*** VIRAL PROTEIN/IMMUNE SYSTEM 22-NOV-20 7KSG ***
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 = 220207192221103606.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 220207192221103606.atom to be opened.
Openam> File opened: 220207192221103606.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 = 3510
First residue number = 23
Last residue number = 113
Number of atoms found = 27691
Mean number per residue = 7.9
Pdbmat> Coordinate statistics:
= 306.615438 +/- 25.966328 From: 250.324000 To: 388.628000
= 305.785045 +/- 24.948912 From: 230.642000 To: 376.071000
= 308.959379 +/- 46.478673 From: 202.314000 To: 410.177000
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 -1.2093 % Filled.
Pdbmat> 10211245 non-zero elements.
Pdbmat> 1116306 atom-atom interactions.
Pdbmat> Number per atom= 80.63 +/- 21.24
Maximum number = 131
Minimum number = 9
Pdbmat> Matrix trace = 2.232612E+07
Pdbmat> Larger element = 509.970
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3510 non-zero elements, NRBL set to 18
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 = 220207192221103606.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 18
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 220207192221103606.atom to be opened.
Openam> file on opening on unit 11:
220207192221103606.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 27691 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 18 residue(s) per block.
Blocpdb> 3510 residues.
Blocpdb> 148 atoms in block 1
Block first atom: 1
Blocpdb> 150 atoms in block 2
Block first atom: 149
Blocpdb> 104 atoms in block 3
Block first atom: 299
Blocpdb> 149 atoms in block 4
Block first atom: 403
Blocpdb> 143 atoms in block 5
Block first atom: 552
Blocpdb> 135 atoms in block 6
Block first atom: 695
Blocpdb> 155 atoms in block 7
Block first atom: 830
Blocpdb> 151 atoms in block 8
Block first atom: 985
Blocpdb> 148 atoms in block 9
Block first atom: 1136
Blocpdb> 157 atoms in block 10
Block first atom: 1284
Blocpdb> 146 atoms in block 11
Block first atom: 1441
Blocpdb> 138 atoms in block 12
Block first atom: 1587
Blocpdb> 83 atoms in block 13
Block first atom: 1725
Blocpdb> 126 atoms in block 14
Block first atom: 1808
Blocpdb> 149 atoms in block 15
Block first atom: 1934
Blocpdb> 129 atoms in block 16
Block first atom: 2083
Blocpdb> 149 atoms in block 17
Block first atom: 2212
Blocpdb> 142 atoms in block 18
Block first atom: 2361
Blocpdb> 155 atoms in block 19
Block first atom: 2503
Blocpdb> 139 atoms in block 20
Block first atom: 2658
Blocpdb> 138 atoms in block 21
Block first atom: 2797
Blocpdb> 140 atoms in block 22
Block first atom: 2935
Blocpdb> 144 atoms in block 23
Block first atom: 3075
Blocpdb> 136 atoms in block 24
Block first atom: 3219
Blocpdb> 167 atoms in block 25
Block first atom: 3355
Blocpdb> 126 atoms in block 26
Block first atom: 3522
Blocpdb> 147 atoms in block 27
Block first atom: 3648
Blocpdb> 145 atoms in block 28
Block first atom: 3795
Blocpdb> 129 atoms in block 29
Block first atom: 3940
Blocpdb> 134 atoms in block 30
Block first atom: 4069
Blocpdb> 146 atoms in block 31
Block first atom: 4203
Blocpdb> 139 atoms in block 32
Block first atom: 4349
Blocpdb> 122 atoms in block 33
Block first atom: 4488
Blocpdb> 73 atoms in block 34
Block first atom: 4610
Blocpdb> 135 atoms in block 35
