*** ***
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 = 2404081256303009666.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 2404081256303009666.atom to be opened.
Openam> File opened: 2404081256303009666.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 = 2798
First residue number = 1
Last residue number = 888
Number of atoms found = 43228
Mean number per residue = 15.4
Pdbmat> Coordinate statistics:
= 31.358720 +/- 70.123446 From: -124.062000 To: 175.258000
= -7.387516 +/- 43.703921 From: -151.925000 To: 82.320000
= 82.321562 +/- 42.468616 From: -15.073000 To: 186.934000
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 -16.4029 % Filled.
Pdbmat> 29672795 non-zero elements.
Pdbmat> 3268723 atom-atom interactions.
Pdbmat> Number per atom= 151.23 +/- 53.29
Maximum number = 318
Minimum number = 19
Pdbmat> Matrix trace = 6.537446E+07
Pdbmat> Larger element = 1117.03
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2798 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 = 2404081256303009666.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 2404081256303009666.atom to be opened.
Openam> file on opening on unit 11:
2404081256303009666.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 43228 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> 2798 residues.
Blocpdb> 237 atoms in block 1
Block first atom: 1
Blocpdb> 226 atoms in block 2
Block first atom: 238
Blocpdb> 192 atoms in block 3
Block first atom: 464
Blocpdb> 203 atoms in block 4
Block first atom: 656
Blocpdb> 217 atoms in block 5
Block first atom: 859
Blocpdb> 229 atoms in block 6
Block first atom: 1076
Blocpdb> 212 atoms in block 7
Block first atom: 1305
Blocpdb> 211 atoms in block 8
Block first atom: 1517
Blocpdb> 215 atoms in block 9
Block first atom: 1728
Blocpdb> 232 atoms in block 10
Block first atom: 1943
Blocpdb> 226 atoms in block 11
Block first atom: 2175
Blocpdb> 211 atoms in block 12
Block first atom: 2401
Blocpdb> 240 atoms in block 13
Block first atom: 2612
Blocpdb> 230 atoms in block 14
Block first atom: 2852
Blocpdb> 233 atoms in block 15
Block first atom: 3082
Blocpdb> 224 atoms in block 16
Block first atom: 3315
Blocpdb> 233 atoms in block 17
Block first atom: 3539
Blocpdb> 231 atoms in block 18
Block first atom: 3772
Blocpdb> 208 atoms in block 19
Block first atom: 4003
Blocpdb> 220 atoms in block 20
Block first atom: 4211
Blocpdb> 197 atoms in block 21
Block first atom: 4431
Blocpdb> 213 atoms in block 22
Block first atom: 4628
Blocpdb> 223 atoms in block 23
Block first atom: 4841
Blocpdb> 200 atoms in block 24
Block first atom: 5064
Blocpdb> 199 atoms in block 25
Block first atom: 5264
Blocpdb> 214 atoms in block 26
Block first atom: 5463
Blocpdb> 218 atoms in block 27
Block first atom: 5677
Blocpdb> 216 atoms in block 28
Block first atom: 5895
Blocpdb> 187 atoms in block 29
Block first atom: 6111
Blocpdb> 221 atoms in block 30
Block first atom: 6298
Blocpdb> 226 atoms in block 31
Block first atom: 6519
Blocpdb> 207 atoms in block 32
Block first atom: 6745
Blocpdb> 216 atoms in block 33
Block first atom: 6952
Blocpdb> 221 atoms in block 34
Block first atom: 7168
Blocpdb> 203 atoms in block 35
Block first atom: 7389
