*** GCCnowat ***
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 = 220209112104107964.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 220209112104107964.atom to be opened.
Openam> File opened: 220209112104107964.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 = 4291
First residue number = 5
Last residue number = 701
Number of atoms found = 33222
Mean number per residue = 7.7
Pdbmat> Coordinate statistics:
= 143.047329 +/- 29.118983 From: 68.487000 To: 215.072000
= 151.314477 +/- 25.870483 From: 82.158000 To: 220.048000
= 143.191467 +/- 28.898764 From: 64.468000 To: 215.077000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'COA ' is not a well known amino-acid.
%Pdbmat-W> residue:'BTI ' is not a well known amino-acid.
%Pdbmat-W> 2 residue(s) not known.
Openam> File opened: pdbmat.xyzm
Pdbmat> Coordinates and masses considered are saved.
Openam> File opened: pdbmat.sdijb
Pdbmat> Matrix statistics:
Pdbmat> The matrix is 1.8580 % Filled.
Pdbmat> 12481133 non-zero elements.
Pdbmat> 1364906 atom-atom interactions.
Pdbmat> Number per atom= 82.17 +/- 19.71
Maximum number = 123
Minimum number = 14
Pdbmat> Matrix trace = 2.729812E+07
Pdbmat> Larger element = 482.707
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
4291 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 = 220209112104107964.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 220209112104107964.atom to be opened.
Openam> file on opening on unit 11:
220209112104107964.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 33222 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> 4291 residues.
Blocpdb> 175 atoms in block 1
Block first atom: 1
Blocpdb> 183 atoms in block 2
Block first atom: 176
Blocpdb> 188 atoms in block 3
Block first atom: 359
Blocpdb> 163 atoms in block 4
Block first atom: 547
Blocpdb> 161 atoms in block 5
Block first atom: 710
Blocpdb> 159 atoms in block 6
Block first atom: 871
Blocpdb> 153 atoms in block 7
Block first atom: 1030
Blocpdb> 155 atoms in block 8
Block first atom: 1183
Blocpdb> 174 atoms in block 9
Block first atom: 1338
Blocpdb> 155 atoms in block 10
Block first atom: 1512
Blocpdb> 180 atoms in block 11
Block first atom: 1667
Blocpdb> 172 atoms in block 12
Block first atom: 1847
Blocpdb> 179 atoms in block 13
Block first atom: 2019
Blocpdb> 172 atoms in block 14
Block first atom: 2198
Blocpdb> 162 atoms in block 15
Block first atom: 2370
Blocpdb> 172 atoms in block 16
Block first atom: 2532
Blocpdb> 166 atoms in block 17
Block first atom: 2704
Blocpdb> 168 atoms in block 18
Block first atom: 2870
Blocpdb> 165 atoms in block 19
Block first atom: 3038
Blocpdb> 159 atoms in block 20
Block first atom: 3203
Blocpdb> 181 atoms in block 21
Block first atom: 3362
Blocpdb> 179 atoms in block 22
Block first atom: 3543
Blocpdb> 181 atoms in block 23
Block first atom: 3722
Blocpdb> 175 atoms in block 24
Block first atom: 3903
Blocpdb> 183 atoms in block 25
Block first atom: 4078
Blocpdb> 188 atoms in block 26
Block first atom: 4261
Blocpdb> 163 atoms in block 27
Block first atom: 4449
Blocpdb> 161 atoms in block 28
Block first atom: 4612
Blocpdb> 159 atoms in block 29
Block first atom: 4773
Blocpdb> 153 atoms in block 30
Block first atom: 4932
Blocpdb> 155 atoms in block 31
