*** 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 = 240504091712309855.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 240504091712309855.atom to be opened.
Openam> File opened: 240504091712309855.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 = 3055
First residue number = 14
Last residue number = 1146
Number of atoms found = 23954
Mean number per residue = 7.8
Pdbmat> Coordinate statistics:
= 152.881942 +/- 24.845306 From: 70.944000 To: 209.985000
= 155.111807 +/- 25.387908 From: 80.845000 To: 215.314000
= 153.318726 +/- 36.417020 From: 63.043000 To: 232.375000
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 2.0081 % Filled.
Pdbmat> 8727809 non-zero elements.
Pdbmat> 953960 atom-atom interactions.
Pdbmat> Number per atom= 79.65 +/- 20.06
Maximum number = 131
Minimum number = 9
Pdbmat> Matrix trace = 1.907920E+07
Pdbmat> Larger element = 500.853
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3055 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 = 240504091712309855.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 240504091712309855.atom to be opened.
Openam> file on opening on unit 11:
240504091712309855.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 23954 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> 3055 residues.
Blocpdb> 30 atoms in block 1
Block first atom: 1
Blocpdb> 128 atoms in block 2
Block first atom: 31
Blocpdb> 132 atoms in block 3
Block first atom: 159
Blocpdb> 142 atoms in block 4
Block first atom: 291
Blocpdb> 7 atoms in block 5
Block first atom: 433
Blocpdb> 133 atoms in block 6
Block first atom: 440
Blocpdb> 129 atoms in block 7
Block first atom: 573
Blocpdb> 119 atoms in block 8
Block first atom: 702
Blocpdb> 128 atoms in block 9
Block first atom: 821
Blocpdb> 54 atoms in block 10
Block first atom: 949
Blocpdb> 135 atoms in block 11
Block first atom: 1003
Blocpdb> 53 atoms in block 12
Block first atom: 1138
Blocpdb> 94 atoms in block 13
Block first atom: 1191
Blocpdb> 141 atoms in block 14
Block first atom: 1285
Blocpdb> 120 atoms in block 15
Block first atom: 1426
Blocpdb> 129 atoms in block 16
Block first atom: 1546
Blocpdb> 120 atoms in block 17
Block first atom: 1675
Blocpdb> 127 atoms in block 18
Block first atom: 1795
Blocpdb> 120 atoms in block 19
Block first atom: 1922
Blocpdb> 131 atoms in block 20
Block first atom: 2042
Blocpdb> 129 atoms in block 21
Block first atom: 2173
Blocpdb> 130 atoms in block 22
Block first atom: 2302
Blocpdb> 104 atoms in block 23
Block first atom: 2432
Blocpdb> 120 atoms in block 24
Block first atom: 2536
Blocpdb> 129 atoms in block 25
Block first atom: 2656
Blocpdb> 120 atoms in block 26
Block first atom: 2785
Blocpdb> 128 atoms in block 27
Block first atom: 2905
Blocpdb> 88 atoms in block 28
Block first atom: 3033
Blocpdb> 145 atoms in block 29
Block first atom: 3121
Blocpdb> 46 atoms in block 30
Block first atom: 3266
Blocpdb> 126 atoms in block 31
Block first atom: 3312
Blocpdb> 137 atoms in block 32
Block first atom: 3438
Blocpdb> 114 atoms in block 33
Block first atom: 3575
Blocpdb> 117 atoms in block 34
Block first atom: 3689
Blocpdb> 137 atoms in block 35
Block first atom: 3806
Blocpdb> 122 atoms in block 36
Block first atom: 3943
Blocpdb> 111 atoms in block 37
Block first atom: 4065
Blocpdb> 120 atoms in block 38