Blocpdb> 242 atoms in block 36
Block first atom: 7592
Blocpdb> 185 atoms in block 37
Block first atom: 7834
Blocpdb> 218 atoms in block 38
Block first atom: 8019
Blocpdb> 222 atoms in block 39
Block first atom: 8237
Blocpdb> 209 atoms in block 40
Block first atom: 8459
Blocpdb> 194 atoms in block 41
Block first atom: 8668
Blocpdb> 238 atoms in block 42
Block first atom: 8862
Blocpdb> 200 atoms in block 43
Block first atom: 9100
Blocpdb> 205 atoms in block 44
Block first atom: 9300
Blocpdb> 215 atoms in block 45
Block first atom: 9505
Blocpdb> 191 atoms in block 46
Block first atom: 9720
Blocpdb> 191 atoms in block 47
Block first atom: 9911
Blocpdb> 213 atoms in block 48
Block first atom: 10102
Blocpdb> 227 atoms in block 49
Block first atom: 10315
Blocpdb> 214 atoms in block 50
Block first atom: 10542
Blocpdb> 224 atoms in block 51
Block first atom: 10756
Blocpdb> 204 atoms in block 52
Block first atom: 10980
Blocpdb> 224 atoms in block 53
Block first atom: 11184
Blocpdb> 204 atoms in block 54
Block first atom: 11408
Blocpdb> 250 atoms in block 55
Block first atom: 11612
Blocpdb> 226 atoms in block 56
Block first atom: 11862
Blocpdb> 201 atoms in block 57
Block first atom: 12088
Blocpdb> 181 atoms in block 58
Block first atom: 12289
Blocpdb> 228 atoms in block 59
Block first atom: 12470
Blocpdb> 220 atoms in block 60
Block first atom: 12698
Blocpdb> 227 atoms in block 61
Block first atom: 12918
Blocpdb> 203 atoms in block 62
Block first atom: 13145
Blocpdb> 217 atoms in block 63
Block first atom: 13348
Blocpdb> 216 atoms in block 64
Block first atom: 13565
Blocpdb> 224 atoms in block 65
Block first atom: 13781
Blocpdb> 202 atoms in block 66
Block first atom: 14005
Blocpdb> 164 atoms in block 67
Block first atom: 14207
Blocpdb> 211 atoms in block 68
Block first atom: 14371
Blocpdb> 224 atoms in block 69
Block first atom: 14582
Blocpdb> 223 atoms in block 70
Block first atom: 14806
Blocpdb> 208 atoms in block 71
Block first atom: 15029
Blocpdb> 215 atoms in block 72
Block first atom: 15237
Blocpdb> 217 atoms in block 73
Block first atom: 15452
Blocpdb> 216 atoms in block 74
Block first atom: 15669
Blocpdb> 241 atoms in block 75
Block first atom: 15885
Blocpdb> 232 atoms in block 76
Block first atom: 16126
Blocpdb> 220 atoms in block 77
Block first atom: 16358
Blocpdb> 206 atoms in block 78
Block first atom: 16578
Blocpdb> 220 atoms in block 79
Block first atom: 16784
Blocpdb> 215 atoms in block 80
Block first atom: 17004
Blocpdb> 171 atoms in block 81
Block first atom: 17219
Blocpdb> 208 atoms in block 82
Block first atom: 17390
Blocpdb> 227 atoms in block 83
Block first atom: 17598
Blocpdb> 188 atoms in block 84
Block first atom: 17825
Blocpdb> 186 atoms in block 85
Block first atom: 18013
Blocpdb> 224 atoms in block 86
Block first atom: 18199
Blocpdb> 198 atoms in block 87
Block first atom: 18423
Blocpdb> 231 atoms in block 88
Block first atom: 18621
Blocpdb> 208 atoms in block 89
Block first atom: 18852
Blocpdb> 215 atoms in block 90
Block first atom: 19060
Blocpdb> 227 atoms in block 91
Block first atom: 19275
Blocpdb> 211 atoms in block 92
Block first atom: 19502
Blocpdb> 226 atoms in block 93
Block first atom: 19713
