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***  mcGAS-dsDNA_ladder-model_n3  ***

LOGs for ID: 22112516010524134

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 = 22112516010524134.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 22112516010524134.atom to be opened. Openam> File opened: 22112516010524134.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 = 7062 First residue number = 149 Last residue number = 20 Number of atoms found = 66231 Mean number per residue = 9.4 Pdbmat> Coordinate statistics: = -5.564493 +/- 137.266404 From: -258.465000 To: 242.477000 = 47.016036 +/- 18.970297 From: 3.561000 To: 101.539000 = 44.882045 +/- 78.927079 From: -115.542000 To: 207.800000 Pdbmat> Masses are all set to one. %Pdbmat-W> residue:'DG ' 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> residue:'DT ' is not a well known amino-acid. %Pdbmat-W> residue:'DA ' is not a well known amino-acid. %Pdbmat-W> residue:'DC ' 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> ........ %Pdbmat-W> 636 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 5.9901 % Filled. Pdbmat> 24691248 non-zero elements. Pdbmat> 2699788 atom-atom interactions. Pdbmat> Number per atom= 81.53 +/- 21.23 Maximum number = 128 Minimum number = 10 Pdbmat> Matrix trace = 5.399576E+07 Pdbmat> Larger element = 524.628 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 7062 non-zero elements, NRBL set to 36 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 = 22112516010524134.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 36 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 22112516010524134.atom to be opened. Openam> file on opening on unit 11: 22112516010524134.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 66231 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 36 residue(s) per block. Blocpdb> 7062 residues. Blocpdb> 302 atoms in block 1 Block first atom: 1 Blocpdb> 297 atoms in block 2 Block first atom: 303 Blocpdb> 305 atoms in block 3 Block first atom: 600 Blocpdb> 286 atoms in block 4 Block first atom: 905 Blocpdb> 274 atoms in block 5 Block first atom: 1191 Blocpdb> 301 atoms in block 6 Block first atom: 1465 Blocpdb> 280 atoms in block 7 Block first atom: 1766 Blocpdb> 312 atoms in block 8 Block first atom: 2046 Blocpdb> 308 atoms in block 9 Block first atom: 2358 Blocpdb> 287 atoms in block 10 Block first atom: 2666 Blocpdb> 302 atoms in block 11 Block first atom: 2953 Blocpdb> 297 atoms in block 12 Block first atom: 3255 Blocpdb> 305 atoms in block 13 Block first atom: 3552 Blocpdb> 286 atoms in block 14 Block first atom: 3857 Blocpdb> 274 atoms in block 15 Block first atom: 4143 Blocpdb> 301 atoms in block 16 Block first atom: 4417 Blocpdb> 280 atoms in block 17 Block first atom: 4718 Blocpdb> 312 atoms in block 18 Block first atom: 4998 Blocpdb> 308 atoms in block 19 Block first atom: 5310 Blocpdb> 287 atoms in block 20 Block first atom: 5618 Blocpdb> 302 atoms in block 21 Block first atom: 5905 Blocpdb> 297 atoms in block 22 Block first atom: 6207 Blocpdb> 305 atoms in block 23 Block first atom: 6504 Blocpdb> 286 atoms in block 24 Block first atom: 6809 Blocpdb> 274 atoms in block 25 Block first atom: 7095 Blocpdb> 301 atoms in block 26 Block first atom: 7369 Blocpdb> 280 atoms in block 27 Block first atom: 7670 Blocpdb> 312 atoms in block 28 Block first atom: 7950 Blocpdb> 