*** ***
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 = 22121818065151613.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 22121818065151613.atom to be opened.
Openam> File opened: 22121818065151613.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 = 4084
First residue number = 5
Last residue number = 166
Number of atoms found = 32038
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 146.533569 +/- 16.702193 From: 97.972000 To: 190.265000
= 147.196863 +/- 21.758019 From: 87.639000 To: 203.101000
= 133.554071 +/- 69.653081 From: 3.437000 To: 284.593000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> residue:'ADP ' is not a well known amino-acid.
%Pdbmat-W> residue:'MG ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 18 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 3.7716 % Filled.
Pdbmat> 12221268 non-zero elements.
Pdbmat> 1336780 atom-atom interactions.
Pdbmat> Number per atom= 83.45 +/- 20.14
Maximum number = 132
Minimum number = 13
Pdbmat> Matrix trace = 2.673560E+07
Pdbmat> Larger element = 511.071
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
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 = 22121818065151613.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 22121818065151613.atom to be opened.
Openam> file on opening on unit 11:
22121818065151613.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 32038 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> 4084 residues.
Blocpdb> 103 atoms in block 1
Block first atom: 1
Blocpdb> 114 atoms in block 2
Block first atom: 104
Blocpdb> 122 atoms in block 3
Block first atom: 218
Blocpdb> 124 atoms in block 4
Block first atom: 340
Blocpdb> 137 atoms in block 5
Block first atom: 464
Blocpdb> 145 atoms in block 6
Block first atom: 601
Blocpdb> 124 atoms in block 7
Block first atom: 746
Blocpdb> 131 atoms in block 8
Block first atom: 870
Blocpdb> 120 atoms in block 9
Block first atom: 1001
Blocpdb> 110 atoms in block 10
Block first atom: 1121
Blocpdb> 131 atoms in block 11
Block first atom: 1231
Blocpdb> 131 atoms in block 12
Block first atom: 1362
Blocpdb> 130 atoms in block 13
Block first atom: 1493
Blocpdb> 131 atoms in block 14
Block first atom: 1623
Blocpdb> 117 atoms in block 15
Block first atom: 1754
Blocpdb> 126 atoms in block 16
Block first atom: 1871
Blocpdb> 123 atoms in block 17
Block first atom: 1997
Blocpdb> 131 atoms in block 18
Block first atom: 2120
Blocpdb> 115 atoms in block 19
Block first atom: 2251
Blocpdb> 120 atoms in block 20
Block first atom: 2366
Blocpdb> 137 atoms in block 21
Block first atom: 2486
Blocpdb> 121 atoms in block 22
Block first atom: 2623
Blocpdb> 129 atoms in block 23
Block first atom: 2744
Blocpdb> 15 atoms in block 24
Block first atom: 2873
Blocpdb> 28 atoms in block 25
Block first atom: 2888
Blocpdb> 103 atoms in block 26
Block first atom: 2916
Blocpdb> 114 atoms in block 27
Block first atom: 3019
Blocpdb> 122 atoms in block 28
Block first atom: 3133
Blocpdb> 124 atoms in block 29
Block first atom: 3255
Blocpdb> 137 atoms in block 30
Block first atom: 3379
Blocpdb> 145 atoms in block 31
Block first atom: 3516
Blocpdb> 124 atoms in block 32
Block first atom: 3661
Blocpdb> 131 atoms in block 33
Block first atom: 3785
Blocpdb> 120 atoms in block 34
Block first atom: 3916
Blocpdb> 110 atoms in block 35
Block first atom: 4036
Blocpdb> 131 atoms in block 36
Block first atom: 4146
Blocpdb> 131 atoms in block 37
Block first atom: 4277
Blocpdb> 130 atoms in block 38