Blocpdb> 229 atoms in block 94
Block first atom: 19939
Blocpdb> 219 atoms in block 95
Block first atom: 20168
Blocpdb> 216 atoms in block 96
Block first atom: 20387
Blocpdb> 207 atoms in block 97
Block first atom: 20603
Blocpdb> 213 atoms in block 98
Block first atom: 20810
Blocpdb> 209 atoms in block 99
Block first atom: 21023
Blocpdb> 241 atoms in block 100
Block first atom: 21232
Blocpdb> 200 atoms in block 101
Block first atom: 21473
Blocpdb> 244 atoms in block 102
Block first atom: 21673
Blocpdb> 206 atoms in block 103
Block first atom: 21917
Blocpdb> 207 atoms in block 104
Block first atom: 22123
Blocpdb> 245 atoms in block 105
Block first atom: 22330
Blocpdb> 236 atoms in block 106
Block first atom: 22575
Blocpdb> 190 atoms in block 107
Block first atom: 22811
Blocpdb> 219 atoms in block 108
Block first atom: 23001
Blocpdb> 218 atoms in block 109
Block first atom: 23220
Blocpdb> 208 atoms in block 110
Block first atom: 23438
Blocpdb> 197 atoms in block 111
Block first atom: 23646
Blocpdb> 209 atoms in block 112
Block first atom: 23843
Blocpdb> 209 atoms in block 113
Block first atom: 24052
Blocpdb> 225 atoms in block 114
Block first atom: 24261
Blocpdb> 228 atoms in block 115
Block first atom: 24486
Blocpdb> 213 atoms in block 116
Block first atom: 24714
Blocpdb> 240 atoms in block 117
Block first atom: 24927
Blocpdb> 226 atoms in block 118
Block first atom: 25167
Blocpdb> 202 atoms in block 119
Block first atom: 25393
Blocpdb> 244 atoms in block 120
Block first atom: 25595
Blocpdb> 220 atoms in block 121
Block first atom: 25839
Blocpdb> 207 atoms in block 122
Block first atom: 26059
Blocpdb> 229 atoms in block 123
Block first atom: 26266
Blocpdb> 237 atoms in block 124
Block first atom: 26495
Blocpdb> 216 atoms in block 125
Block first atom: 26732
Blocpdb> 201 atoms in block 126
Block first atom: 26948
Blocpdb> 200 atoms in block 127
Block first atom: 27149
Blocpdb> 196 atoms in block 128
Block first atom: 27349
Blocpdb> 248 atoms in block 129
Block first atom: 27545
Blocpdb> 232 atoms in block 130
Block first atom: 27793
Blocpdb> 206 atoms in block 131
Block first atom: 28025
Blocpdb> 196 atoms in block 132
Block first atom: 28231
Blocpdb> 197 atoms in block 133
Block first atom: 28427
Blocpdb> 200 atoms in block 134
Block first atom: 28624
Blocpdb> 195 atoms in block 135
Block first atom: 28824
Blocpdb> 185 atoms in block 136
Block first atom: 29019
Blocpdb> 173 atoms in block 137
Block first atom: 29204
Blocpdb> 244 atoms in block 138
Block first atom: 29377
Blocpdb> 208 atoms in block 139
Block first atom: 29621
Blocpdb> 237 atoms in block 140
Block first atom: 29829
Blocpdb> 205 atoms in block 141
Block first atom: 30066
Blocpdb> 233 atoms in block 142
Block first atom: 30271
Blocpdb> 211 atoms in block 143
Block first atom: 30504
Blocpdb> 189 atoms in block 144
Block first atom: 30715
Blocpdb> 216 atoms in block 145
Block first atom: 30904
Blocpdb> 228 atoms in block 146
Block first atom: 31120
Blocpdb> 240 atoms in block 147
Block first atom: 31348
Blocpdb> 211 atoms in block 148
Block first atom: 31588
Blocpdb> 235 atoms in block 149
Block first atom: 31799
Blocpdb> 237 atoms in block 150
Block first atom: 32034
