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***  rec.pdb  ***

LOGs for ID: 210108173056143434

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 = 210108173056143434.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 210108173056143434.atom to be opened. Openam> File opened: 210108173056143434.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 = 4380 First residue number = 28 Last residue number = 989 Number of atoms found = 40818 Mean number per residue = 9.3 Pdbmat> Coordinate statistics: = 229.479580 +/- 30.144359 From: 148.642000 To: 299.493000 = 216.635237 +/- 22.910970 From: 161.765000 To: 280.688000 = 158.613928 +/- 42.683606 From: 61.333000 To: 247.529000 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 1.9444 % Filled. Pdbmat> 20515760 non-zero elements. Pdbmat> 2252708 atom-atom interactions. Pdbmat> Number per atom= 110.38 +/- 30.38 Maximum number = 194 Minimum number = 9 Pdbmat> Matrix trace = 4.505416E+07 Pdbmat> Larger element = 707.166 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 4380 non-zero elements, NRBL set to 22 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 = 210108173056143434.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 22 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 210108173056143434.atom to be opened. Openam> file on opening on unit 11: 210108173056143434.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 40818 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 22 residue(s) per block. Blocpdb> 4380 residues. Blocpdb> 190 atoms in block 1 Block first atom: 1 Blocpdb> 201 atoms in block 2 Block first atom: 191 Blocpdb> 211 atoms in block 3 Block first atom: 392 Blocpdb> 197 atoms in block 4 Block first atom: 603 Blocpdb> 235 atoms in block 5 Block first atom: 800 Blocpdb> 225 atoms in block 6 Block first atom: 1035 Blocpdb> 211 atoms in block 7 Block first atom: 1260 Blocpdb> 200 atoms in block 8 Block first atom: 1471 Blocpdb> 216 atoms in block 9 Block first atom: 1671 Blocpdb> 229 atoms in block 10 Block first atom: 1887 Blocpdb> 205 atoms in block 11 Block first atom: 2116 Blocpdb> 201 atoms in block 12 Block first atom: 2321 Blocpdb> 199 atoms in block 13 Block first atom: 2522 Blocpdb> 211 atoms in block 14 Block first atom: 2721 Blocpdb> 204 atoms in block 15 Block first atom: 2932 Blocpdb> 206 atoms in block 16 Block first atom: 3136 Blocpdb> 208 atoms in block 17 Block first atom: 3342 Blocpdb> 194 atoms in block 18 Block first atom: 3550 Blocpdb> 214 atoms in block 19 Block first atom: 3744 Blocpdb> 195 atoms in block 20 Block first atom: 3958 Blocpdb> 202 atoms in block 21 Block first atom: 4153 Blocpdb> 212 atoms in block 22 Block first atom: 4355 Blocpdb> 195 atoms in block 23 Block first atom: 4567 Blocpdb> 201 atoms in block 24 Block first atom: 4762 Blocpdb> 193 atoms in block 25 Block first atom: 4963 Blocpdb> 211 atoms in block 26 Block first atom: 5156 Blocpdb> 183 atoms in block 27 Block first atom: 5367 Blocpdb> 196 atoms in block 28 Block first atom: 5550 Blocpdb> 236 atoms in block 29 Block first atom: 5746 Blocpdb> 214 atoms in block 30 Block first atom: 5982 Blocpdb> 220 atoms in block 31 Block first atom: 6196 Blocpdb> 59 atoms in block 32 Block first atom: 6416 Blocpdb> 200 atoms