*** ***
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 = 2401041723143859387.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 2401041723143859387.atom to be opened.
Openam> File opened: 2401041723143859387.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 = 2065
First residue number = 1
Last residue number = 413
Number of atoms found = 29794
Mean number per residue = 14.4
Pdbmat> Coordinate statistics:
= 19.353800 +/- 31.689164 From: -46.208000 To: 100.322000
= 13.476416 +/- 36.132129 From: -66.475000 To: 92.826000
= -3.325943 +/- 33.853627 From: -85.641000 To: 99.047000
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 -7.2454 % Filled.
Pdbmat> 21761797 non-zero elements.
Pdbmat> 2398522 atom-atom interactions.
Pdbmat> Number per atom= 161.01 +/- 98.31
Maximum number = 705
Minimum number = 18
Pdbmat> Matrix trace = 4.797044E+07
Pdbmat> Larger element = 2548.89
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2065 non-zero elements, NRBL set to 11
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 = 2401041723143859387.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 11
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 2401041723143859387.atom to be opened.
Openam> file on opening on unit 11:
2401041723143859387.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 29794 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 11 residue(s) per block.
Blocpdb> 2065 residues.
Blocpdb> 152 atoms in block 1
Block first atom: 1
Blocpdb> 162 atoms in block 2
Block first atom: 153
Blocpdb> 154 atoms in block 3
Block first atom: 315
Blocpdb> 139 atoms in block 4
Block first atom: 469
Blocpdb> 129 atoms in block 5
Block first atom: 608
Blocpdb> 157 atoms in block 6
Block first atom: 737
Blocpdb> 181 atoms in block 7
Block first atom: 894
Blocpdb> 170 atoms in block 8
Block first atom: 1075
Blocpdb> 139 atoms in block 9
Block first atom: 1245
Blocpdb> 159 atoms in block 10
Block first atom: 1384
Blocpdb> 161 atoms in block 11
Block first atom: 1543
Blocpdb> 150 atoms in block 12
Block first atom: 1704
Blocpdb> 186 atoms in block 13
Block first atom: 1854
Blocpdb> 158 atoms in block 14
Block first atom: 2040
Blocpdb> 144 atoms in block 15
Block first atom: 2198
Blocpdb> 161 atoms in block 16
Block first atom: 2342
Blocpdb> 139 atoms in block 17
Block first atom: 2503
Blocpdb> 180 atoms in block 18
Block first atom: 2642
Blocpdb> 143 atoms in block 19
Block first atom: 2822
Blocpdb> 193 atoms in block 20
Block first atom: 2965
Blocpdb> 156 atoms in block 21
Block first atom: 3158
Blocpdb> 184 atoms in block 22
Block first atom: 3314
Blocpdb> 217 atoms in block 23
Block first atom: 3498
Blocpdb> 143 atoms in block 24
Block first atom: 3715
Blocpdb> 175 atoms in block 25
Block first atom: 3858
Blocpdb> 156 atoms in block 26
Block first atom: 4033
Blocpdb> 193 atoms in block 27
Block first atom: 4189
Blocpdb> 199 atoms in block 28
Block first atom: 4382
Blocpdb> 165 atoms in block 29
Block first atom: 4581
Blocpdb> 121 atoms in block 30
Block first atom: 4746
Blocpdb> 128 atoms in block 31
Block first atom: 4867
Blocpdb> 116 atoms in block 32
Block first atom: 4995
Blocpdb> 154 atoms in block 33
Block first atom: 5111
Blocpdb> 154 atoms in block 34
Block first atom: 5265
Blocpdb> 163 atoms in block 35
Block first atom: 5419
Blocpdb> 150 atoms in block 36
Block first atom: 5582
Blocpdb> 149 atoms in block 37
Block first atom: 5732
Blocpdb> 82 atoms in block 38
Block first atom: 5881
Blocpdb> 152 atoms in block 39
Block first atom: 5963
Blocpdb> 162 atoms in block 40
Block first atom: 6115
Blocpdb> 154 atoms in block 41
Block first atom: 6277
Blocpdb> 139 atoms in block 42
Block first atom: 6431
Blocpdb> 129 atoms in block 43
Block first atom: 6570
Blocpdb> 157 atoms in block 44
Block first atom: 6699
Blocpdb> 181 atoms in block 45
Block first atom: 6856
Blocpdb> 170 atoms in block 46
Block first atom: 7037
Blocpdb> 139 atoms in block 47
Block first atom: 7207
Blocpdb> 159 atoms in block 48
Block first atom: 7346
Blocpdb> 161 atoms in block 49
Block first atom: 7505
Blocpdb> 150 atoms in block 50