Block first atom: 4408
Blocpdb> 131 atoms in block 39
Block first atom: 4538
Blocpdb> 117 atoms in block 40
Block first atom: 4669
Blocpdb> 126 atoms in block 41
Block first atom: 4786
Blocpdb> 123 atoms in block 42
Block first atom: 4912
Blocpdb> 131 atoms in block 43
Block first atom: 5035
Blocpdb> 115 atoms in block 44
Block first atom: 5166
Blocpdb> 120 atoms in block 45
Block first atom: 5281
Blocpdb> 137 atoms in block 46
Block first atom: 5401
Blocpdb> 121 atoms in block 47
Block first atom: 5538
Blocpdb> 129 atoms in block 48
Block first atom: 5659
Blocpdb> 15 atoms in block 49
Block first atom: 5788
Blocpdb> 28 atoms in block 50
Block first atom: 5803
Blocpdb> 103 atoms in block 51
Block first atom: 5831
Blocpdb> 114 atoms in block 52
Block first atom: 5934
Blocpdb> 122 atoms in block 53
Block first atom: 6048
Blocpdb> 124 atoms in block 54
Block first atom: 6170
Blocpdb> 137 atoms in block 55
Block first atom: 6294
Blocpdb> 145 atoms in block 56
Block first atom: 6431
Blocpdb> 124 atoms in block 57
Block first atom: 6576
Blocpdb> 131 atoms in block 58
Block first atom: 6700
Blocpdb> 120 atoms in block 59
Block first atom: 6831
Blocpdb> 110 atoms in block 60
Block first atom: 6951
Blocpdb> 131 atoms in block 61
Block first atom: 7061
Blocpdb> 131 atoms in block 62
Block first atom: 7192
Blocpdb> 130 atoms in block 63
Block first atom: 7323
Blocpdb> 131 atoms in block 64
Block first atom: 7453
Blocpdb> 117 atoms in block 65
Block first atom: 7584
Blocpdb> 126 atoms in block 66
Block first atom: 7701
Blocpdb> 123 atoms in block 67
Block first atom: 7827
Blocpdb> 131 atoms in block 68
Block first atom: 7950
Blocpdb> 115 atoms in block 69
Block first atom: 8081
Blocpdb> 120 atoms in block 70
Block first atom: 8196
Blocpdb> 137 atoms in block 71
Block first atom: 8316
Blocpdb> 121 atoms in block 72
Block first atom: 8453
Blocpdb> 129 atoms in block 73
Block first atom: 8574
Blocpdb> 15 atoms in block 74
Block first atom: 8703
Blocpdb> 28 atoms in block 75
Block first atom: 8718
Blocpdb> 103 atoms in block 76
Block first atom: 8746
Blocpdb> 114 atoms in block 77
Block first atom: 8849
Blocpdb> 29 atoms in block 78
Block first atom: 8963
Blocpdb> 75 atoms in block 79
Block first atom: 8992
Blocpdb> 135 atoms in block 80
Block first atom: 9067
Blocpdb> 150 atoms in block 81
Block first atom: 9202
Blocpdb> 121 atoms in block 82
Block first atom: 9352
Blocpdb> 136 atoms in block 83
Block first atom: 9473
Blocpdb> 122 atoms in block 84
Block first atom: 9609
Blocpdb> 104 atoms in block 85
Block first atom: 9731
Blocpdb> 127 atoms in block 86
Block first atom: 9835
Blocpdb> 131 atoms in block 87
Block first atom: 9962
Blocpdb> 131 atoms in block 88
Block first atom: 10093
Blocpdb> 134 atoms in block 89
Block first atom: 10224
Blocpdb> 112 atoms in block 90
Block first atom: 10358
Blocpdb> 130 atoms in block 91
Block first atom: 10470
Blocpdb> 127 atoms in block 92
Block first atom: 10600
Blocpdb> 123 atoms in block 93
Block first atom: 10727
Blocpdb> 121 atoms in block 94
Block first atom: 10850
Blocpdb> 125 atoms in block 95
Block first atom: 10971
Blocpdb> 122 atoms in block 96
Block first atom: 11096
Blocpdb> 118 atoms in block 97
Block first atom: 11218
Blocpdb> 138 atoms in block 98
Block first atom: 11336
Blocpdb> 57 atoms in block 99
Block first atom: 11474
Blocpdb> 28 atoms in block 100
Block first atom: 11531
Blocpdb> 114 atoms in block 101
Block first atom: 11559
Blocpdb> 129 atoms in block 102
