*** ***
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 = 22090213271411502.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 22090213271411502.atom to be opened.
Openam> File opened: 22090213271411502.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 = 3128
First residue number = 1
Last residue number = 329
Number of atoms found = 48612
Mean number per residue = 15.5
Pdbmat> Coordinate statistics:
= 197.042748 +/- 40.159973 From: 102.076000 To: 288.096000
= 207.659165 +/- 35.335222 From: 115.879000 To: 292.107000
= 270.918385 +/- 30.570787 From: 191.245000 To: 341.694000
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 -34.4780 % Filled.
Pdbmat> 35607439 non-zero elements.
Pdbmat> 3924598 atom-atom interactions.
Pdbmat> Number per atom= 161.47 +/- 50.31
Maximum number = 256
Minimum number = 17
Pdbmat> Matrix trace = 7.849196E+07
Pdbmat> Larger element = 910.592
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3128 non-zero elements, NRBL set to 16
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 = 22090213271411502.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 16
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 22090213271411502.atom to be opened.
Openam> file on opening on unit 11:
22090213271411502.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 48612 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 16 residue(s) per block.
Blocpdb> 3128 residues.
Blocpdb> 247 atoms in block 1
Block first atom: 1
Blocpdb> 254 atoms in block 2
Block first atom: 248
Blocpdb> 239 atoms in block 3
Block first atom: 502
Blocpdb> 238 atoms in block 4
Block first atom: 741
Blocpdb> 252 atoms in block 5
Block first atom: 979
Blocpdb> 227 atoms in block 6
Block first atom: 1231
Blocpdb> 272 atoms in block 7
Block first atom: 1458
Blocpdb> 251 atoms in block 8
Block first atom: 1730
Blocpdb> 247 atoms in block 9
Block first atom: 1981
Blocpdb> 263 atoms in block 10
Block first atom: 2228
Blocpdb> 247 atoms in block 11
Block first atom: 2491
Blocpdb> 243 atoms in block 12
Block first atom: 2738
Blocpdb> 273 atoms in block 13
Block first atom: 2981
Blocpdb> 263 atoms in block 14
Block first atom: 3254
Blocpdb> 254 atoms in block 15
Block first atom: 3517
Blocpdb> 267 atoms in block 16
Block first atom: 3771
Blocpdb> 270 atoms in block 17
Block first atom: 4038
Blocpdb> 253 atoms in block 18
Block first atom: 4308
Blocpdb> 258 atoms in block 19
Block first atom: 4561
Blocpdb> 245 atoms in block 20
Block first atom: 4819
Blocpdb> 239 atoms in block 21
Block first atom: 5064
Blocpdb> 262 atoms in block 22
Block first atom: 5303
Blocpdb> 271 atoms in block 23
Block first atom: 5565
Blocpdb> 234 atoms in block 24
Block first atom: 5836
Blocpdb> 268 atoms in block 25
Block first atom: 6070
Blocpdb> 272 atoms in block 26
Block first atom: 6338
Blocpdb> 265 atoms in block 27
Block first atom: 6610
Blocpdb> 254 atoms in block 28
Block first atom: 6875
Blocpdb> 241 atoms in block 29
Block first atom: 7129
Blocpdb> 244 atoms in block 30
Block first atom: 7370
Blocpdb> 263 atoms in block 31
Block first atom: 7614
Blocpdb> 242 atoms in block 32
Block first atom: 7877
Blocpdb> 233 atoms in block 33
Block first atom: 8119
Blocpdb> 271 atoms in block 34
Block first atom: 8352
Blocpdb> 223 atoms in block 35
Block first atom: 8623
Blocpdb> 256 atoms in block 36
Block first atom: 8846
Blocpdb> 269 atoms in block 37
Block first atom: 9102
Blocpdb> 232 atoms in block 38
Block first atom: 9371
Blocpdb> 266 atoms in block 39
Block first atom: 9603
Blocpdb> 267 atoms in block 40
Block first atom: 9869
Blocpdb> 242 atoms in block 41
Block first atom: 10136
Blocpdb> 231 atoms in block 42
Block first atom: 10378
Blocpdb> 235 atoms in block 43
Block first atom: 10609
Blocpdb> 296 atoms in block 44
Block first atom: 10844
Blocpdb> 294 atoms in block 45
Block first atom: 11140
Blocpdb> 245 atoms in block 46
Block first atom: 11434
Blocpdb> 220 atoms in block 47
Block first atom: 11679
Blocpdb> 221 atoms in block 48
Block first atom: 11899
Blocpdb> 256 atoms in block 49
Block first atom: 12120
Blocpdb> 218 atoms in block 50
Block first atom: 12376
Blocpdb> 246 atoms in block 51
Block first atom: 12594
Blocpdb> 270 atoms in block 52
Block first atom: 12840
