*** STRUCTURAL PROTEIN 25-JAN-13 2M3T ***
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 = 2209191901321061.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 2209191901321061.atom to be opened.
Openam> File opened: 2209191901321061.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 = 3738
First residue number = 1
Last residue number = 178
Number of atoms found = 60207
Mean number per residue = 16.1
Pdbmat> Coordinate statistics:
= -34.937914 +/- 6.996141 From: -55.098000 To: -17.039000
= -20.084395 +/- 11.445717 From: -47.047000 To: 10.947000
= -20.641383 +/- 10.878510 From: -43.382000 To: 4.857000
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 ******** % Filled.
Pdbmat> 891021003 non-zero elements.
Pdbmat> 98979866 atom-atom interactions.
Pdbmat> Number per atom= 3287.99 +/- 1029.24
Maximum number = 5397
Minimum number = 89
Pdbmat> Matrix trace = 1.979597E+09
Pdbmat> Larger element = 18944.5
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3738 non-zero elements, NRBL set to 19
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 = 2209191901321061.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 19
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 2209191901321061.atom to be opened.
Openam> file on opening on unit 11:
2209191901321061.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 60207 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 19 residue(s) per block.
Blocpdb> 3738 residues.
Blocpdb> 304 atoms in block 1
Block first atom: 1
Blocpdb> 287 atoms in block 2
Block first atom: 305
Blocpdb> 286 atoms in block 3
Block first atom: 592
Blocpdb> 329 atoms in block 4
Block first atom: 878
Blocpdb> 287 atoms in block 5
Block first atom: 1207
Blocpdb> 294 atoms in block 6
Block first atom: 1494
Blocpdb> 312 atoms in block 7
Block first atom: 1788
Blocpdb> 336 atoms in block 8
Block first atom: 2100
Blocpdb> 302 atoms in block 9
Block first atom: 2436
Blocpdb> 130 atoms in block 10
Block first atom: 2738
Blocpdb> 304 atoms in block 11
Block first atom: 2868
Blocpdb> 287 atoms in block 12
Block first atom: 3172
Blocpdb> 286 atoms in block 13
Block first atom: 3459
Blocpdb> 329 atoms in block 14
Block first atom: 3745
Blocpdb> 287 atoms in block 15
Block first atom: 4074
Blocpdb> 294 atoms in block 16
Block first atom: 4361
Blocpdb> 312 atoms in block 17
Block first atom: 4655
Blocpdb> 336 atoms in block 18
Block first atom: 4967
Blocpdb> 302 atoms in block 19
Block first atom: 5303
Blocpdb> 130 atoms in block 20
Block first atom: 5605
Blocpdb> 304 atoms in block 21
Block first atom: 5735
Blocpdb> 287 atoms in block 22
Block first atom: 6039
Blocpdb> 286 atoms in block 23
Block first atom: 6326
Blocpdb> 329 atoms in block 24
Block first atom: 6612
Blocpdb> 287 atoms in block 25
Block first atom: 6941
Blocpdb> 294 atoms in block 26
Block first atom: 7228
Blocpdb> 312 atoms in block 27
Block first atom: 7522
Blocpdb> 336 atoms in block 28
Block first atom: 7834
Blocpdb> 302 atoms in block 29
Block first atom: 8170
Blocpdb> 130 atoms in block 30
Block first atom: 8472
Blocpdb> 304 atoms in block 31
Block first atom: 8602
Blocpdb> 287 atoms in block 32
Block first atom: 8906
Blocpdb> 286 atoms in block 33
Block first atom: 9193
Blocpdb> 329 atoms in block 34
Block first atom: 9479
Blocpdb> 287 atoms in block 35
Block first atom: 9808
Blocpdb> 294 atoms in block 36
