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LOGs for ID: 22121818065151613

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 = 22121818065151613.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 22121818065151613.atom to be opened. Openam> File opened: 22121818065151613.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 = 4084 First residue number = 5 Last residue number = 166 Number of atoms found = 32038 Mean number per residue = 7.8 Pdbmat> Coordinate statistics: = 146.533569 +/- 16.702193 From: 97.972000 To: 190.265000 = 147.196863 +/- 21.758019 From: 87.639000 To: 203.101000 = 133.554071 +/- 69.653081 From: 3.437000 To: 284.593000 Pdbmat> Masses are all set to one. %Pdbmat-W> residue:'MG ' is not a well known amino-acid. %Pdbmat-W> residue:'ADP ' is not a well known amino-acid. %Pdbmat-W> residue:'MG ' is not a well known amino-acid. %Pdbmat-W> residue:'ADP ' is not a well known amino-acid. %Pdbmat-W> residue:'MG ' is not a well known amino-acid. %Pdbmat-W> residue:'ADP ' is not a well known amino-acid. %Pdbmat-W> residue:'MG ' is not a well known amino-acid. %Pdbmat-W> residue:'ADP ' is not a well known amino-acid. %Pdbmat-W> residue:'MG ' is not a well known amino-acid. %Pdbmat-W> ........ %Pdbmat-W> 18 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 3.7716 % Filled. Pdbmat> 12221268 non-zero elements. Pdbmat> 1336780 atom-atom interactions. Pdbmat> Number per atom= 83.45 +/- 20.14 Maximum number = 132 Minimum number = 13 Pdbmat> Matrix trace = 2.673560E+07 Pdbmat> Larger element = 511.071 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. 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 = 22121818065151613.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 16 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 22121818065151613.atom to be opened. Openam> file on opening on unit 11: 22121818065151613.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 32038 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 16 residue(s) per block. Blocpdb> 4084 residues. Blocpdb> 103 atoms in block 1 Block first atom: 1 Blocpdb> 114 atoms in block 2 Block first atom: 104 Blocpdb> 122 atoms in block 3 Block first atom: 218 Blocpdb> 124 atoms in block 4 Block first atom: 340 Blocpdb> 137 atoms in block 5 Block first atom: 464 Blocpdb> 145 atoms in block 6 Block first atom: 601 Blocpdb> 124 atoms in block 7 Block first atom: 746 Blocpdb> 131 atoms in block 8 Block first atom: 870 Blocpdb> 120 atoms in block 9 Block first atom: 1001 Blocpdb> 110 atoms in block 10 Block first atom: 1121 Blocpdb> 131 atoms in block 11 Block first atom: 1231 Blocpdb> 131 atoms in block 12 Block first atom: 1362 Blocpdb> 130 atoms in block 13 Block first atom: 1493 Blocpdb> 131 atoms in block 14 Block first atom: 1623 Blocpdb> 117 atoms in block 15 Block first atom: 1754 Blocpdb> 126 atoms in block 16 Block first atom: 1871 Blocpdb> 123 atoms in block 17 Block first atom: 1997 Blocpdb> 131 atoms in block 18 Block first atom: 2120 Blocpdb> 115 atoms in block 19 Block first atom: 2251 Blocpdb> 120 atoms in block 20 Block first atom: 2366 Blocpdb> 137 atoms in block 21 Block first atom: 2486 Blocpdb> 121 atoms in block 22 Block first atom: 2623 Blocpdb> 129 atoms in block 23 Block first atom: 2744 Blocpdb> 15 atoms in block 24 Block first atom: 2873 Blocpdb> 28 atoms in block 25 Block first atom: 2888 Blocpdb> 103 atoms in block 26 Block first atom: 2916 Blocpdb> 114 atoms in block 27 Block first atom: 3019 Blocpdb> 122 atoms in block 28 Block first atom: 3133 Blocpdb> 124 atoms in block 29 Block first atom: 3255 Blocpdb> 