Blocpdb> 234 atoms in block 53
Block first atom: 13110
Blocpdb> 224 atoms in block 54
Block first atom: 13344
Blocpdb> 157 atoms in block 55
Block first atom: 13568
Blocpdb> 257 atoms in block 56
Block first atom: 13725
Blocpdb> 237 atoms in block 57
Block first atom: 13982
Blocpdb> 249 atoms in block 58
Block first atom: 14219
Blocpdb> 246 atoms in block 59
Block first atom: 14468
Blocpdb> 234 atoms in block 60
Block first atom: 14714
Blocpdb> 244 atoms in block 61
Block first atom: 14948
Blocpdb> 267 atoms in block 62
Block first atom: 15192
Blocpdb> 255 atoms in block 63
Block first atom: 15459
Blocpdb> 235 atoms in block 64
Block first atom: 15714
Blocpdb> 253 atoms in block 65
Block first atom: 15949
Blocpdb> 235 atoms in block 66
Block first atom: 16202
Blocpdb> 206 atoms in block 67
Block first atom: 16437
Blocpdb> 270 atoms in block 68
Block first atom: 16643
Blocpdb> 243 atoms in block 69
Block first atom: 16913
Blocpdb> 252 atoms in block 70
Block first atom: 17156
Blocpdb> 283 atoms in block 71
Block first atom: 17408
Blocpdb> 235 atoms in block 72
Block first atom: 17691
Blocpdb> 270 atoms in block 73
Block first atom: 17926
Blocpdb> 210 atoms in block 74
Block first atom: 18196
Blocpdb> 272 atoms in block 75
Block first atom: 18406
Blocpdb> 192 atoms in block 76
Block first atom: 18678
Blocpdb> 221 atoms in block 77
Block first atom: 18870
Blocpdb> 114 atoms in block 78
Block first atom: 19091
Blocpdb> 276 atoms in block 79
Block first atom: 19205
Blocpdb> 291 atoms in block 80
Block first atom: 19481
Blocpdb> 276 atoms in block 81
Block first atom: 19772
Blocpdb> 253 atoms in block 82
Block first atom: 20048
Blocpdb> 253 atoms in block 83
Block first atom: 20301
Blocpdb> 205 atoms in block 84
Block first atom: 20554
Blocpdb> 244 atoms in block 85
Block first atom: 20759
Blocpdb> 274 atoms in block 86
Block first atom: 21003
Blocpdb> 257 atoms in block 87
Block first atom: 21277
Blocpdb> 228 atoms in block 88
Block first atom: 21534
Blocpdb> 234 atoms in block 89
Block first atom: 21762
Blocpdb> 256 atoms in block 90
Block first atom: 21996
Blocpdb> 251 atoms in block 91
Block first atom: 22252
Blocpdb> 211 atoms in block 92
Block first atom: 22503
Blocpdb> 260 atoms in block 93
Block first atom: 22714
Blocpdb> 257 atoms in block 94
Block first atom: 22974
Blocpdb> 243 atoms in block 95
Block first atom: 23231
Blocpdb> 222 atoms in block 96
Block first atom: 23474
Blocpdb> 234 atoms in block 97
Block first atom: 23696
Blocpdb> 232 atoms in block 98
Block first atom: 23930
Blocpdb> 145 atoms in block 99
Block first atom: 24162
Blocpdb> 247 atoms in block 100
Block first atom: 24307
Blocpdb> 254 atoms in block 101
Block first atom: 24554
Blocpdb> 239 atoms in block 102
Block first atom: 24808
Blocpdb> 238 atoms in block 103
Block first atom: 25047
Blocpdb> 252 atoms in block 104
Block first atom: 25285
Blocpdb> 227 atoms in block 105
Block first atom: 25537
Blocpdb> 272 atoms in block 106
Block first atom: 25764
Blocpdb> 251 atoms in block 107
Block first atom: 26036
Blocpdb> 247 atoms in block 108
Block first atom: 26287
Blocpdb> 263 atoms in block 109
Block first atom: 26534
Blocpdb> 247 atoms in block 110
Block first atom: 26797
Blocpdb> 243 atoms in block 111
Block first atom: 27044
Blocpdb> 273 atoms in block 112
Block first atom: 27287
Blocpdb> 263 atoms in block 113
Block first atom: 27560
Blocpdb> 254 atoms in block 114
Block first atom: 27823
Blocpdb> 267 atoms in block 115
Block first atom: 28077
Blocpdb> 270 atoms in block 116
Block first atom: 28344
Blocpdb> 253 atoms in block 117
Block first atom: 28614
Blocpdb> 258 atoms in block 118
Block first atom: 28867
Blocpdb> 245 atoms in block 119
Block first atom: 29125
Blocpdb> 239 atoms in block 120
Block first atom: 29370
Blocpdb> 262 atoms in block 121
Block first atom: 29609
Blocpdb> 271 atoms in block 122
Block first atom: 29871
Blocpdb> 234 atoms in block 123
Block first atom: 30142
Blocpdb> 268 atoms in block 124
Block first atom: 30376
Blocpdb> 272 atoms in block 125
Block first atom: 30644
Blocpdb> 265 atoms in block 126
Block first atom: 30916
Blocpdb> 254 atoms in block 127
Block first atom: 31181
Blocpdb> 241 atoms in block 128
Block first atom: 31435
Blocpdb> 244 atoms in block 129
