CNRS Nantes University UFIP UFIP
home |  start a new run |  job status |  references&downloads |  examples |  help  

Should you encounter any unexpected behaviour,
please let us know.


***  VIRAL PROTEIN/IMMUNE SYSTEM 22-NOV-20 7KSG  ***

LOGs for ID: 220207192221103606

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 = 220207192221103606.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 220207192221103606.atom to be opened. Openam> File opened: 220207192221103606.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 = 3510 First residue number = 23 Last residue number = 113 Number of atoms found = 27691 Mean number per residue = 7.9 Pdbmat> Coordinate statistics: = 306.615438 +/- 25.966328 From: 250.324000 To: 388.628000 = 305.785045 +/- 24.948912 From: 230.642000 To: 376.071000 = 308.959379 +/- 46.478673 From: 202.314000 To: 410.177000 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 -1.2093 % Filled. Pdbmat> 10211245 non-zero elements. Pdbmat> 1116306 atom-atom interactions. Pdbmat> Number per atom= 80.63 +/- 21.24 Maximum number = 131 Minimum number = 9 Pdbmat> Matrix trace = 2.232612E+07 Pdbmat> Larger element = 509.970 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 3510 non-zero elements, NRBL set to 18 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 = 220207192221103606.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 18 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 220207192221103606.atom to be opened. Openam> file on opening on unit 11: 220207192221103606.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 27691 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 18 residue(s) per block. Blocpdb> 3510 residues. Blocpdb> 148 atoms in block 1 Block first atom: 1 Blocpdb> 150 atoms in block 2 Block first atom: 149 Blocpdb> 104 atoms in block 3 Block first atom: 299 Blocpdb> 149 atoms in block 4 Block first atom: 403 Blocpdb> 143 atoms in block 5 Block first atom: 552 Blocpdb> 135 atoms in block 6 Block first atom: 695 Blocpdb> 155 atoms in block 7 Block first atom: 830 Blocpdb> 151 atoms in block 8 Block first atom: 985 Blocpdb> 148 atoms in block 9 Block first atom: 1136 Blocpdb> 157 atoms in block 10 Block first atom: 1284 Blocpdb> 146 atoms in block 11 Block first atom: 1441 Blocpdb> 138 atoms in block 12 Block first atom: 1587 Blocpdb> 83 atoms in block 13 Block first atom: 1725 Blocpdb> 126 atoms in block 14 Block first atom: 1808 Blocpdb> 149 atoms in block 15 Block first atom: 1934 Blocpdb> 129 atoms in block 16 Block first atom: 2083 Blocpdb> 149 atoms in block 17 Block first atom: 2212 Blocpdb> 142 atoms in block 18 Block first atom: 2361 Blocpdb> 155 atoms in block 19 Block first atom: 2503 Blocpdb> 139 atoms in block 20 Block first atom: 2658 Blocpdb> 138 atoms in block 21 Block first atom: 2797 Blocpdb> 140 atoms in block 22 Block first atom: 2935 Blocpdb> 144 atoms in block 23 Block first atom: 3075 Blocpdb> 136 atoms in block 24 Block first atom: 3219 Blocpdb> 167 atoms in block 25 Block first atom: 3355 Blocpdb> 126 atoms in block 26 Block first atom: 3522 Blocpdb> 147 atoms in block 27 Block first atom: 3648 Blocpdb> 145 atoms in block 28 Block first atom: 3795 Blocpdb> 129 atoms in block 29 Block first atom: 3940 Blocpdb> 134 atoms in block 30 Block first atom: 4069 Blocpdb> 146 atoms in block 31 Block first