137 atoms in block 30 Block first atom: 3379 Blocpdb> 145 atoms in block 31 Block first atom: 3516 Blocpdb> 124 atoms in block 32 Block first atom: 3661 Blocpdb> 131 atoms in block 33 Block first atom: 3785 Blocpdb> 120 atoms in block 34 Block first atom: 3916 Blocpdb> 110 atoms in block 35 Block first atom: 4036 Blocpdb> 131 atoms in block 36 Block first atom: 4146 Blocpdb> 131 atoms in block 37 Block first atom: 4277 Blocpdb> 130 atoms in block 38 Block first atom: 4408 Blocpdb> 131 atoms in block 39 Block first atom: 4538 Blocpdb> 117 atoms in block 40 Block first atom: 4669 Blocpdb> 126 atoms in block 41 Block first atom: 4786 Blocpdb> 123 atoms in block 42 Block first atom: 4912 Blocpdb> 131 atoms in block 43 Block first atom: 5035 Blocpdb> 115 atoms in block 44 Block first atom: 5166 Blocpdb> 120 atoms in block 45 Block first atom: 5281 Blocpdb> 137 atoms in block 46 Block first atom: 5401 Blocpdb> 121 atoms in block 47 Block first atom: 5538 Blocpdb> 129 atoms in block 48 Block first atom: 5659 Blocpdb> 15 atoms in block 49 Block first atom: 5788 Blocpdb> 28 atoms in block 50 Block first atom: 5803 Blocpdb> 103 atoms in block 51 Block first atom: 5831 Blocpdb> 114 atoms in block 52 Block first atom: 5934 Blocpdb> 122 atoms in block 53 Block first atom: 6048 Blocpdb> 124 atoms in block 54 Block first atom: 6170 Blocpdb> 137 atoms in block 55 Block first atom: 6294 Blocpdb> 145 atoms in block 56 Block first atom: 6431 Blocpdb> 124 atoms in block 57 Block first atom: 6576 Blocpdb> 131 atoms in block 58 Block first atom: 6700 Blocpdb> 120 atoms in block 59 Block first atom: 6831 Blocpdb> 110 atoms in block 60 Block first atom: 6951 Blocpdb> 131 atoms in block 61 Block first atom: 7061 Blocpdb> 131 atoms in block 62 Block first atom: 7192 Blocpdb> 130 atoms in block 63 Block first atom: 7323 Blocpdb> 131 atoms in block 64 Block first atom: 7453 Blocpdb> 117 atoms in block 65 Block first atom: 7584 Blocpdb> 126 atoms in block 66 Block first atom: 7701 Blocpdb> 123 atoms in block 67 Block first atom: 7827 Blocpdb> 131 atoms in block 68 Block first atom: 7950 Blocpdb> 115 atoms in block 69 Block first atom: 8081 Blocpdb> 120 atoms in block 70 Block first atom: 8196 Blocpdb> 137 atoms in block 71 Block first atom: 8316 Blocpdb> 121 atoms in block 72 Block first atom: 8453 Blocpdb> 129 atoms in block 73 Block first atom: 8574 Blocpdb> 15 atoms in block 74 Block first atom: 8703 Blocpdb> 28 atoms in block 75 Block first atom: 8718 Blocpdb> 103 atoms in block 76 Block first atom: 8746 Blocpdb> 114 atoms in block 77 Block first atom: 8849 Blocpdb> 29 atoms in block 78 Block first atom: 8963 Blocpdb> 75 atoms in block 79 Block first atom: 8992 Blocpdb> 135 atoms in block 80 Block first atom: 9067 Blocpdb> 150 atoms in block 81 Block first atom: 9202 Blocpdb> 121 atoms in block 82 Block first atom: 9352 Blocpdb> 136 atoms in block 83 Block first atom: 9473 Blocpdb> 122 atoms in block 84 Block first atom: 9609 Blocpdb> 104 atoms in block 85 Block first atom: 9731 Blocpdb> 127 atoms in block 86 Block first atom: 9835 Blocpdb> 131 atoms in block 87 Block first atom: 9962 Blocpdb> 131 atoms in block 88 Block first atom: 10093 Blocpdb> 134 atoms in block 89 Block first atom: 10224 Blocpdb> 112 atoms in block 90 Block first atom: 10358 Blocpdb> 130 atoms in block 91 Block first atom: 10470 Blocpdb> 127 atoms in block 92 Block first atom: 10600 Blocpdb> 123 atoms in block 93 Block first atom: 10727 Blocpdb> 121 atoms in block 94 Block first atom: 10850 Blocpdb> 125 atoms in block 95 Block first atom: 10971 Blocpdb> 122 atoms in block 96 Block