Block first atom: 31676
Blocpdb> 263 atoms in block 130
Block first atom: 31920
Blocpdb> 242 atoms in block 131
Block first atom: 32183
Blocpdb> 233 atoms in block 132
Block first atom: 32425
Blocpdb> 271 atoms in block 133
Block first atom: 32658
Blocpdb> 223 atoms in block 134
Block first atom: 32929
Blocpdb> 256 atoms in block 135
Block first atom: 33152
Blocpdb> 269 atoms in block 136
Block first atom: 33408
Blocpdb> 232 atoms in block 137
Block first atom: 33677
Blocpdb> 266 atoms in block 138
Block first atom: 33909
Blocpdb> 267 atoms in block 139
Block first atom: 34175
Blocpdb> 242 atoms in block 140
Block first atom: 34442
Blocpdb> 231 atoms in block 141
Block first atom: 34684
Blocpdb> 235 atoms in block 142
Block first atom: 34915
Blocpdb> 296 atoms in block 143
Block first atom: 35150
Blocpdb> 294 atoms in block 144
Block first atom: 35446
Blocpdb> 245 atoms in block 145
Block first atom: 35740
Blocpdb> 220 atoms in block 146
Block first atom: 35985
Blocpdb> 221 atoms in block 147
Block first atom: 36205
Blocpdb> 256 atoms in block 148
Block first atom: 36426
Blocpdb> 218 atoms in block 149
Block first atom: 36682
Blocpdb> 246 atoms in block 150
Block first atom: 36900
Blocpdb> 270 atoms in block 151
Block first atom: 37146
Blocpdb> 234 atoms in block 152
Block first atom: 37416
Blocpdb> 224 atoms in block 153
Block first atom: 37650
Blocpdb> 157 atoms in block 154
Block first atom: 37874
Blocpdb> 257 atoms in block 155
Block first atom: 38031
Blocpdb> 237 atoms in block 156
Block first atom: 38288
Blocpdb> 249 atoms in block 157
Block first atom: 38525
Blocpdb> 246 atoms in block 158
Block first atom: 38774
Blocpdb> 234 atoms in block 159
Block first atom: 39020
Blocpdb> 244 atoms in block 160
Block first atom: 39254
Blocpdb> 267 atoms in block 161
Block first atom: 39498
Blocpdb> 255 atoms in block 162
Block first atom: 39765
Blocpdb> 235 atoms in block 163
Block first atom: 40020
Blocpdb> 253 atoms in block 164
Block first atom: 40255
Blocpdb> 235 atoms in block 165
Block first atom: 40508
Blocpdb> 206 atoms in block 166
Block first atom: 40743
Blocpdb> 270 atoms in block 167
Block first atom: 40949
Blocpdb> 243 atoms in block 168
Block first atom: 41219
Blocpdb> 252 atoms in block 169
Block first atom: 41462
Blocpdb> 283 atoms in block 170
Block first atom: 41714
Blocpdb> 235 atoms in block 171
Block first atom: 41997
Blocpdb> 270 atoms in block 172
Block first atom: 42232
Blocpdb> 210 atoms in block 173
Block first atom: 42502
Blocpdb> 272 atoms in block 174
Block first atom: 42712
Blocpdb> 192 atoms in block 175
Block first atom: 42984
Blocpdb> 221 atoms in block 176
Block first atom: 43176
Blocpdb> 114 atoms in block 177
Block first atom: 43397
Blocpdb> 276 atoms in block 178
Block first atom: 43511
Blocpdb> 291 atoms in block 179
Block first atom: 43787
Blocpdb> 276 atoms in block 180
Block first atom: 44078
Blocpdb> 253 atoms in block 181
Block first atom: 44354
Blocpdb> 253 atoms in block 182
Block first atom: 44607
Blocpdb> 205 atoms in block 183
Block first atom: 44860
Blocpdb> 244 atoms in block 184
Block first atom: 45065
Blocpdb> 274 atoms in block 185
Block first atom: 45309
Blocpdb> 257 atoms in block 186
Block first atom: 45583
Blocpdb> 228 atoms in block 187
Block first atom: 45840
Blocpdb> 234 atoms in block 188
Block first atom: 46068
Blocpdb> 256 atoms in block 189
Block first atom: 46302
Blocpdb> 251 atoms in block 190
Block first atom: 46558
Blocpdb> 211 atoms in block 191
Block first atom: 46809
Blocpdb> 260 atoms in block 192
Block first atom: 47020
Blocpdb> 257 atoms in block 193
Block first atom: 47280
Blocpdb> 243 atoms in block 194
Block first atom: 47537
Blocpdb> 222 atoms in block 195
Block first atom: 47780
Blocpdb> 234 atoms in block 196
Block first atom: 48002
Blocpdb> 232 atoms in block 197
Block first atom: 48236
Blocpdb> 145 atoms in block 198
Block first atom: 48467
Blocpdb> 198 blocks.
Blocpdb> At most, 296 atoms in each of them.
Blocpdb> At least, 114 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: 130290913 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 0m0.184s
user 0m0.176s
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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