*** Histone pretein ***
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 = 2405231922143008260.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 2405231922143008260.atom to be opened.
Openam> File opened: 2405231922143008260.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 = 2128
First residue number = 38
Last residue number = 73
Number of atoms found = 24301
Mean number per residue = 11.4
Pdbmat> Coordinate statistics:
= -38.905631 +/- 26.119440 From: -98.320000 To: 20.746000
= 2.994016 +/- 23.827365 From: -52.030000 To: 56.729000
= 49.110035 +/- 30.044290 From: -11.818000 To: 106.784000
Pdbmat> Masses are all set to one.
%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:'DA ' 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:'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> ........
%Pdbmat-W> 588 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 1.7701 % Filled.
Pdbmat> 9027248 non-zero elements.
Pdbmat> 986988 atom-atom interactions.
Pdbmat> Number per atom= 81.23 +/- 21.75
Maximum number = 133
Minimum number = 12
Pdbmat> Matrix trace = 1.973976E+07
Pdbmat> Larger element = 518.719
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
2128 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 = 2405231922143008260.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 2405231922143008260.atom to be opened.
Openam> file on opening on unit 11:
2405231922143008260.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 24301 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> 2128 residues.
Blocpdb> 89 atoms in block 1
Block first atom: 1
Blocpdb> 102 atoms in block 2
Block first atom: 90
Blocpdb> 98 atoms in block 3
Block first atom: 192
Blocpdb> 92 atoms in block 4
Block first atom: 290
Blocpdb> 84 atoms in block 5
Block first atom: 382
Blocpdb> 83 atoms in block 6
Block first atom: 466
Blocpdb> 85 atoms in block 7
Block first atom: 549
Blocpdb> 91 atoms in block 8
Block first atom: 634
Blocpdb> 84 atoms in block 9
Block first atom: 725
Blocpdb> 81 atoms in block 10
Block first atom: 809
Blocpdb> 92 atoms in block 11
Block first atom: 890
Blocpdb> 86 atoms in block 12
Block first atom: 982
Blocpdb> 93 atoms in block 13
Block first atom: 1068
Blocpdb> 90 atoms in block 14
Block first atom: 1161
Blocpdb> 82 atoms in block 15
Block first atom: 1251
Blocpdb> 94 atoms in block 16
Block first atom: 1333
Blocpdb> 9 atoms in block 17
Block first atom: 1427
Blocpdb> 87 atoms in block 18
Block first atom: 1436
Blocpdb> 93 atoms in block 19
Block first atom: 1523
Blocpdb> 74 atoms in block 20
Block first atom: 1616
Blocpdb> 88 atoms in block 21
Block first atom: 1690
Blocpdb> 76 atoms in block 22
Block first atom: 1778
Blocpdb> 91 atoms in block 23
Block first atom: 1854
Blocpdb> 94 atoms in block 24
Block first atom: 1945
Blocpdb> 87 atoms in block 25
Block first atom: 2039
Blocpdb> 75 atoms in block 26
Block first atom: 2126
Blocpdb> 39 atoms in block 27
Block first atom: 2201
Blocpdb> 95 atoms in block 28
Block first atom: 2240
Blocpdb> 98 atoms in block 29
Block first atom: 2335
Blocpdb> 77 atoms in block 30
Block first atom: 2433
Blocpdb> 85 atoms in block 31
Block first atom: 2510
Blocpdb> 87 atoms in block 32