Block first atom: 5085
Blocpdb> 174 atoms in block 32
Block first atom: 5240
Blocpdb> 155 atoms in block 33
Block first atom: 5414
Blocpdb> 180 atoms in block 34
Block first atom: 5569
Blocpdb> 172 atoms in block 35
Block first atom: 5749
Blocpdb> 179 atoms in block 36
Block first atom: 5921
Blocpdb> 172 atoms in block 37
Block first atom: 6100
Blocpdb> 162 atoms in block 38
Block first atom: 6272
Blocpdb> 172 atoms in block 39
Block first atom: 6434
Blocpdb> 166 atoms in block 40
Block first atom: 6606
Blocpdb> 168 atoms in block 41
Block first atom: 6772
Blocpdb> 165 atoms in block 42
Block first atom: 6940
Blocpdb> 159 atoms in block 43
Block first atom: 7105
Blocpdb> 181 atoms in block 44
Block first atom: 7264
Blocpdb> 179 atoms in block 45
Block first atom: 7445
Blocpdb> 181 atoms in block 46
Block first atom: 7624
Blocpdb> 175 atoms in block 47
Block first atom: 7805
Blocpdb> 183 atoms in block 48
Block first atom: 7980
Blocpdb> 188 atoms in block 49
Block first atom: 8163
Blocpdb> 163 atoms in block 50
Block first atom: 8351
Blocpdb> 161 atoms in block 51
Block first atom: 8514
Blocpdb> 159 atoms in block 52
Block first atom: 8675
Blocpdb> 153 atoms in block 53
Block first atom: 8834
Blocpdb> 155 atoms in block 54
Block first atom: 8987
Blocpdb> 174 atoms in block 55
Block first atom: 9142
Blocpdb> 155 atoms in block 56
Block first atom: 9316
Blocpdb> 180 atoms in block 57
Block first atom: 9471
Blocpdb> 172 atoms in block 58
Block first atom: 9651
Blocpdb> 179 atoms in block 59
Block first atom: 9823
Blocpdb> 172 atoms in block 60
Block first atom: 10002
Blocpdb> 162 atoms in block 61
Block first atom: 10174
Blocpdb> 172 atoms in block 62
Block first atom: 10336
Blocpdb> 166 atoms in block 63
Block first atom: 10508
Blocpdb> 168 atoms in block 64
Block first atom: 10674
Blocpdb> 165 atoms in block 65
Block first atom: 10842
Blocpdb> 159 atoms in block 66
Block first atom: 11007
Blocpdb> 181 atoms in block 67
Block first atom: 11166
Blocpdb> 179 atoms in block 68
Block first atom: 11347
Blocpdb> 181 atoms in block 69
Block first atom: 11526
Blocpdb> 175 atoms in block 70
Block first atom: 11707
Blocpdb> 183 atoms in block 71
Block first atom: 11882
Blocpdb> 188 atoms in block 72
Block first atom: 12065
Blocpdb> 163 atoms in block 73
Block first atom: 12253
Blocpdb> 161 atoms in block 74
Block first atom: 12416
Blocpdb> 159 atoms in block 75
Block first atom: 12577
Blocpdb> 153 atoms in block 76
Block first atom: 12736
Blocpdb> 155 atoms in block 77
Block first atom: 12889
Blocpdb> 174 atoms in block 78
Block first atom: 13044
Blocpdb> 155 atoms in block 79
Block first atom: 13218
Blocpdb> 180 atoms in block 80
Block first atom: 13373
Blocpdb> 172 atoms in block 81
Block first atom: 13553
Blocpdb> 179 atoms in block 82
Block first atom: 13725
Blocpdb> 172 atoms in block 83
Block first atom: 13904
Blocpdb> 162 atoms in block 84
Block first atom: 14076
Blocpdb> 172 atoms in block 85
Block first atom: 14238
Blocpdb> 166 atoms in block 86
Block first atom: 14410
Blocpdb> 168 atoms in block 87
Block first atom: 14576
Blocpdb> 165 atoms in block 88
Block first atom: 14744
Blocpdb> 159 atoms in block 89
Block first atom: 14909
Blocpdb> 181 atoms in block 90
Block first atom: 15068
Blocpdb> 179 atoms in block 91
