*** GLYCOGEN PHOSPHORYLASE 13-NOV-90 1GPA ***
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 = 22120817044743600.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 22120817044743600.atom to be opened.
Openam> File opened: 22120817044743600.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 = 3307
First residue number = 10
Last residue number = 837
Number of atoms found = 26889
Mean number per residue = 8.1
Pdbmat> Coordinate statistics:
= 74.069539 +/- 27.916572 From: 4.146000 To: 134.476000
= 22.851852 +/- 27.122857 From: -36.461000 To: 81.464000
= 39.738300 +/- 26.853904 From: -29.571000 To: 96.988000
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 -1.0246 % Filled.
Pdbmat> 10670026 non-zero elements.
Pdbmat> 1167808 atom-atom interactions.
Pdbmat> Number per atom= 86.86 +/- 20.47
Maximum number = 136
Minimum number = 12
Pdbmat> Matrix trace = 2.335616E+07
Pdbmat> Larger element = 530.856
Pdbmat> 0 elements larger than +/- 1.0E+10
Pdbmat> Normal end.
automatic determination of NRBL (NRBL = nresidues/200 + 1)
3307 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 = 22120817044743600.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 22120817044743600.atom to be opened.
Openam> file on opening on unit 11:
22120817044743600.atom
Blocpdb> Coordinate file in PDB format.
Blocpdb> 26889 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> 3307 residues.
Blocpdb> 37 atoms in block 1
Block first atom: 1
Blocpdb> 131 atoms in block 2
Block first atom: 38
Blocpdb> 142 atoms in block 3
Block first atom: 169
Blocpdb> 144 atoms in block 4
Block first atom: 311
Blocpdb> 164 atoms in block 5
Block first atom: 455
Blocpdb> 148 atoms in block 6
Block first atom: 619
Blocpdb> 126 atoms in block 7
Block first atom: 767
Blocpdb> 131 atoms in block 8
Block first atom: 893
Blocpdb> 116 atoms in block 9
Block first atom: 1024
Blocpdb> 136 atoms in block 10
Block first atom: 1140
Blocpdb> 143 atoms in block 11
Block first atom: 1276
Blocpdb> 145 atoms in block 12
Block first atom: 1419
Blocpdb> 140 atoms in block 13
Block first atom: 1564
Blocpdb> 134 atoms in block 14
Block first atom: 1704
Blocpdb> 137 atoms in block 15
Block first atom: 1838
Blocpdb> 135 atoms in block 16
Block first atom: 1975
Blocpdb> 134 atoms in block 17
Block first atom: 2110
Blocpdb> 139 atoms in block 18
Block first atom: 2244
Blocpdb> 144 atoms in block 19
Block first atom: 2383
Blocpdb> 136 atoms in block 20
Block first atom: 2527
Blocpdb> 132 atoms in block 21
Block first atom: 2663
Blocpdb> 148 atoms in block 22
Block first atom: 2795
Blocpdb> 140 atoms in block 23
Block first atom: 2943
Blocpdb> 147 atoms in block 24
Block first atom: 3083
Blocpdb> 133 atoms in block 25
Block first atom: 3230
Blocpdb> 140 atoms in block 26
Block first atom: 3363
Blocpdb> 114 atoms in block 27
Block first atom: 3503
Blocpdb> 153 atoms in block 28
Block first atom: 3617
Blocpdb> 143 atoms in block 29
Block first atom: 3770
Blocpdb> 133 atoms in block 30
Block first atom: 3913
Blocpdb> 143 atoms in block 31
Block first atom: 4046
Blocpdb> 138 atoms in block 32
Block first atom: 4189
Blocpdb> 150 atoms in block 33
Block first atom: 4327
Blocpdb> 150 atoms in block 34
