*** rec.pdb ***
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 = 210108173056143434.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 210108173056143434.atom to be opened.
Openam> File opened: 210108173056143434.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 = 4380
First residue number = 28
Last residue number = 989
Number of atoms found = 40818
Mean number per residue = 9.3
Pdbmat> Coordinate statistics:
= 229.479580 +/- 30.144359 From: 148.642000 To: 299.493000
= 216.635237 +/- 22.910970 From: 161.765000 To: 280.688000
= 158.613928 +/- 42.683606 From: 61.333000 To: 247.529000
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 1.9444 % Filled.
Pdbmat> 20515760 non-zero elements.
Pdbmat> 2252708 atom-atom interactions.
Pdbmat> Number per atom= 110.38 +/- 30.38
Maximum number = 194
Minimum number = 9
Pdbmat> Matrix trace = 4.505416E+07
Pdbmat> Larger element = 707.166
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4380 non-zero elements, NRBL set to 22
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 = 210108173056143434.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 22
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 210108173056143434.atom to be opened.
Openam> file on opening on unit 11:
210108173056143434.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 40818 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 22 residue(s) per block.
Blocpdb> 4380 residues.
Blocpdb> 190 atoms in block 1
Block first atom: 1
Blocpdb> 201 atoms in block 2
Block first atom: 191
Blocpdb> 211 atoms in block 3
Block first atom: 392
Blocpdb> 197 atoms in block 4
Block first atom: 603
Blocpdb> 235 atoms in block 5
Block first atom: 800
Blocpdb> 225 atoms in block 6
Block first atom: 1035
Blocpdb> 211 atoms in block 7
Block first atom: 1260
Blocpdb> 200 atoms in block 8
Block first atom: 1471
Blocpdb> 216 atoms in block 9
Block first atom: 1671
Blocpdb> 229 atoms in block 10
Block first atom: 1887
Blocpdb> 205 atoms in block 11
Block first atom: 2116
Blocpdb> 201 atoms in block 12
Block first atom: 2321
Blocpdb> 199 atoms in block 13
Block first atom: 2522
Blocpdb> 211 atoms in block 14
Block first atom: 2721
Blocpdb> 204 atoms in block 15
Block first atom: 2932
Blocpdb> 206 atoms in block 16
Block first atom: 3136
Blocpdb> 208 atoms in block 17
Block first atom: 3342
Blocpdb> 194 atoms in block 18
Block first atom: 3550
Blocpdb> 214 atoms in block 19
Block first atom: 3744
Blocpdb> 195 atoms in block 20
Block first atom: 3958
Blocpdb> 202 atoms in block 21
Block first atom: 4153
Blocpdb> 212 atoms in block 22
Block first atom: 4355
Blocpdb> 195 atoms in block 23
Block first atom: 4567
Blocpdb> 201 atoms in block 24
Block first atom: 4762
Blocpdb> 193 atoms in block 25
Block first atom: 4963
Blocpdb> 211 atoms in block 26
Block first atom: 5156
Blocpdb> 183 atoms in block 27
Block first atom: 5367
Blocpdb> 196 atoms in block 28
Block first atom: 5550
Blocpdb> 236 atoms in block 29
Block first atom: 5746
Blocpdb> 214 atoms in block 30
Block first atom: 5982
Blocpdb> 220 atoms in block 31
Block first atom: 6196
Blocpdb> 59 atoms in block 32
Block first atom: 6416
Blocpdb> 200 atoms in block 33
Block first atom: 6475
Blocpdb> 201 atoms in block 34
