb> 227 atoms in block 97
Block first atom: 24089
Blocpdb> 249 atoms in block 98
Block first atom: 24316
Blocpdb> 262 atoms in block 99
Block first atom: 24565
Blocpdb> 211 atoms in block 100
Block first atom: 24827
Blocpdb> 264 atoms in block 101
Block first atom: 25038
Blocpdb> 244 atoms in block 102
Block first atom: 25302
Blocpdb> 254 atoms in block 103
Block first atom: 25546
Blocpdb> 266 atoms in block 104
Block first atom: 25800
Blocpdb> 255 atoms in block 105
Block first atom: 26066
Blocpdb> 226 atoms in block 106
Block first atom: 26321
Blocpdb> 261 atoms in block 107
Block first atom: 26547
Blocpdb> 249 atoms in block 108
Block first atom: 26808
Blocpdb> 254 atoms in block 109
Block first atom: 27057
Blocpdb> 266 atoms in block 110
Block first atom: 27311
Blocpdb> 251 atoms in block 111
Block first atom: 27577
Blocpdb> 247 atoms in block 112
Block first atom: 27828
Blocpdb> 252 atoms in block 113
Block first atom: 28075
Blocpdb> 268 atoms in block 114
Block first atom: 28327
Blocpdb> 259 atoms in block 115
Block first atom: 28595
Blocpdb> 250 atoms in block 116
Block first atom: 28854
Blocpdb> 234 atoms in block 117
Block first atom: 29104
Blocpdb> 237 atoms in block 118
Block first atom: 29338
Blocpdb> 267 atoms in block 119
Block first atom: 29575
Blocpdb> 273 atoms in block 120
Block first atom: 29842
Blocpdb> 235 atoms in block 121
Block first atom: 30115
Blocpdb> 227 atoms in block 122
Block first atom: 30350
Blocpdb> 249 atoms in block 123
Block first atom: 30577
Blocpdb> 262 atoms in block 124
Block first atom: 30826
Blocpdb> 211 atoms in block 125
Block first atom: 31088
Blocpdb> 264 atoms in block 126
Block first atom: 31299
Blocpdb> 244 atoms in block 127
Block first atom: 31563
Blocpdb> 254 atoms in block 128
Block first atom: 31807
Blocpdb> 266 atoms in block 129
Block first atom: 32061
Blocpdb> 255 atoms in block 130
Block first atom: 32327
Blocpdb> 226 atoms in block 131
Block first atom: 32582
Blocpdb> 261 atoms in block 132
Block first atom: 32808
Blocpdb> 249 atoms in block 133
Block first atom: 33069
Blocpdb> 254 atoms in block 134
Block first atom: 33318
Blocpdb> 266 atoms in block 135
Block first atom: 33572
Blocpdb> 251 atoms in block 136
Block first atom: 33838
Blocpdb> 247 atoms in block 137
Block first atom: 34089
Blocpdb> 252 atoms in block 138
Block first atom: 34336
Blocpdb> 268 atoms in block 139
Block first atom: 34588
Blocpdb> 259 atoms in block 140
Block first atom: 34856
Blocpdb> 250 atoms in block 141
Block first atom: 35115
Blocpdb> 234 atoms in block 142
Block first atom: 35365
Blocpdb> 237 atoms in block 143
Block first atom: 35599
Blocpdb> 267 atoms in block 144
Block first atom: 35836
Blocpdb> 273 atoms in block 145
Block first atom: 36103
Blocpdb> 235 atoms in block 146
Block first atom: 36376
Blocpdb> 227 atoms in block 147
Block first atom: 36611
Blocpdb> 249 atoms in block 148
Block first atom: 36838
Blocpdb> 262 atoms in block 149
Block first atom: 37087
Blocpdb> 211 atoms in block 150
Block first atom: 37349
Blocpdb> 264 atoms in block 151
Block first atom: 37560
Blocpdb> 244 atoms in block 152
Block first atom: 37824
Blocpdb> 254 atoms in block 153
Block first atom: 38068
Blocpdb> 266 atoms in block 154
Block first atom: 38322
Blocpdb> 255 atoms in block 155
Block first atom: 38588
Blocpdb> 226 atoms in block 156
Block first atom: 38843
Blocpdb> 261 atoms in block 157
Block first atom: 39069
Blocpdb> 249 atoms in block 158
Block first atom: 39330
Blocpdb> 254 atoms in block 159
Block first atom: 39579
Blocpdb> 266 atoms in block 160
Block first atom: 39833
Blocpdb> 251 atoms in block 161
Block first atom: 40099
Blocpdb> 247 atoms in block 162
Block first atom: 40350
Blocpdb> 252 atoms in block 163
Block first atom: 40597
Blocpdb> 268 atoms in block 164
Block first atom: 40849
Blocpdb> 259 atoms in block 165
Block first atom: 41117
Blocpdb> 250 atoms in block 166
Block first atom: 41376
Blocpdb> 234 atoms in block 167
Block first atom: 41626
Blocpdb> 237 atoms in block 168
Block first atom: 41860
Blocpdb> 267 atoms in block 169
Block first atom: 42097
Blocpdb> 273 atoms in block 170
Block first atom: 42364
Blocpdb> 235 atoms in block 171
Block first atom: 42637
Blocpdb> 227 atoms in block 172
Block first atom: 42872
Blocpdb> 249 atoms in block 173
Block first atom: 43099
Blocpdb> 262 atoms in block 174
Block first atom: 43348
Blocpdb> 211 atoms in block 175
Block first atom: 43610
Blocpdb> 260 atoms in block 176
Block first atom: 43821
Blocpdb> 245 atoms in block 177
Block first atom: 44081
Blocpdb> 256 atoms in block 178
Block first atom: 44326
Blocpdb> 267 atoms in block 179
Block first atom: 44582
Blocpdb> 257 atoms in block 180
Block first atom: 44849
Blocpdb> 224 atoms in block 181
Block first atom: 45106
Blocpdb> 265 atoms in block 182
Block first atom: 45330
Blocpdb> 244 atoms in block 183
Block first atom: 45595
Blocpdb> 251 atoms in block 184
Block first atom: 45839
Blocpdb> 267 atoms in block 185
Block first atom: 46090
Blocpdb> 248 atoms in block 186
Block first atom: 46357
Blocpdb> 249 atoms in block 187
Block first atom: 46605
Blocpdb> 253 atoms in block 188
Block first atom: 46854
Blocpdb> 262 atoms in block 189
Block first atom: 47107
Blocpdb> 267 atoms in block 190
Block first atom: 47369
Blocpdb> 251 atoms in block 191
Block first atom: 47636
Blocpdb> 239 atoms in block 192
Block first atom: 47887
Blocpdb> 228 atoms in block 193
Block first atom: 48126
Blocpdb> 264 atoms in block 194
Block first atom: 48354
Blocpdb> 279 atoms in block 195
Block first atom: 48618
Blocpdb> 236 atoms in block 196
Block first atom: 48897
Blocpdb> 229 atoms in block 197
Block first atom: 49133
Blocpdb> 249 atoms in block 198
Block first atom: 49362
Blocpdb> 265 atoms in block 199
Block first atom: 49611
Blocpdb> 220 atoms in block 200
Block first atom: 49875
Blocpdb> 200 blocks.
Blocpdb> At most, 279 atoms in each of them.
Blocpdb> At least, 199 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: 126489115 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 0m0.261s
user 0m0.249s
sys 0m0.012s
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 8th, 2025.
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