first atom: 11096 Blocpdb> 118 atoms in block 97 Block first atom: 11218 Blocpdb> 138 atoms in block 98 Block first atom: 11336 Blocpdb> 57 atoms in block 99 Block first atom: 11474 Blocpdb> 28 atoms in block 100 Block first atom: 11531 Blocpdb> 114 atoms in block 101 Block first atom: 11559 Blocpdb> 129 atoms in block 102 Block first atom: 11673 Blocpdb> 127 atoms in block 103 Block first atom: 11802 Blocpdb> 134 atoms in block 104 Block first atom: 11929 Blocpdb> 134 atoms in block 105 Block first atom: 12063 Blocpdb> 115 atoms in block 106 Block first atom: 12197 Blocpdb> 125 atoms in block 107 Block first atom: 12312 Blocpdb> 120 atoms in block 108 Block first atom: 12437 Blocpdb> 133 atoms in block 109 Block first atom: 12557 Blocpdb> 121 atoms in block 110 Block first atom: 12690 Blocpdb> 118 atoms in block 111 Block first atom: 12811 Blocpdb> 111 atoms in block 112 Block first atom: 12929 Blocpdb> 28 atoms in block 113 Block first atom: 13040 Blocpdb> 114 atoms in block 114 Block first atom: 13068 Blocpdb> 129 atoms in block 115 Block first atom: 13182 Blocpdb> 127 atoms in block 116 Block first atom: 13311 Blocpdb> 134 atoms in block 117 Block first atom: 13438 Blocpdb> 134 atoms in block 118 Block first atom: 13572 Blocpdb> 115 atoms in block 119 Block first atom: 13706 Blocpdb> 125 atoms in block 120 Block first atom: 13821 Blocpdb> 120 atoms in block 121 Block first atom: 13946 Blocpdb> 133 atoms in block 122 Block first atom: 14066 Blocpdb> 121 atoms in block 123 Block first atom: 14199 Blocpdb> 118 atoms in block 124 Block first atom: 14320 Blocpdb> 111 atoms in block 125 Block first atom: 14438 Blocpdb> 28 atoms in block 126 Block first atom: 14549 Blocpdb> 103 atoms in block 127 Block first atom: 14577 Blocpdb> 114 atoms in block 128 Block first atom: 14680 Blocpdb> 29 atoms in block 129 Block first atom: 14794 Blocpdb> 75 atoms in block 130 Block first atom: 14823 Blocpdb> 135 atoms in block 131 Block first atom: 14898 Blocpdb> 150 atoms in block 132 Block first atom: 15033 Blocpdb> 121 atoms in block 133 Block first atom: 15183 Blocpdb> 136 atoms in block 134 Block first atom: 15304 Blocpdb> 122 atoms in block 135 Block first atom: 15440 Blocpdb> 15 atoms in block 136 Block first atom: 15562 Blocpdb> 120 atoms in block 137 Block first atom: 15577 Blocpdb> 133 atoms in block 138 Block first atom: 15697 Blocpdb> 51 atoms in block 139 Block first atom: 15830 Blocpdb> 103 atoms in block 140 Block first atom: 15881 Blocpdb> 114 atoms in block 141 Block first atom: 15984 Blocpdb> 29 atoms in block 142 Block first atom: 16098 Blocpdb> 75 atoms in block 143 Block first atom: 16127 Blocpdb> 135 atoms in block 144 Block first atom: 16202 Blocpdb> 150 atoms in block 145 Block first atom: 16337 Blocpdb> 121 atoms in block 146 Block first atom: 16487 Blocpdb> 136 atoms in block 147 Block first atom: 16608 Blocpdb> 122 atoms in block 148 Block first atom: 16744 Blocpdb> 15 atoms in block 149 Block first atom: 16866 Blocpdb> 120 atoms in block 150 Block first atom: 16881 Blocpdb> 133 atoms in block 151 Block first atom: 17001 Blocpdb> 51 atoms in block 152 Block first atom: 17134 Blocpdb> 113 atoms in block 153 Block first atom: 17185 Blocpdb> 134 atoms in block 154 Block first atom: 17298 Blocpdb> 127 atoms in block 155 Block first atom: 17432 Blocpdb> 116 atoms in block 156 Block first atom: 17559 Blocpdb> 135 atoms in block 157 Block first atom: 17675 Blocpdb> 132 atoms in block 158 Block first atom: 17810 Blocpdb> 130 atoms in block 159 Block first atom: 17942 Blocpdb> 121 atoms in block 160 Block first atom: 18072 Blocpdb> 137 