Block first atom: 10095
Blocpdb> 312 atoms in block 37
Block first atom: 10389
Blocpdb> 336 atoms in block 38
Block first atom: 10701
Blocpdb> 302 atoms in block 39
Block first atom: 11037
Blocpdb> 130 atoms in block 40
Block first atom: 11339
Blocpdb> 304 atoms in block 41
Block first atom: 11469
Blocpdb> 287 atoms in block 42
Block first atom: 11773
Blocpdb> 286 atoms in block 43
Block first atom: 12060
Blocpdb> 329 atoms in block 44
Block first atom: 12346
Blocpdb> 287 atoms in block 45
Block first atom: 12675
Blocpdb> 294 atoms in block 46
Block first atom: 12962
Blocpdb> 312 atoms in block 47
Block first atom: 13256
Blocpdb> 336 atoms in block 48
Block first atom: 13568
Blocpdb> 302 atoms in block 49
Block first atom: 13904
Blocpdb> 130 atoms in block 50
Block first atom: 14206
Blocpdb> 304 atoms in block 51
Block first atom: 14336
Blocpdb> 287 atoms in block 52
Block first atom: 14640
Blocpdb> 286 atoms in block 53
Block first atom: 14927
Blocpdb> 329 atoms in block 54
Block first atom: 15213
Blocpdb> 287 atoms in block 55
Block first atom: 15542
Blocpdb> 294 atoms in block 56
Block first atom: 15829
Blocpdb> 312 atoms in block 57
Block first atom: 16123
Blocpdb> 336 atoms in block 58
Block first atom: 16435
Blocpdb> 302 atoms in block 59
Block first atom: 16771
Blocpdb> 130 atoms in block 60
Block first atom: 17073
Blocpdb> 304 atoms in block 61
Block first atom: 17203
Blocpdb> 287 atoms in block 62
Block first atom: 17507
Blocpdb> 286 atoms in block 63
Block first atom: 17794
Blocpdb> 329 atoms in block 64
Block first atom: 18080
Blocpdb> 287 atoms in block 65
Block first atom: 18409
Blocpdb> 294 atoms in block 66
Block first atom: 18696
Blocpdb> 312 atoms in block 67
Block first atom: 18990
Blocpdb> 336 atoms in block 68
Block first atom: 19302
Blocpdb> 302 atoms in block 69
Block first atom: 19638
Blocpdb> 130 atoms in block 70
Block first atom: 19940
Blocpdb> 304 atoms in block 71
Block first atom: 20070
Blocpdb> 287 atoms in block 72
Block first atom: 20374
Blocpdb> 286 atoms in block 73
Block first atom: 20661
Blocpdb> 329 atoms in block 74
Block first atom: 20947
Blocpdb> 287 atoms in block 75
Block first atom: 21276
Blocpdb> 294 atoms in block 76
Block first atom: 21563
Blocpdb> 312 atoms in block 77
Block first atom: 21857
Blocpdb> 336 atoms in block 78
Block first atom: 22169
Blocpdb> 302 atoms in block 79
Block first atom: 22505
Blocpdb> 130 atoms in block 80
Block first atom: 22807
Blocpdb> 304 atoms in block 81
Block first atom: 22937
Blocpdb> 287 atoms in block 82
Block first atom: 23241
Blocpdb> 286 atoms in block 83
Block first atom: 23528
Blocpdb> 329 atoms in block 84
Block first atom: 23814
Blocpdb> 287 atoms in block 85
Block first atom: 24143
Blocpdb> 294 atoms in block 86
Block first atom: 24430
Blocpdb> 312 atoms in block 87
Block first atom: 24724
Blocpdb> 336 atoms in block 88
Block first atom: 25036
Blocpdb> 302 atoms in block 89
Block first atom: 25372
Blocpdb> 130 atoms in block 90
Block first atom: 25674
Blocpdb> 304 atoms in block 91
Block first atom: 25804
Blocpdb> 287 atoms in block 92
Block first atom: 26108
Blocpdb> 286 atoms in block 93
Block first atom: 26395
Blocpdb> 329 atoms in block 94
Block first atom: 26681
Blocpdb> 287 atoms in block 95
Block first atom: 27010
Blocpdb> 294 atoms in block 96
Block first atom: 27297
Blocpdb> 312 atoms in block 97