308 atoms in block 29 Block first atom: 8262 Blocpdb> 287 atoms in block 30 Block first atom: 8570 Blocpdb> 302 atoms in block 31 Block first atom: 8857 Blocpdb> 297 atoms in block 32 Block first atom: 9159 Blocpdb> 305 atoms in block 33 Block first atom: 9456 Blocpdb> 286 atoms in block 34 Block first atom: 9761 Blocpdb> 274 atoms in block 35 Block first atom: 10047 Blocpdb> 301 atoms in block 36 Block first atom: 10321 Blocpdb> 280 atoms in block 37 Block first atom: 10622 Blocpdb> 312 atoms in block 38 Block first atom: 10902 Blocpdb> 308 atoms in block 39 Block first atom: 11214 Blocpdb> 287 atoms in block 40 Block first atom: 11522 Blocpdb> 302 atoms in block 41 Block first atom: 11809 Blocpdb> 297 atoms in block 42 Block first atom: 12111 Blocpdb> 305 atoms in block 43 Block first atom: 12408 Blocpdb> 286 atoms in block 44 Block first atom: 12713 Blocpdb> 274 atoms in block 45 Block first atom: 12999 Blocpdb> 301 atoms in block 46 Block first atom: 13273 Blocpdb> 280 atoms in block 47 Block first atom: 13574 Blocpdb> 312 atoms in block 48 Block first atom: 13854 Blocpdb> 308 atoms in block 49 Block first atom: 14166 Blocpdb> 287 atoms in block 50 Block first atom: 14474 Blocpdb> 302 atoms in block 51 Block first atom: 14761 Blocpdb> 297 atoms in block 52 Block first atom: 15063 Blocpdb> 305 atoms in block 53 Block first atom: 15360 Blocpdb> 286 atoms in block 54 Block first atom: 15665 Blocpdb> 274 atoms in block 55 Block first atom: 15951 Blocpdb> 301 atoms in block 56 Block first atom: 16225 Blocpdb> 280 atoms in block 57 Block first atom: 16526 Blocpdb> 312 atoms in block 58 Block first atom: 16806 Blocpdb> 308 atoms in block 59 Block first atom: 17118 Blocpdb> 287 atoms in block 60 Block first atom: 17426 Blocpdb> 738 atoms in block 61 Block first atom: 17713 Blocpdb> 19 atoms in block 62 Block first atom: 18451 Blocpdb> 738 atoms in block 63 Block first atom: 18470 Blocpdb> 738 atoms in block 64 Block first atom: 19208 Blocpdb> 738 atoms in block 65 Block first atom: 19946 Blocpdb> 350 atoms in block 66 Block first atom: 20684 Blocpdb> 347 atoms in block 67 Block first atom: 21034 Blocpdb> 350 atoms in block 68 Block first atom: 21381 Blocpdb> 347 atoms in block 69 Block first atom: 21731 Blocpdb> 302 atoms in block 70 Block first atom: 22078 Blocpdb> 297 atoms in block 71 Block first atom: 22380 Blocpdb> 305 atoms in block 72 Block first atom: 22677 Blocpdb> 286 atoms in block 73 Block first atom: 22982 Blocpdb> 274 atoms in block 74 Block first atom: 23268 Blocpdb> 301 atoms in block 75 Block first atom: 23542 Blocpdb> 280 atoms in block 76 Block first atom: 23843 Blocpdb> 312 atoms in block 77 Block first atom: 24123 Blocpdb> 308 atoms in block 78 Block first atom: 24435 Blocpdb> 287 atoms in block 79 Block first atom: 24743 Blocpdb> 302 atoms in block 80 Block first atom: 25030 Blocpdb> 297 atoms in block 81 Block first atom: 25332 Blocpdb> 305 atoms in block 82 Block first atom: 25629 Blocpdb> 286 atoms in block 83 Block first atom: 25934 Blocpdb> 274 atoms in block 84 Block first atom: 26220 Blocpdb> 301 atoms in block 85 Block first atom: 26494 Blocpdb> 280 atoms in block 86 Block first atom: 26795 Blocpdb> 312 atoms in block 87 Block first atom: 27075 Blocpdb> 308 atoms in block 88 Block first atom: 27387 Blocpdb> 287 atoms in block 89 Block first atom: 27695 Blocpdb> 302 atoms in block 