Block first atom: 4683
Blocpdb> 114 atoms in block 36
Block first atom: 4818
Blocpdb> 130 atoms in block 37
Block first atom: 4932
Blocpdb> 135 atoms in block 38
Block first atom: 5062
Blocpdb> 131 atoms in block 39
Block first atom: 5197
Blocpdb> 138 atoms in block 40
Block first atom: 5328
Blocpdb> 139 atoms in block 41
Block first atom: 5466
Blocpdb> 147 atoms in block 42
Block first atom: 5605
Blocpdb> 141 atoms in block 43
Block first atom: 5752
Blocpdb> 102 atoms in block 44
Block first atom: 5893
Blocpdb> 137 atoms in block 45
Block first atom: 5995
Blocpdb> 128 atoms in block 46
Block first atom: 6132
Blocpdb> 138 atoms in block 47
Block first atom: 6260
Blocpdb> 143 atoms in block 48
Block first atom: 6398
Blocpdb> 125 atoms in block 49
Block first atom: 6541
Blocpdb> 135 atoms in block 50
Block first atom: 6666
Blocpdb> 132 atoms in block 51
Block first atom: 6801
Blocpdb> 144 atoms in block 52
Block first atom: 6933
Blocpdb> 143 atoms in block 53
Block first atom: 7077
Blocpdb> 130 atoms in block 54
Block first atom: 7220
Blocpdb> 143 atoms in block 55
Block first atom: 7350
Blocpdb> 136 atoms in block 56
Block first atom: 7493
Blocpdb> 137 atoms in block 57
Block first atom: 7629
Blocpdb> 150 atoms in block 58
Block first atom: 7766
Blocpdb> 148 atoms in block 59
Block first atom: 7916
Blocpdb> 137 atoms in block 60
Block first atom: 8064
Blocpdb> 32 atoms in block 61
Block first atom: 8201
Blocpdb> 139 atoms in block 62
Block first atom: 8233
Blocpdb> 154 atoms in block 63
Block first atom: 8372
Blocpdb> 154 atoms in block 64
Block first atom: 8526
Blocpdb> 25 atoms in block 65
Block first atom: 8680
Blocpdb> 149 atoms in block 66
Block first atom: 8705
Blocpdb> 143 atoms in block 67
Block first atom: 8854
Blocpdb> 135 atoms in block 68
Block first atom: 8997
Blocpdb> 155 atoms in block 69
Block first atom: 9132
Blocpdb> 151 atoms in block 70
Block first atom: 9287
Blocpdb> 148 atoms in block 71
Block first atom: 9438
Blocpdb> 157 atoms in block 72
Block first atom: 9586
Blocpdb> 146 atoms in block 73
Block first atom: 9743
Blocpdb> 138 atoms in block 74
Block first atom: 9889
Blocpdb> 83 atoms in block 75
Block first atom: 10027
Blocpdb> 126 atoms in block 76
Block first atom: 10110
Blocpdb> 149 atoms in block 77
Block first atom: 10236
Blocpdb> 129 atoms in block 78
Block first atom: 10385
Blocpdb> 149 atoms in block 79
Block first atom: 10514
Blocpdb> 139 atoms in block 80
Block first atom: 10663
Blocpdb> 155 atoms in block 81
Block first atom: 10802
Blocpdb> 139 atoms in block 82
Block first atom: 10957
Blocpdb> 138 atoms in block 83
Block first atom: 11096
Blocpdb> 140 atoms in block 84
Block first atom: 11234
Blocpdb> 144 atoms in block 85
Block first atom: 11374
Blocpdb> 136 atoms in block 86
Block first atom: 11518
Blocpdb> 167 atoms in block 87
Block first atom: 11654
Blocpdb> 126 atoms in block 88
Block first atom: 11821
Blocpdb> 147 atoms in block 89
Block first atom: 11947
Blocpdb> 140 atoms in block 90
Block first atom: 12094
Blocpdb> 129 atoms in block 91
Block first atom: 12234
Blocpdb> 134 atoms in block 92
Block first atom: 12363
Blocpdb> 146 atoms in block 93
Block first atom: 12497
Blocpdb> 139 atoms in block 94
Block first atom: 12643
Blocpdb> 122 atoms in block 95
Block first atom: 12782
