*** CELL ADHESION/BLOOD CLOTTING 22-NOV-08 3FCS ***
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 = 2603111356512110508.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 2603111356512110508.atom to be opened.
Openam> File opened: 2603111356512110508.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 = 3101
First residue number = 1
Last residue number = 612
Number of atoms found = 23821
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= -24.148151 +/- 42.718284 From: -114.869000 To: 65.019000
= -27.052607 +/- 44.036741 From: -113.466000 To: 66.218000
= -37.052761 +/- 46.433520 From: -134.568000 To: 64.896000
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 2.1748 % Filled.
Pdbmat> 8830514 non-zero elements.
Pdbmat> 965454 atom-atom interactions.
Pdbmat> Number per atom= 81.06 +/- 22.80
Maximum number = 132
Minimum number = 7
Pdbmat> Matrix trace = 1.930908E+07
Pdbmat> Larger element = 495.568
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3101 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 = 2603111356512110508.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 2603111356512110508.atom to be opened.
Openam> file on opening on unit 11:
2603111356512110508.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 23821 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> 3101 residues.
Blocpdb> 121 atoms in block 1
Block first atom: 1
Blocpdb> 132 atoms in block 2
Block first atom: 122
Blocpdb> 111 atoms in block 3
Block first atom: 254
Blocpdb> 119 atoms in block 4
Block first atom: 365
Blocpdb> 127 atoms in block 5
Block first atom: 484
Blocpdb> 118 atoms in block 6
Block first atom: 611
Blocpdb> 126 atoms in block 7
Block first atom: 729
Blocpdb> 128 atoms in block 8
Block first atom: 855
Blocpdb> 125 atoms in block 9
Block first atom: 983
Blocpdb> 131 atoms in block 10
Block first atom: 1108
Blocpdb> 128 atoms in block 11
Block first atom: 1239
Blocpdb> 126 atoms in block 12
Block first atom: 1367
Blocpdb> 120 atoms in block 13
Block first atom: 1493
Blocpdb> 126 atoms in block 14
Block first atom: 1613
Blocpdb> 131 atoms in block 15
Block first atom: 1739
Blocpdb> 120 atoms in block 16
Block first atom: 1870
Blocpdb> 123 atoms in block 17
Block first atom: 1990
Blocpdb> 156 atoms in block 18
Block first atom: 2113
Blocpdb> 117 atoms in block 19
Block first atom: 2269
Blocpdb> 125 atoms in block 20
Block first atom: 2386
Blocpdb> 130 atoms in block 21
Block first atom: 2511
Blocpdb> 111 atoms in block 22
Block first atom: 2641
Blocpdb> 120 atoms in block 23
Block first atom: 2752
Blocpdb> 110 atoms in block 24
Block first atom: 2872
Blocpdb> 120 atoms in block 25
Block first atom: 2982
Blocpdb> 115 atoms in block 26
Block first atom: 3102
Blocpdb> 123 atoms in block 27
Block first atom: 3217
Blocpdb> 116 atoms in block 28
Block first atom: 3340
Blocpdb> 122 atoms in block 29
Block first atom: 3456
Blocpdb> 116 atoms in block 30
Block first atom: 3578
Blocpdb> 113 atoms in block 31
Block first atom: 3694
Blocpdb> 137 atoms in block 32
Block first atom: 3807
Blocpdb> 130 atoms in block 33
Block first atom: 3944
Blocpdb> 111 atoms in block 34
Block first atom: 4074
Blocpdb> 133 atoms in block 35
Block first atom: 4185
Blocpdb> 117 atoms in block 36
Block first atom: 4318
Blocpdb> 121 atoms in block 37
Block first atom: 4435
Blocpdb> 124 atoms in block 38
Block first atom: 4556
Blocpdb> 113 atoms in block 39
Block first atom: 4680
Blocpdb> 116 atoms in block 40
Block first atom: 4793
Blocpdb> 115 atoms in block 41
Block first atom: 4909
Blocpdb> 142 atoms in block 42
Block first atom: 5024
Blocpdb> 130 atoms in block 43
Block first atom: 5166
Blocpdb> 116 atoms in block 44
Block first atom: 5296
Blocpdb> 115 atoms in block 45
Block first atom: 5412
Blocpdb> 127 atoms in block 46
Block first atom: 5527
Blocpdb> 123 atoms in block 47
Block first atom: 5654
Blocpdb> 75 atoms in block 48
Block first atom: 5777
Blocpdb> 132 atoms in block 49
Block first atom: 5852
Blocpdb> 115 atoms in block 50
Block first atom: 5984
Blocpdb> 125 atoms in block 51
Block first atom: 6099
Blocpdb> 122 atoms in block 52
Block first atom: 6224
%Blocpdb-Wn> 2 atoms in block 53 i.e., less than what is required for a rigid body.