Block first atom: 2595
Blocpdb> 89 atoms in block 33
Block first atom: 2682
Blocpdb> 91 atoms in block 34
Block first atom: 2771
Blocpdb> 79 atoms in block 35
Block first atom: 2862
Blocpdb> 78 atoms in block 36
Block first atom: 2941
Blocpdb> 10 atoms in block 37
Block first atom: 3019
Blocpdb> 89 atoms in block 38
Block first atom: 3029
Blocpdb> 102 atoms in block 39
Block first atom: 3118
Blocpdb> 98 atoms in block 40
Block first atom: 3220
Blocpdb> 92 atoms in block 41
Block first atom: 3318
Blocpdb> 84 atoms in block 42
Block first atom: 3410
Blocpdb> 83 atoms in block 43
Block first atom: 3494
Blocpdb> 85 atoms in block 44
Block first atom: 3577
Blocpdb> 91 atoms in block 45
Block first atom: 3662
Blocpdb> 84 atoms in block 46
Block first atom: 3753
Blocpdb> 100 atoms in block 47
Block first atom: 3837
Blocpdb> 83 atoms in block 48
Block first atom: 3937
Blocpdb> 83 atoms in block 49
Block first atom: 4020
Blocpdb> 91 atoms in block 50
Block first atom: 4103
Blocpdb> 89 atoms in block 51
Block first atom: 4194
Blocpdb> 93 atoms in block 52
Block first atom: 4283
Blocpdb> 89 atoms in block 53
Block first atom: 4376
Blocpdb> 66 atoms in block 54
Block first atom: 4465
Blocpdb> 81 atoms in block 55
Block first atom: 4531
Blocpdb> 93 atoms in block 56
Block first atom: 4612
Blocpdb> 85 atoms in block 57
Block first atom: 4705
Blocpdb> 77 atoms in block 58
Block first atom: 4790
Blocpdb> 83 atoms in block 59
Block first atom: 4867
Blocpdb> 89 atoms in block 60
Block first atom: 4950
Blocpdb> 92 atoms in block 61
Block first atom: 5039
Blocpdb> 89 atoms in block 62
Block first atom: 5131
Blocpdb> 75 atoms in block 63
Block first atom: 5220
Blocpdb> 79 atoms in block 64
Block first atom: 5295
Blocpdb> 99 atoms in block 65
Block first atom: 5374
Blocpdb> 93 atoms in block 66
Block first atom: 5473
Blocpdb> 75 atoms in block 67
Block first atom: 5566
Blocpdb> 94 atoms in block 68
Block first atom: 5641
Blocpdb> 83 atoms in block 69
Block first atom: 5735
Blocpdb> 91 atoms in block 70
Block first atom: 5818
Blocpdb> 82 atoms in block 71
Block first atom: 5909
Blocpdb> 76 atoms in block 72
Block first atom: 5991
Blocpdb> 63 atoms in block 73
Block first atom: 6067
Blocpdb> 219 atoms in block 74
Block first atom: 6130
Blocpdb> 223 atoms in block 75
Block first atom: 6349
Blocpdb> 227 atoms in block 76
Block first atom: 6572
Blocpdb> 227 atoms in block 77
Block first atom: 6799
Blocpdb> 221 atoms in block 78
Block first atom: 7026
Blocpdb> 225 atoms in block 79
Block first atom: 7247
Blocpdb> 226 atoms in block 80
Block first atom: 7472
Blocpdb> 226 atoms in block 81
Block first atom: 7698
Blocpdb> 229 atoms in block 82
Block first atom: 7924
Blocpdb> 224 atoms in block 83
Block first atom: 8153
Blocpdb> 222 atoms in block 84
Block first atom: 8377
Blocpdb> 229 atoms in block 85
Block first atom: 8599
Blocpdb> 230 atoms in block 86
Block first atom: 8828
Blocpdb> 83 atoms in block 87
Block first atom: 9058
Blocpdb> 219 atoms in block 88
Block first atom: 9141
Blocpdb> 223 atoms in block 89
Block first atom: 9360
Blocpdb> 227 atoms in block 90
Block first atom: 9583
Blocpdb> 227 atoms in block 91
Block first atom: 9810
Blocpdb> 221 atoms in block 92
