*** TRANSFERASE 15-FEB-17 5N6I ***
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 = 22112810424473367.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 22112810424473367.atom to be opened.
Openam> File opened: 22112810424473367.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 = 2354
First residue number = 149
Last residue number = 20
Number of atoms found = 22077
Mean number per residue = 9.4
Pdbmat> Coordinate statistics:
= -3.275522 +/- 45.625238 From: -93.916000 To: 89.935000
= 47.016036 +/- 18.970297 From: 3.561000 To: 101.539000
= 44.222865 +/- 29.948512 From: -28.931000 To: 115.542000
Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'DG ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA ' is not a well known amino-acid.
%Pdbmat-W> ........
%Pdbmat-W> 212 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 17.9344 % Filled.
Pdbmat> 8217950 non-zero elements.
Pdbmat> 898537 atom-atom interactions.
Pdbmat> Number per atom= 81.40 +/- 21.35
Maximum number = 128
Minimum number = 10
Pdbmat> Matrix trace = 1.797074E+07
Pdbmat> Larger element = 524.628
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2354 non-zero elements, NRBL set to 12
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 = 22112810424473367.atom
Eigenvector OUTPut file = matrix.eigenrtb
Nb of VECTors required = 106
EigeNVALues chosen = LOWE
Type of SUBStructuring = NONE
Nb of residues per BLOck = 12
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 22112810424473367.atom to be opened.
Openam> file on opening on unit 11:
22112810424473367.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 22077 atoms picked in pdb file.
Blocpdb> All masses set to unity.
Blocpdb> Coordinate file is rewritten.
Blocpdb> Substructuring:
Blocpdb> 12 residue(s) per block.
Blocpdb> 2354 residues.
Blocpdb> 103 atoms in block 1
Block first atom: 1
Blocpdb> 92 atoms in block 2
Block first atom: 104
Blocpdb> 107 atoms in block 3
Block first atom: 196
Blocpdb> 100 atoms in block 4
Block first atom: 303
Blocpdb> 95 atoms in block 5
Block first atom: 403
Blocpdb> 102 atoms in block 6
Block first atom: 498
Blocpdb> 105 atoms in block 7
Block first atom: 600
Blocpdb> 109 atoms in block 8
Block first atom: 705
Blocpdb> 91 atoms in block 9
Block first atom: 814
Blocpdb> 97 atoms in block 10
Block first atom: 905
Blocpdb> 101 atoms in block 11
Block first atom: 1002
Blocpdb> 88 atoms in block 12
Block first atom: 1103
Blocpdb> 95 atoms in block 13
Block first atom: 1191
Blocpdb> 86 atoms in block 14
Block first atom: 1286
Blocpdb> 93 atoms in block 15
Block first atom: 1372
Blocpdb> 96 atoms in block 16
Block first atom: 1465
Blocpdb> 105 atoms in block 17
Block first atom: 1561
Blocpdb> 100 atoms in block 18
Block first atom: 1666
Blocpdb> 102 atoms in block 19
Block first atom: 1766
Blocpdb> 88 atoms in block 20
Block first atom: 1868
Blocpdb> 90 atoms in block 21
Block first atom: 1956
Blocpdb> 109 atoms in block 22
Block first atom: 2046
Blocpdb> 100 atoms in block 23
Block first atom: 2155
Blocpdb> 103 atoms in block 24
Block first atom: 2255
Blocpdb> 97 atoms in block 25
Block first atom: 2358
Blocpdb> 102 atoms in block 26
Block first atom: 2455
Blocpdb> 109 atoms in block 27
Block first atom: 2557
Blocpdb> 106 atoms in block 28