Block first atom: 6675
Blocpdb> 195 atoms in block 35
Block first atom: 6876
Blocpdb> 224 atoms in block 36
Block first atom: 7071
Blocpdb> 198 atoms in block 37
Block first atom: 7295
Blocpdb> 208 atoms in block 38
Block first atom: 7493
Blocpdb> 227 atoms in block 39
Block first atom: 7701
Blocpdb> 220 atoms in block 40
Block first atom: 7928
Blocpdb> 178 atoms in block 41
Block first atom: 8148
Blocpdb> 211 atoms in block 42
Block first atom: 8326
Blocpdb> 207 atoms in block 43
Block first atom: 8537
Blocpdb> 203 atoms in block 44
Block first atom: 8744
Blocpdb> 230 atoms in block 45
Block first atom: 8947
Blocpdb> 198 atoms in block 46
Block first atom: 9177
Blocpdb> 223 atoms in block 47
Block first atom: 9375
Blocpdb> 195 atoms in block 48
Block first atom: 9598
Blocpdb> 196 atoms in block 49
Block first atom: 9793
Blocpdb> 186 atoms in block 50
Block first atom: 9989
Blocpdb> 200 atoms in block 51
Block first atom: 10175
Blocpdb> 191 atoms in block 52
Block first atom: 10375
Blocpdb> 208 atoms in block 53
Block first atom: 10566
Blocpdb> 195 atoms in block 54
Block first atom: 10774
Blocpdb> 198 atoms in block 55
Block first atom: 10969
Blocpdb> 234 atoms in block 56
Block first atom: 11167
Blocpdb> 193 atoms in block 57
Block first atom: 11401
Blocpdb> 214 atoms in block 58
Block first atom: 11594
Blocpdb> 186 atoms in block 59
Block first atom: 11808
Blocpdb> 196 atoms in block 60
Block first atom: 11994
Blocpdb> 183 atoms in block 61
Block first atom: 12190
Blocpdb> 202 atoms in block 62
Block first atom: 12373
Blocpdb> 227 atoms in block 63
Block first atom: 12575
Blocpdb> 193 atoms in block 64
Block first atom: 12802
Blocpdb> 209 atoms in block 65
Block first atom: 12995
Blocpdb> 206 atoms in block 66
Block first atom: 13204
Blocpdb> 205 atoms in block 67
Block first atom: 13410
Blocpdb> 207 atoms in block 68
Block first atom: 13615
Blocpdb> 201 atoms in block 69
Block first atom: 13822
Blocpdb> 197 atoms in block 70
Block first atom: 14023
Blocpdb> 223 atoms in block 71
Block first atom: 14220
Blocpdb> 206 atoms in block 72
Block first atom: 14443
Blocpdb> 201 atoms in block 73
Block first atom: 14649
Blocpdb> 223 atoms in block 74
Block first atom: 14850
Blocpdb> 202 atoms in block 75
Block first atom: 15073
Blocpdb> 114 atoms in block 76
Block first atom: 15275
Blocpdb> 202 atoms in block 77
Block first atom: 15389
Blocpdb> 195 atoms in block 78
Block first atom: 15591
Blocpdb> 208 atoms in block 79
Block first atom: 15786
Blocpdb> 202 atoms in block 80
Block first atom: 15994
Blocpdb> 200 atoms in block 81
Block first atom: 16196
Blocpdb> 209 atoms in block 82
Block first atom: 16396
Blocpdb> 196 atoms in block 83
Block first atom: 16605
Blocpdb> 222 atoms in block 84
Block first atom: 16801
Blocpdb> 203 atoms in block 85
Block first atom: 17023
Blocpdb> 183 atoms in block 86
Block first atom: 17226
Blocpdb> 201 atoms in block 87
Block first atom: 17409
Blocpdb> 230 atoms in block 88
Block first atom: 17610
Blocpdb> 199 atoms in block 89
Block first atom: 17840
Blocpdb> 178 atoms in block 90
Block first atom: 18039
Blocpdb> 203 atoms in block 91
Block first atom: 18217
Blocpdb> 199 atoms in block 92
Block first atom: 18420
Blocpdb> 216 atoms in block 93
Block first atom: 18619