%Blocpdb-Wn> Last atom in this block is the 6347th, in residue A 839
%Blocpdb-Wn> It will be merged with next block.
Blocpdb> 113 atoms in block 53
Block first atom: 6346
Blocpdb> 122 atoms in block 54
Block first atom: 6459
Blocpdb> 139 atoms in block 55
Block first atom: 6581
Blocpdb> 146 atoms in block 56
Block first atom: 6720
Blocpdb> 121 atoms in block 57
Block first atom: 6866
Blocpdb> 47 atoms in block 58
Block first atom: 6987
Blocpdb> 111 atoms in block 59
Block first atom: 7034
Blocpdb> 115 atoms in block 60
Block first atom: 7145
Blocpdb> 125 atoms in block 61
Block first atom: 7260
Blocpdb> 121 atoms in block 62
Block first atom: 7385
Blocpdb> 76 atoms in block 63
Block first atom: 7506
Blocpdb> 130 atoms in block 64
Block first atom: 7582
Blocpdb> 136 atoms in block 65
Block first atom: 7712
Blocpdb> 135 atoms in block 66
Block first atom: 7848
Blocpdb> 126 atoms in block 67
Block first atom: 7983
Blocpdb> 126 atoms in block 68
Block first atom: 8109
Blocpdb> 127 atoms in block 69
Block first atom: 8235
Blocpdb> 128 atoms in block 70
Block first atom: 8362
Blocpdb> 135 atoms in block 71
Block first atom: 8490
Blocpdb> 120 atoms in block 72
Block first atom: 8625
Blocpdb> 126 atoms in block 73
Block first atom: 8745
Blocpdb> 125 atoms in block 74
Block first atom: 8871
Blocpdb> 118 atoms in block 75
Block first atom: 8996
Blocpdb> 115 atoms in block 76
Block first atom: 9114
Blocpdb> 126 atoms in block 77
Block first atom: 9229
Blocpdb> 129 atoms in block 78
Block first atom: 9355
Blocpdb> 121 atoms in block 79
Block first atom: 9484
Blocpdb> 121 atoms in block 80
Block first atom: 9605
Blocpdb> 134 atoms in block 81
Block first atom: 9726
Blocpdb> 116 atoms in block 82
Block first atom: 9860
Blocpdb> 115 atoms in block 83
Block first atom: 9976
Blocpdb> 128 atoms in block 84
Block first atom: 10091
Blocpdb> 122 atoms in block 85
Block first atom: 10219
Blocpdb> 118 atoms in block 86
Block first atom: 10341
Blocpdb> 116 atoms in block 87
Block first atom: 10459
Blocpdb> 101 atoms in block 88
Block first atom: 10575
Blocpdb> 124 atoms in block 89
Block first atom: 10676
Blocpdb> 110 atoms in block 90
Block first atom: 10800
Blocpdb> 127 atoms in block 91
Block first atom: 10910
Blocpdb> 111 atoms in block 92
Block first atom: 11037
Blocpdb> 125 atoms in block 93
Block first atom: 11148
Blocpdb> 114 atoms in block 94
Block first atom: 11273
Blocpdb> 109 atoms in block 95
Block first atom: 11387
Blocpdb> 113 atoms in block 96
Block first atom: 11496
Blocpdb> 130 atoms in block 97
Block first atom: 11609
Blocpdb> 133 atoms in block 98
Block first atom: 11739
Blocpdb> 125 atoms in block 99
Block first atom: 11872
Blocpdb> 137 atoms in block 100
Block first atom: 11997
Blocpdb> 120 atoms in block 101
Block first atom: 12134
Blocpdb> 121 atoms in block 102
Block first atom: 12254
Blocpdb> 132 atoms in block 103