90 Block first atom: 27982 Blocpdb> 297 atoms in block 91 Block first atom: 28284 Blocpdb> 305 atoms in block 92 Block first atom: 28581 Blocpdb> 286 atoms in block 93 Block first atom: 28886 Blocpdb> 274 atoms in block 94 Block first atom: 29172 Blocpdb> 301 atoms in block 95 Block first atom: 29446 Blocpdb> 280 atoms in block 96 Block first atom: 29747 Blocpdb> 312 atoms in block 97 Block first atom: 30027 Blocpdb> 308 atoms in block 98 Block first atom: 30339 Blocpdb> 287 atoms in block 99 Block first atom: 30647 Blocpdb> 302 atoms in block 100 Block first atom: 30934 Blocpdb> 297 atoms in block 101 Block first atom: 31236 Blocpdb> 305 atoms in block 102 Block first atom: 31533 Blocpdb> 286 atoms in block 103 Block first atom: 31838 Blocpdb> 274 atoms in block 104 Block first atom: 32124 Blocpdb> 301 atoms in block 105 Block first atom: 32398 Blocpdb> 280 atoms in block 106 Block first atom: 32699 Blocpdb> 312 atoms in block 107 Block first atom: 32979 Blocpdb> 308 atoms in block 108 Block first atom: 33291 Blocpdb> 287 atoms in block 109 Block first atom: 33599 Blocpdb> 302 atoms in block 110 Block first atom: 33886 Blocpdb> 297 atoms in block 111 Block first atom: 34188 Blocpdb> 305 atoms in block 112 Block first atom: 34485 Blocpdb> 286 atoms in block 113 Block first atom: 34790 Blocpdb> 274 atoms in block 114 Block first atom: 35076 Blocpdb> 301 atoms in block 115 Block first atom: 35350 Blocpdb> 280 atoms in block 116 Block first atom: 35651 Blocpdb> 312 atoms in block 117 Block first atom: 35931 Blocpdb> 308 atoms in block 118 Block first atom: 36243 Blocpdb> 287 atoms in block 119 Block first atom: 36551 Blocpdb> 302 atoms in block 120 Block first atom: 36838 Blocpdb> 297 atoms in block 121 Block first atom: 37140 Blocpdb> 305 atoms in block 122 Block first atom: 37437 Blocpdb> 286 atoms in block 123 Block first atom: 37742 Blocpdb> 274 atoms in block 124 Block first atom: 38028 Blocpdb> 301 atoms in block 125 Block first atom: 38302 Blocpdb> 280 atoms in block 126 Block first atom: 38603 Blocpdb> 312 atoms in block 127 Block first atom: 38883 Blocpdb> 308 atoms in block 128 Block first atom: 39195 Blocpdb> 287 atoms in block 129 Block first atom: 39503 Blocpdb> 738 atoms in block 130 Block first atom: 39790 Blocpdb> 19 atoms in block 131 Block first atom: 40528 Blocpdb> 738 atoms in block 132 Block first atom: 40547 Blocpdb> 738 atoms in block 133 Block first atom: 41285 Blocpdb> 738 atoms in block 134 Block first atom: 42023 Blocpdb> 350 atoms in block 135 Block first atom: 42761 Blocpdb> 347 atoms in block 136 Block first atom: 43111 Blocpdb> 350 atoms in block 137 Block first atom: 43458 Blocpdb> 347 atoms in block 138 Block first atom: 43808 Blocpdb> 302 atoms in block 139 Block first atom: 44155 Blocpdb> 297 atoms in block 140 Block first atom: 44457 Blocpdb> 305 atoms in block 141 Block first atom: 44754 Blocpdb> 286 atoms in block 142 Block first atom: 45059 Blocpdb> 274 atoms in block 143 Block first atom: 45345 Blocpdb> 301 atoms in block 144 Block first atom: 45619 Blocpdb> 280 atoms in block 145 Block first atom: 45920 Blocpdb> 312 atoms in block 146 Block first atom: 46200 Blocpdb> 308 atoms in block 147 Block first atom: 46512 Blocpdb> 287 atoms in block 148 Block first atom: 46820 Blocpdb> 302 atoms in block 149 Block first atom: 47107 Blocpdb> 297 atoms in block 150 Block first atom: 