*** IMMUNE SYSTEM/AGONIST 27-DEC-18 6NIG ***
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 = 2403131902523096026.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 2403131902523096026.atom to be opened.
Openam> File opened: 2403131902523096026.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 = 2186
First residue number = 27
Last residue number = 575
Number of atoms found = 34995
Mean number per residue = 16.0
Pdbmat> Coordinate statistics:
= 5.156747 +/- 15.725756 From: -30.710000 To: 41.402000
= 47.888914 +/- 29.193952 From: -13.880000 To: 108.919000
= 103.997284 +/- 31.181560 From: 36.730000 To: 171.320000
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 -2.8466 % Filled.
Pdbmat> 26514920 non-zero elements.
Pdbmat> 2923265 atom-atom interactions.
Pdbmat> Number per atom= 167.07 +/- 47.30
Maximum number = 264
Minimum number = 22
Pdbmat> Matrix trace = 5.846530E+07
Pdbmat> Larger element = 897.583
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2186 non-zero elements, NRBL set to 11
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 = 2403131902523096026.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 11
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 2403131902523096026.atom to be opened.
Openam> file on opening on unit 11:
2403131902523096026.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 34995 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 11 residue(s) per block.
Blocpdb> 2186 residues.
Blocpdb> 158 atoms in block 1
Block first atom: 1
Blocpdb> 135 atoms in block 2
Block first atom: 159
Blocpdb> 164 atoms in block 3
Block first atom: 294
Blocpdb> 172 atoms in block 4
Block first atom: 458
Blocpdb> 178 atoms in block 5
Block first atom: 630
Blocpdb> 162 atoms in block 6
Block first atom: 808
Blocpdb> 151 atoms in block 7
Block first atom: 970
Blocpdb> 177 atoms in block 8
Block first atom: 1121
Blocpdb> 173 atoms in block 9
Block first atom: 1298
Blocpdb> 180 atoms in block 10
Block first atom: 1471
Blocpdb> 169 atoms in block 11
Block first atom: 1651
Blocpdb> 190 atoms in block 12
Block first atom: 1820
Blocpdb> 193 atoms in block 13
Block first atom: 2010
Blocpdb> 173 atoms in block 14
Block first atom: 2203
Blocpdb> 161 atoms in block 15
Block first atom: 2376
Blocpdb> 178 atoms in block 16
Block first atom: 2537
Blocpdb> 204 atoms in block 17
Block first atom: 2715
Blocpdb> 169 atoms in block 18
Block first atom: 2919
Blocpdb> 172 atoms in block 19
Block first atom: 3088
Blocpdb> 141 atoms in block 20
Block first atom: 3260
Blocpdb> 198 atoms in block 21
Block first atom: 3401
Blocpdb> 181 atoms in block 22
Block first atom: 3599
Blocpdb> 183 atoms in block 23
Block first atom: 3780
Blocpdb> 158 atoms in block 24
Block first atom: 3963
Blocpdb> 164 atoms in block 25
Block first atom: 4121
Blocpdb> 168 atoms in block 26
Block first atom: 4285
Blocpdb> 220 atoms in block 27
Block first atom: 4453
Blocpdb> 181 atoms in block 28
Block first atom: 4673
Blocpdb> 190 atoms in block 29
Block first atom: 4854
Blocpdb> 183 atoms in block 30
Block first atom: 5044
Blocpdb> 185 atoms in block 31
Block first atom: 5227
Blocpdb> 187 atoms in block 32
Block first atom: 5412
Blocpdb> 153 atoms in block 33
