*** sars ***
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 = 240504092832310531.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 240504092832310531.atom to be opened.
Openam> File opened: 240504092832310531.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 = 3303
First residue number = 14
Last residue number = 1139
Number of atoms found = 25782
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 154.055613 +/- 23.537160 From: 92.146000 To: 232.164000
= 154.072462 +/- 23.538937 From: 77.461000 To: 219.702000
= 152.962263 +/- 35.923059 From: 85.212000 To: 239.191000
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 1.1891 % Filled.
Pdbmat> 10033009 non-zero elements.
Pdbmat> 1097768 atom-atom interactions.
Pdbmat> Number per atom= 85.16 +/- 20.97
Maximum number = 131
Minimum number = 17
Pdbmat> Matrix trace = 2.195536E+07
Pdbmat> Larger element = 516.155
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3303 non-zero elements, NRBL set to 17
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 = 240504092832310531.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 17
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 240504092832310531.atom to be opened.
Openam> file on opening on unit 11:
240504092832310531.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 25782 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 17 residue(s) per block.
Blocpdb> 3303 residues.
Blocpdb> 133 atoms in block 1
Block first atom: 1
Blocpdb> 142 atoms in block 2
Block first atom: 134
Blocpdb> 146 atoms in block 3
Block first atom: 276
Blocpdb> 134 atoms in block 4
Block first atom: 422
Blocpdb> 132 atoms in block 5
Block first atom: 556
Blocpdb> 137 atoms in block 6
Block first atom: 688
Blocpdb> 126 atoms in block 7
Block first atom: 825
Blocpdb> 149 atoms in block 8
Block first atom: 951
Blocpdb> 141 atoms in block 9
Block first atom: 1100
Blocpdb> 142 atoms in block 10
Block first atom: 1241
Blocpdb> 146 atoms in block 11
Block first atom: 1383
Blocpdb> 144 atoms in block 12
Block first atom: 1529
Blocpdb> 125 atoms in block 13
Block first atom: 1673
Blocpdb> 143 atoms in block 14
Block first atom: 1798
Blocpdb> 114 atoms in block 15
Block first atom: 1941
Blocpdb> 146 atoms in block 16
Block first atom: 2055
Blocpdb> 121 atoms in block 17
Block first atom: 2201
Blocpdb> 142 atoms in block 18
Block first atom: 2322
Blocpdb> 134 atoms in block 19
Block first atom: 2464
Blocpdb> 140 atoms in block 20
Block first atom: 2598
Blocpdb> 140 atoms in block 21
Block first atom: 2738
Blocpdb> 127 atoms in block 22
Block first atom: 2878
Blocpdb> 135 atoms in block 23
Block first atom: 3005
Blocpdb> 130 atoms in block 24
Block first atom: 3140
Blocpdb> 136 atoms in block 25
Block first atom: 3270
Blocpdb> 141 atoms in block 26
Block first atom: 3406
Blocpdb> 146 atoms in block 27
Block first atom: 3547
Blocpdb> 125 atoms in block 28
Block first atom: 3693
Blocpdb> 135 atoms in block 29
Block first atom: 3818
Blocpdb> 135 atoms in block 30
Block first atom: 3953
Blocpdb> 125 atoms in block 31
Block first atom: 4088
Blocpdb> 126 atoms in block 32
Block first atom: 4213
Blocpdb> 141 atoms in block 33
Block first atom: 4339
Blocpdb> 129 atoms in block 34
Block first atom: 4480
Blocpdb> 117 atoms in block 35
Block first atom: 4609
Blocpdb> 77 atoms in block 36
Block first atom: 4726
Blocpdb> 136 atoms in block 37
Block first atom: 4803
Blocpdb> 129 atoms in block 38
Block first atom: 4939
Blocpdb> 74 atoms in block 39
Block first atom: 5068
Blocpdb> 122 atoms in block 40
Block first atom: 5142
Blocpdb> 127 atoms in block 41
Block first atom: 5264
Blocpdb> 124 atoms in block 42
Block first atom: 5391
Blocpdb> 133 atoms in block 43
Block first atom: 5515
Blocpdb> 123 atoms in block 44
Block first atom: 5648
Blocpdb> 145 atoms in block 45
Block first atom: 5771
Blocpdb> 133 atoms in block 46
Block first atom: 5916
Blocpdb> 140 atoms in block 47
Block first atom: 6049
Blocpdb> 128 atoms in block 48
Block first atom: 6189
Blocpdb> 125 atoms in block 49
Block first atom: 6317
Blocpdb> 131 atoms in block 50
Block first atom: 6442
Blocpdb> 112 atoms in block 51
Block first atom: 6573
Blocpdb> 137 atoms in block 52
Block first atom: 6685
