*** ***
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 = 22112810583194754.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 22112810583194754.atom to be opened.
Openam> File opened: 22112810583194754.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 = 3146
First residue number = 149
Last residue number = 38
Number of atoms found = 29558
Mean number per residue = 9.4
Pdbmat> Coordinate statistics:
= 74.280500 +/- 61.958168 From: -46.153000 To: 194.714000
= 49.505141 +/- 20.788101 From: 3.561000 To: 101.539000
= 89.434500 +/- 38.391757 From: 0.881000 To: 177.988000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'DG ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 290 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is -3.0345 % Filled.
Pdbmat> 11027058 non-zero elements.
Pdbmat> 1205725 atom-atom interactions.
Pdbmat> Number per atom= 81.58 +/- 21.26
Maximum number = 127
Minimum number = 11
Pdbmat> Matrix trace = 2.411450E+07
Pdbmat> Larger element = 520.033
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3146 non-zero elements, NRBL set to 16
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 = 22112810583194754.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 16
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 22112810583194754.atom to be opened.
Openam> file on opening on unit 11:
22112810583194754.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 29558 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 16 residue(s) per block.
Blocpdb> 3146 residues.
Blocpdb> 139 atoms in block 1
Block first atom: 1
Blocpdb> 126 atoms in block 2
Block first atom: 140
Blocpdb> 137 atoms in block 3
Block first atom: 266
Blocpdb> 130 atoms in block 4
Block first atom: 403
Blocpdb> 140 atoms in block 5
Block first atom: 533
Blocpdb> 141 atoms in block 6
Block first atom: 673
Blocpdb> 117 atoms in block 7
Block first atom: 814
Blocpdb> 139 atoms in block 8
Block first atom: 931
Blocpdb> 121 atoms in block 9
Block first atom: 1070
Blocpdb> 124 atoms in block 10
Block first atom: 1191
Blocpdb> 123 atoms in block 11
Block first atom: 1315
Blocpdb> 123 atoms in block 12
Block first atom: 1438
Blocpdb> 134 atoms in block 13
Block first atom: 1561
Blocpdb> 137 atoms in block 14
Block first atom: 1695
Blocpdb> 124 atoms in block 15
Block first atom: 1832
Blocpdb> 127 atoms in block 16
Block first atom: 1956
Blocpdb> 134 atoms in block 17
Block first atom: 2083
Blocpdb> 141 atoms in block 18
Block first atom: 2217
Blocpdb> 133 atoms in block 19
Block first atom: 2358
Blocpdb> 140 atoms in block 20
Block first atom: 2491
Blocpdb> 141 atoms in block 21
Block first atom: 2631
Blocpdb> 136 atoms in block 22
Block first atom: 2772
Blocpdb> 45 atoms in block 23
Block first atom: 2908
Blocpdb> 139 atoms in block 24
Block first atom: 2953
Blocpdb> 126 atoms in block 25
Block first atom: 3092
Blocpdb> 137 atoms in block 26
Block first atom: 3218
Blocpdb> 130 atoms in block 27
Block first atom: 3355
Blocpdb> 140 atoms in block 28
Block first atom: 3485
Blocpdb> 141 atoms in block 29
Block first atom: 3625
Blocpdb> 117 atoms in block 30
Block first atom: 3766
Blocpdb> 139 atoms in block 31
Block first atom: 3883
Blocpdb> 121 atoms in block 32
Block first atom: 4022
Blocpdb> 124 atoms in block 33
Block first atom: 4143
Blocpdb> 123 atoms in block 34