Blocpdb> 73 atoms in block 96
Block first atom: 12904
Blocpdb> 135 atoms in block 97
Block first atom: 12977
Blocpdb> 114 atoms in block 98
Block first atom: 13112
Blocpdb> 130 atoms in block 99
Block first atom: 13226
Blocpdb> 135 atoms in block 100
Block first atom: 13356
Blocpdb> 131 atoms in block 101
Block first atom: 13491
Blocpdb> 138 atoms in block 102
Block first atom: 13622
Blocpdb> 139 atoms in block 103
Block first atom: 13760
Blocpdb> 147 atoms in block 104
Block first atom: 13899
Blocpdb> 141 atoms in block 105
Block first atom: 14046
Blocpdb> 102 atoms in block 106
Block first atom: 14187
Blocpdb> 137 atoms in block 107
Block first atom: 14289
Blocpdb> 128 atoms in block 108
Block first atom: 14426
Blocpdb> 138 atoms in block 109
Block first atom: 14554
Blocpdb> 143 atoms in block 110
Block first atom: 14692
Blocpdb> 125 atoms in block 111
Block first atom: 14835
Blocpdb> 135 atoms in block 112
Block first atom: 14960
Blocpdb> 132 atoms in block 113
Block first atom: 15095
Blocpdb> 144 atoms in block 114
Block first atom: 15227
Blocpdb> 143 atoms in block 115
Block first atom: 15371
Blocpdb> 130 atoms in block 116
Block first atom: 15514
Blocpdb> 143 atoms in block 117
Block first atom: 15644
Blocpdb> 136 atoms in block 118
Block first atom: 15787
Blocpdb> 137 atoms in block 119
Block first atom: 15923
Blocpdb> 150 atoms in block 120
Block first atom: 16060
Blocpdb> 148 atoms in block 121
Block first atom: 16210
Blocpdb> 137 atoms in block 122
Block first atom: 16358
Blocpdb> 32 atoms in block 123
Block first atom: 16495
Blocpdb> 139 atoms in block 124
Block first atom: 16527
Blocpdb> 154 atoms in block 125
Block first atom: 16666
Blocpdb> 154 atoms in block 126
Block first atom: 16820
Blocpdb> 25 atoms in block 127
Block first atom: 16974
Blocpdb> 149 atoms in block 128
Block first atom: 16999
Blocpdb> 143 atoms in block 129
Block first atom: 17148
Blocpdb> 135 atoms in block 130
Block first atom: 17291
Blocpdb> 155 atoms in block 131
Block first atom: 17426
Blocpdb> 151 atoms in block 132
Block first atom: 17581
Blocpdb> 148 atoms in block 133
Block first atom: 17732
Blocpdb> 157 atoms in block 134
Block first atom: 17880
Blocpdb> 146 atoms in block 135
Block first atom: 18037
Blocpdb> 138 atoms in block 136
Block first atom: 18183
Blocpdb> 83 atoms in block 137
Block first atom: 18321
Blocpdb> 126 atoms in block 138
Block first atom: 18404
Blocpdb> 149 atoms in block 139
Block first atom: 18530
Blocpdb> 129 atoms in block 140
Block first atom: 18679
Blocpdb> 149 atoms in block 141
Block first atom: 18808
Blocpdb> 142 atoms in block 142
Block first atom: 18957
Blocpdb> 155 atoms in block 143
Block first atom: 19099
Blocpdb> 139 atoms in block 144
Block first atom: 19254
Blocpdb> 138 atoms in block 145
Block first atom: 19393
Blocpdb> 140 atoms in block 146
Block first atom: 19531
Blocpdb> 144 atoms in block 147
Block first atom: 19671
Blocpdb> 136 atoms in block 148
Block first atom: 19815
Blocpdb> 167 atoms in block 149
Block first atom: 19951
Blocpdb> 126 atoms in block 150
Block first atom: 20118
Blocpdb> 147 atoms in block 151
Block first atom: 20244
Blocpdb> 140 atoms in block 152
Block first atom: 20391
Blocpdb> 129 atoms in block 153
Block first atom: 20531
Blocpdb> 134 atoms in block 154
Block first atom: 20660