atom: 4203 Blocpdb> 139 atoms in block 32 Block first atom: 4349 Blocpdb> 122 atoms in block 33 Block first atom: 4488 Blocpdb> 73 atoms in block 34 Block first atom: 4610 Blocpdb> 135 atoms in block 35 Block first atom: 4683 Blocpdb> 114 atoms in block 36 Block first atom: 4818 Blocpdb> 130 atoms in block 37 Block first atom: 4932 Blocpdb> 135 atoms in block 38 Block first atom: 5062 Blocpdb> 131 atoms in block 39 Block first atom: 5197 Blocpdb> 138 atoms in block 40 Block first atom: 5328 Blocpdb> 139 atoms in block 41 Block first atom: 5466 Blocpdb> 147 atoms in block 42 Block first atom: 5605 Blocpdb> 141 atoms in block 43 Block first atom: 5752 Blocpdb> 102 atoms in block 44 Block first atom: 5893 Blocpdb> 137 atoms in block 45 Block first atom: 5995 Blocpdb> 128 atoms in block 46 Block first atom: 6132 Blocpdb> 138 atoms in block 47 Block first atom: 6260 Blocpdb> 143 atoms in block 48 Block first atom: 6398 Blocpdb> 125 atoms in block 49 Block first atom: 6541 Blocpdb> 135 atoms in block 50 Block first atom: 6666 Blocpdb> 132 atoms in block 51 Block first atom: 6801 Blocpdb> 144 atoms in block 52 Block first atom: 6933 Blocpdb> 143 atoms in block 53 Block first atom: 7077 Blocpdb> 130 atoms in block 54 Block first atom: 7220 Blocpdb> 143 atoms in block 55 Block first atom: 7350 Blocpdb> 136 atoms in block 56 Block first atom: 7493 Blocpdb> 137 atoms in block 57 Block first atom: 7629 Blocpdb> 150 atoms in block 58 Block first atom: 7766 Blocpdb> 148 atoms in block 59 Block first atom: 7916 Blocpdb> 137 atoms in block 60 Block first atom: 8064 Blocpdb> 32 atoms in block 61 Block first atom: 8201 Blocpdb> 139 atoms in block 62 Block first atom: 8233 Blocpdb> 154 atoms in block 63 Block first atom: 8372 Blocpdb> 154 atoms in block 64 Block first atom: 8526 Blocpdb> 25 atoms in block 65 Block first atom: 8680 Blocpdb> 149 atoms in block 66 Block first atom: 8705 Blocpdb> 143 atoms in block 67 Block first atom: 8854 Blocpdb> 135 atoms in block 68 Block first atom: 8997 Blocpdb> 155 atoms in block 69 Block first atom: 9132 Blocpdb> 151 atoms in block 70 Block first atom: 9287 Blocpdb> 148 atoms in block 71 Block first atom: 9438 Blocpdb> 157 atoms in block 72 Block first atom: 9586 Blocpdb> 146 atoms in block 73 Block first atom: 9743 Blocpdb> 138 atoms in block 74 Block first atom: 9889 Blocpdb> 83 atoms in block 75 Block first atom: 10027 Blocpdb> 126 atoms in block 76 Block first atom: 10110 Blocpdb> 149 atoms in block 77 Block first atom: 10236 Blocpdb> 129 atoms in block 78 Block first atom: 10385 Blocpdb> 149 atoms in block 79 Block first atom: 10514 Blocpdb> 139 atoms in block 80 Block first atom: 10663 Blocpdb> 155 atoms in block 81 Block first atom: 10802 Blocpdb> 139 atoms in block 82 Block first atom: 10957 Blocpdb> 138 atoms in block 83 Block first atom: 11096 Blocpdb> 140 atoms in block 84 Block first atom: 11234 Blocpdb> 144 atoms in block 85 Block first atom: 11374 Blocpdb> 136 atoms in block 86 Block first atom: 11518 Blocpdb> 167 atoms in block 87 Block first atom: 11654 Blocpdb> 126 atoms in block 88 Block first atom: 11821 Blocpdb> 147 atoms in block 89 Block first atom: 11947 Blocpdb> 140 atoms in block 90 Block first atom: 12094 Blocpdb> 129 atoms in block 91 Block first atom: 12234 Blocpdb> 134 atoms in block 92 Block first atom: 12363 Blocpdb> 146 atoms in