Blocpdb> 210 atoms in block 151
Block first atom: 32271
Blocpdb> 215 atoms in block 152
Block first atom: 32481
Blocpdb> 219 atoms in block 153
Block first atom: 32696
Blocpdb> 228 atoms in block 154
Block first atom: 32915
Blocpdb> 176 atoms in block 155
Block first atom: 33143
Blocpdb> 174 atoms in block 156
Block first atom: 33319
Blocpdb> 227 atoms in block 157
Block first atom: 33493
Blocpdb> 245 atoms in block 158
Block first atom: 33720
Blocpdb> 186 atoms in block 159
Block first atom: 33965
Blocpdb> 222 atoms in block 160
Block first atom: 34151
Blocpdb> 222 atoms in block 161
Block first atom: 34373
Blocpdb> 208 atoms in block 162
Block first atom: 34595
Blocpdb> 262 atoms in block 163
Block first atom: 34803
Blocpdb> 223 atoms in block 164
Block first atom: 35065
Blocpdb> 221 atoms in block 165
Block first atom: 35288
Blocpdb> 234 atoms in block 166
Block first atom: 35509
Blocpdb> 212 atoms in block 167
Block first atom: 35743
Blocpdb> 220 atoms in block 168
Block first atom: 35955
Blocpdb> 203 atoms in block 169
Block first atom: 36175
Blocpdb> 203 atoms in block 170
Block first atom: 36378
Blocpdb> 246 atoms in block 171
Block first atom: 36581
Blocpdb> 214 atoms in block 172
Block first atom: 36827
Blocpdb> 212 atoms in block 173
Block first atom: 37041
Blocpdb> 221 atoms in block 174
Block first atom: 37253
Blocpdb> 197 atoms in block 175
Block first atom: 37474
Blocpdb> 228 atoms in block 176
Block first atom: 37671
Blocpdb> 224 atoms in block 177
Block first atom: 37899
Blocpdb> 226 atoms in block 178
Block first atom: 38123
Blocpdb> 186 atoms in block 179
Block first atom: 38349
Blocpdb> 220 atoms in block 180
Block first atom: 38535
Blocpdb> 246 atoms in block 181
Block first atom: 38755
Blocpdb> 206 atoms in block 182
Block first atom: 39001
Blocpdb> 215 atoms in block 183
Block first atom: 39207
Blocpdb> 209 atoms in block 184
Block first atom: 39422
Blocpdb> 215 atoms in block 185
Block first atom: 39631
Blocpdb> 227 atoms in block 186
Block first atom: 39846
Blocpdb> 214 atoms in block 187
Block first atom: 40073
Blocpdb> 221 atoms in block 188
Block first atom: 40287
Blocpdb> 201 atoms in block 189
Block first atom: 40508
Blocpdb> 217 atoms in block 190
Block first atom: 40709
Blocpdb> 205 atoms in block 191
Block first atom: 40926
Blocpdb> 239 atoms in block 192
Block first atom: 41131
Blocpdb> 223 atoms in block 193
Block first atom: 41370
Blocpdb> 183 atoms in block 194
Block first atom: 41593
Blocpdb> 214 atoms in block 195
Block first atom: 41776
Blocpdb> 222 atoms in block 196
Block first atom: 41990
Blocpdb> 198 atoms in block 197
Block first atom: 42212
Blocpdb> 263 atoms in block 198
Block first atom: 42410
Blocpdb> 234 atoms in block 199
Block first atom: 42673
Blocpdb> 231 atoms in block 200
Block first atom: 42907
Blocpdb> 91 atoms in block 201
Block first atom: 43137
Blocpdb> 201 blocks.
Blocpdb> At most, 263 atoms in each of them.
Blocpdb> At least, 91 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: 102943198 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 0m0.188s
user 0m0.172s
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).
Last modification: April 25th, 2023.
|