Block first atom: 4477
Blocpdb> 144 atoms in block 35
Block first atom: 4627
Blocpdb> 128 atoms in block 36
Block first atom: 4771
Blocpdb> 129 atoms in block 37
Block first atom: 4899
Blocpdb> 130 atoms in block 38
Block first atom: 5028
Blocpdb> 135 atoms in block 39
Block first atom: 5158
Blocpdb> 112 atoms in block 40
Block first atom: 5293
Blocpdb> 123 atoms in block 41
Block first atom: 5405
Blocpdb> 136 atoms in block 42
Block first atom: 5528
Blocpdb> 138 atoms in block 43
Block first atom: 5664
Blocpdb> 155 atoms in block 44
Block first atom: 5802
Blocpdb> 135 atoms in block 45
Block first atom: 5957
Blocpdb> 152 atoms in block 46
Block first atom: 6092
Blocpdb> 145 atoms in block 47
Block first atom: 6244
Blocpdb> 136 atoms in block 48
Block first atom: 6389
Blocpdb> 140 atoms in block 49
Block first atom: 6525
Blocpdb> 58 atoms in block 50
Block first atom: 6665
Blocpdb> 37 atoms in block 51
Block first atom: 6723
Blocpdb> 30 atoms in block 52
Block first atom: 6760
Blocpdb> 150 atoms in block 53
Block first atom: 6790
Blocpdb> 144 atoms in block 54
Block first atom: 6940
Blocpdb> 146 atoms in block 55
Block first atom: 7084
Blocpdb> 161 atoms in block 56
Block first atom: 7230
Blocpdb> 135 atoms in block 57
Block first atom: 7391
Blocpdb> 132 atoms in block 58
Block first atom: 7526
Blocpdb> 116 atoms in block 59
Block first atom: 7658
Blocpdb> 122 atoms in block 60
Block first atom: 7774
Blocpdb> 140 atoms in block 61
Block first atom: 7896
Blocpdb> 152 atoms in block 62
Block first atom: 8036
Blocpdb> 146 atoms in block 63
Block first atom: 8188
Blocpdb> 127 atoms in block 64
Block first atom: 8334
Blocpdb> 139 atoms in block 65
Block first atom: 8461
Blocpdb> 140 atoms in block 66
Block first atom: 8600
Blocpdb> 128 atoms in block 67
Block first atom: 8740
Blocpdb> 140 atoms in block 68
Block first atom: 8868
Blocpdb> 144 atoms in block 69
Block first atom: 9008
Blocpdb> 140 atoms in block 70
Block first atom: 9152
Blocpdb> 131 atoms in block 71
Block first atom: 9292
Blocpdb> 144 atoms in block 72
Block first atom: 9423
Blocpdb> 137 atoms in block 73
Block first atom: 9567
Blocpdb> 142 atoms in block 74
Block first atom: 9704
Blocpdb> 153 atoms in block 75
Block first atom: 9846
Blocpdb> 133 atoms in block 76
Block first atom: 9999
Blocpdb> 130 atoms in block 77
Block first atom: 10132
Blocpdb> 121 atoms in block 78
Block first atom: 10262
Blocpdb> 156 atoms in block 79
Block first atom: 10383
Blocpdb> 138 atoms in block 80
Block first atom: 10539
Blocpdb> 131 atoms in block 81
Block first atom: 10677
Blocpdb> 143 atoms in block 82
Block first atom: 10808
Blocpdb> 141 atoms in block 83
Block first atom: 10951
Blocpdb> 146 atoms in block 84
Block first atom: 11092
Blocpdb> 152 atoms in block 85
Block first atom: 11238
Blocpdb> 145 atoms in block 86
Block first atom: 11390
Blocpdb> 121 atoms in block 87
Block first atom: 11535
Blocpdb> 130 atoms in block 88
Block first atom: 11656
Blocpdb> 144 atoms in block 89
Block first atom: 11786
Blocpdb> 123 atoms in block 90
Block first atom: 11930
Blocpdb> 118 atoms in block 91
Block first atom: 12053
Blocpdb> 114 atoms in block 92
Block first atom: 12171
Blocpdb> 139 atoms in block 93