Block first atom: 5599
Blocpdb> 183 atoms in block 34
Block first atom: 5752
Blocpdb> 177 atoms in block 35
Block first atom: 5935
Blocpdb> 179 atoms in block 36
Block first atom: 6112
Blocpdb> 170 atoms in block 37
Block first atom: 6291
Blocpdb> 184 atoms in block 38
Block first atom: 6461
Blocpdb> 165 atoms in block 39
Block first atom: 6645
Blocpdb> 175 atoms in block 40
Block first atom: 6810
Blocpdb> 180 atoms in block 41
Block first atom: 6985
Blocpdb> 205 atoms in block 42
Block first atom: 7165
Blocpdb> 166 atoms in block 43
Block first atom: 7370
Blocpdb> 199 atoms in block 44
Block first atom: 7536
Blocpdb> 176 atoms in block 45
Block first atom: 7735
Blocpdb> 190 atoms in block 46
Block first atom: 7911
Blocpdb> 171 atoms in block 47
Block first atom: 8101
Blocpdb> 197 atoms in block 48
Block first atom: 8272
Blocpdb> 128 atoms in block 49
Block first atom: 8469
Blocpdb> 149 atoms in block 50
Block first atom: 8597
Blocpdb> 158 atoms in block 51
Block first atom: 8746
Blocpdb> 135 atoms in block 52
Block first atom: 8904
Blocpdb> 164 atoms in block 53
Block first atom: 9039
Blocpdb> 172 atoms in block 54
Block first atom: 9203
Blocpdb> 178 atoms in block 55
Block first atom: 9375
Blocpdb> 162 atoms in block 56
Block first atom: 9553
Blocpdb> 151 atoms in block 57
Block first atom: 9715
Blocpdb> 177 atoms in block 58
Block first atom: 9866
Blocpdb> 173 atoms in block 59
Block first atom: 10043
Blocpdb> 180 atoms in block 60
Block first atom: 10216
Blocpdb> 169 atoms in block 61
Block first atom: 10396
Blocpdb> 190 atoms in block 62
Block first atom: 10565
Blocpdb> 193 atoms in block 63
Block first atom: 10755
Blocpdb> 173 atoms in block 64
Block first atom: 10948
Blocpdb> 161 atoms in block 65
Block first atom: 11121
Blocpdb> 179 atoms in block 66
Block first atom: 11282
Blocpdb> 204 atoms in block 67
Block first atom: 11461
Blocpdb> 169 atoms in block 68
Block first atom: 11665
Blocpdb> 172 atoms in block 69
Block first atom: 11834
Blocpdb> 163 atoms in block 70
Block first atom: 12006
Blocpdb> 199 atoms in block 71
Block first atom: 12169
Blocpdb> 179 atoms in block 72
Block first atom: 12368
Blocpdb> 180 atoms in block 73
Block first atom: 12547
Blocpdb> 170 atoms in block 74
Block first atom: 12727
Blocpdb> 121 atoms in block 75
Block first atom: 12897
Blocpdb> 170 atoms in block 76
Block first atom: 13018
Blocpdb> 221 atoms in block 77
Block first atom: 13188
Blocpdb> 176 atoms in block 78
Block first atom: 13409
Blocpdb> 197 atoms in block 79
Block first atom: 13585
Blocpdb> 178 atoms in block 80
Block first atom: 13782
Blocpdb> 183 atoms in block 81
Block first atom: 13960
Blocpdb> 183 atoms in block 82
Block first atom: 14143
Blocpdb> 156 atoms in block 83
Block first atom: 14326
Blocpdb> 188 atoms in block 84
Block first atom: 14482
Blocpdb> 180 atoms in block 85
Block first atom: 14670
Blocpdb> 168 atoms in block 86
Block first atom: 14850
Blocpdb> 173 atoms in block 87
Block first atom: 15018
Blocpdb> 184 atoms in block 88
Block first atom: 15191
Blocpdb> 173 atoms in block 89
Block first atom: 15375
Blocpdb> 167 atoms in block 90
Block first atom: 15548
Blocpdb> 185 atoms in block 91
Block first atom: 15715
Blocpdb> 203 atoms in block 92