Block first atom: 2666
Blocpdb> 105 atoms in block 29
Block first atom: 2772
Blocpdb> 76 atoms in block 30
Block first atom: 2877
Blocpdb> 103 atoms in block 31
Block first atom: 2953
Blocpdb> 92 atoms in block 32
Block first atom: 3056
Blocpdb> 107 atoms in block 33
Block first atom: 3148
Blocpdb> 100 atoms in block 34
Block first atom: 3255
Blocpdb> 95 atoms in block 35
Block first atom: 3355
Blocpdb> 102 atoms in block 36
Block first atom: 3450
Blocpdb> 105 atoms in block 37
Block first atom: 3552
Blocpdb> 109 atoms in block 38
Block first atom: 3657
Blocpdb> 91 atoms in block 39
Block first atom: 3766
Blocpdb> 97 atoms in block 40
Block first atom: 3857
Blocpdb> 101 atoms in block 41
Block first atom: 3954
Blocpdb> 88 atoms in block 42
Block first atom: 4055
Blocpdb> 95 atoms in block 43
Block first atom: 4143
Blocpdb> 86 atoms in block 44
Block first atom: 4238
Blocpdb> 93 atoms in block 45
Block first atom: 4324
Blocpdb> 96 atoms in block 46
Block first atom: 4417
Blocpdb> 105 atoms in block 47
Block first atom: 4513
Blocpdb> 100 atoms in block 48
Block first atom: 4618
Blocpdb> 102 atoms in block 49
Block first atom: 4718
Blocpdb> 88 atoms in block 50
Block first atom: 4820
Blocpdb> 90 atoms in block 51
Block first atom: 4908
Blocpdb> 109 atoms in block 52
Block first atom: 4998
Blocpdb> 100 atoms in block 53
Block first atom: 5107
Blocpdb> 103 atoms in block 54
Block first atom: 5207
Blocpdb> 97 atoms in block 55
Block first atom: 5310
Blocpdb> 102 atoms in block 56
Block first atom: 5407
Blocpdb> 109 atoms in block 57
Block first atom: 5509
Blocpdb> 106 atoms in block 58
Block first atom: 5618
Blocpdb> 105 atoms in block 59
Block first atom: 5724
Blocpdb> 76 atoms in block 60
Block first atom: 5829
Blocpdb> 103 atoms in block 61
Block first atom: 5905
Blocpdb> 92 atoms in block 62
Block first atom: 6008
Blocpdb> 107 atoms in block 63
Block first atom: 6100
Blocpdb> 100 atoms in block 64
Block first atom: 6207
Blocpdb> 95 atoms in block 65
Block first atom: 6307
Blocpdb> 102 atoms in block 66
Block first atom: 6402
Blocpdb> 105 atoms in block 67
Block first atom: 6504
Blocpdb> 109 atoms in block 68
Block first atom: 6609
Blocpdb> 91 atoms in block 69
Block first atom: 6718
Blocpdb> 97 atoms in block 70
Block first atom: 6809
Blocpdb> 101 atoms in block 71
Block first atom: 6906
Blocpdb> 88 atoms in block 72
Block first atom: 7007
Blocpdb> 95 atoms in block 73
Block first atom: 7095
Blocpdb> 86 atoms in block 74
Block first atom: 7190
Blocpdb> 93 atoms in block 75
Block first atom: 7276
Blocpdb> 96 atoms in block 76
Block first atom: 7369
Blocpdb> 105 atoms in block 77
Block first atom: 7465
Blocpdb> 100 atoms in block 78
Block first atom: 7570
Blocpdb> 102 atoms in block 79
Block first atom: 7670
Blocpdb> 88 atoms in block 80
Block first atom: 7772
Blocpdb> 90 atoms in block 81
Block first atom: 7860
Blocpdb> 109 atoms in block 82
Block first atom: 7950
Blocpdb> 100 atoms in block 83
Block first atom: 8059
Blocpdb> 103 atoms in block 84
Block first atom: 8159
Blocpdb> 97 atoms in block 85
Block first atom: 8262
Blocpdb> 102 atoms in block 86
Block first atom: 8359
Blocpdb> 109 atoms in block 87
Block first atom: 8461
Blocpdb> 106 atoms in block 88
Block first atom: 8570
Blocpdb> 105 atoms in block 89