Block first atom: 11673
Blocpdb> 127 atoms in block 103
Block first atom: 11802
Blocpdb> 134 atoms in block 104
Block first atom: 11929
Blocpdb> 134 atoms in block 105
Block first atom: 12063
Blocpdb> 115 atoms in block 106
Block first atom: 12197
Blocpdb> 125 atoms in block 107
Block first atom: 12312
Blocpdb> 120 atoms in block 108
Block first atom: 12437
Blocpdb> 133 atoms in block 109
Block first atom: 12557
Blocpdb> 121 atoms in block 110
Block first atom: 12690
Blocpdb> 118 atoms in block 111
Block first atom: 12811
Blocpdb> 111 atoms in block 112
Block first atom: 12929
Blocpdb> 28 atoms in block 113
Block first atom: 13040
Blocpdb> 114 atoms in block 114
Block first atom: 13068
Blocpdb> 129 atoms in block 115
Block first atom: 13182
Blocpdb> 127 atoms in block 116
Block first atom: 13311
Blocpdb> 134 atoms in block 117
Block first atom: 13438
Blocpdb> 134 atoms in block 118
Block first atom: 13572
Blocpdb> 115 atoms in block 119
Block first atom: 13706
Blocpdb> 125 atoms in block 120
Block first atom: 13821
Blocpdb> 120 atoms in block 121
Block first atom: 13946
Blocpdb> 133 atoms in block 122
Block first atom: 14066
Blocpdb> 121 atoms in block 123
Block first atom: 14199
Blocpdb> 118 atoms in block 124
Block first atom: 14320
Blocpdb> 111 atoms in block 125
Block first atom: 14438
Blocpdb> 28 atoms in block 126
Block first atom: 14549
Blocpdb> 103 atoms in block 127
Block first atom: 14577
Blocpdb> 114 atoms in block 128
Block first atom: 14680
Blocpdb> 29 atoms in block 129
Block first atom: 14794
Blocpdb> 75 atoms in block 130
Block first atom: 14823
Blocpdb> 135 atoms in block 131
Block first atom: 14898
Blocpdb> 150 atoms in block 132
Block first atom: 15033
Blocpdb> 121 atoms in block 133
Block first atom: 15183
Blocpdb> 136 atoms in block 134
Block first atom: 15304
Blocpdb> 122 atoms in block 135
Block first atom: 15440
Blocpdb> 15 atoms in block 136
Block first atom: 15562
Blocpdb> 120 atoms in block 137
Block first atom: 15577
Blocpdb> 133 atoms in block 138
Block first atom: 15697
Blocpdb> 51 atoms in block 139
Block first atom: 15830
Blocpdb> 103 atoms in block 140
Block first atom: 15881
Blocpdb> 114 atoms in block 141
Block first atom: 15984
Blocpdb> 29 atoms in block 142
Block first atom: 16098
Blocpdb> 75 atoms in block 143
Block first atom: 16127
Blocpdb> 135 atoms in block 144
Block first atom: 16202
Blocpdb> 150 atoms in block 145
Block first atom: 16337
Blocpdb> 121 atoms in block 146
Block first atom: 16487
Blocpdb> 136 atoms in block 147
Block first atom: 16608
Blocpdb> 122 atoms in block 148
Block first atom: 16744
Blocpdb> 15 atoms in block 149
Block first atom: 16866
Blocpdb> 120 atoms in block 150
Block first atom: 16881
Blocpdb> 133 atoms in block 151
Block first atom: 17001
Blocpdb> 51 atoms in block 152
Block first atom: 17134
Blocpdb> 113 atoms in block 153
Block first atom: 17185
Blocpdb> 134 atoms in block 154
Block first atom: 17298
Blocpdb> 127 atoms in block 155
Block first atom: 17432
Blocpdb> 116 atoms in block 156
Block first atom: 17559
Blocpdb> 135 atoms in block 157
Block first atom: 17675
Blocpdb> 132 atoms in block 158
Block first atom: 17810
Blocpdb> 130 atoms in block 159
Block first atom: 17942
Blocpdb> 121 atoms in block 160
Block first atom: 18072
Blocpdb> 137 atoms in block 161
Block first atom: 18193
Blocpdb> 109 atoms in block 162
Block first atom: 18330
Blocpdb> 29 atoms in block 163
Block first atom: 18439
Blocpdb> 103 atoms in block 164
Block first atom: 18468