Block first atom: 15900
Blocpdb> 168 atoms in block 93
Block first atom: 16103
Blocpdb> 202 atoms in block 94
Block first atom: 16271
Blocpdb> 168 atoms in block 95
Block first atom: 16473
Blocpdb> 190 atoms in block 96
Block first atom: 16641
Blocpdb> 176 atoms in block 97
Block first atom: 16831
Blocpdb> 193 atoms in block 98
Block first atom: 17007
Blocpdb> 135 atoms in block 99
Block first atom: 17200
Blocpdb> 127 atoms in block 100
Block first atom: 17335
Blocpdb> 158 atoms in block 101
Block first atom: 17462
Blocpdb> 135 atoms in block 102
Block first atom: 17620
Blocpdb> 164 atoms in block 103
Block first atom: 17755
Blocpdb> 172 atoms in block 104
Block first atom: 17919
Blocpdb> 178 atoms in block 105
Block first atom: 18091
Blocpdb> 162 atoms in block 106
Block first atom: 18269
Blocpdb> 151 atoms in block 107
Block first atom: 18431
Blocpdb> 178 atoms in block 108
Block first atom: 18582
Blocpdb> 173 atoms in block 109
Block first atom: 18760
Blocpdb> 180 atoms in block 110
Block first atom: 18933
Blocpdb> 169 atoms in block 111
Block first atom: 19113
Blocpdb> 190 atoms in block 112
Block first atom: 19282
Blocpdb> 193 atoms in block 113
Block first atom: 19472
Blocpdb> 173 atoms in block 114
Block first atom: 19665
Blocpdb> 161 atoms in block 115
Block first atom: 19838
Blocpdb> 179 atoms in block 116
Block first atom: 19999
Blocpdb> 204 atoms in block 117
Block first atom: 20178
Blocpdb> 169 atoms in block 118
Block first atom: 20382
Blocpdb> 172 atoms in block 119
Block first atom: 20551
Blocpdb> 163 atoms in block 120
Block first atom: 20723
Blocpdb> 199 atoms in block 121
Block first atom: 20886
Blocpdb> 179 atoms in block 122
Block first atom: 21085
Blocpdb> 180 atoms in block 123
Block first atom: 21264
Blocpdb> 170 atoms in block 124
Block first atom: 21444
Blocpdb> 147 atoms in block 125
Block first atom: 21614
Blocpdb> 178 atoms in block 126
Block first atom: 21761
Blocpdb> 215 atoms in block 127
Block first atom: 21939
Blocpdb> 186 atoms in block 128
Block first atom: 22154
Blocpdb> 193 atoms in block 129
Block first atom: 22340
Blocpdb> 177 atoms in block 130
Block first atom: 22533
Blocpdb> 191 atoms in block 131
Block first atom: 22710
Blocpdb> 184 atoms in block 132
Block first atom: 22901
Blocpdb> 150 atoms in block 133
Block first atom: 23085
Blocpdb> 189 atoms in block 134
Block first atom: 23235
Blocpdb> 169 atoms in block 135
Block first atom: 23424
Blocpdb> 184 atoms in block 136
Block first atom: 23593
Blocpdb> 160 atoms in block 137
Block first atom: 23777
Blocpdb> 197 atoms in block 138
Block first atom: 23937
Blocpdb> 162 atoms in block 139
Block first atom: 24134
Blocpdb> 175 atoms in block 140
Block first atom: 24296
Blocpdb> 177 atoms in block 141
Block first atom: 24471
Blocpdb> 203 atoms in block 142
Block first atom: 24648
Blocpdb> 168 atoms in block 143
Block first atom: 24851
Blocpdb> 197 atoms in block 144
Block first atom: 25019
Blocpdb> 176 atoms in block 145
Block first atom: 25216
Blocpdb> 195 atoms in block 146
Block first atom: 25392
Blocpdb> 164 atoms in block 147
Block first atom: 25587
Blocpdb> 196 atoms in block 148
Block first atom: 25751
Blocpdb> 143 atoms in block 149
Block first atom: 25947