Block first atom: 27591
Blocpdb> 336 atoms in block 98
Block first atom: 27903
Blocpdb> 302 atoms in block 99
Block first atom: 28239
Blocpdb> 130 atoms in block 100
Block first atom: 28541
Blocpdb> 304 atoms in block 101
Block first atom: 28671
Blocpdb> 287 atoms in block 102
Block first atom: 28975
Blocpdb> 286 atoms in block 103
Block first atom: 29262
Blocpdb> 329 atoms in block 104
Block first atom: 29548
Blocpdb> 287 atoms in block 105
Block first atom: 29877
Blocpdb> 294 atoms in block 106
Block first atom: 30164
Blocpdb> 312 atoms in block 107
Block first atom: 30458
Blocpdb> 336 atoms in block 108
Block first atom: 30770
Blocpdb> 302 atoms in block 109
Block first atom: 31106
Blocpdb> 130 atoms in block 110
Block first atom: 31408
Blocpdb> 304 atoms in block 111
Block first atom: 31538
Blocpdb> 287 atoms in block 112
Block first atom: 31842
Blocpdb> 286 atoms in block 113
Block first atom: 32129
Blocpdb> 329 atoms in block 114
Block first atom: 32415
Blocpdb> 287 atoms in block 115
Block first atom: 32744
Blocpdb> 294 atoms in block 116
Block first atom: 33031
Blocpdb> 312 atoms in block 117
Block first atom: 33325
Blocpdb> 336 atoms in block 118
Block first atom: 33637
Blocpdb> 302 atoms in block 119
Block first atom: 33973
Blocpdb> 130 atoms in block 120
Block first atom: 34275
Blocpdb> 304 atoms in block 121
Block first atom: 34405
Blocpdb> 287 atoms in block 122
Block first atom: 34709
Blocpdb> 286 atoms in block 123
Block first atom: 34996
Blocpdb> 329 atoms in block 124
Block first atom: 35282
Blocpdb> 287 atoms in block 125
Block first atom: 35611
Blocpdb> 294 atoms in block 126
Block first atom: 35898
Blocpdb> 312 atoms in block 127
Block first atom: 36192
Blocpdb> 336 atoms in block 128
Block first atom: 36504
Blocpdb> 302 atoms in block 129
Block first atom: 36840
Blocpdb> 130 atoms in block 130
Block first atom: 37142
Blocpdb> 304 atoms in block 131
Block first atom: 37272
Blocpdb> 287 atoms in block 132
Block first atom: 37576
Blocpdb> 286 atoms in block 133
Block first atom: 37863
Blocpdb> 329 atoms in block 134
Block first atom: 38149
Blocpdb> 287 atoms in block 135
Block first atom: 38478
Blocpdb> 294 atoms in block 136
Block first atom: 38765
Blocpdb> 312 atoms in block 137
Block first atom: 39059
Blocpdb> 336 atoms in block 138
Block first atom: 39371
Blocpdb> 302 atoms in block 139
Block first atom: 39707
Blocpdb> 130 atoms in block 140
Block first atom: 40009
Blocpdb> 304 atoms in block 141
Block first atom: 40139
Blocpdb> 287 atoms in block 142
Block first atom: 40443
Blocpdb> 286 atoms in block 143
Block first atom: 40730
Blocpdb> 329 atoms in block 144
Block first atom: 41016
Blocpdb> 287 atoms in block 145
Block first atom: 41345
Blocpdb> 294 atoms in block 146
Block first atom: 41632
Blocpdb> 312 atoms in block 147
Block first atom: 41926
Blocpdb> 336 atoms in block 148
Block first atom: 42238
Blocpdb> 302 atoms in block 149
Block first atom: 42574
Blocpdb> 130 atoms in block 150
Block first atom: 42876
Blocpdb> 304 atoms in block 151
Block first atom: 43006
Blocpdb> 287 atoms in block 152
Block first atom: 43310
Blocpdb> 286 atoms in block 153
Block first atom: 43597
Blocpdb> 329 atoms in block 154
Block first atom: 43883
Blocpdb> 287 atoms in block 155
Block first atom: 44212
Blocpdb> 294 atoms in block 156
Block first atom: 44499