atoms in block 161 Block first atom: 18193 Blocpdb> 109 atoms in block 162 Block first atom: 18330 Blocpdb> 29 atoms in block 163 Block first atom: 18439 Blocpdb> 103 atoms in block 164 Block first atom: 18468 Blocpdb> 114 atoms in block 165 Block first atom: 18571 Blocpdb> 29 atoms in block 166 Block first atom: 18685 Blocpdb> 75 atoms in block 167 Block first atom: 18714 Blocpdb> 135 atoms in block 168 Block first atom: 18789 Blocpdb> 150 atoms in block 169 Block first atom: 18924 Blocpdb> 121 atoms in block 170 Block first atom: 19074 Blocpdb> 136 atoms in block 171 Block first atom: 19195 Blocpdb> 122 atoms in block 172 Block first atom: 19331 Blocpdb> 104 atoms in block 173 Block first atom: 19453 Blocpdb> 127 atoms in block 174 Block first atom: 19557 Blocpdb> 131 atoms in block 175 Block first atom: 19684 Blocpdb> 131 atoms in block 176 Block first atom: 19815 Blocpdb> 134 atoms in block 177 Block first atom: 19946 Blocpdb> 112 atoms in block 178 Block first atom: 20080 Blocpdb> 130 atoms in block 179 Block first atom: 20192 Blocpdb> 127 atoms in block 180 Block first atom: 20322 Blocpdb> 123 atoms in block 181 Block first atom: 20449 Blocpdb> 121 atoms in block 182 Block first atom: 20572 Blocpdb> 125 atoms in block 183 Block first atom: 20693 Blocpdb> 122 atoms in block 184 Block first atom: 20818 Blocpdb> 118 atoms in block 185 Block first atom: 20940 Blocpdb> 138 atoms in block 186 Block first atom: 21058 Blocpdb> 57 atoms in block 187 Block first atom: 21196 Blocpdb> 28 atoms in block 188 Block first atom: 21253 Blocpdb> 103 atoms in block 189 Block first atom: 21281 Blocpdb> 114 atoms in block 190 Block first atom: 21384 Blocpdb> 29 atoms in block 191 Block first atom: 21498 Blocpdb> 75 atoms in block 192 Block first atom: 21527 Blocpdb> 135 atoms in block 193 Block first atom: 21602 Blocpdb> 150 atoms in block 194 Block first atom: 21737 Blocpdb> 121 atoms in block 195 Block first atom: 21887 Blocpdb> 136 atoms in block 196 Block first atom: 22008 Blocpdb> 122 atoms in block 197 Block first atom: 22144 Blocpdb> 104 atoms in block 198 Block first atom: 22266 Blocpdb> 127 atoms in block 199 Block first atom: 22370 Blocpdb> 131 atoms in block 200 Block first atom: 22497 Blocpdb> 131 atoms in block 201 Block first atom: 22628 Blocpdb> 134 atoms in block 202 Block first atom: 22759 Blocpdb> 112 atoms in block 203 Block first atom: 22893 Blocpdb> 130 atoms in block 204 Block first atom: 23005 Blocpdb> 127 atoms in block 205 Block first atom: 23135 Blocpdb> 123 atoms in block 206 Block first atom: 23262 Blocpdb> 121 atoms in block 207 Block first atom: 23385 Blocpdb> 125 atoms in block 208 Block first atom: 23506 Blocpdb> 122 atoms in block 209 Block first atom: 23631 Blocpdb> 118 atoms in block 210 Block first atom: 23753 Blocpdb> 138 atoms in block 211 Block first atom: 23871 Blocpdb> 57 atoms in block 212 Block first atom: 24009 Blocpdb> 28 atoms in block 213 Block first atom: 24066 Blocpdb> 103 atoms in block 214 Block first atom: 24094 Blocpdb> 114 atoms in block 215 Block first atom: 24197 Blocpdb> 29 atoms in block 216 Block first atom: 24311 Blocpdb> 75 atoms in block 217 Block first atom: 24340 Blocpdb> 135 atoms in block 218 Block first atom: 24415 Blocpdb> 150 atoms in block 219 Block first atom: 24550 Blocpdb> 121 atoms in block 220 Block first atom: 24700 Blocpdb> 136 atoms in block 221 Block first atom: 24821 Blocpdb> 122 atoms in block 222 Block first atom: 24957 Blocpdb> 104 atoms in block 223 Block first atom: 25079 Blocpdb> 127 atoms in block 224 Block first atom: 25183 Blocpdb> 131 atoms in block 225 Block