Block first atom: 4267
Blocpdb> 123 atoms in block 35
Block first atom: 4390
Blocpdb> 134 atoms in block 36
Block first atom: 4513
Blocpdb> 137 atoms in block 37
Block first atom: 4647
Blocpdb> 124 atoms in block 38
Block first atom: 4784
Blocpdb> 127 atoms in block 39
Block first atom: 4908
Blocpdb> 134 atoms in block 40
Block first atom: 5035
Blocpdb> 141 atoms in block 41
Block first atom: 5169
Blocpdb> 133 atoms in block 42
Block first atom: 5310
Blocpdb> 140 atoms in block 43
Block first atom: 5443
Blocpdb> 141 atoms in block 44
Block first atom: 5583
Blocpdb> 136 atoms in block 45
Block first atom: 5724
Blocpdb> 45 atoms in block 46
Block first atom: 5860
Blocpdb> 139 atoms in block 47
Block first atom: 5905
Blocpdb> 126 atoms in block 48
Block first atom: 6044
Blocpdb> 137 atoms in block 49
Block first atom: 6170
Blocpdb> 130 atoms in block 50
Block first atom: 6307
Blocpdb> 140 atoms in block 51
Block first atom: 6437
Blocpdb> 141 atoms in block 52
Block first atom: 6577
Blocpdb> 117 atoms in block 53
Block first atom: 6718
Blocpdb> 139 atoms in block 54
Block first atom: 6835
Blocpdb> 121 atoms in block 55
Block first atom: 6974
Blocpdb> 124 atoms in block 56
Block first atom: 7095
Blocpdb> 123 atoms in block 57
Block first atom: 7219
Blocpdb> 123 atoms in block 58
Block first atom: 7342
Blocpdb> 134 atoms in block 59
Block first atom: 7465
Blocpdb> 137 atoms in block 60
Block first atom: 7599
Blocpdb> 124 atoms in block 61
Block first atom: 7736
Blocpdb> 127 atoms in block 62
Block first atom: 7860
Blocpdb> 134 atoms in block 63
Block first atom: 7987
Blocpdb> 141 atoms in block 64
Block first atom: 8121
Blocpdb> 133 atoms in block 65
Block first atom: 8262
Blocpdb> 140 atoms in block 66
Block first atom: 8395
Blocpdb> 141 atoms in block 67
Block first atom: 8535
Blocpdb> 136 atoms in block 68
Block first atom: 8676
Blocpdb> 45 atoms in block 69
Block first atom: 8812
Blocpdb> 139 atoms in block 70
Block first atom: 8857
Blocpdb> 126 atoms in block 71
Block first atom: 8996
Blocpdb> 137 atoms in block 72
Block first atom: 9122
Blocpdb> 130 atoms in block 73
Block first atom: 9259
Blocpdb> 140 atoms in block 74
Block first atom: 9389
Blocpdb> 141 atoms in block 75
Block first atom: 9529
Blocpdb> 117 atoms in block 76
Block first atom: 9670
Blocpdb> 139 atoms in block 77
Block first atom: 9787
Blocpdb> 121 atoms in block 78
Block first atom: 9926
Blocpdb> 124 atoms in block 79
Block first atom: 10047
Blocpdb> 123 atoms in block 80
Block first atom: 10171
Blocpdb> 123 atoms in block 81
Block first atom: 10294
Blocpdb> 134 atoms in block 82
Block first atom: 10417
Blocpdb> 137 atoms in block 83
Block first atom: 10551
Blocpdb> 124 atoms in block 84
Block first atom: 10688
Blocpdb> 127 atoms in block 85
Block first atom: 10812
Blocpdb> 134 atoms in block 86
Block first atom: 10939
Blocpdb> 141 atoms in block 87
Block first atom: 11073
Blocpdb> 133 atoms in block 88
Block first atom: 11214
Blocpdb> 140 atoms in block 89
Block first atom: 11347
Blocpdb> 141 atoms in block 90
Block first atom: 11487
Blocpdb> 136 atoms in block 91
Block first atom: 11628
Blocpdb> 45 atoms in block 92
Block first atom: 11764
Blocpdb> 327 atoms in block 93
Block first atom: 11809
Blocpdb> 328 atoms in block 94
Block first atom: 12136
Blocpdb> 102 atoms in block 95
Block first atom: 12464