Block first atom: 8676
Blocpdb> 76 atoms in block 90
Block first atom: 8781
Blocpdb> 103 atoms in block 91
Block first atom: 8857
Blocpdb> 92 atoms in block 92
Block first atom: 8960
Blocpdb> 107 atoms in block 93
Block first atom: 9052
Blocpdb> 100 atoms in block 94
Block first atom: 9159
Blocpdb> 95 atoms in block 95
Block first atom: 9259
Blocpdb> 102 atoms in block 96
Block first atom: 9354
Blocpdb> 105 atoms in block 97
Block first atom: 9456
Blocpdb> 109 atoms in block 98
Block first atom: 9561
Blocpdb> 91 atoms in block 99
Block first atom: 9670
Blocpdb> 97 atoms in block 100
Block first atom: 9761
Blocpdb> 101 atoms in block 101
Block first atom: 9858
Blocpdb> 88 atoms in block 102
Block first atom: 9959
Blocpdb> 95 atoms in block 103
Block first atom: 10047
Blocpdb> 86 atoms in block 104
Block first atom: 10142
Blocpdb> 93 atoms in block 105
Block first atom: 10228
Blocpdb> 96 atoms in block 106
Block first atom: 10321
Blocpdb> 105 atoms in block 107
Block first atom: 10417
Blocpdb> 100 atoms in block 108
Block first atom: 10522
Blocpdb> 102 atoms in block 109
Block first atom: 10622
Blocpdb> 88 atoms in block 110
Block first atom: 10724
Blocpdb> 90 atoms in block 111
Block first atom: 10812
Blocpdb> 109 atoms in block 112
Block first atom: 10902
Blocpdb> 100 atoms in block 113
Block first atom: 11011
Blocpdb> 103 atoms in block 114
Block first atom: 11111
Blocpdb> 97 atoms in block 115
Block first atom: 11214
Blocpdb> 102 atoms in block 116
Block first atom: 11311
Blocpdb> 109 atoms in block 117
Block first atom: 11413
Blocpdb> 106 atoms in block 118
Block first atom: 11522
Blocpdb> 105 atoms in block 119
Block first atom: 11628
Blocpdb> 76 atoms in block 120
Block first atom: 11733
Blocpdb> 103 atoms in block 121
Block first atom: 11809
Blocpdb> 92 atoms in block 122
Block first atom: 11912
Blocpdb> 107 atoms in block 123
Block first atom: 12004
Blocpdb> 100 atoms in block 124
Block first atom: 12111
Blocpdb> 95 atoms in block 125
Block first atom: 12211
Blocpdb> 102 atoms in block 126
Block first atom: 12306
Blocpdb> 105 atoms in block 127
Block first atom: 12408
Blocpdb> 109 atoms in block 128
Block first atom: 12513
Blocpdb> 91 atoms in block 129
Block first atom: 12622
Blocpdb> 97 atoms in block 130
Block first atom: 12713
Blocpdb> 101 atoms in block 131
Block first atom: 12810
Blocpdb> 88 atoms in block 132
Block first atom: 12911
Blocpdb> 95 atoms in block 133
Block first atom: 12999
Blocpdb> 86 atoms in block 134
Block first atom: 13094
Blocpdb> 93 atoms in block 135
Block first atom: 13180
Blocpdb> 96 atoms in block 136
Block first atom: 13273
Blocpdb> 105 atoms in block 137
Block first atom: 13369
Blocpdb> 100 atoms in block 138
Block first atom: 13474
Blocpdb> 102 atoms in block 139
Block first atom: 13574
Blocpdb> 88 atoms in block 140
Block first atom: 13676
Blocpdb> 90 atoms in block 141
Block first atom: 13764
Blocpdb> 109 atoms in block 142
Block first atom: 13854
Blocpdb> 100 atoms in block 143
Block first atom: 13963
Blocpdb> 103 atoms in block 144
Block first atom: 14063
Blocpdb> 97 atoms in block 145
Block first atom: 14166
Blocpdb> 102 atoms in block 146
Block first atom: 14263
Blocpdb> 109 atoms in block 147
Block first atom: 14365
Blocpdb> 106 atoms in block 148