in block 33 Block first atom: 6475 Blocpdb> 201 atoms in block 34 Block first atom: 6675 Blocpdb> 195 atoms in block 35 Block first atom: 6876 Blocpdb> 224 atoms in block 36 Block first atom: 7071 Blocpdb> 198 atoms in block 37 Block first atom: 7295 Blocpdb> 208 atoms in block 38 Block first atom: 7493 Blocpdb> 227 atoms in block 39 Block first atom: 7701 Blocpdb> 220 atoms in block 40 Block first atom: 7928 Blocpdb> 178 atoms in block 41 Block first atom: 8148 Blocpdb> 211 atoms in block 42 Block first atom: 8326 Blocpdb> 207 atoms in block 43 Block first atom: 8537 Blocpdb> 203 atoms in block 44 Block first atom: 8744 Blocpdb> 230 atoms in block 45 Block first atom: 8947 Blocpdb> 198 atoms in block 46 Block first atom: 9177 Blocpdb> 223 atoms in block 47 Block first atom: 9375 Blocpdb> 195 atoms in block 48 Block first atom: 9598 Blocpdb> 196 atoms in block 49 Block first atom: 9793 Blocpdb> 186 atoms in block 50 Block first atom: 9989 Blocpdb> 200 atoms in block 51 Block first atom: 10175 Blocpdb> 191 atoms in block 52 Block first atom: 10375 Blocpdb> 208 atoms in block 53 Block first atom: 10566 Blocpdb> 195 atoms in block 54 Block first atom: 10774 Blocpdb> 198 atoms in block 55 Block first atom: 10969 Blocpdb> 234 atoms in block 56 Block first atom: 11167 Blocpdb> 193 atoms in block 57 Block first atom: 11401 Blocpdb> 214 atoms in block 58 Block first atom: 11594 Blocpdb> 186 atoms in block 59 Block first atom: 11808 Blocpdb> 196 atoms in block 60 Block first atom: 11994 Blocpdb> 183 atoms in block 61 Block first atom: 12190 Blocpdb> 202 atoms in block 62 Block first atom: 12373 Blocpdb> 227 atoms in block 63 Block first atom: 12575 Blocpdb> 193 atoms in block 64 Block first atom: 12802 Blocpdb> 209 atoms in block 65 Block first atom: 12995 Blocpdb> 206 atoms in block 66 Block first atom: 13204 Blocpdb> 205 atoms in block 67 Block first atom: 13410 Blocpdb> 207 atoms in block 68 Block first atom: 13615 Blocpdb> 201 atoms in block 69 Block first atom: 13822 Blocpdb> 197 atoms in block 70 Block first atom: 14023 Blocpdb> 223 atoms in block 71 Block first atom: 14220 Blocpdb> 206 atoms in block 72 Block first atom: 14443 Blocpdb> 201 atoms in block 73 Block first atom: 14649 Blocpdb> 223 atoms in block 74 Block first atom: 14850 Blocpdb> 202 atoms in block 75 Block first atom: 15073 Blocpdb> 114 atoms in block 76 Block first atom: 15275 Blocpdb> 202 atoms in block 77 Block first atom: 15389 Blocpdb> 195 atoms in block 78 Block first atom: 15591 Blocpdb> 208 atoms in block 79 Block first atom: 15786 Blocpdb> 202 atoms in block 80 Block first atom: 15994 Blocpdb> 200 atoms in block 81 Block first atom: 16196 Blocpdb> 209 atoms in block 82 Block first atom: 16396 Blocpdb> 196 atoms in block 83 Block first atom: 16605 Blocpdb> 222 atoms in block 84 Block first atom: 16801 Blocpdb> 203 atoms in block 85 Block first atom: 17023 Blocpdb> 183 atoms in block 86 Block first atom: 17226 Blocpdb> 201 atoms in block 87 Block first atom: 17409 Blocpdb> 230 atoms in block 88 Block first atom: 17610 Blocpdb> 199 atoms in block 89 Block first atom: 17840 Blocpdb> 178 atoms in block 90 Block first atom: 18039 Blocpdb> 203 atoms in block 91 Block first atom: 18217 Blocpdb> 199 atoms in block 92 Block first atom: 