Block first atom: 12375
Blocpdb> 111 atoms in block 104
Block first atom: 12507
Blocpdb> 119 atoms in block 105
Block first atom: 12618
Blocpdb> 127 atoms in block 106
Block first atom: 12737
Blocpdb> 118 atoms in block 107
Block first atom: 12864
Blocpdb> 126 atoms in block 108
Block first atom: 12982
Blocpdb> 128 atoms in block 109
Block first atom: 13108
Blocpdb> 125 atoms in block 110
Block first atom: 13236
Blocpdb> 131 atoms in block 111
Block first atom: 13361
Blocpdb> 128 atoms in block 112
Block first atom: 13492
Blocpdb> 126 atoms in block 113
Block first atom: 13620
Blocpdb> 120 atoms in block 114
Block first atom: 13746
Blocpdb> 136 atoms in block 115
Block first atom: 13866
Blocpdb> 131 atoms in block 116
Block first atom: 14002
Blocpdb> 120 atoms in block 117
Block first atom: 14133
Blocpdb> 123 atoms in block 118
Block first atom: 14253
Blocpdb> 145 atoms in block 119
Block first atom: 14376
Blocpdb> 117 atoms in block 120
Block first atom: 14521
Blocpdb> 133 atoms in block 121
Block first atom: 14638
Blocpdb> 130 atoms in block 122
Block first atom: 14771
Blocpdb> 111 atoms in block 123
Block first atom: 14901
Blocpdb> 120 atoms in block 124
Block first atom: 15012
Blocpdb> 110 atoms in block 125
Block first atom: 15132
Blocpdb> 120 atoms in block 126
Block first atom: 15242
Blocpdb> 126 atoms in block 127
Block first atom: 15362
Blocpdb> 123 atoms in block 128
Block first atom: 15488
Blocpdb> 116 atoms in block 129
Block first atom: 15611
Blocpdb> 122 atoms in block 130
Block first atom: 15727
Blocpdb> 116 atoms in block 131
Block first atom: 15849
Blocpdb> 113 atoms in block 132
Block first atom: 15965
Blocpdb> 140 atoms in block 133
Block first atom: 16078
Blocpdb> 130 atoms in block 134
Block first atom: 16218
Blocpdb> 111 atoms in block 135
Block first atom: 16348
Blocpdb> 141 atoms in block 136
Block first atom: 16459
Blocpdb> 117 atoms in block 137
Block first atom: 16600
Blocpdb> 121 atoms in block 138
Block first atom: 16717
Blocpdb> 124 atoms in block 139
Block first atom: 16838
Blocpdb> 113 atoms in block 140
Block first atom: 16962
Blocpdb> 116 atoms in block 141
Block first atom: 17075
Blocpdb> 115 atoms in block 142
Block first atom: 17191
Blocpdb> 118 atoms in block 143
Block first atom: 17306
Blocpdb> 130 atoms in block 144
Block first atom: 17424
Blocpdb> 116 atoms in block 145
Block first atom: 17554
Blocpdb> 115 atoms in block 146
Block first atom: 17670
Blocpdb> 127 atoms in block 147
Block first atom: 17785
Blocpdb> 123 atoms in block 148
Block first atom: 17912
Blocpdb> 37 atoms in block 149
Block first atom: 18035
Blocpdb> 122 atoms in block 150
Block first atom: 18072
Blocpdb> 119 atoms in block 151
Block first atom: 18194
Blocpdb> 128 atoms in block 152
Block first atom: 18313
Blocpdb> 96 atoms in block 153
Block first atom: 18441
Blocpdb> 106 atoms in block 154
Block first atom: 18537