Blocpdb> 329 atoms in block 96
Block first atom: 12566
Blocpdb> 327 atoms in block 97
Block first atom: 12895
Blocpdb> 82 atoms in block 98
Block first atom: 13222
Blocpdb> 327 atoms in block 99
Block first atom: 13304
Blocpdb> 328 atoms in block 100
Block first atom: 13631
Blocpdb> 83 atoms in block 101
Block first atom: 13959
Blocpdb> 329 atoms in block 102
Block first atom: 14042
Blocpdb> 327 atoms in block 103
Block first atom: 14371
Blocpdb> 82 atoms in block 104
Block first atom: 14698
Blocpdb> 139 atoms in block 105
Block first atom: 14780
Blocpdb> 126 atoms in block 106
Block first atom: 14919
Blocpdb> 137 atoms in block 107
Block first atom: 15045
Blocpdb> 130 atoms in block 108
Block first atom: 15182
Blocpdb> 140 atoms in block 109
Block first atom: 15312
Blocpdb> 141 atoms in block 110
Block first atom: 15452
Blocpdb> 117 atoms in block 111
Block first atom: 15593
Blocpdb> 139 atoms in block 112
Block first atom: 15710
Blocpdb> 121 atoms in block 113
Block first atom: 15849
Blocpdb> 124 atoms in block 114
Block first atom: 15970
Blocpdb> 123 atoms in block 115
Block first atom: 16094
Blocpdb> 123 atoms in block 116
Block first atom: 16217
Blocpdb> 134 atoms in block 117
Block first atom: 16340
Blocpdb> 137 atoms in block 118
Block first atom: 16474
Blocpdb> 124 atoms in block 119
Block first atom: 16611
Blocpdb> 127 atoms in block 120
Block first atom: 16735
Blocpdb> 134 atoms in block 121
Block first atom: 16862
Blocpdb> 141 atoms in block 122
Block first atom: 16996
Blocpdb> 133 atoms in block 123
Block first atom: 17137
Blocpdb> 140 atoms in block 124
Block first atom: 17270
Blocpdb> 141 atoms in block 125
Block first atom: 17410
Blocpdb> 136 atoms in block 126
Block first atom: 17551
Blocpdb> 45 atoms in block 127
Block first atom: 17687
Blocpdb> 139 atoms in block 128
Block first atom: 17732
Blocpdb> 126 atoms in block 129
Block first atom: 17871
Blocpdb> 137 atoms in block 130
Block first atom: 17997
Blocpdb> 130 atoms in block 131
Block first atom: 18134
Blocpdb> 140 atoms in block 132
Block first atom: 18264
Blocpdb> 141 atoms in block 133
Block first atom: 18404
Blocpdb> 117 atoms in block 134
Block first atom: 18545
Blocpdb> 139 atoms in block 135
Block first atom: 18662
Blocpdb> 121 atoms in block 136
Block first atom: 18801
Blocpdb> 124 atoms in block 137
Block first atom: 18922
Blocpdb> 123 atoms in block 138
Block first atom: 19046
Blocpdb> 123 atoms in block 139
Block first atom: 19169
Blocpdb> 134 atoms in block 140
Block first atom: 19292
Blocpdb> 137 atoms in block 141
Block first atom: 19426
Blocpdb> 124 atoms in block 142
Block first atom: 19563
Blocpdb> 127 atoms in block 143
Block first atom: 19687
Blocpdb> 134 atoms in block 144
Block first atom: 19814
Blocpdb> 141 atoms in block 145
Block first atom: 19948
Blocpdb> 133 atoms in block 146
Block first atom: 20089
Blocpdb> 140 atoms in block 147
Block first atom: 20222
Blocpdb> 141 atoms in block 148
Block first atom: 20362
Blocpdb> 136 atoms in block 149
Block first atom: 20503
Blocpdb> 45 atoms in block 150
Block first atom: 20639
Blocpdb> 139 atoms in block 151
Block first atom: 20684
Blocpdb> 126 atoms in block 152
Block first atom: 20823
Blocpdb> 137 atoms in block 153
Block first atom: 20949
Blocpdb> 130 atoms in block 154
Block first atom: 21086