Blocpdb> 135 atoms in block 53
Block first atom: 6822
Blocpdb> 120 atoms in block 54
Block first atom: 6957
Blocpdb> 125 atoms in block 55
Block first atom: 7077
Blocpdb> 123 atoms in block 56
Block first atom: 7202
Blocpdb> 136 atoms in block 57
Block first atom: 7325
Blocpdb> 140 atoms in block 58
Block first atom: 7461
Blocpdb> 123 atoms in block 59
Block first atom: 7601
Blocpdb> 128 atoms in block 60
Block first atom: 7724
Blocpdb> 132 atoms in block 61
Block first atom: 7852
Blocpdb> 135 atoms in block 62
Block first atom: 7984
Blocpdb> 132 atoms in block 63
Block first atom: 8119
Blocpdb> 150 atoms in block 64
Block first atom: 8251
Blocpdb> 125 atoms in block 65
Block first atom: 8401
Blocpdb> 69 atoms in block 66
Block first atom: 8526
Blocpdb> 133 atoms in block 67
Block first atom: 8595
Blocpdb> 142 atoms in block 68
Block first atom: 8728
Blocpdb> 146 atoms in block 69
Block first atom: 8870
Blocpdb> 134 atoms in block 70
Block first atom: 9016
Blocpdb> 132 atoms in block 71
Block first atom: 9150
Blocpdb> 137 atoms in block 72
Block first atom: 9282
Blocpdb> 126 atoms in block 73
Block first atom: 9419
Blocpdb> 149 atoms in block 74
Block first atom: 9545
Blocpdb> 141 atoms in block 75
Block first atom: 9694
Blocpdb> 142 atoms in block 76
Block first atom: 9835
Blocpdb> 146 atoms in block 77
Block first atom: 9977
Blocpdb> 144 atoms in block 78
Block first atom: 10123
Blocpdb> 125 atoms in block 79
Block first atom: 10267
Blocpdb> 143 atoms in block 80
Block first atom: 10392
Blocpdb> 114 atoms in block 81
Block first atom: 10535
Blocpdb> 146 atoms in block 82
Block first atom: 10649
Blocpdb> 121 atoms in block 83
Block first atom: 10795
Blocpdb> 142 atoms in block 84
Block first atom: 10916
Blocpdb> 134 atoms in block 85
Block first atom: 11058
Blocpdb> 140 atoms in block 86
Block first atom: 11192
Blocpdb> 140 atoms in block 87
Block first atom: 11332
Blocpdb> 127 atoms in block 88
Block first atom: 11472
Blocpdb> 135 atoms in block 89
Block first atom: 11599
Blocpdb> 130 atoms in block 90
Block first atom: 11734
Blocpdb> 136 atoms in block 91
Block first atom: 11864
Blocpdb> 141 atoms in block 92
Block first atom: 12000
Blocpdb> 146 atoms in block 93
Block first atom: 12141
Blocpdb> 125 atoms in block 94
Block first atom: 12287
Blocpdb> 135 atoms in block 95
Block first atom: 12412
Blocpdb> 135 atoms in block 96
Block first atom: 12547
Blocpdb> 125 atoms in block 97
Block first atom: 12682
Blocpdb> 126 atoms in block 98
Block first atom: 12807
Blocpdb> 141 atoms in block 99
Block first atom: 12933
Blocpdb> 129 atoms in block 100
Block first atom: 13074
Blocpdb> 117 atoms in block 101
Block first atom: 13203
Blocpdb> 77 atoms in block 102
Block first atom: 13320
Blocpdb> 136 atoms in block 103
Block first atom: 13397
Blocpdb> 129 atoms in block 104
Block first atom: 13533
Blocpdb> 74 atoms in block 105
Block first atom: 13662
Blocpdb> 122 atoms in block 106
Block first atom: 13736
Blocpdb> 127 atoms in block 107
Block first atom: 13858
Blocpdb> 124 atoms in block 108
Block first atom: 13985
Blocpdb> 133 atoms in block 109
Block first atom: 14109
Blocpdb> 123 atoms in block 110
Block first atom: 14242
Blocpdb> 145 atoms in block 111
Block first atom: 14365
Blocpdb> 133 atoms in block 112
Block first atom: 14510
Blocpdb> 140 atoms in block 113
Block first atom: 14643
Blocpdb> 128 atoms in block 114
Block first atom: 14783
Blocpdb> 125 atoms in block 115
Block first atom: 14911
Blocpdb> 131 atoms in block 116
Block first atom: 15036
Blocpdb> 112 atoms in block 117
Block first atom: 15167
Blocpdb> 137 atoms in block 118
Block first atom: 15279
Blocpdb> 135 atoms in block 119
Block first atom: 15416
Blocpdb> 120 atoms in block 120
Block first atom: 15551
Blocpdb> 125 atoms in block 121
Block first atom: 15671
Blocpdb> 123 atoms in block 122
Block first atom: 15796
Blocpdb> 136 atoms in block 123
Block first atom: 15919
Blocpdb> 140 atoms in block 124
Block first atom: 16055
Blocpdb> 123 atoms in block 125
Block first atom: 16195
Blocpdb> 128 atoms in block 126
Block first atom: 16318
Blocpdb> 132 atoms in block 127
Block first atom: 16446
Blocpdb> 135 atoms in block 128
Block first atom: 16578
Blocpdb> 132 atoms in block 129
Block first atom: 16713