18420 Blocpdb> 216 atoms in block 93 Block first atom: 18619 Blocpdb> 187 atoms in block 94 Block first atom: 18835 Blocpdb> 214 atoms in block 95 Block first atom: 19022 Blocpdb> 207 atoms in block 96 Block first atom: 19236 Blocpdb> 209 atoms in block 97 Block first atom: 19443 Blocpdb> 186 atoms in block 98 Block first atom: 19652 Blocpdb> 209 atoms in block 99 Block first atom: 19838 Blocpdb> 194 atoms in block 100 Block first atom: 20047 Blocpdb> 169 atoms in block 101 Block first atom: 20241 Blocpdb> 202 atoms in block 102 Block first atom: 20410 Blocpdb> 195 atoms in block 103 Block first atom: 20612 Blocpdb> 208 atoms in block 104 Block first atom: 20807 Blocpdb> 202 atoms in block 105 Block first atom: 21015 Blocpdb> 200 atoms in block 106 Block first atom: 21217 Blocpdb> 209 atoms in block 107 Block first atom: 21417 Blocpdb> 196 atoms in block 108 Block first atom: 21626 Blocpdb> 222 atoms in block 109 Block first atom: 21822 Blocpdb> 203 atoms in block 110 Block first atom: 22044 Blocpdb> 183 atoms in block 111 Block first atom: 22247 Blocpdb> 201 atoms in block 112 Block first atom: 22430 Blocpdb> 230 atoms in block 113 Block first atom: 22631 Blocpdb> 199 atoms in block 114 Block first atom: 22861 Blocpdb> 178 atoms in block 115 Block first atom: 23060 Blocpdb> 203 atoms in block 116 Block first atom: 23238 Blocpdb> 199 atoms in block 117 Block first atom: 23441 Blocpdb> 216 atoms in block 118 Block first atom: 23640 Blocpdb> 187 atoms in block 119 Block first atom: 23856 Blocpdb> 214 atoms in block 120 Block first atom: 24043 Blocpdb> 207 atoms in block 121 Block first atom: 24257 Blocpdb> 209 atoms in block 122 Block first atom: 24464 Blocpdb> 186 atoms in block 123 Block first atom: 24673 Blocpdb> 209 atoms in block 124 Block first atom: 24859 Blocpdb> 194 atoms in block 125 Block first atom: 25068 Blocpdb> 169 atoms in block 126 Block first atom: 25262 Blocpdb> 190 atoms in block 127 Block first atom: 25431 Blocpdb> 201 atoms in block 128 Block first atom: 25621 Blocpdb> 211 atoms in block 129 Block first atom: 25822 Blocpdb> 197 atoms in block 130 Block first atom: 26033 Blocpdb> 235 atoms in block 131 Block first atom: 26230 Blocpdb> 225 atoms in block 132 Block first atom: 26465 Blocpdb> 211 atoms in block 133 Block first atom: 26690 Blocpdb> 200 atoms in block 134 Block first atom: 26901 Blocpdb> 216 atoms in block 135 Block first atom: 27101 Blocpdb> 229 atoms in block 136 Block first atom: 27317 Blocpdb> 205 atoms in block 137 Block first atom: 27546 Blocpdb> 201 atoms in block 138 Block first atom: 27751 Blocpdb> 199 atoms in block 139 Block first atom: 27952 Blocpdb> 211 atoms in block 140 Block first atom: 28151 Blocpdb> 204 atoms in block 141 Block first atom: 28362 Blocpdb> 206 atoms in block 142 Block first atom: 28566 Blocpdb> 208 atoms in block 143 Block first atom: 28772 Blocpdb> 194 atoms in block 144 Block first atom: 28980 Blocpdb> 214 atoms in block 145 Block first atom: 29174 Blocpdb> 195 atoms in block 146 Block first atom: 29388 Blocpdb> 202 atoms in block 147 Block first atom: 29583 Blocpdb> 212 atoms in block 148 Block first atom: 29785 Blocpdb> 195 atoms in block 149 Block first atom: 29997 Blocpdb> 201 atoms in block 150 Block first atom: 30192 Blocpdb> 