Block first atom: 7666
Blocpdb> 186 atoms in block 51
Block first atom: 7816
Blocpdb> 158 atoms in block 52
Block first atom: 8002
Blocpdb> 144 atoms in block 53
Block first atom: 8160
Blocpdb> 161 atoms in block 54
Block first atom: 8304
Blocpdb> 139 atoms in block 55
Block first atom: 8465
Blocpdb> 180 atoms in block 56
Block first atom: 8604
Blocpdb> 143 atoms in block 57
Block first atom: 8784
Blocpdb> 193 atoms in block 58
Block first atom: 8927
Blocpdb> 156 atoms in block 59
Block first atom: 9120
Blocpdb> 184 atoms in block 60
Block first atom: 9276
Blocpdb> 217 atoms in block 61
Block first atom: 9460
Blocpdb> 142 atoms in block 62
Block first atom: 9677
Blocpdb> 175 atoms in block 63
Block first atom: 9819
Blocpdb> 155 atoms in block 64
Block first atom: 9994
Blocpdb> 193 atoms in block 65
Block first atom: 10149
Blocpdb> 199 atoms in block 66
Block first atom: 10342
Blocpdb> 165 atoms in block 67
Block first atom: 10541
Blocpdb> 121 atoms in block 68
Block first atom: 10706
Blocpdb> 128 atoms in block 69
Block first atom: 10827
Blocpdb> 116 atoms in block 70
Block first atom: 10955
Blocpdb> 154 atoms in block 71
Block first atom: 11071
Blocpdb> 154 atoms in block 72
Block first atom: 11225
Blocpdb> 163 atoms in block 73
Block first atom: 11379
Blocpdb> 150 atoms in block 74
Block first atom: 11542
Blocpdb> 149 atoms in block 75
Block first atom: 11692
Blocpdb> 82 atoms in block 76
Block first atom: 11841
Blocpdb> 152 atoms in block 77
Block first atom: 11923
Blocpdb> 162 atoms in block 78
Block first atom: 12075
Blocpdb> 154 atoms in block 79
Block first atom: 12237
Blocpdb> 139 atoms in block 80
Block first atom: 12391
Blocpdb> 129 atoms in block 81
Block first atom: 12530
Blocpdb> 157 atoms in block 82
Block first atom: 12659
Blocpdb> 181 atoms in block 83
Block first atom: 12816
Blocpdb> 170 atoms in block 84
Block first atom: 12997
Blocpdb> 139 atoms in block 85
Block first atom: 13167
Blocpdb> 159 atoms in block 86
Block first atom: 13306
Blocpdb> 161 atoms in block 87
Block first atom: 13465
Blocpdb> 150 atoms in block 88
Block first atom: 13626
Blocpdb> 186 atoms in block 89
Block first atom: 13776
Blocpdb> 158 atoms in block 90
Block first atom: 13962
Blocpdb> 144 atoms in block 91
Block first atom: 14120
Blocpdb> 161 atoms in block 92
Block first atom: 14264
Blocpdb> 139 atoms in block 93
Block first atom: 14425
Blocpdb> 180 atoms in block 94
Block first atom: 14564
Blocpdb> 143 atoms in block 95
Block first atom: 14744
Blocpdb> 193 atoms in block 96
Block first atom: 14887
Blocpdb> 156 atoms in block 97
Block first atom: 15080
Blocpdb> 184 atoms in block 98
Block first atom: 15236
Blocpdb> 217 atoms in block 99
Block first atom: 15420
Blocpdb> 141 atoms in block 100
Block first atom: 15637
Blocpdb> 175 atoms in block 101
Block first atom: 15778
Blocpdb> 154 atoms in block 102
Block first atom: 15953
Blocpdb> 193 atoms in block 103
Block first atom: 16107
Blocpdb> 199 atoms in block 104
Block first atom: 16300
Blocpdb> 165 atoms in block 105
Block first atom: 16499
Blocpdb> 121 atoms in block 106
Block first atom: 16664
Blocpdb> 128 atoms in block 107
Block first atom: 16785
Blocpdb> 116 atoms in block 108
Block first atom: 16913
Blocpdb> 154 atoms in block 109
Block first atom: 17029
Blocpdb> 154 atoms in block 110
Block first atom: 17183
Blocpdb> 163 atoms in block 111
Block first atom: 17337
Blocpdb> 150 atoms in block 112
Block first atom: 17500
Blocpdb> 149 atoms in block 113
Block first atom: 17650
Blocpdb> 82 atoms in block 114
Block first atom: 17799
Blocpdb> 152 atoms in block 115
Block first atom: 17881
Blocpdb> 162 atoms in block 116
Block first atom: 18033
Blocpdb> 154 atoms in block 117
Block first atom: 18195
Blocpdb> 139 atoms in block 118
Block first atom: 18349
Blocpdb> 129 atoms in block 119
Block first atom: 18488
Blocpdb> 157 atoms in block 120
Block first atom: 18617
Blocpdb> 181 atoms in block 121
Block first atom: 18774
Blocpdb> 170 atoms in block 122
Block first atom: 18955
Blocpdb> 139 atoms in block 123
Block first atom: 19125
Blocpdb> 159 atoms in block 124