Blocpdb> 114 atoms in block 165
Block first atom: 18571
Blocpdb> 29 atoms in block 166
Block first atom: 18685
Blocpdb> 75 atoms in block 167
Block first atom: 18714
Blocpdb> 135 atoms in block 168
Block first atom: 18789
Blocpdb> 150 atoms in block 169
Block first atom: 18924
Blocpdb> 121 atoms in block 170
Block first atom: 19074
Blocpdb> 136 atoms in block 171
Block first atom: 19195
Blocpdb> 122 atoms in block 172
Block first atom: 19331
Blocpdb> 104 atoms in block 173
Block first atom: 19453
Blocpdb> 127 atoms in block 174
Block first atom: 19557
Blocpdb> 131 atoms in block 175
Block first atom: 19684
Blocpdb> 131 atoms in block 176
Block first atom: 19815
Blocpdb> 134 atoms in block 177
Block first atom: 19946
Blocpdb> 112 atoms in block 178
Block first atom: 20080
Blocpdb> 130 atoms in block 179
Block first atom: 20192
Blocpdb> 127 atoms in block 180
Block first atom: 20322
Blocpdb> 123 atoms in block 181
Block first atom: 20449
Blocpdb> 121 atoms in block 182
Block first atom: 20572
Blocpdb> 125 atoms in block 183
Block first atom: 20693
Blocpdb> 122 atoms in block 184
Block first atom: 20818
Blocpdb> 118 atoms in block 185
Block first atom: 20940
Blocpdb> 138 atoms in block 186
Block first atom: 21058
Blocpdb> 57 atoms in block 187
Block first atom: 21196
Blocpdb> 28 atoms in block 188
Block first atom: 21253
Blocpdb> 103 atoms in block 189
Block first atom: 21281
Blocpdb> 114 atoms in block 190
Block first atom: 21384
Blocpdb> 29 atoms in block 191
Block first atom: 21498
Blocpdb> 75 atoms in block 192
Block first atom: 21527
Blocpdb> 135 atoms in block 193
Block first atom: 21602
Blocpdb> 150 atoms in block 194
Block first atom: 21737
Blocpdb> 121 atoms in block 195
Block first atom: 21887
Blocpdb> 136 atoms in block 196
Block first atom: 22008
Blocpdb> 122 atoms in block 197
Block first atom: 22144
Blocpdb> 104 atoms in block 198
Block first atom: 22266
Blocpdb> 127 atoms in block 199
Block first atom: 22370
Blocpdb> 131 atoms in block 200
Block first atom: 22497
Blocpdb> 131 atoms in block 201
Block first atom: 22628
Blocpdb> 134 atoms in block 202
Block first atom: 22759
Blocpdb> 112 atoms in block 203
Block first atom: 22893
Blocpdb> 130 atoms in block 204
Block first atom: 23005
Blocpdb> 127 atoms in block 205
Block first atom: 23135
Blocpdb> 123 atoms in block 206
Block first atom: 23262
Blocpdb> 121 atoms in block 207
Block first atom: 23385
Blocpdb> 125 atoms in block 208
Block first atom: 23506
Blocpdb> 122 atoms in block 209
Block first atom: 23631
Blocpdb> 118 atoms in block 210
Block first atom: 23753
Blocpdb> 138 atoms in block 211
Block first atom: 23871
Blocpdb> 57 atoms in block 212
Block first atom: 24009
Blocpdb> 28 atoms in block 213
Block first atom: 24066
Blocpdb> 103 atoms in block 214
Block first atom: 24094
Blocpdb> 114 atoms in block 215
Block first atom: 24197
Blocpdb> 29 atoms in block 216
Block first atom: 24311
Blocpdb> 75 atoms in block 217
Block first atom: 24340
Blocpdb> 135 atoms in block 218
Block first atom: 24415
Blocpdb> 150 atoms in block 219
Block first atom: 24550
Blocpdb> 121 atoms in block 220
Block first atom: 24700
Blocpdb> 136 atoms in block 221
Block first atom: 24821
Blocpdb> 122 atoms in block 222
Block first atom: 24957
Blocpdb> 104 atoms in block 223
Block first atom: 25079
Blocpdb> 127 atoms in block 224
Block first atom: 25183
Blocpdb> 131 atoms in block 225
Block first atom: 25310
Blocpdb> 131 atoms in block 226
Block first atom: 25441