Blocpdb> 187 atoms in block 94
Block first atom: 18835
Blocpdb> 214 atoms in block 95
Block first atom: 19022
Blocpdb> 207 atoms in block 96
Block first atom: 19236
Blocpdb> 209 atoms in block 97
Block first atom: 19443
Blocpdb> 186 atoms in block 98
Block first atom: 19652
Blocpdb> 209 atoms in block 99
Block first atom: 19838
Blocpdb> 194 atoms in block 100
Block first atom: 20047
Blocpdb> 169 atoms in block 101
Block first atom: 20241
Blocpdb> 202 atoms in block 102
Block first atom: 20410
Blocpdb> 195 atoms in block 103
Block first atom: 20612
Blocpdb> 208 atoms in block 104
Block first atom: 20807
Blocpdb> 202 atoms in block 105
Block first atom: 21015
Blocpdb> 200 atoms in block 106
Block first atom: 21217
Blocpdb> 209 atoms in block 107
Block first atom: 21417
Blocpdb> 196 atoms in block 108
Block first atom: 21626
Blocpdb> 222 atoms in block 109
Block first atom: 21822
Blocpdb> 203 atoms in block 110
Block first atom: 22044
Blocpdb> 183 atoms in block 111
Block first atom: 22247
Blocpdb> 201 atoms in block 112
Block first atom: 22430
Blocpdb> 230 atoms in block 113
Block first atom: 22631
Blocpdb> 199 atoms in block 114
Block first atom: 22861
Blocpdb> 178 atoms in block 115
Block first atom: 23060
Blocpdb> 203 atoms in block 116
Block first atom: 23238
Blocpdb> 199 atoms in block 117
Block first atom: 23441
Blocpdb> 216 atoms in block 118
Block first atom: 23640
Blocpdb> 187 atoms in block 119
Block first atom: 23856
Blocpdb> 214 atoms in block 120
Block first atom: 24043
Blocpdb> 207 atoms in block 121
Block first atom: 24257
Blocpdb> 209 atoms in block 122
Block first atom: 24464
Blocpdb> 186 atoms in block 123
Block first atom: 24673
Blocpdb> 209 atoms in block 124
Block first atom: 24859
Blocpdb> 194 atoms in block 125
Block first atom: 25068
Blocpdb> 169 atoms in block 126
Block first atom: 25262
Blocpdb> 190 atoms in block 127
Block first atom: 25431
Blocpdb> 201 atoms in block 128
Block first atom: 25621
Blocpdb> 211 atoms in block 129
Block first atom: 25822
Blocpdb> 197 atoms in block 130
Block first atom: 26033
Blocpdb> 235 atoms in block 131
Block first atom: 26230
Blocpdb> 225 atoms in block 132
Block first atom: 26465
Blocpdb> 211 atoms in block 133
Block first atom: 26690
Blocpdb> 200 atoms in block 134
Block first atom: 26901
Blocpdb> 216 atoms in block 135
Block first atom: 27101
Blocpdb> 229 atoms in block 136
Block first atom: 27317
Blocpdb> 205 atoms in block 137
Block first atom: 27546
Blocpdb> 201 atoms in block 138
Block first atom: 27751
Blocpdb> 199 atoms in block 139
Block first atom: 27952
Blocpdb> 211 atoms in block 140
Block first atom: 28151
Blocpdb> 204 atoms in block 141
Block first atom: 28362
Blocpdb> 206 atoms in block 142
Block first atom: 28566
Blocpdb> 208 atoms in block 143
Block first atom: 28772
Blocpdb> 194 atoms in block 144
Block first atom: 28980
Blocpdb> 214 atoms in block 145
Block first atom: 29174
Blocpdb> 195 atoms in block 146
Block first atom: 29388
Blocpdb> 202 atoms in block 147
Block first atom: 29583
Blocpdb> 212 atoms in block 148
Block first atom: 29785
Blocpdb> 195 atoms in block 149
Block first atom: 29997
Blocpdb> 201 atoms in block 150
Block first atom: 30192
Blocpdb> 193 atoms in block 151
Block first atom: 30393