Block first atom: 4176
Blocpdb> 6 atoms in block 39
Block first atom: 4296
Blocpdb> 119 atoms in block 40
Block first atom: 4302
Blocpdb> 112 atoms in block 41
Block first atom: 4421
Blocpdb> 34 atoms in block 42
Block first atom: 4533
Blocpdb> 115 atoms in block 43
Block first atom: 4567
Blocpdb> 121 atoms in block 44
Block first atom: 4682
Blocpdb> 116 atoms in block 45
Block first atom: 4803
Blocpdb> 117 atoms in block 46
Block first atom: 4919
Blocpdb> 127 atoms in block 47
Block first atom: 5036
Blocpdb> 124 atoms in block 48
Block first atom: 5163
Blocpdb> 130 atoms in block 49
Block first atom: 5287
Blocpdb> 126 atoms in block 50
Block first atom: 5417
Blocpdb> 94 atoms in block 51
Block first atom: 5543
Blocpdb> 120 atoms in block 52
Block first atom: 5637
Blocpdb> 117 atoms in block 53
Block first atom: 5757
Blocpdb> 112 atoms in block 54
Block first atom: 5874
Blocpdb> 125 atoms in block 55
Block first atom: 5986
Blocpdb> 136 atoms in block 56
Block first atom: 6111
Blocpdb> 83 atoms in block 57
Block first atom: 6247
Blocpdb> 117 atoms in block 58
Block first atom: 6330
Blocpdb> 116 atoms in block 59
Block first atom: 6447
Blocpdb> 124 atoms in block 60
Block first atom: 6563
Blocpdb> 133 atoms in block 61
Block first atom: 6687
Blocpdb> 121 atoms in block 62
Block first atom: 6820
Blocpdb> 117 atoms in block 63
Block first atom: 6941
Blocpdb> 126 atoms in block 64
Block first atom: 7058
Blocpdb> 123 atoms in block 65
Block first atom: 7184
Blocpdb> 118 atoms in block 66
Block first atom: 7307
Blocpdb> 137 atoms in block 67
Block first atom: 7425
Blocpdb> 136 atoms in block 68
Block first atom: 7562
Blocpdb> 114 atoms in block 69
Block first atom: 7698
Blocpdb> 90 atoms in block 70
Block first atom: 7812
Blocpdb> 38 atoms in block 71
Block first atom: 7902
Blocpdb> 128 atoms in block 72
Block first atom: 7940
Blocpdb> 132 atoms in block 73
Block first atom: 8068
Blocpdb> 142 atoms in block 74
Block first atom: 8200
Blocpdb> 7 atoms in block 75
Block first atom: 8342
Blocpdb> 133 atoms in block 76
Block first atom: 8349
Blocpdb> 129 atoms in block 77
Block first atom: 8482
Blocpdb> 119 atoms in block 78
Block first atom: 8611
Blocpdb> 7 atoms in block 79
Block first atom: 8730
Blocpdb> 129 atoms in block 80
Block first atom: 8737
Blocpdb> 41 atoms in block 81
Block first atom: 8866
Blocpdb> 116 atoms in block 82
Block first atom: 8907
Blocpdb> 125 atoms in block 83
Block first atom: 9023
Blocpdb> 143 atoms in block 84
Block first atom: 9148
Blocpdb> 133 atoms in block 85
Block first atom: 9291
Blocpdb> 116 atoms in block 86
Block first atom: 9424
Blocpdb> 109 atoms in block 87
Block first atom: 9540
Blocpdb> 120 atoms in block 88
Block first atom: 9649
Blocpdb> 130 atoms in block 89
Block first atom: 9769
Blocpdb> 118 atoms in block 90
Block first atom: 9899
Blocpdb> 132 atoms in block 91
Block first atom: 10017
Blocpdb> 127 atoms in block 92
Block first atom: 10149
Blocpdb> 126 atoms in block 93
Block first atom: 10276
Blocpdb> 126 atoms in block 94
Block first atom: 10402
Blocpdb> 120 atoms in block 95
Block first atom: 10528
Blocpdb> 129 atoms in block 96
Block first atom: 10648
Blocpdb> 120 atoms in block 97
Block first atom: 10777
Blocpdb> 128 atoms in block 98
Block first atom: 10897
Blocpdb> 123 atoms in block 99
Block first atom: 11025