Block first atom: 15249
Blocpdb> 181 atoms in block 92
Block first atom: 15428
Blocpdb> 175 atoms in block 93
Block first atom: 15609
Blocpdb> 183 atoms in block 94
Block first atom: 15784
Blocpdb> 188 atoms in block 95
Block first atom: 15967
Blocpdb> 163 atoms in block 96
Block first atom: 16155
Blocpdb> 161 atoms in block 97
Block first atom: 16318
Blocpdb> 159 atoms in block 98
Block first atom: 16479
Blocpdb> 153 atoms in block 99
Block first atom: 16638
Blocpdb> 155 atoms in block 100
Block first atom: 16791
Blocpdb> 174 atoms in block 101
Block first atom: 16946
Blocpdb> 155 atoms in block 102
Block first atom: 17120
Blocpdb> 180 atoms in block 103
Block first atom: 17275
Blocpdb> 172 atoms in block 104
Block first atom: 17455
Blocpdb> 179 atoms in block 105
Block first atom: 17627
Blocpdb> 172 atoms in block 106
Block first atom: 17806
Blocpdb> 162 atoms in block 107
Block first atom: 17978
Blocpdb> 172 atoms in block 108
Block first atom: 18140
Blocpdb> 166 atoms in block 109
Block first atom: 18312
Blocpdb> 168 atoms in block 110
Block first atom: 18478
Blocpdb> 165 atoms in block 111
Block first atom: 18646
Blocpdb> 159 atoms in block 112
Block first atom: 18811
Blocpdb> 181 atoms in block 113
Block first atom: 18970
Blocpdb> 179 atoms in block 114
Block first atom: 19151
Blocpdb> 181 atoms in block 115
Block first atom: 19330
Blocpdb> 175 atoms in block 116
Block first atom: 19511
Blocpdb> 183 atoms in block 117
Block first atom: 19686
Blocpdb> 188 atoms in block 118
Block first atom: 19869
Blocpdb> 163 atoms in block 119
Block first atom: 20057
Blocpdb> 161 atoms in block 120
Block first atom: 20220
Blocpdb> 159 atoms in block 121
Block first atom: 20381
Blocpdb> 153 atoms in block 122
Block first atom: 20540
Blocpdb> 155 atoms in block 123
Block first atom: 20693
Blocpdb> 174 atoms in block 124
Block first atom: 20848
Blocpdb> 155 atoms in block 125
Block first atom: 21022
Blocpdb> 180 atoms in block 126
Block first atom: 21177
Blocpdb> 172 atoms in block 127
Block first atom: 21357
Blocpdb> 179 atoms in block 128
Block first atom: 21529
Blocpdb> 172 atoms in block 129
Block first atom: 21708
Blocpdb> 162 atoms in block 130
Block first atom: 21880
Blocpdb> 172 atoms in block 131
Block first atom: 22042
Blocpdb> 166 atoms in block 132
Block first atom: 22214
Blocpdb> 168 atoms in block 133
Block first atom: 22380
Blocpdb> 165 atoms in block 134
Block first atom: 22548
Blocpdb> 159 atoms in block 135
Block first atom: 22713
Blocpdb> 181 atoms in block 136
Block first atom: 22872
Blocpdb> 179 atoms in block 137
Block first atom: 23053
Blocpdb> 181 atoms in block 138
Block first atom: 23232
Blocpdb> 159 atoms in block 139
Block first atom: 23413
Blocpdb> 183 atoms in block 140
Block first atom: 23572
Blocpdb> 63 atoms in block 141
Block first atom: 23755
Blocpdb> 159 atoms in block 142
Block first atom: 23818
Blocpdb> 161 atoms in block 143
Block first atom: 23977
Blocpdb> 164 atoms in block 144
Block first atom: 24138
Blocpdb> 166 atoms in block 145
Block first atom: 24302
Blocpdb> 166 atoms in block 146
Block first atom: 24468
Blocpdb> 172 atoms in block 147
Block first atom: 24634
Blocpdb> 152 atoms in block 148
Block first atom: 24806
Blocpdb> 20 atoms in block 149