Blocpdb> 146 atoms in block 155
Block first atom: 20794
Blocpdb> 18 atoms in block 156
Block first atom: 20940
Blocpdb> 123 atoms in block 157
Block first atom: 20958
Blocpdb> 138 atoms in block 158
Block first atom: 21081
Blocpdb> 7 atoms in block 159
Block first atom: 21219
Blocpdb> 135 atoms in block 160
Block first atom: 21226
Blocpdb> 114 atoms in block 161
Block first atom: 21361
Blocpdb> 130 atoms in block 162
Block first atom: 21475
Blocpdb> 135 atoms in block 163
Block first atom: 21605
Blocpdb> 131 atoms in block 164
Block first atom: 21740
Blocpdb> 138 atoms in block 165
Block first atom: 21871
Blocpdb> 139 atoms in block 166
Block first atom: 22009
Blocpdb> 147 atoms in block 167
Block first atom: 22148
Blocpdb> 141 atoms in block 168
Block first atom: 22295
Blocpdb> 102 atoms in block 169
Block first atom: 22436
Blocpdb> 137 atoms in block 170
Block first atom: 22538
Blocpdb> 128 atoms in block 171
Block first atom: 22675
Blocpdb> 138 atoms in block 172
Block first atom: 22803
Blocpdb> 143 atoms in block 173
Block first atom: 22941
Blocpdb> 125 atoms in block 174
Block first atom: 23084
Blocpdb> 135 atoms in block 175
Block first atom: 23209
Blocpdb> 132 atoms in block 176
Block first atom: 23344
Blocpdb> 144 atoms in block 177
Block first atom: 23476
Blocpdb> 143 atoms in block 178
Block first atom: 23620
Blocpdb> 130 atoms in block 179
Block first atom: 23763
Blocpdb> 143 atoms in block 180
Block first atom: 23893
Blocpdb> 136 atoms in block 181
Block first atom: 24036
Blocpdb> 137 atoms in block 182
Block first atom: 24172
Blocpdb> 150 atoms in block 183
Block first atom: 24309
Blocpdb> 148 atoms in block 184
Block first atom: 24459
Blocpdb> 137 atoms in block 185
Block first atom: 24607
Blocpdb> 32 atoms in block 186
Block first atom: 24744
Blocpdb> 118 atoms in block 187
Block first atom: 24776
Blocpdb> 136 atoms in block 188
Block first atom: 24894
Blocpdb> 140 atoms in block 189
Block first atom: 25030
Blocpdb> 146 atoms in block 190
Block first atom: 25170
Blocpdb> 160 atoms in block 191
Block first atom: 25316
Blocpdb> 239 atoms in block 192
Block first atom: 25476
Blocpdb> 33 atoms in block 193
Block first atom: 25715
Blocpdb> 118 atoms in block 194
Block first atom: 25748
Blocpdb> 136 atoms in block 195
Block first atom: 25866
Blocpdb> 140 atoms in block 196
Block first atom: 26002
Blocpdb> 146 atoms in block 197
Block first atom: 26142
Blocpdb> 160 atoms in block 198
Block first atom: 26288
Blocpdb> 239 atoms in block 199
Block first atom: 26448
Blocpdb> 33 atoms in block 200
Block first atom: 26687
Blocpdb> 118 atoms in block 201
Block first atom: 26720
Blocpdb> 136 atoms in block 202
Block first atom: 26838
Blocpdb> 140 atoms in block 203
Block first atom: 26974
Blocpdb> 146 atoms in block 204
Block first atom: 27114
Blocpdb> 160 atoms in block 205
Block first atom: 27260
Blocpdb> 239 atoms in block 206
Block first atom: 27420
Blocpdb> 33 atoms in block 207
Block first atom: 27658
Blocpdb> 207 blocks.
Blocpdb> At most, 239 atoms in each of them.
Blocpdb> At least, 7 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: 60077431 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 0m0.174s
user 0m0.168s
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: October 18th, 2018.
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