Block first atom: 12285
Blocpdb> 153 atoms in block 94
Block first atom: 12424
Blocpdb> 137 atoms in block 95
Block first atom: 12577
Blocpdb> 144 atoms in block 96
Block first atom: 12714
Blocpdb> 155 atoms in block 97
Block first atom: 12858
Blocpdb> 148 atoms in block 98
Block first atom: 13013
Blocpdb> 130 atoms in block 99
Block first atom: 13161
Blocpdb> 138 atoms in block 100
Block first atom: 13291
Blocpdb> 17 atoms in block 101
Block first atom: 13429
Blocpdb> 37 atoms in block 102
Block first atom: 13446
Blocpdb> 131 atoms in block 103
Block first atom: 13483
Blocpdb> 142 atoms in block 104
Block first atom: 13614
Blocpdb> 144 atoms in block 105
Block first atom: 13756
Blocpdb> 164 atoms in block 106
Block first atom: 13900
Blocpdb> 148 atoms in block 107
Block first atom: 14064
Blocpdb> 126 atoms in block 108
Block first atom: 14212
Blocpdb> 131 atoms in block 109
Block first atom: 14338
Blocpdb> 116 atoms in block 110
Block first atom: 14469
Blocpdb> 136 atoms in block 111
Block first atom: 14585
Blocpdb> 143 atoms in block 112
Block first atom: 14721
Blocpdb> 145 atoms in block 113
Block first atom: 14864
Blocpdb> 140 atoms in block 114
Block first atom: 15009
Blocpdb> 134 atoms in block 115
Block first atom: 15149
Blocpdb> 137 atoms in block 116
Block first atom: 15283
Blocpdb> 135 atoms in block 117
Block first atom: 15420
Blocpdb> 134 atoms in block 118
Block first atom: 15555
Blocpdb> 139 atoms in block 119
Block first atom: 15689
Blocpdb> 144 atoms in block 120
Block first atom: 15828
Blocpdb> 136 atoms in block 121
Block first atom: 15972
Blocpdb> 132 atoms in block 122
Block first atom: 16108
Blocpdb> 148 atoms in block 123
Block first atom: 16240
Blocpdb> 140 atoms in block 124
Block first atom: 16388
Blocpdb> 147 atoms in block 125
Block first atom: 16528
Blocpdb> 133 atoms in block 126
Block first atom: 16675
Blocpdb> 140 atoms in block 127
Block first atom: 16808
Blocpdb> 114 atoms in block 128
Block first atom: 16948
Blocpdb> 153 atoms in block 129
Block first atom: 17062
Blocpdb> 143 atoms in block 130
Block first atom: 17215
Blocpdb> 133 atoms in block 131
Block first atom: 17358
Blocpdb> 143 atoms in block 132
Block first atom: 17491
Blocpdb> 138 atoms in block 133
Block first atom: 17634
Blocpdb> 150 atoms in block 134
Block first atom: 17772
Blocpdb> 150 atoms in block 135
Block first atom: 17922
Blocpdb> 144 atoms in block 136
Block first atom: 18072
Blocpdb> 128 atoms in block 137
Block first atom: 18216
Blocpdb> 129 atoms in block 138
Block first atom: 18344
Blocpdb> 130 atoms in block 139
Block first atom: 18473
Blocpdb> 135 atoms in block 140
Block first atom: 18603
Blocpdb> 112 atoms in block 141
Block first atom: 18738
Blocpdb> 123 atoms in block 142
Block first atom: 18850
Blocpdb> 136 atoms in block 143
Block first atom: 18973
Blocpdb> 138 atoms in block 144
Block first atom: 19109
Blocpdb> 155 atoms in block 145
Block first atom: 19247
Blocpdb> 135 atoms in block 146
Block first atom: 19402
Blocpdb> 152 atoms in block 147
Block first atom: 19537
Blocpdb> 145 atoms in block 148
Block first atom: 19689
Blocpdb> 136 atoms in block 149
Block first atom: 19834
Blocpdb> 140 atoms in block 150