Blocpdb> 156 atoms in block 150
Block first atom: 26090
Blocpdb> 158 atoms in block 151
Block first atom: 26246
Blocpdb> 135 atoms in block 152
Block first atom: 26404
Blocpdb> 164 atoms in block 153
Block first atom: 26539
Blocpdb> 172 atoms in block 154
Block first atom: 26703
Blocpdb> 178 atoms in block 155
Block first atom: 26875
Blocpdb> 162 atoms in block 156
Block first atom: 27053
Blocpdb> 151 atoms in block 157
Block first atom: 27215
Blocpdb> 178 atoms in block 158
Block first atom: 27366
Blocpdb> 173 atoms in block 159
Block first atom: 27544
Blocpdb> 180 atoms in block 160
Block first atom: 27717
Blocpdb> 169 atoms in block 161
Block first atom: 27897
Blocpdb> 190 atoms in block 162
Block first atom: 28066
Blocpdb> 193 atoms in block 163
Block first atom: 28256
Blocpdb> 173 atoms in block 164
Block first atom: 28449
Blocpdb> 161 atoms in block 165
Block first atom: 28622
Blocpdb> 178 atoms in block 166
Block first atom: 28783
Blocpdb> 204 atoms in block 167
Block first atom: 28961
Blocpdb> 169 atoms in block 168
Block first atom: 29165
Blocpdb> 172 atoms in block 169
Block first atom: 29334
Blocpdb> 181 atoms in block 170
Block first atom: 29506
Blocpdb> 199 atoms in block 171
Block first atom: 29687
Blocpdb> 179 atoms in block 172
Block first atom: 29886
Blocpdb> 180 atoms in block 173
Block first atom: 30065
Blocpdb> 170 atoms in block 174
Block first atom: 30245
Blocpdb> 121 atoms in block 175
Block first atom: 30415
Blocpdb> 167 atoms in block 176
Block first atom: 30536
Blocpdb> 220 atoms in block 177
Block first atom: 30703
Blocpdb> 181 atoms in block 178
Block first atom: 30923
Blocpdb> 190 atoms in block 179
Block first atom: 31104
Blocpdb> 183 atoms in block 180
Block first atom: 31294
Blocpdb> 185 atoms in block 181
Block first atom: 31477
Blocpdb> 187 atoms in block 182
Block first atom: 31662
Blocpdb> 153 atoms in block 183
Block first atom: 31849
Blocpdb> 183 atoms in block 184
Block first atom: 32002
Blocpdb> 177 atoms in block 185
Block first atom: 32185
Blocpdb> 179 atoms in block 186
Block first atom: 32362
Blocpdb> 170 atoms in block 187
Block first atom: 32541
Blocpdb> 184 atoms in block 188
Block first atom: 32711
Blocpdb> 165 atoms in block 189
Block first atom: 32895
Blocpdb> 175 atoms in block 190
Block first atom: 33060
Blocpdb> 180 atoms in block 191
Block first atom: 33235
Blocpdb> 205 atoms in block 192
Block first atom: 33415
Blocpdb> 166 atoms in block 193
Block first atom: 33620
Blocpdb> 199 atoms in block 194
Block first atom: 33786
Blocpdb> 176 atoms in block 195
Block first atom: 33985
Blocpdb> 190 atoms in block 196
Block first atom: 34161
Blocpdb> 171 atoms in block 197
Block first atom: 34351
Blocpdb> 197 atoms in block 198
Block first atom: 34522
Blocpdb> 128 atoms in block 199
Block first atom: 34719
Blocpdb> 149 atoms in block 200
Block first atom: 34846
Blocpdb> 200 blocks.
Blocpdb> At most, 221 atoms in each of them.
Blocpdb> At least, 121 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: 70044625 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 0m0.185s
user 0m0.181s
sys 0m0.004s
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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