Blocpdb> 122 atoms in block 155
Block first atom: 18643
Blocpdb> 139 atoms in block 156
Block first atom: 18765
Blocpdb> 135 atoms in block 157
Block first atom: 18904
Blocpdb> 121 atoms in block 158
Block first atom: 19039
Blocpdb> 47 atoms in block 159
Block first atom: 19160
Blocpdb> 111 atoms in block 160
Block first atom: 19207
Blocpdb> 115 atoms in block 161
Block first atom: 19318
Blocpdb> 125 atoms in block 162
Block first atom: 19433
Blocpdb> 130 atoms in block 163
Block first atom: 19558
Blocpdb> 80 atoms in block 164
Block first atom: 19688
Blocpdb> 130 atoms in block 165
Block first atom: 19768
Blocpdb> 136 atoms in block 166
Block first atom: 19898
Blocpdb> 135 atoms in block 167
Block first atom: 20034
Blocpdb> 126 atoms in block 168
Block first atom: 20169
Blocpdb> 126 atoms in block 169
Block first atom: 20295
Blocpdb> 127 atoms in block 170
Block first atom: 20421
Blocpdb> 128 atoms in block 171
Block first atom: 20548
Blocpdb> 135 atoms in block 172
Block first atom: 20676
Blocpdb> 120 atoms in block 173
Block first atom: 20811
Blocpdb> 126 atoms in block 174
Block first atom: 20931
Blocpdb> 132 atoms in block 175
Block first atom: 21057
Blocpdb> 118 atoms in block 176
Block first atom: 21189
Blocpdb> 115 atoms in block 177
Block first atom: 21307
Blocpdb> 126 atoms in block 178
Block first atom: 21422
Blocpdb> 129 atoms in block 179
Block first atom: 21548
Blocpdb> 123 atoms in block 180
Block first atom: 21677
Blocpdb> 121 atoms in block 181
Block first atom: 21800
Blocpdb> 134 atoms in block 182
Block first atom: 21921
Blocpdb> 116 atoms in block 183
Block first atom: 22055
Blocpdb> 115 atoms in block 184
Block first atom: 22171
Blocpdb> 128 atoms in block 185
Block first atom: 22286
Blocpdb> 122 atoms in block 186
Block first atom: 22414
Blocpdb> 118 atoms in block 187
Block first atom: 22536
Blocpdb> 116 atoms in block 188
Block first atom: 22654
Blocpdb> 101 atoms in block 189
Block first atom: 22770
Blocpdb> 124 atoms in block 190
Block first atom: 22871
Blocpdb> 110 atoms in block 191
Block first atom: 22995
Blocpdb> 127 atoms in block 192
Block first atom: 23105
Blocpdb> 111 atoms in block 193
Block first atom: 23232
Blocpdb> 125 atoms in block 194
Block first atom: 23343
Blocpdb> 114 atoms in block 195
Block first atom: 23468
Blocpdb> 109 atoms in block 196
Block first atom: 23582
Blocpdb> 113 atoms in block 197
Block first atom: 23691
Blocpdb> 18 atoms in block 198
Block first atom: 23803
Blocpdb> 198 blocks.
Blocpdb> At most, 156 atoms in each of them.
Blocpdb> At least, 18 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: 33663709 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 0m0.127s
user 0m0.118s
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).
Between 2015 and 2025, it was hosted by US2B (Nantes).
Last modification: december 26th, 2025.
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