first atom: 25310 Blocpdb> 131 atoms in block 226 Block first atom: 25441 Blocpdb> 134 atoms in block 227 Block first atom: 25572 Blocpdb> 112 atoms in block 228 Block first atom: 25706 Blocpdb> 130 atoms in block 229 Block first atom: 25818 Blocpdb> 127 atoms in block 230 Block first atom: 25948 Blocpdb> 123 atoms in block 231 Block first atom: 26075 Blocpdb> 121 atoms in block 232 Block first atom: 26198 Blocpdb> 125 atoms in block 233 Block first atom: 26319 Blocpdb> 122 atoms in block 234 Block first atom: 26444 Blocpdb> 118 atoms in block 235 Block first atom: 26566 Blocpdb> 138 atoms in block 236 Block first atom: 26684 Blocpdb> 57 atoms in block 237 Block first atom: 26822 Blocpdb> 28 atoms in block 238 Block first atom: 26879 Blocpdb> 113 atoms in block 239 Block first atom: 26907 Blocpdb> 134 atoms in block 240 Block first atom: 27020 Blocpdb> 127 atoms in block 241 Block first atom: 27154 Blocpdb> 116 atoms in block 242 Block first atom: 27281 Blocpdb> 135 atoms in block 243 Block first atom: 27397 Blocpdb> 132 atoms in block 244 Block first atom: 27532 Blocpdb> 130 atoms in block 245 Block first atom: 27664 Blocpdb> 121 atoms in block 246 Block first atom: 27794 Blocpdb> 137 atoms in block 247 Block first atom: 27915 Blocpdb> 109 atoms in block 248 Block first atom: 28052 Blocpdb> 29 atoms in block 249 Block first atom: 28161 Blocpdb> 113 atoms in block 250 Block first atom: 28190 Blocpdb> 134 atoms in block 251 Block first atom: 28303 Blocpdb> 127 atoms in block 252 Block first atom: 28437 Blocpdb> 116 atoms in block 253 Block first atom: 28564 Blocpdb> 135 atoms in block 254 Block first atom: 28680 Blocpdb> 132 atoms in block 255 Block first atom: 28815 Blocpdb> 130 atoms in block 256 Block first atom: 28947 Blocpdb> 121 atoms in block 257 Block first atom: 29077 Blocpdb> 137 atoms in block 258 Block first atom: 29198 Blocpdb> 109 atoms in block 259 Block first atom: 29335 Blocpdb> 29 atoms in block 260 Block first atom: 29444 Blocpdb> 113 atoms in block 261 Block first atom: 29473 Blocpdb> 134 atoms in block 262 Block first atom: 29586 Blocpdb> 127 atoms in block 263 Block first atom: 29720 Blocpdb> 116 atoms in block 264 Block first atom: 29847 Blocpdb> 135 atoms in block 265 Block first atom: 29963 Blocpdb> 132 atoms in block 266 Block first atom: 30098 Blocpdb> 130 atoms in block 267 Block first atom: 30230 Blocpdb> 121 atoms in block 268 Block first atom: 30360 Blocpdb> 137 atoms in block 269 Block first atom: 30481 Blocpdb> 109 atoms in block 270 Block first atom: 30618 Blocpdb> 29 atoms in block 271 Block first atom: 30727 Blocpdb> 113 atoms in block 272 Block first atom: 30756 Blocpdb> 134 atoms in block 273 Block first atom: 30869 Blocpdb> 127 atoms in block 274 Block first atom: 31003 Blocpdb> 116 atoms in block 275 Block first atom: 31130 Blocpdb> 135 atoms in block 276 Block first atom: 31246 Blocpdb> 132 atoms in block 277 Block first atom: 31381 Blocpdb> 130 atoms in block 278 Block first atom: 31513 Blocpdb> 121 atoms in block 279 Block first atom: 31643 Blocpdb> 137 atoms in block 280 Block first atom: 31764 Blocpdb> 109 atoms in block 281 Block first atom: 31901 Blocpdb> 29 atoms in block 282 Block first atom: 32009 Blocpdb> 282 blocks. Blocpdb> At most, 150 atoms in each of them. Blocpdb> At least, 15 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: 43453801 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 0m0.192s user 0m0.184s sys 0m0.004s




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It was developed by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: October 18th, 2018.