*** AMS-059 ***
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 = 2403181605463770136.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 2403181605463770136.atom to be opened.
Openam> File opened: 2403181605463770136.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 = 1307
First residue number = 1
Last residue number = 213
Number of atoms found = 20311
Mean number per residue = 15.5
Pdbmat> Coordinate statistics:
= 76.690944 +/- 25.855781 From: 12.250000 To: 129.456000
= 111.867298 +/- 21.352565 From: 55.252000 To: 161.025000
= 137.052035 +/- 39.804088 From: 65.714000 To: 227.970000
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 -4.9362 % Filled.
Pdbmat> 14366315 non-zero elements.
Pdbmat> 1582991 atom-atom interactions.
Pdbmat> Number per atom= 155.88 +/- 48.63
Maximum number = 251
Minimum number = 20
Pdbmat> Matrix trace = 3.165982E+07
Pdbmat> Larger element = 921.547
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
1307 non-zero elements, NRBL set to 7
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 = 2403181605463770136.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 7
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 2403181605463770136.atom to be opened.
Openam> file on opening on unit 11:
2403181605463770136.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 20311 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 7 residue(s) per block.
Blocpdb> 1307 residues.
Blocpdb> 113 atoms in block 1
Block first atom: 1
Blocpdb> 106 atoms in block 2
Block first atom: 114
Blocpdb> 104 atoms in block 3
Block first atom: 220
Blocpdb> 89 atoms in block 4
Block first atom: 324
Blocpdb> 116 atoms in block 5
Block first atom: 413
Blocpdb> 119 atoms in block 6
Block first atom: 529
Blocpdb> 111 atoms in block 7
Block first atom: 648
Blocpdb> 115 atoms in block 8
Block first atom: 759
Blocpdb> 115 atoms in block 9
Block first atom: 874
Blocpdb> 101 atoms in block 10
Block first atom: 989
Blocpdb> 99 atoms in block 11
Block first atom: 1090
Blocpdb> 164 atoms in block 12
Block first atom: 1189
Blocpdb> 106 atoms in block 13
Block first atom: 1353
Blocpdb> 101 atoms in block 14
Block first atom: 1459
Blocpdb> 268 atoms in block 15
Block first atom: 1560
Blocpdb> 97 atoms in block 16
Block first atom: 1828
Blocpdb> 89 atoms in block 17
Block first atom: 1925
Blocpdb> 104 atoms in block 18
Block first atom: 2014
Blocpdb> 87 atoms in block 19
Block first atom: 2118
Blocpdb> 77 atoms in block 20
Block first atom: 2205
Blocpdb> 124 atoms in block 21
Block first atom: 2282
Blocpdb> 110 atoms in block 22
Block first atom: 2406
Blocpdb> 86 atoms in block 23
Block first atom: 2516
Blocpdb> 99 atoms in block 24
Block first atom: 2602
Blocpdb> 100 atoms in block 25
Block first atom: 2701
Blocpdb> 105 atoms in block 26
Block first atom: 2801
Blocpdb> 96 atoms in block 27
Block first atom: 2906
Blocpdb> 102 atoms in block 28
Block first atom: 3002
Blocpdb> 108 atoms in block 29
Block first atom: 3104
Blocpdb> 124 atoms in block 30
Block first atom: 3212
Blocpdb> 101 atoms in block 31
Block first atom: 3336
Blocpdb> 107 atoms in block 32
Block first atom: 3437
Blocpdb> 102 atoms in block 33
Block first atom: 3544
Blocpdb> 94 atoms in block 34
Block first atom: 3646
Blocpdb> 118 atoms in block 35
Block first atom: 3740
Blocpdb> 118 atoms in block 36
Block first atom: 3858
Blocpdb> 101 atoms in block 37
Block first atom: 3976
Blocpdb> 100 atoms in block 38
Block first atom: 4077
Blocpdb> 125 atoms in block 39
Block first atom: 4177
Blocpdb> 103 atoms in block 40
Block first atom: 4302
Blocpdb> 114 atoms in block 41
Block first atom: 4405
Blocpdb> 117 atoms in block 42
Block first atom: 4519
Blocpdb> 118 atoms in block 43
Block first atom: 4636
Blocpdb> 115 atoms in block 44
Block first atom: 4754
Blocpdb> 122 atoms in block 45
Block first atom: 4869
Blocpdb> 117 atoms in block 46
Block first atom: 4991
Blocpdb> 101 atoms in block 47
Block first atom: 5108
Blocpdb> 120 atoms in block 48
Block first atom: 5209
Blocpdb> 108 atoms in block 49