Blocpdb> 312 atoms in block 157
Block first atom: 44793
Blocpdb> 336 atoms in block 158
Block first atom: 45105
Blocpdb> 302 atoms in block 159
Block first atom: 45441
Blocpdb> 130 atoms in block 160
Block first atom: 45743
Blocpdb> 304 atoms in block 161
Block first atom: 45873
Blocpdb> 287 atoms in block 162
Block first atom: 46177
Blocpdb> 286 atoms in block 163
Block first atom: 46464
Blocpdb> 329 atoms in block 164
Block first atom: 46750
Blocpdb> 287 atoms in block 165
Block first atom: 47079
Blocpdb> 294 atoms in block 166
Block first atom: 47366
Blocpdb> 312 atoms in block 167
Block first atom: 47660
Blocpdb> 336 atoms in block 168
Block first atom: 47972
Blocpdb> 302 atoms in block 169
Block first atom: 48308
Blocpdb> 130 atoms in block 170
Block first atom: 48610
Blocpdb> 304 atoms in block 171
Block first atom: 48740
Blocpdb> 287 atoms in block 172
Block first atom: 49044
Blocpdb> 286 atoms in block 173
Block first atom: 49331
Blocpdb> 329 atoms in block 174
Block first atom: 49617
Blocpdb> 287 atoms in block 175
Block first atom: 49946
Blocpdb> 294 atoms in block 176
Block first atom: 50233
Blocpdb> 312 atoms in block 177
Block first atom: 50527
Blocpdb> 336 atoms in block 178
Block first atom: 50839
Blocpdb> 302 atoms in block 179
Block first atom: 51175
Blocpdb> 130 atoms in block 180
Block first atom: 51477
Blocpdb> 304 atoms in block 181
Block first atom: 51607
Blocpdb> 287 atoms in block 182
Block first atom: 51911
Blocpdb> 286 atoms in block 183
Block first atom: 52198
Blocpdb> 329 atoms in block 184
Block first atom: 52484
Blocpdb> 287 atoms in block 185
Block first atom: 52813
Blocpdb> 294 atoms in block 186
Block first atom: 53100
Blocpdb> 312 atoms in block 187
Block first atom: 53394
Blocpdb> 336 atoms in block 188
Block first atom: 53706
Blocpdb> 302 atoms in block 189
Block first atom: 54042
Blocpdb> 130 atoms in block 190
Block first atom: 54344
Blocpdb> 304 atoms in block 191
Block first atom: 54474
Blocpdb> 287 atoms in block 192
Block first atom: 54778
Blocpdb> 286 atoms in block 193
Block first atom: 55065
Blocpdb> 329 atoms in block 194
Block first atom: 55351
Blocpdb> 287 atoms in block 195
Block first atom: 55680
Blocpdb> 294 atoms in block 196
Block first atom: 55967
Blocpdb> 312 atoms in block 197
Block first atom: 56261
Blocpdb> 336 atoms in block 198
Block first atom: 56573
Blocpdb> 302 atoms in block 199
Block first atom: 56909
Blocpdb> 130 atoms in block 200
Block first atom: 57211
Blocpdb> 304 atoms in block 201
Block first atom: 57341
Blocpdb> 287 atoms in block 202
Block first atom: 57645
Blocpdb> 286 atoms in block 203
Block first atom: 57932
Blocpdb> 329 atoms in block 204
Block first atom: 58218
Blocpdb> 287 atoms in block 205
Block first atom: 58547
Blocpdb> 294 atoms in block 206
Block first atom: 58834
Blocpdb> 312 atoms in block 207
Block first atom: 59128
Blocpdb> 336 atoms in block 208
Block first atom: 59440
Blocpdb> 302 atoms in block 209
Block first atom: 59776
Blocpdb> 130 atoms in block 210
Block first atom: 60077
Blocpdb> 210 blocks.
Blocpdb> At most, 336 atoms in each of them.
Blocpdb> At least, 130 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: 183082033 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 0m0.744s
user 0m0.292s
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.
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