Block first atom: 10037
Blocpdb> 225 atoms in block 93
Block first atom: 10258
Blocpdb> 225 atoms in block 94
Block first atom: 10483
Blocpdb> 226 atoms in block 95
Block first atom: 10708
Blocpdb> 229 atoms in block 96
Block first atom: 10934
Blocpdb> 224 atoms in block 97
Block first atom: 11163
Blocpdb> 222 atoms in block 98
Block first atom: 11387
Blocpdb> 229 atoms in block 99
Block first atom: 11609
Blocpdb> 230 atoms in block 100
Block first atom: 11838
Blocpdb> 83 atoms in block 101
Block first atom: 12068
Blocpdb> 90 atoms in block 102
Block first atom: 12151
Blocpdb> 101 atoms in block 103
Block first atom: 12241
Blocpdb> 99 atoms in block 104
Block first atom: 12342
Blocpdb> 92 atoms in block 105
Block first atom: 12441
Blocpdb> 84 atoms in block 106
Block first atom: 12533
Blocpdb> 83 atoms in block 107
Block first atom: 12617
Blocpdb> 88 atoms in block 108
Block first atom: 12700
Blocpdb> 87 atoms in block 109
Block first atom: 12788
Blocpdb> 93 atoms in block 110
Block first atom: 12875
Blocpdb> 81 atoms in block 111
Block first atom: 12968
Blocpdb> 92 atoms in block 112
Block first atom: 13049
Blocpdb> 86 atoms in block 113
Block first atom: 13141
Blocpdb> 93 atoms in block 114
Block first atom: 13227
Blocpdb> 90 atoms in block 115
Block first atom: 13320
Blocpdb> 82 atoms in block 116
Block first atom: 13410
Blocpdb> 94 atoms in block 117
Block first atom: 13492
Blocpdb> 9 atoms in block 118
Block first atom: 13586
Blocpdb> 87 atoms in block 119
Block first atom: 13595
Blocpdb> 93 atoms in block 120
Block first atom: 13682
Blocpdb> 74 atoms in block 121
Block first atom: 13775
Blocpdb> 88 atoms in block 122
Block first atom: 13849
Blocpdb> 76 atoms in block 123
Block first atom: 13937
Blocpdb> 91 atoms in block 124
Block first atom: 14013
Blocpdb> 94 atoms in block 125
Block first atom: 14104
Blocpdb> 87 atoms in block 126
Block first atom: 14198
Blocpdb> 75 atoms in block 127
Block first atom: 14285
Blocpdb> 55 atoms in block 128
Block first atom: 14360
Blocpdb> 99 atoms in block 129
Block first atom: 14415
Blocpdb> 93 atoms in block 130
Block first atom: 14514
Blocpdb> 75 atoms in block 131
Block first atom: 14607
Blocpdb> 94 atoms in block 132
Block first atom: 14682
Blocpdb> 83 atoms in block 133
Block first atom: 14776
Blocpdb> 91 atoms in block 134
Block first atom: 14859
Blocpdb> 82 atoms in block 135
Block first atom: 14950
Blocpdb> 76 atoms in block 136
Block first atom: 15032
Blocpdb> 63 atoms in block 137
Block first atom: 15108
Blocpdb> 89 atoms in block 138
Block first atom: 15171
Blocpdb> 102 atoms in block 139
Block first atom: 15260
Blocpdb> 98 atoms in block 140
Block first atom: 15362
Blocpdb> 92 atoms in block 141
Block first atom: 15460
Blocpdb> 84 atoms in block 142
Block first atom: 15552
Blocpdb> 83 atoms in block 143
Block first atom: 15636
Blocpdb> 85 atoms in block 144
Block first atom: 15719
Blocpdb> 91 atoms in block 145
Block first atom: 15804
Blocpdb> 84 atoms in block 146
Block first atom: 15895
Blocpdb> 100 atoms in block 147
Block first atom: 15979
Blocpdb> 87 atoms in block 148
Block first atom: 16079
Blocpdb> 80 atoms in block 149
Block first atom: 16166
Blocpdb> 92 atoms in block 150