Block first atom: 5329
Blocpdb> 109 atoms in block 50
Block first atom: 5437
Blocpdb> 121 atoms in block 51
Block first atom: 5546
Blocpdb> 106 atoms in block 52
Block first atom: 5667
Blocpdb> 111 atoms in block 53
Block first atom: 5773
Blocpdb> 111 atoms in block 54
Block first atom: 5884
Blocpdb> 92 atoms in block 55
Block first atom: 5995
Blocpdb> 113 atoms in block 56
Block first atom: 6087
Blocpdb> 88 atoms in block 57
Block first atom: 6200
Blocpdb> 132 atoms in block 58
Block first atom: 6288
Blocpdb> 123 atoms in block 59
Block first atom: 6420
Blocpdb> 102 atoms in block 60
Block first atom: 6543
Blocpdb> 96 atoms in block 61
Block first atom: 6645
Blocpdb> 119 atoms in block 62
Block first atom: 6741
Blocpdb> 107 atoms in block 63
Block first atom: 6860
Blocpdb> 30 atoms in block 64
Block first atom: 6967
Blocpdb> 103 atoms in block 65
Block first atom: 6997
Blocpdb> 95 atoms in block 66
Block first atom: 7100
Blocpdb> 106 atoms in block 67
Block first atom: 7195
Blocpdb> 88 atoms in block 68
Block first atom: 7301
Blocpdb> 143 atoms in block 69
Block first atom: 7389
Blocpdb> 111 atoms in block 70
Block first atom: 7532
Blocpdb> 109 atoms in block 71
Block first atom: 7643
Blocpdb> 107 atoms in block 72
Block first atom: 7752
Blocpdb> 104 atoms in block 73
Block first atom: 7859
Blocpdb> 107 atoms in block 74
Block first atom: 7963
Blocpdb> 91 atoms in block 75
Block first atom: 8070
Blocpdb> 107 atoms in block 76
Block first atom: 8161
Blocpdb> 113 atoms in block 77
Block first atom: 8268
Blocpdb> 105 atoms in block 78
Block first atom: 8381
Blocpdb> 90 atoms in block 79
Block first atom: 8486
Blocpdb> 105 atoms in block 80
Block first atom: 8576
Blocpdb> 104 atoms in block 81
Block first atom: 8681
Blocpdb> 99 atoms in block 82
Block first atom: 8785
Blocpdb> 106 atoms in block 83
Block first atom: 8884
Blocpdb> 107 atoms in block 84
Block first atom: 8990
Blocpdb> 98 atoms in block 85
Block first atom: 9097
Blocpdb> 100 atoms in block 86
Block first atom: 9195
Blocpdb> 100 atoms in block 87
Block first atom: 9295
Blocpdb> 106 atoms in block 88
Block first atom: 9395
Blocpdb> 102 atoms in block 89
Block first atom: 9501
Blocpdb> 106 atoms in block 90
Block first atom: 9603
Blocpdb> 121 atoms in block 91
Block first atom: 9709
Blocpdb> 110 atoms in block 92
Block first atom: 9830
Blocpdb> 94 atoms in block 93
Block first atom: 9940
Blocpdb> 105 atoms in block 94
Block first atom: 10034
Blocpdb> 38 atoms in block 95
Block first atom: 10139
Blocpdb> 113 atoms in block 96
Block first atom: 10177
Blocpdb> 106 atoms in block 97
Block first atom: 10290
Blocpdb> 104 atoms in block 98
Block first atom: 10396
Blocpdb> 89 atoms in block 99
Block first atom: 10500
Blocpdb> 116 atoms in block 100
Block first atom: 10589
Blocpdb> 119 atoms in block 101
Block first atom: 10705
Blocpdb> 111 atoms in block 102
Block first atom: 10824
Blocpdb> 115 atoms in block 103
Block first atom: 10935
Blocpdb> 115 atoms in block 104
Block first atom: 11050
Blocpdb> 101 atoms in block 105
Block first atom: 11165
Blocpdb> 99 atoms in block 106
Block first atom: 11266
Blocpdb> 164 atoms in block 107
Block first atom: 11365
Blocpdb> 106 atoms in block 108
Block first atom: 11529
Blocpdb> 101 atoms in block 109
Block first atom: 11635
Blocpdb> 268 atoms in block 110
Block first atom: 11736
Blocpdb> 97 atoms in block 111
Block first atom: 12004
Blocpdb> 89 atoms in block 112
Block first atom: 12101
Blocpdb> 104 atoms in block 113
Block first atom: 12190
Blocpdb> 87 atoms in block 114
Block first atom: 12294
Blocpdb> 77 atoms in block 115
Block first atom: 12381
Blocpdb> 124 atoms in block 116
Block first atom: 12458
Blocpdb> 110 atoms in block 117
Block first atom: 12582
Blocpdb> 86 atoms in block 118
Block first atom: 12692
Blocpdb> 99 atoms in block 119
Block first atom: 12778
Blocpdb> 100 atoms in block 120
Block first atom: 12877
Blocpdb> 105 atoms in block 121
Block first atom: 12977
Blocpdb> 96 atoms in block 122
Block first atom: 13082
Blocpdb> 102 atoms in block 123
Block first atom: 13178