Blocpdb> 150 atoms in block 130
Block first atom: 16845
Blocpdb> 125 atoms in block 131
Block first atom: 16995
Blocpdb> 69 atoms in block 132
Block first atom: 17120
Blocpdb> 133 atoms in block 133
Block first atom: 17189
Blocpdb> 142 atoms in block 134
Block first atom: 17322
Blocpdb> 146 atoms in block 135
Block first atom: 17464
Blocpdb> 134 atoms in block 136
Block first atom: 17610
Blocpdb> 132 atoms in block 137
Block first atom: 17744
Blocpdb> 137 atoms in block 138
Block first atom: 17876
Blocpdb> 126 atoms in block 139
Block first atom: 18013
Blocpdb> 149 atoms in block 140
Block first atom: 18139
Blocpdb> 141 atoms in block 141
Block first atom: 18288
Blocpdb> 142 atoms in block 142
Block first atom: 18429
Blocpdb> 146 atoms in block 143
Block first atom: 18571
Blocpdb> 144 atoms in block 144
Block first atom: 18717
Blocpdb> 125 atoms in block 145
Block first atom: 18861
Blocpdb> 143 atoms in block 146
Block first atom: 18986
Blocpdb> 114 atoms in block 147
Block first atom: 19129
Blocpdb> 146 atoms in block 148
Block first atom: 19243
Blocpdb> 121 atoms in block 149
Block first atom: 19389
Blocpdb> 142 atoms in block 150
Block first atom: 19510
Blocpdb> 134 atoms in block 151
Block first atom: 19652
Blocpdb> 140 atoms in block 152
Block first atom: 19786
Blocpdb> 140 atoms in block 153
Block first atom: 19926
Blocpdb> 127 atoms in block 154
Block first atom: 20066
Blocpdb> 135 atoms in block 155
Block first atom: 20193
Blocpdb> 130 atoms in block 156
Block first atom: 20328
Blocpdb> 136 atoms in block 157
Block first atom: 20458
Blocpdb> 141 atoms in block 158
Block first atom: 20594
Blocpdb> 146 atoms in block 159
Block first atom: 20735
Blocpdb> 125 atoms in block 160
Block first atom: 20881
Blocpdb> 135 atoms in block 161
Block first atom: 21006
Blocpdb> 135 atoms in block 162
Block first atom: 21141
Blocpdb> 125 atoms in block 163
Block first atom: 21276
Blocpdb> 126 atoms in block 164
Block first atom: 21401
Blocpdb> 141 atoms in block 165
Block first atom: 21527
Blocpdb> 129 atoms in block 166
Block first atom: 21668
Blocpdb> 117 atoms in block 167
Block first atom: 21797
Blocpdb> 77 atoms in block 168
Block first atom: 21914
Blocpdb> 136 atoms in block 169
Block first atom: 21991
Blocpdb> 129 atoms in block 170
Block first atom: 22127
Blocpdb> 74 atoms in block 171
Block first atom: 22256
Blocpdb> 122 atoms in block 172
Block first atom: 22330
Blocpdb> 127 atoms in block 173
Block first atom: 22452
Blocpdb> 124 atoms in block 174
Block first atom: 22579
Blocpdb> 133 atoms in block 175
Block first atom: 22703
Blocpdb> 123 atoms in block 176
Block first atom: 22836
Blocpdb> 145 atoms in block 177
Block first atom: 22959
Blocpdb> 133 atoms in block 178
Block first atom: 23104
Blocpdb> 140 atoms in block 179
Block first atom: 23237
Blocpdb> 128 atoms in block 180
Block first atom: 23377
Blocpdb> 125 atoms in block 181
Block first atom: 23505
Blocpdb> 131 atoms in block 182
Block first atom: 23630
Blocpdb> 112 atoms in block 183
Block first atom: 23761
Blocpdb> 137 atoms in block 184
Block first atom: 23873
Blocpdb> 135 atoms in block 185
Block first atom: 24010
Blocpdb> 120 atoms in block 186
Block first atom: 24145
Blocpdb> 125 atoms in block 187
Block first atom: 24265
Blocpdb> 123 atoms in block 188
Block first atom: 24390
Blocpdb> 136 atoms in block 189
Block first atom: 24513
Blocpdb> 140 atoms in block 190
Block first atom: 24649
Blocpdb> 123 atoms in block 191
Block first atom: 24789
Blocpdb> 128 atoms in block 192
Block first atom: 24912
Blocpdb> 132 atoms in block 193
Block first atom: 25040
Blocpdb> 135 atoms in block 194
Block first atom: 25172
Blocpdb> 132 atoms in block 195
Block first atom: 25307
Blocpdb> 150 atoms in block 196
Block first atom: 25439
Blocpdb> 125 atoms in block 197
Block first atom: 25589
Blocpdb> 69 atoms in block 198
Block first atom: 25713
Blocpdb> 198 blocks.
Blocpdb> At most, 150 atoms in each of them.
Blocpdb> At least, 69 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: 35008201 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 0m0.134s
user 0m0.126s
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: April 25th, 2023.
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