Block first atom: 14474
Blocpdb> 105 atoms in block 149
Block first atom: 14580
Blocpdb> 76 atoms in block 150
Block first atom: 14685
Blocpdb> 103 atoms in block 151
Block first atom: 14761
Blocpdb> 92 atoms in block 152
Block first atom: 14864
Blocpdb> 107 atoms in block 153
Block first atom: 14956
Blocpdb> 100 atoms in block 154
Block first atom: 15063
Blocpdb> 95 atoms in block 155
Block first atom: 15163
Blocpdb> 102 atoms in block 156
Block first atom: 15258
Blocpdb> 105 atoms in block 157
Block first atom: 15360
Blocpdb> 109 atoms in block 158
Block first atom: 15465
Blocpdb> 91 atoms in block 159
Block first atom: 15574
Blocpdb> 97 atoms in block 160
Block first atom: 15665
Blocpdb> 101 atoms in block 161
Block first atom: 15762
Blocpdb> 88 atoms in block 162
Block first atom: 15863
Blocpdb> 95 atoms in block 163
Block first atom: 15951
Blocpdb> 86 atoms in block 164
Block first atom: 16046
Blocpdb> 93 atoms in block 165
Block first atom: 16132
Blocpdb> 96 atoms in block 166
Block first atom: 16225
Blocpdb> 105 atoms in block 167
Block first atom: 16321
Blocpdb> 100 atoms in block 168
Block first atom: 16426
Blocpdb> 102 atoms in block 169
Block first atom: 16526
Blocpdb> 88 atoms in block 170
Block first atom: 16628
Blocpdb> 90 atoms in block 171
Block first atom: 16716
Blocpdb> 109 atoms in block 172
Block first atom: 16806
Blocpdb> 100 atoms in block 173
Block first atom: 16915
Blocpdb> 103 atoms in block 174
Block first atom: 17015
Blocpdb> 97 atoms in block 175
Block first atom: 17118
Blocpdb> 102 atoms in block 176
Block first atom: 17215
Blocpdb> 109 atoms in block 177
Block first atom: 17317
Blocpdb> 106 atoms in block 178
Block first atom: 17426
Blocpdb> 105 atoms in block 179
Block first atom: 17532
Blocpdb> 76 atoms in block 180
Block first atom: 17637
Blocpdb> 247 atoms in block 181
Block first atom: 17713
Blocpdb> 246 atoms in block 182
Block first atom: 17960
Blocpdb> 245 atoms in block 183
Block first atom: 18206
Blocpdb> 19 atoms in block 184
Block first atom: 18451
Blocpdb> 247 atoms in block 185
Block first atom: 18470
Blocpdb> 246 atoms in block 186
Block first atom: 18717
Blocpdb> 245 atoms in block 187
Block first atom: 18963
Blocpdb> 247 atoms in block 188
Block first atom: 19208
Blocpdb> 246 atoms in block 189
Block first atom: 19455
Blocpdb> 245 atoms in block 190
Block first atom: 19701
Blocpdb> 247 atoms in block 191
Block first atom: 19946
Blocpdb> 246 atoms in block 192
Block first atom: 20193
Blocpdb> 245 atoms in block 193
Block first atom: 20439
Blocpdb> 247 atoms in block 194
Block first atom: 20684
Blocpdb> 103 atoms in block 195
Block first atom: 20931
Blocpdb> 246 atoms in block 196
Block first atom: 21034
Blocpdb> 101 atoms in block 197
Block first atom: 21280
Blocpdb> 247 atoms in block 198
Block first atom: 21381
Blocpdb> 103 atoms in block 199
Block first atom: 21628
Blocpdb> 246 atoms in block 200
Block first atom: 21731
Blocpdb> 101 atoms in block 201
Block first atom: 21976
Blocpdb> 201 blocks.
Blocpdb> At most, 247 atoms in each of them.
Blocpdb> At least, 19 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: 49626253 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 0m0.144s
user 0m0.140s
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.
|