Block first atom: 19970
Blocpdb> 58 atoms in block 151
Block first atom: 20110
Blocpdb> 37 atoms in block 152
Block first atom: 20168
Blocpdb> 131 atoms in block 153
Block first atom: 20205
Blocpdb> 142 atoms in block 154
Block first atom: 20336
Blocpdb> 144 atoms in block 155
Block first atom: 20478
Blocpdb> 164 atoms in block 156
Block first atom: 20622
Blocpdb> 148 atoms in block 157
Block first atom: 20786
Blocpdb> 126 atoms in block 158
Block first atom: 20934
Blocpdb> 131 atoms in block 159
Block first atom: 21060
Blocpdb> 116 atoms in block 160
Block first atom: 21191
Blocpdb> 136 atoms in block 161
Block first atom: 21307
Blocpdb> 143 atoms in block 162
Block first atom: 21443
Blocpdb> 145 atoms in block 163
Block first atom: 21586
Blocpdb> 140 atoms in block 164
Block first atom: 21731
Blocpdb> 134 atoms in block 165
Block first atom: 21871
Blocpdb> 137 atoms in block 166
Block first atom: 22005
Blocpdb> 135 atoms in block 167
Block first atom: 22142
Blocpdb> 134 atoms in block 168
Block first atom: 22277
Blocpdb> 139 atoms in block 169
Block first atom: 22411
Blocpdb> 144 atoms in block 170
Block first atom: 22550
Blocpdb> 136 atoms in block 171
Block first atom: 22694
Blocpdb> 132 atoms in block 172
Block first atom: 22830
Blocpdb> 148 atoms in block 173
Block first atom: 22962
Blocpdb> 140 atoms in block 174
Block first atom: 23110
Blocpdb> 147 atoms in block 175
Block first atom: 23250
Blocpdb> 133 atoms in block 176
Block first atom: 23397
Blocpdb> 140 atoms in block 177
Block first atom: 23530
Blocpdb> 114 atoms in block 178
Block first atom: 23670
Blocpdb> 153 atoms in block 179
Block first atom: 23784
Blocpdb> 143 atoms in block 180
Block first atom: 23937
Blocpdb> 133 atoms in block 181
Block first atom: 24080
Blocpdb> 143 atoms in block 182
Block first atom: 24213
Blocpdb> 138 atoms in block 183
Block first atom: 24356
Blocpdb> 150 atoms in block 184
Block first atom: 24494
Blocpdb> 150 atoms in block 185
Block first atom: 24644
Blocpdb> 144 atoms in block 186
Block first atom: 24794
Blocpdb> 128 atoms in block 187
Block first atom: 24938
Blocpdb> 129 atoms in block 188
Block first atom: 25066
Blocpdb> 130 atoms in block 189
Block first atom: 25195
Blocpdb> 135 atoms in block 190
Block first atom: 25325
Blocpdb> 112 atoms in block 191
Block first atom: 25460
Blocpdb> 123 atoms in block 192
Block first atom: 25572
Blocpdb> 136 atoms in block 193
Block first atom: 25695
Blocpdb> 138 atoms in block 194
Block first atom: 25831
Blocpdb> 155 atoms in block 195
Block first atom: 25969
Blocpdb> 135 atoms in block 196
Block first atom: 26124
Blocpdb> 152 atoms in block 197
Block first atom: 26259
Blocpdb> 145 atoms in block 198
Block first atom: 26411
Blocpdb> 136 atoms in block 199
Block first atom: 26556
Blocpdb> 140 atoms in block 200
Block first atom: 26692
Blocpdb> 58 atoms in block 201
Block first atom: 26831
Blocpdb> 201 blocks.
Blocpdb> At most, 164 atoms in each of them.
Blocpdb> At least, 17 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: 39930229 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 0m0.171s
user 0m0.168s
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: October 18th, 2018.
|