block 93 Block first atom: 12497 Blocpdb> 139 atoms in block 94 Block first atom: 12643 Blocpdb> 122 atoms in block 95 Block first atom: 12782 Blocpdb> 73 atoms in block 96 Block first atom: 12904 Blocpdb> 135 atoms in block 97 Block first atom: 12977 Blocpdb> 114 atoms in block 98 Block first atom: 13112 Blocpdb> 130 atoms in block 99 Block first atom: 13226 Blocpdb> 135 atoms in block 100 Block first atom: 13356 Blocpdb> 131 atoms in block 101 Block first atom: 13491 Blocpdb> 138 atoms in block 102 Block first atom: 13622 Blocpdb> 139 atoms in block 103 Block first atom: 13760 Blocpdb> 147 atoms in block 104 Block first atom: 13899 Blocpdb> 141 atoms in block 105 Block first atom: 14046 Blocpdb> 102 atoms in block 106 Block first atom: 14187 Blocpdb> 137 atoms in block 107 Block first atom: 14289 Blocpdb> 128 atoms in block 108 Block first atom: 14426 Blocpdb> 138 atoms in block 109 Block first atom: 14554 Blocpdb> 143 atoms in block 110 Block first atom: 14692 Blocpdb> 125 atoms in block 111 Block first atom: 14835 Blocpdb> 135 atoms in block 112 Block first atom: 14960 Blocpdb> 132 atoms in block 113 Block first atom: 15095 Blocpdb> 144 atoms in block 114 Block first atom: 15227 Blocpdb> 143 atoms in block 115 Block first atom: 15371 Blocpdb> 130 atoms in block 116 Block first atom: 15514 Blocpdb> 143 atoms in block 117 Block first atom: 15644 Blocpdb> 136 atoms in block 118 Block first atom: 15787 Blocpdb> 137 atoms in block 119 Block first atom: 15923 Blocpdb> 150 atoms in block 120 Block first atom: 16060 Blocpdb> 148 atoms in block 121 Block first atom: 16210 Blocpdb> 137 atoms in block 122 Block first atom: 16358 Blocpdb> 32 atoms in block 123 Block first atom: 16495 Blocpdb> 139 atoms in block 124 Block first atom: 16527 Blocpdb> 154 atoms in block 125 Block first atom: 16666 Blocpdb> 154 atoms in block 126 Block first atom: 16820 Blocpdb> 25 atoms in block 127 Block first atom: 16974 Blocpdb> 149 atoms in block 128 Block first atom: 16999 Blocpdb> 143 atoms in block 129 Block first atom: 17148 Blocpdb> 135 atoms in block 130 Block first atom: 17291 Blocpdb> 155 atoms in block 131 Block first atom: 17426 Blocpdb> 151 atoms in block 132 Block first atom: 17581 Blocpdb> 148 atoms in block 133 Block first atom: 17732 Blocpdb> 157 atoms in block 134 Block first atom: 17880 Blocpdb> 146 atoms in block 135 Block first atom: 18037 Blocpdb> 138 atoms in block 136 Block first atom: 18183 Blocpdb> 83 atoms in block 137 Block first atom: 18321 Blocpdb> 126 atoms in block 138 Block first atom: 18404 Blocpdb> 149 atoms in block 139 Block first atom: 18530 Blocpdb> 129 atoms in block 140 Block first atom: 18679 Blocpdb> 149 atoms in block 141 Block first atom: 18808 Blocpdb> 142 atoms in block 142 Block first atom: 18957 Blocpdb> 155 atoms in block 143 Block first atom: 19099 Blocpdb> 139 atoms in block 144 Block first atom: 19254 Blocpdb> 138 atoms in block 145 Block first atom: 19393 Blocpdb> 140 atoms in block 146 Block first atom: 19531 Blocpdb> 144 atoms in block 147 Block first atom: 19671 Blocpdb> 136 atoms in block 148 Block first atom: 19815 Blocpdb> 167 atoms in block 149 Block first atom: 19951 Blocpdb> 126 atoms in block 150 Block first atom: 20118 Blocpdb> 147 atoms in block 151 Block first atom: 20244 Blocpdb> 140 atoms in block 152 Block first atom: 20391 Blocpdb> 129 