Block first atom: 19264
Blocpdb> 161 atoms in block 125
Block first atom: 19423
Blocpdb> 150 atoms in block 126
Block first atom: 19584
Blocpdb> 186 atoms in block 127
Block first atom: 19734
Blocpdb> 158 atoms in block 128
Block first atom: 19920
Blocpdb> 144 atoms in block 129
Block first atom: 20078
Blocpdb> 161 atoms in block 130
Block first atom: 20222
Blocpdb> 139 atoms in block 131
Block first atom: 20383
Blocpdb> 180 atoms in block 132
Block first atom: 20522
Blocpdb> 142 atoms in block 133
Block first atom: 20702
Blocpdb> 193 atoms in block 134
Block first atom: 20844
Blocpdb> 155 atoms in block 135
Block first atom: 21037
Blocpdb> 184 atoms in block 136
Block first atom: 21192
Blocpdb> 217 atoms in block 137
Block first atom: 21376
Blocpdb> 141 atoms in block 138
Block first atom: 21593
Blocpdb> 175 atoms in block 139
Block first atom: 21734
Blocpdb> 154 atoms in block 140
Block first atom: 21909
Blocpdb> 193 atoms in block 141
Block first atom: 22063
Blocpdb> 199 atoms in block 142
Block first atom: 22256
Blocpdb> 165 atoms in block 143
Block first atom: 22455
Blocpdb> 121 atoms in block 144
Block first atom: 22620
Blocpdb> 128 atoms in block 145
Block first atom: 22741
Blocpdb> 116 atoms in block 146
Block first atom: 22869
Blocpdb> 154 atoms in block 147
Block first atom: 22985
Blocpdb> 154 atoms in block 148
Block first atom: 23139
Blocpdb> 163 atoms in block 149
Block first atom: 23293
Blocpdb> 150 atoms in block 150
Block first atom: 23456
Blocpdb> 149 atoms in block 151
Block first atom: 23606
Blocpdb> 82 atoms in block 152
Block first atom: 23755
Blocpdb> 152 atoms in block 153
Block first atom: 23837
Blocpdb> 162 atoms in block 154
Block first atom: 23989
Blocpdb> 154 atoms in block 155
Block first atom: 24151
Blocpdb> 139 atoms in block 156
Block first atom: 24305
Blocpdb> 129 atoms in block 157
Block first atom: 24444
Blocpdb> 157 atoms in block 158
Block first atom: 24573
Blocpdb> 181 atoms in block 159
Block first atom: 24730
Blocpdb> 170 atoms in block 160
Block first atom: 24911
Blocpdb> 139 atoms in block 161
Block first atom: 25081
Blocpdb> 159 atoms in block 162
Block first atom: 25220
Blocpdb> 161 atoms in block 163
Block first atom: 25379
Blocpdb> 150 atoms in block 164
Block first atom: 25540
Blocpdb> 186 atoms in block 165
Block first atom: 25690
Blocpdb> 158 atoms in block 166
Block first atom: 25876
Blocpdb> 144 atoms in block 167
Block first atom: 26034
Blocpdb> 161 atoms in block 168
Block first atom: 26178
Blocpdb> 139 atoms in block 169
Block first atom: 26339
Blocpdb> 180 atoms in block 170
Block first atom: 26478
Blocpdb> 143 atoms in block 171
Block first atom: 26658
Blocpdb> 193 atoms in block 172
Block first atom: 26801
Blocpdb> 156 atoms in block 173
Block first atom: 26994
Blocpdb> 184 atoms in block 174
Block first atom: 27150
Blocpdb> 217 atoms in block 175
Block first atom: 27334
Blocpdb> 141 atoms in block 176
Block first atom: 27551
Blocpdb> 175 atoms in block 177
Block first atom: 27692
Blocpdb> 154 atoms in block 178
Block first atom: 27867
Blocpdb> 193 atoms in block 179
Block first atom: 28021
Blocpdb> 199 atoms in block 180
Block first atom: 28214
Blocpdb> 165 atoms in block 181
Block first atom: 28413
Blocpdb> 121 atoms in block 182
Block first atom: 28578
Blocpdb> 128 atoms in block 183
Block first atom: 28699
Blocpdb> 116 atoms in block 184
Block first atom: 28827
Blocpdb> 154 atoms in block 185
Block first atom: 28943
Blocpdb> 154 atoms in block 186
Block first atom: 29097
Blocpdb> 163 atoms in block 187
Block first atom: 29251
Blocpdb> 150 atoms in block 188
Block first atom: 29414
Blocpdb> 149 atoms in block 189
Block first atom: 29564
Blocpdb> 82 atoms in block 190
Block first atom: 29712
Blocpdb> 190 blocks.
Blocpdb> At most, 217 atoms in each of them.
Blocpdb> At least, 82 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: 58611484 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 0m0.136s
user 0m0.132s
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: April 25th, 2023.
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