Blocpdb> 134 atoms in block 227
Block first atom: 25572
Blocpdb> 112 atoms in block 228
Block first atom: 25706
Blocpdb> 130 atoms in block 229
Block first atom: 25818
Blocpdb> 127 atoms in block 230
Block first atom: 25948
Blocpdb> 123 atoms in block 231
Block first atom: 26075
Blocpdb> 121 atoms in block 232
Block first atom: 26198
Blocpdb> 125 atoms in block 233
Block first atom: 26319
Blocpdb> 122 atoms in block 234
Block first atom: 26444
Blocpdb> 118 atoms in block 235
Block first atom: 26566
Blocpdb> 138 atoms in block 236
Block first atom: 26684
Blocpdb> 57 atoms in block 237
Block first atom: 26822
Blocpdb> 28 atoms in block 238
Block first atom: 26879
Blocpdb> 113 atoms in block 239
Block first atom: 26907
Blocpdb> 134 atoms in block 240
Block first atom: 27020
Blocpdb> 127 atoms in block 241
Block first atom: 27154
Blocpdb> 116 atoms in block 242
Block first atom: 27281
Blocpdb> 135 atoms in block 243
Block first atom: 27397
Blocpdb> 132 atoms in block 244
Block first atom: 27532
Blocpdb> 130 atoms in block 245
Block first atom: 27664
Blocpdb> 121 atoms in block 246
Block first atom: 27794
Blocpdb> 137 atoms in block 247
Block first atom: 27915
Blocpdb> 109 atoms in block 248
Block first atom: 28052
Blocpdb> 29 atoms in block 249
Block first atom: 28161
Blocpdb> 113 atoms in block 250
Block first atom: 28190
Blocpdb> 134 atoms in block 251
Block first atom: 28303
Blocpdb> 127 atoms in block 252
Block first atom: 28437
Blocpdb> 116 atoms in block 253
Block first atom: 28564
Blocpdb> 135 atoms in block 254
Block first atom: 28680
Blocpdb> 132 atoms in block 255
Block first atom: 28815
Blocpdb> 130 atoms in block 256
Block first atom: 28947
Blocpdb> 121 atoms in block 257
Block first atom: 29077
Blocpdb> 137 atoms in block 258
Block first atom: 29198
Blocpdb> 109 atoms in block 259
Block first atom: 29335
Blocpdb> 29 atoms in block 260
Block first atom: 29444
Blocpdb> 113 atoms in block 261
Block first atom: 29473
Blocpdb> 134 atoms in block 262
Block first atom: 29586
Blocpdb> 127 atoms in block 263
Block first atom: 29720
Blocpdb> 116 atoms in block 264
Block first atom: 29847
Blocpdb> 135 atoms in block 265
Block first atom: 29963
Blocpdb> 132 atoms in block 266
Block first atom: 30098
Blocpdb> 130 atoms in block 267
Block first atom: 30230
Blocpdb> 121 atoms in block 268
Block first atom: 30360
Blocpdb> 137 atoms in block 269
Block first atom: 30481
Blocpdb> 109 atoms in block 270
Block first atom: 30618
Blocpdb> 29 atoms in block 271
Block first atom: 30727
Blocpdb> 113 atoms in block 272
Block first atom: 30756
Blocpdb> 134 atoms in block 273
Block first atom: 30869
Blocpdb> 127 atoms in block 274
Block first atom: 31003
Blocpdb> 116 atoms in block 275
Block first atom: 31130
Blocpdb> 135 atoms in block 276
Block first atom: 31246
Blocpdb> 132 atoms in block 277
Block first atom: 31381
Blocpdb> 130 atoms in block 278
Block first atom: 31513
Blocpdb> 121 atoms in block 279
Block first atom: 31643
Blocpdb> 137 atoms in block 280
Block first atom: 31764
Blocpdb> 109 atoms in block 281
Block first atom: 31901
Blocpdb> 29 atoms in block 282
Block first atom: 32009
Blocpdb> 282 blocks.
Blocpdb> At most, 150 atoms in each of them.
Blocpdb> At least, 15 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: 43453801 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 0m0.192s
user 0m0.184s
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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