Block first atom: 16246
Blocpdb> 89 atoms in block 151
Block first atom: 16338
Blocpdb> 93 atoms in block 152
Block first atom: 16427
Blocpdb> 87 atoms in block 153
Block first atom: 16520
Blocpdb> 75 atoms in block 154
Block first atom: 16607
Blocpdb> 81 atoms in block 155
Block first atom: 16682
Blocpdb> 93 atoms in block 156
Block first atom: 16763
Blocpdb> 85 atoms in block 157
Block first atom: 16856
Blocpdb> 77 atoms in block 158
Block first atom: 16941
Blocpdb> 83 atoms in block 159
Block first atom: 17018
Blocpdb> 89 atoms in block 160
Block first atom: 17101
Blocpdb> 92 atoms in block 161
Block first atom: 17190
Blocpdb> 89 atoms in block 162
Block first atom: 17282
Blocpdb> 75 atoms in block 163
Block first atom: 17371
Blocpdb> 79 atoms in block 164
Block first atom: 17446
Blocpdb> 99 atoms in block 165
Block first atom: 17525
Blocpdb> 93 atoms in block 166
Block first atom: 17624
Blocpdb> 75 atoms in block 167
Block first atom: 17717
Blocpdb> 94 atoms in block 168
Block first atom: 17792
Blocpdb> 83 atoms in block 169
Block first atom: 17886
Blocpdb> 91 atoms in block 170
Block first atom: 17969
Blocpdb> 82 atoms in block 171
Block first atom: 18060
Blocpdb> 76 atoms in block 172
Block first atom: 18142
Blocpdb> 63 atoms in block 173
Block first atom: 18218
Blocpdb> 219 atoms in block 174
Block first atom: 18281
Blocpdb> 223 atoms in block 175
Block first atom: 18500
Blocpdb> 227 atoms in block 176
Block first atom: 18723
Blocpdb> 227 atoms in block 177
Block first atom: 18950
Blocpdb> 221 atoms in block 178
Block first atom: 19177
Blocpdb> 225 atoms in block 179
Block first atom: 19398
Blocpdb> 226 atoms in block 180
Block first atom: 19623
Blocpdb> 226 atoms in block 181
Block first atom: 19849
Blocpdb> 229 atoms in block 182
Block first atom: 20075
Blocpdb> 224 atoms in block 183
Block first atom: 20304
Blocpdb> 222 atoms in block 184
Block first atom: 20528
Blocpdb> 229 atoms in block 185
Block first atom: 20750
Blocpdb> 230 atoms in block 186
Block first atom: 20979
Blocpdb> 83 atoms in block 187
Block first atom: 21209
Blocpdb> 219 atoms in block 188
Block first atom: 21292
Blocpdb> 223 atoms in block 189
Block first atom: 21511
Blocpdb> 227 atoms in block 190
Block first atom: 21734
Blocpdb> 227 atoms in block 191
Block first atom: 21961
Blocpdb> 221 atoms in block 192
Block first atom: 22188
Blocpdb> 225 atoms in block 193
Block first atom: 22409
Blocpdb> 225 atoms in block 194
Block first atom: 22634
Blocpdb> 226 atoms in block 195
Block first atom: 22859
Blocpdb> 229 atoms in block 196
Block first atom: 23085
Blocpdb> 224 atoms in block 197
Block first atom: 23314
Blocpdb> 222 atoms in block 198
Block first atom: 23538
Blocpdb> 229 atoms in block 199
Block first atom: 23760
Blocpdb> 230 atoms in block 200
Block first atom: 23989
Blocpdb> 83 atoms in block 201
Block first atom: 24218
Blocpdb> 201 blocks.
Blocpdb> At most, 230 atoms in each of them.
Blocpdb> At least, 9 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: 50779171 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 0m0.127s
user 0m0.123s
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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