atoms in block 153 Block first atom: 20531 Blocpdb> 134 atoms in block 154 Block first atom: 20660 Blocpdb> 146 atoms in block 155 Block first atom: 20794 Blocpdb> 18 atoms in block 156 Block first atom: 20940 Blocpdb> 123 atoms in block 157 Block first atom: 20958 Blocpdb> 138 atoms in block 158 Block first atom: 21081 Blocpdb> 7 atoms in block 159 Block first atom: 21219 Blocpdb> 135 atoms in block 160 Block first atom: 21226 Blocpdb> 114 atoms in block 161 Block first atom: 21361 Blocpdb> 130 atoms in block 162 Block first atom: 21475 Blocpdb> 135 atoms in block 163 Block first atom: 21605 Blocpdb> 131 atoms in block 164 Block first atom: 21740 Blocpdb> 138 atoms in block 165 Block first atom: 21871 Blocpdb> 139 atoms in block 166 Block first atom: 22009 Blocpdb> 147 atoms in block 167 Block first atom: 22148 Blocpdb> 141 atoms in block 168 Block first atom: 22295 Blocpdb> 102 atoms in block 169 Block first atom: 22436 Blocpdb> 137 atoms in block 170 Block first atom: 22538 Blocpdb> 128 atoms in block 171 Block first atom: 22675 Blocpdb> 138 atoms in block 172 Block first atom: 22803 Blocpdb> 143 atoms in block 173 Block first atom: 22941 Blocpdb> 125 atoms in block 174 Block first atom: 23084 Blocpdb> 135 atoms in block 175 Block first atom: 23209 Blocpdb> 132 atoms in block 176 Block first atom: 23344 Blocpdb> 144 atoms in block 177 Block first atom: 23476 Blocpdb> 143 atoms in block 178 Block first atom: 23620 Blocpdb> 130 atoms in block 179 Block first atom: 23763 Blocpdb> 143 atoms in block 180 Block first atom: 23893 Blocpdb> 136 atoms in block 181 Block first atom: 24036 Blocpdb> 137 atoms in block 182 Block first atom: 24172 Blocpdb> 150 atoms in block 183 Block first atom: 24309 Blocpdb> 148 atoms in block 184 Block first atom: 24459 Blocpdb> 137 atoms in block 185 Block first atom: 24607 Blocpdb> 32 atoms in block 186 Block first atom: 24744 Blocpdb> 118 atoms in block 187 Block first atom: 24776 Blocpdb> 136 atoms in block 188 Block first atom: 24894 Blocpdb> 140 atoms in block 189 Block first atom: 25030 Blocpdb> 146 atoms in block 190 Block first atom: 25170 Blocpdb> 160 atoms in block 191 Block first atom: 25316 Blocpdb> 239 atoms in block 192 Block first atom: 25476 Blocpdb> 33 atoms in block 193 Block first atom: 25715 Blocpdb> 118 atoms in block 194 Block first atom: 25748 Blocpdb> 136 atoms in block 195 Block first atom: 25866 Blocpdb> 140 atoms in block 196 Block first atom: 26002 Blocpdb> 146 atoms in block 197 Block first atom: 26142 Blocpdb> 160 atoms in block 198 Block first atom: 26288 Blocpdb> 239 atoms in block 199 Block first atom: 26448 Blocpdb> 33 atoms in block 200 Block first atom: 26687 Blocpdb> 118 atoms in block 201 Block first atom: 26720 Blocpdb> 136 atoms in block 202 Block first atom: 26838 Blocpdb> 140 atoms in block 203 Block first atom: 26974 Blocpdb> 146 atoms in block 204 Block first atom: 27114 Blocpdb> 160 atoms in block 205 Block first atom: 27260 Blocpdb> 239 atoms in block 206 Block first atom: 27420 Blocpdb> 33 atoms in block 207 Block first atom: 27658 Blocpdb> 207 blocks. Blocpdb> At most, 239 atoms in each of them. Blocpdb> At least, 7 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: 60077431 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 0m0.174s user 0m0.168s 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.