Blocpdb> 211 atoms in block 152
Block first atom: 30586
Blocpdb> 183 atoms in block 153
Block first atom: 30797
Blocpdb> 196 atoms in block 154
Block first atom: 30980
Blocpdb> 236 atoms in block 155
Block first atom: 31176
Blocpdb> 214 atoms in block 156
Block first atom: 31412
Blocpdb> 220 atoms in block 157
Block first atom: 31626
Blocpdb> 59 atoms in block 158
Block first atom: 31846
Blocpdb> 200 atoms in block 159
Block first atom: 31905
Blocpdb> 201 atoms in block 160
Block first atom: 32105
Blocpdb> 195 atoms in block 161
Block first atom: 32306
Blocpdb> 224 atoms in block 162
Block first atom: 32501
Blocpdb> 198 atoms in block 163
Block first atom: 32725
Blocpdb> 208 atoms in block 164
Block first atom: 32923
Blocpdb> 227 atoms in block 165
Block first atom: 33131
Blocpdb> 220 atoms in block 166
Block first atom: 33358
Blocpdb> 178 atoms in block 167
Block first atom: 33578
Blocpdb> 211 atoms in block 168
Block first atom: 33756
Blocpdb> 207 atoms in block 169
Block first atom: 33967
Blocpdb> 203 atoms in block 170
Block first atom: 34174
Blocpdb> 230 atoms in block 171
Block first atom: 34377
Blocpdb> 198 atoms in block 172
Block first atom: 34607
Blocpdb> 223 atoms in block 173
Block first atom: 34805
Blocpdb> 195 atoms in block 174
Block first atom: 35028
Blocpdb> 196 atoms in block 175
Block first atom: 35223
Blocpdb> 186 atoms in block 176
Block first atom: 35419
Blocpdb> 200 atoms in block 177
Block first atom: 35605
Blocpdb> 191 atoms in block 178
Block first atom: 35805
Blocpdb> 208 atoms in block 179
Block first atom: 35996
Blocpdb> 195 atoms in block 180
Block first atom: 36204
Blocpdb> 198 atoms in block 181
Block first atom: 36399
Blocpdb> 234 atoms in block 182
Block first atom: 36597
Blocpdb> 193 atoms in block 183
Block first atom: 36831
Blocpdb> 214 atoms in block 184
Block first atom: 37024
Blocpdb> 186 atoms in block 185
Block first atom: 37238
Blocpdb> 196 atoms in block 186
Block first atom: 37424
Blocpdb> 183 atoms in block 187
Block first atom: 37620
Blocpdb> 202 atoms in block 188
Block first atom: 37803
Blocpdb> 227 atoms in block 189
Block first atom: 38005
Blocpdb> 193 atoms in block 190
Block first atom: 38232
Blocpdb> 209 atoms in block 191
Block first atom: 38425
Blocpdb> 206 atoms in block 192
Block first atom: 38634
Blocpdb> 205 atoms in block 193
Block first atom: 38840
Blocpdb> 207 atoms in block 194
Block first atom: 39045
Blocpdb> 201 atoms in block 195
Block first atom: 39252
Blocpdb> 197 atoms in block 196
Block first atom: 39453
Blocpdb> 223 atoms in block 197
Block first atom: 39650
Blocpdb> 206 atoms in block 198
Block first atom: 39873
Blocpdb> 201 atoms in block 199
Block first atom: 40079
Blocpdb> 223 atoms in block 200
Block first atom: 40280
Blocpdb> 202 atoms in block 201
Block first atom: 40503
Blocpdb> 114 atoms in block 202
Block first atom: 40704
Blocpdb> 202 blocks.
Blocpdb> At most, 236 atoms in each of them.
Blocpdb> At least, 59 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: 87198697 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 0m0.219s
user 0m0.208s
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).
Last modification: October 18th, 2018.
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