Block first atom: 24958
Blocpdb> 159 atoms in block 150
Block first atom: 24978
Blocpdb> 181 atoms in block 151
Block first atom: 25137
Blocpdb> 169 atoms in block 152
Block first atom: 25318
Blocpdb> 169 atoms in block 153
Block first atom: 25487
Blocpdb> 159 atoms in block 154
Block first atom: 25656
Blocpdb> 167 atoms in block 155
Block first atom: 25815
Blocpdb> 157 atoms in block 156
Block first atom: 25982
Blocpdb> 163 atoms in block 157
Block first atom: 26139
Blocpdb> 167 atoms in block 158
Block first atom: 26302
Blocpdb> 90 atoms in block 159
Block first atom: 26469
Blocpdb> 163 atoms in block 160
Block first atom: 26559
Blocpdb> 177 atoms in block 161
Block first atom: 26722
Blocpdb> 170 atoms in block 162
Block first atom: 26899
Blocpdb> 160 atoms in block 163
Block first atom: 27069
Blocpdb> 163 atoms in block 164
Block first atom: 27229
Blocpdb> 170 atoms in block 165
Block first atom: 27392
Blocpdb> 158 atoms in block 166
Block first atom: 27562
Blocpdb> 165 atoms in block 167
Block first atom: 27720
Blocpdb> 160 atoms in block 168
Block first atom: 27885
Blocpdb> 63 atoms in block 169
Block first atom: 28045
Blocpdb> 159 atoms in block 170
Block first atom: 28108
Blocpdb> 181 atoms in block 171
Block first atom: 28267
Blocpdb> 169 atoms in block 172
Block first atom: 28448
Blocpdb> 169 atoms in block 173
Block first atom: 28617
Blocpdb> 159 atoms in block 174
Block first atom: 28786
Blocpdb> 167 atoms in block 175
Block first atom: 28945
Blocpdb> 157 atoms in block 176
Block first atom: 29112
Blocpdb> 163 atoms in block 177
Block first atom: 29269
Blocpdb> 167 atoms in block 178
Block first atom: 29432
Blocpdb> 90 atoms in block 179
Block first atom: 29599
Blocpdb> 160 atoms in block 180
Block first atom: 29689
Blocpdb> 184 atoms in block 181
Block first atom: 29849
Blocpdb> 165 atoms in block 182
Block first atom: 30033
Blocpdb> 168 atoms in block 183
Block first atom: 30198
Blocpdb> 162 atoms in block 184
Block first atom: 30366
Blocpdb> 166 atoms in block 185
Block first atom: 30528
Blocpdb> 158 atoms in block 186
Block first atom: 30694
Blocpdb> 163 atoms in block 187
Block first atom: 30852
Blocpdb> 166 atoms in block 188
Block first atom: 31015
Blocpdb> 82 atoms in block 189
Block first atom: 31181
Blocpdb> 159 atoms in block 190
Block first atom: 31263
Blocpdb> 181 atoms in block 191
Block first atom: 31422
Blocpdb> 169 atoms in block 192
Block first atom: 31603
Blocpdb> 169 atoms in block 193
Block first atom: 31772
Blocpdb> 159 atoms in block 194
Block first atom: 31941
Blocpdb> 167 atoms in block 195
Block first atom: 32100
Blocpdb> 157 atoms in block 196
Block first atom: 32267
Blocpdb> 163 atoms in block 197
Block first atom: 32424
Blocpdb> 167 atoms in block 198
Block first atom: 32587
Blocpdb> 90 atoms in block 199
Block first atom: 32754
Blocpdb> 288 atoms in block 200
Block first atom: 32844
Blocpdb> 91 atoms in block 201
Block first atom: 33131
Blocpdb> 201 blocks.
Blocpdb> At most, 288 atoms in each of them.
Blocpdb> At least, 20 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: 86857921 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 0m0.188s
user 0m0.184s
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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