Blocpdb> 148 atoms in block 100
Block first atom: 11148
Blocpdb> 19 atoms in block 101
Block first atom: 11296
Blocpdb> 126 atoms in block 102
Block first atom: 11315
Blocpdb> 137 atoms in block 103
Block first atom: 11441
Blocpdb> 114 atoms in block 104
Block first atom: 11578
Blocpdb> 117 atoms in block 105
Block first atom: 11692
Blocpdb> 137 atoms in block 106
Block first atom: 11809
Blocpdb> 122 atoms in block 107
Block first atom: 11946
Blocpdb> 111 atoms in block 108
Block first atom: 12068
Blocpdb> 120 atoms in block 109
Block first atom: 12179
Blocpdb> 6 atoms in block 110
Block first atom: 12299
Blocpdb> 118 atoms in block 111
Block first atom: 12305
Blocpdb> 114 atoms in block 112
Block first atom: 12423
Blocpdb> 39 atoms in block 113
Block first atom: 12537
Blocpdb> 115 atoms in block 114
Block first atom: 12576
Blocpdb> 121 atoms in block 115
Block first atom: 12691
Blocpdb> 116 atoms in block 116
Block first atom: 12812
Blocpdb> 117 atoms in block 117
Block first atom: 12928
Blocpdb> 127 atoms in block 118
Block first atom: 13045
Blocpdb> 124 atoms in block 119
Block first atom: 13172
Blocpdb> 130 atoms in block 120
Block first atom: 13296
Blocpdb> 126 atoms in block 121
Block first atom: 13426
Blocpdb> 94 atoms in block 122
Block first atom: 13552
Blocpdb> 120 atoms in block 123
Block first atom: 13646
Blocpdb> 117 atoms in block 124
Block first atom: 13766
Blocpdb> 112 atoms in block 125
Block first atom: 13883
Blocpdb> 125 atoms in block 126
Block first atom: 13995
Blocpdb> 136 atoms in block 127
Block first atom: 14120
Blocpdb> 83 atoms in block 128
Block first atom: 14256
Blocpdb> 117 atoms in block 129
Block first atom: 14339
Blocpdb> 116 atoms in block 130
Block first atom: 14456
Blocpdb> 124 atoms in block 131
Block first atom: 14572
Blocpdb> 133 atoms in block 132
Block first atom: 14696
Blocpdb> 121 atoms in block 133
Block first atom: 14829
Blocpdb> 117 atoms in block 134
Block first atom: 14950
Blocpdb> 126 atoms in block 135
Block first atom: 15067
Blocpdb> 123 atoms in block 136
Block first atom: 15193
Blocpdb> 118 atoms in block 137
Block first atom: 15316
Blocpdb> 137 atoms in block 138
Block first atom: 15434
Blocpdb> 136 atoms in block 139
Block first atom: 15571
Blocpdb> 114 atoms in block 140
Block first atom: 15707
Blocpdb> 90 atoms in block 141
Block first atom: 15821
Blocpdb> 125 atoms in block 142
Block first atom: 15911
Blocpdb> 137 atoms in block 143
Block first atom: 16036
Blocpdb> 131 atoms in block 144
Block first atom: 16173
Blocpdb> 79 atoms in block 145
Block first atom: 16304
Blocpdb> 133 atoms in block 146
Block first atom: 16383
Blocpdb> 129 atoms in block 147
Block first atom: 16516
Blocpdb> 106 atoms in block 148
Block first atom: 16645
Blocpdb> 132 atoms in block 149
Block first atom: 16751
Blocpdb> 45 atoms in block 150
Block first atom: 16883
Blocpdb> 135 atoms in block 151
Block first atom: 16928
Blocpdb> 74 atoms in block 152
Block first atom: 17063
Blocpdb> 143 atoms in block 153
Block first atom: 17137
Blocpdb> 133 atoms in block 154
Block first atom: 17280
Blocpdb> 116 atoms in block 155
Block first atom: 17413
Blocpdb> 103 atoms in block 156
Block first atom: 17529
Blocpdb> 120 atoms in block 157
Block first atom: 17632
Blocpdb> 130 atoms in block 158
Block first atom: 17752