Blocpdb> 140 atoms in block 155
Block first atom: 21216
Blocpdb> 141 atoms in block 156
Block first atom: 21356
Blocpdb> 117 atoms in block 157
Block first atom: 21497
Blocpdb> 139 atoms in block 158
Block first atom: 21614
Blocpdb> 121 atoms in block 159
Block first atom: 21753
Blocpdb> 124 atoms in block 160
Block first atom: 21874
Blocpdb> 123 atoms in block 161
Block first atom: 21998
Blocpdb> 123 atoms in block 162
Block first atom: 22121
Blocpdb> 134 atoms in block 163
Block first atom: 22244
Blocpdb> 137 atoms in block 164
Block first atom: 22378
Blocpdb> 124 atoms in block 165
Block first atom: 22515
Blocpdb> 127 atoms in block 166
Block first atom: 22639
Blocpdb> 134 atoms in block 167
Block first atom: 22766
Blocpdb> 141 atoms in block 168
Block first atom: 22900
Blocpdb> 133 atoms in block 169
Block first atom: 23041
Blocpdb> 140 atoms in block 170
Block first atom: 23174
Blocpdb> 141 atoms in block 171
Block first atom: 23314
Blocpdb> 136 atoms in block 172
Block first atom: 23455
Blocpdb> 45 atoms in block 173
Block first atom: 23591
Blocpdb> 139 atoms in block 174
Block first atom: 23636
Blocpdb> 126 atoms in block 175
Block first atom: 23775
Blocpdb> 137 atoms in block 176
Block first atom: 23901
Blocpdb> 130 atoms in block 177
Block first atom: 24038
Blocpdb> 140 atoms in block 178
Block first atom: 24168
Blocpdb> 141 atoms in block 179
Block first atom: 24308
Blocpdb> 117 atoms in block 180
Block first atom: 24449
Blocpdb> 139 atoms in block 181
Block first atom: 24566
Blocpdb> 121 atoms in block 182
Block first atom: 24705
Blocpdb> 124 atoms in block 183
Block first atom: 24826
Blocpdb> 123 atoms in block 184
Block first atom: 24950
Blocpdb> 123 atoms in block 185
Block first atom: 25073
Blocpdb> 134 atoms in block 186
Block first atom: 25196
Blocpdb> 137 atoms in block 187
Block first atom: 25330
Blocpdb> 124 atoms in block 188
Block first atom: 25467
Blocpdb> 127 atoms in block 189
Block first atom: 25591
Blocpdb> 134 atoms in block 190
Block first atom: 25718
Blocpdb> 141 atoms in block 191
Block first atom: 25852
Blocpdb> 133 atoms in block 192
Block first atom: 25993
Blocpdb> 140 atoms in block 193
Block first atom: 26126
Blocpdb> 141 atoms in block 194
Block first atom: 26266
Blocpdb> 136 atoms in block 195
Block first atom: 26407
Blocpdb> 45 atoms in block 196
Block first atom: 26543
Blocpdb> 327 atoms in block 197
Block first atom: 26588
Blocpdb> 328 atoms in block 198
Block first atom: 26915
Blocpdb> 102 atoms in block 199
Block first atom: 27243
Blocpdb> 329 atoms in block 200
Block first atom: 27345
Blocpdb> 327 atoms in block 201
Block first atom: 27674
Blocpdb> 82 atoms in block 202
Block first atom: 28001
Blocpdb> 327 atoms in block 203
Block first atom: 28083
Blocpdb> 328 atoms in block 204
Block first atom: 28410
Blocpdb> 83 atoms in block 205
Block first atom: 28738
Blocpdb> 329 atoms in block 206
Block first atom: 28821
Blocpdb> 327 atoms in block 207
Block first atom: 29150
Blocpdb> 82 atoms in block 208
Block first atom: 29476
Blocpdb> 208 blocks.
Blocpdb> At most, 329 atoms in each of them.
Blocpdb> At least, 45 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: 88495408 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 0m0.181s
user 0m0.180s
sys 0m0.000s
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: October 18th, 2018.
|