193 atoms in block 151 Block first atom: 30393 Blocpdb> 211 atoms in block 152 Block first atom: 30586 Blocpdb> 183 atoms in block 153 Block first atom: 30797 Blocpdb> 196 atoms in block 154 Block first atom: 30980 Blocpdb> 236 atoms in block 155 Block first atom: 31176 Blocpdb> 214 atoms in block 156 Block first atom: 31412 Blocpdb> 220 atoms in block 157 Block first atom: 31626 Blocpdb> 59 atoms in block 158 Block first atom: 31846 Blocpdb> 200 atoms in block 159 Block first atom: 31905 Blocpdb> 201 atoms in block 160 Block first atom: 32105 Blocpdb> 195 atoms in block 161 Block first atom: 32306 Blocpdb> 224 atoms in block 162 Block first atom: 32501 Blocpdb> 198 atoms in block 163 Block first atom: 32725 Blocpdb> 208 atoms in block 164 Block first atom: 32923 Blocpdb> 227 atoms in block 165 Block first atom: 33131 Blocpdb> 220 atoms in block 166 Block first atom: 33358 Blocpdb> 178 atoms in block 167 Block first atom: 33578 Blocpdb> 211 atoms in block 168 Block first atom: 33756 Blocpdb> 207 atoms in block 169 Block first atom: 33967 Blocpdb> 203 atoms in block 170 Block first atom: 34174 Blocpdb> 230 atoms in block 171 Block first atom: 34377 Blocpdb> 198 atoms in block 172 Block first atom: 34607 Blocpdb> 223 atoms in block 173 Block first atom: 34805 Blocpdb> 195 atoms in block 174 Block first atom: 35028 Blocpdb> 196 atoms in block 175 Block first atom: 35223 Blocpdb> 186 atoms in block 176 Block first atom: 35419 Blocpdb> 200 atoms in block 177 Block first atom: 35605 Blocpdb> 191 atoms in block 178 Block first atom: 35805 Blocpdb> 208 atoms in block 179 Block first atom: 35996 Blocpdb> 195 atoms in block 180 Block first atom: 36204 Blocpdb> 198 atoms in block 181 Block first atom: 36399 Blocpdb> 234 atoms in block 182 Block first atom: 36597 Blocpdb> 193 atoms in block 183 Block first atom: 36831 Blocpdb> 214 atoms in block 184 Block first atom: 37024 Blocpdb> 186 atoms in block 185 Block first atom: 37238 Blocpdb> 196 atoms in block 186 Block first atom: 37424 Blocpdb> 183 atoms in block 187 Block first atom: 37620 Blocpdb> 202 atoms in block 188 Block first atom: 37803 Blocpdb> 227 atoms in block 189 Block first atom: 38005 Blocpdb> 193 atoms in block 190 Block first atom: 38232 Blocpdb> 209 atoms in block 191 Block first atom: 38425 Blocpdb> 206 atoms in block 192 Block first atom: 38634 Blocpdb> 205 atoms in block 193 Block first atom: 38840 Blocpdb> 207 atoms in block 194 Block first atom: 39045 Blocpdb> 201 atoms in block 195 Block first atom: 39252 Blocpdb> 197 atoms in block 196 Block first atom: 39453 Blocpdb> 223 atoms in block 197 Block first atom: 39650 Blocpdb> 206 atoms in block 198 Block first atom: 39873 Blocpdb> 201 atoms in block 199 Block first atom: 40079 Blocpdb> 223 atoms in block 200 Block first atom: 40280 Blocpdb> 202 atoms in block 201 Block first atom: 40503 Blocpdb> 114 atoms in block 202 Block first atom: 40704 Blocpdb> 202 blocks. Blocpdb> At most, 236 atoms in each of them. Blocpdb> At least, 59 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: 87198697 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 0m0.219s user 0m0.208s sys 0m0.008s




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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.