Blocpdb> 118 atoms in block 159
Block first atom: 17882
Blocpdb> 132 atoms in block 160
Block first atom: 18000
Blocpdb> 127 atoms in block 161
Block first atom: 18132
Blocpdb> 38 atoms in block 162
Block first atom: 18259
Blocpdb> 138 atoms in block 163
Block first atom: 18297
Blocpdb> 65 atoms in block 164
Block first atom: 18435
Blocpdb> 120 atoms in block 165
Block first atom: 18500
Blocpdb> 129 atoms in block 166
Block first atom: 18620
Blocpdb> 120 atoms in block 167
Block first atom: 18749
Blocpdb> 128 atoms in block 168
Block first atom: 18869
Blocpdb> 123 atoms in block 169
Block first atom: 18997
Blocpdb> 148 atoms in block 170
Block first atom: 19120
Blocpdb> 113 atoms in block 171
Block first atom: 19268
Blocpdb> 126 atoms in block 172
Block first atom: 19381
Blocpdb> 137 atoms in block 173
Block first atom: 19507
Blocpdb> 114 atoms in block 174
Block first atom: 19644
Blocpdb> 117 atoms in block 175
Block first atom: 19758
Blocpdb> 137 atoms in block 176
Block first atom: 19875
Blocpdb> 122 atoms in block 177
Block first atom: 20012
Blocpdb> 111 atoms in block 178
Block first atom: 20134
Blocpdb> 120 atoms in block 179
Block first atom: 20245
Blocpdb> 6 atoms in block 180
Block first atom: 20365
Blocpdb> 119 atoms in block 181
Block first atom: 20371
Blocpdb> 112 atoms in block 182
Block first atom: 20490
Blocpdb> 34 atoms in block 183
Block first atom: 20602
Blocpdb> 115 atoms in block 184
Block first atom: 20636
Blocpdb> 121 atoms in block 185
Block first atom: 20751
Blocpdb> 116 atoms in block 186
Block first atom: 20872
Blocpdb> 117 atoms in block 187
Block first atom: 20988
Blocpdb> 127 atoms in block 188
Block first atom: 21105
Blocpdb> 124 atoms in block 189
Block first atom: 21232
Blocpdb> 130 atoms in block 190
Block first atom: 21356
Blocpdb> 126 atoms in block 191
Block first atom: 21486
Blocpdb> 94 atoms in block 192
Block first atom: 21612
Blocpdb> 119 atoms in block 193
Block first atom: 21706
Blocpdb> 117 atoms in block 194
Block first atom: 21825
Blocpdb> 115 atoms in block 195
Block first atom: 21942
Blocpdb> 124 atoms in block 196
Block first atom: 22057
Blocpdb> 130 atoms in block 197
Block first atom: 22181
Blocpdb> 72 atoms in block 198
Block first atom: 22311
Blocpdb> 117 atoms in block 199
Block first atom: 22383
Blocpdb> 116 atoms in block 200
Block first atom: 22500
Blocpdb> 124 atoms in block 201
Block first atom: 22616
Blocpdb> 133 atoms in block 202
Block first atom: 22740
Blocpdb> 121 atoms in block 203
Block first atom: 22873
Blocpdb> 117 atoms in block 204
Block first atom: 22994
Blocpdb> 126 atoms in block 205
Block first atom: 23111
Blocpdb> 123 atoms in block 206
Block first atom: 23237
Blocpdb> 118 atoms in block 207
Block first atom: 23360
Blocpdb> 137 atoms in block 208
Block first atom: 23478
Blocpdb> 136 atoms in block 209
Block first atom: 23615
Blocpdb> 114 atoms in block 210
Block first atom: 23751
Blocpdb> 90 atoms in block 211
Block first atom: 23864
Blocpdb> 211 blocks.
Blocpdb> At most, 148 atoms in each of them.
Blocpdb> At least, 6 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: 32103865 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 0m0.111s
user 0m0.111s
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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