Blocpdb> 108 atoms in block 124
Block first atom: 13280
Blocpdb> 124 atoms in block 125
Block first atom: 13388
Blocpdb> 101 atoms in block 126
Block first atom: 13512
Blocpdb> 107 atoms in block 127
Block first atom: 13613
Blocpdb> 102 atoms in block 128
Block first atom: 13720
Blocpdb> 94 atoms in block 129
Block first atom: 13822
Blocpdb> 118 atoms in block 130
Block first atom: 13916
Blocpdb> 118 atoms in block 131
Block first atom: 14034
Blocpdb> 101 atoms in block 132
Block first atom: 14152
Blocpdb> 101 atoms in block 133
Block first atom: 14253
Blocpdb> 125 atoms in block 134
Block first atom: 14354
Blocpdb> 103 atoms in block 135
Block first atom: 14479
Blocpdb> 114 atoms in block 136
Block first atom: 14582
Blocpdb> 117 atoms in block 137
Block first atom: 14696
Blocpdb> 118 atoms in block 138
Block first atom: 14813
Blocpdb> 115 atoms in block 139
Block first atom: 14931
Blocpdb> 122 atoms in block 140
Block first atom: 15046
Blocpdb> 117 atoms in block 141
Block first atom: 15168
Blocpdb> 101 atoms in block 142
Block first atom: 15285
Blocpdb> 120 atoms in block 143
Block first atom: 15386
Blocpdb> 108 atoms in block 144
Block first atom: 15506
Blocpdb> 109 atoms in block 145
Block first atom: 15614
Blocpdb> 121 atoms in block 146
Block first atom: 15723
Blocpdb> 106 atoms in block 147
Block first atom: 15844
Blocpdb> 111 atoms in block 148
Block first atom: 15950
Blocpdb> 111 atoms in block 149
Block first atom: 16061
Blocpdb> 92 atoms in block 150
Block first atom: 16172
Blocpdb> 113 atoms in block 151
Block first atom: 16264
Blocpdb> 88 atoms in block 152
Block first atom: 16377
Blocpdb> 132 atoms in block 153
Block first atom: 16465
Blocpdb> 123 atoms in block 154
Block first atom: 16597
Blocpdb> 102 atoms in block 155
Block first atom: 16720
Blocpdb> 96 atoms in block 156
Block first atom: 16822
Blocpdb> 120 atoms in block 157
Block first atom: 16918
Blocpdb> 94 atoms in block 158
Block first atom: 17038
Blocpdb> 103 atoms in block 159
Block first atom: 17132
Blocpdb> 95 atoms in block 160
Block first atom: 17235
Blocpdb> 106 atoms in block 161
Block first atom: 17330
Blocpdb> 88 atoms in block 162
Block first atom: 17436
Blocpdb> 143 atoms in block 163
Block first atom: 17524
Blocpdb> 111 atoms in block 164
Block first atom: 17667
Blocpdb> 109 atoms in block 165
Block first atom: 17778
Blocpdb> 107 atoms in block 166
Block first atom: 17887
Blocpdb> 104 atoms in block 167
Block first atom: 17994
Blocpdb> 107 atoms in block 168
Block first atom: 18098
Blocpdb> 91 atoms in block 169
Block first atom: 18205
Blocpdb> 107 atoms in block 170
Block first atom: 18296
Blocpdb> 113 atoms in block 171
Block first atom: 18403
Blocpdb> 105 atoms in block 172
Block first atom: 18516
Blocpdb> 90 atoms in block 173
Block first atom: 18621
Blocpdb> 105 atoms in block 174
Block first atom: 18711
Blocpdb> 104 atoms in block 175
Block first atom: 18816
Blocpdb> 99 atoms in block 176
Block first atom: 18920
Blocpdb> 106 atoms in block 177
Block first atom: 19019
Blocpdb> 107 atoms in block 178
Block first atom: 19125
Blocpdb> 98 atoms in block 179
Block first atom: 19232
Blocpdb> 100 atoms in block 180
Block first atom: 19330
Blocpdb> 100 atoms in block 181
Block first atom: 19430
Blocpdb> 106 atoms in block 182
Block first atom: 19530
Blocpdb> 102 atoms in block 183
Block first atom: 19636
Blocpdb> 106 atoms in block 184
Block first atom: 19738
Blocpdb> 121 atoms in block 185
Block first atom: 19844
Blocpdb> 110 atoms in block 186
Block first atom: 19965
Blocpdb> 94 atoms in block 187
Block first atom: 20075
Blocpdb> 105 atoms in block 188
Block first atom: 20169
Blocpdb> 38 atoms in block 189
Block first atom: 20273
Blocpdb> 189 blocks.
Blocpdb> At most, 268 atoms in each of them.
Blocpdb> At least, 30 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: 49636549 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 0m0.101s
user 0m0.101s
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: April 25th, 2023.
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