47409 Blocpdb> 305 atoms in block 151 Block first atom: 47706 Blocpdb> 286 atoms in block 152 Block first atom: 48011 Blocpdb> 274 atoms in block 153 Block first atom: 48297 Blocpdb> 301 atoms in block 154 Block first atom: 48571 Blocpdb> 280 atoms in block 155 Block first atom: 48872 Blocpdb> 312 atoms in block 156 Block first atom: 49152 Blocpdb> 308 atoms in block 157 Block first atom: 49464 Blocpdb> 287 atoms in block 158 Block first atom: 49772 Blocpdb> 302 atoms in block 159 Block first atom: 50059 Blocpdb> 297 atoms in block 160 Block first atom: 50361 Blocpdb> 305 atoms in block 161 Block first atom: 50658 Blocpdb> 286 atoms in block 162 Block first atom: 50963 Blocpdb> 274 atoms in block 163 Block first atom: 51249 Blocpdb> 301 atoms in block 164 Block first atom: 51523 Blocpdb> 280 atoms in block 165 Block first atom: 51824 Blocpdb> 312 atoms in block 166 Block first atom: 52104 Blocpdb> 308 atoms in block 167 Block first atom: 52416 Blocpdb> 287 atoms in block 168 Block first atom: 52724 Blocpdb> 302 atoms in block 169 Block first atom: 53011 Blocpdb> 297 atoms in block 170 Block first atom: 53313 Blocpdb> 305 atoms in block 171 Block first atom: 53610 Blocpdb> 286 atoms in block 172 Block first atom: 53915 Blocpdb> 274 atoms in block 173 Block first atom: 54201 Blocpdb> 301 atoms in block 174 Block first atom: 54475 Blocpdb> 280 atoms in block 175 Block first atom: 54776 Blocpdb> 312 atoms in block 176 Block first atom: 55056 Blocpdb> 308 atoms in block 177 Block first atom: 55368 Blocpdb> 287 atoms in block 178 Block first atom: 55676 Blocpdb> 302 atoms in block 179 Block first atom: 55963 Blocpdb> 297 atoms in block 180 Block first atom: 56265 Blocpdb> 305 atoms in block 181 Block first atom: 56562 Blocpdb> 286 atoms in block 182 Block first atom: 56867 Blocpdb> 274 atoms in block 183 Block first atom: 57153 Blocpdb> 301 atoms in block 184 Block first atom: 57427 Blocpdb> 280 atoms in block 185 Block first atom: 57728 Blocpdb> 312 atoms in block 186 Block first atom: 58008 Blocpdb> 308 atoms in block 187 Block first atom: 58320 Blocpdb> 287 atoms in block 188 Block first atom: 58628 Blocpdb> 302 atoms in block 189 Block first atom: 58915 Blocpdb> 297 atoms in block 190 Block first atom: 59217 Blocpdb> 305 atoms in block 191 Block first atom: 59514 Blocpdb> 286 atoms in block 192 Block first atom: 59819 Blocpdb> 274 atoms in block 193 Block first atom: 60105 Blocpdb> 301 atoms in block 194 Block first atom: 60379 Blocpdb> 280 atoms in block 195 Block first atom: 60680 Blocpdb> 312 atoms in block 196 Block first atom: 60960 Blocpdb> 308 atoms in block 197 Block first atom: 61272 Blocpdb> 287 atoms in block 198 Block first atom: 61580 Blocpdb> 738 atoms in block 199 Block first atom: 61867 Blocpdb> 19 atoms in block 200 Block first atom: 62605 Blocpdb> 738 atoms in block 201 Block first atom: 62624 Blocpdb> 738 atoms in block 202 Block first atom: 63362 Blocpdb> 738 atoms in block 203 Block first atom: 64100 Blocpdb> 350 atoms in block 204 Block first atom: 64838 Blocpdb> 347 atoms in block 205 Block first atom: 65188 Blocpdb> 350 atoms in block 206 Block first atom: 65535 Blocpdb> 347 atoms in block 207 Block first atom: 65884 Blocpdb> 207 blocks. Blocpdb> At most, 738 atoms in each of them. Blocpdb> At least, 19 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> IIWKMX up to: 9903593 Maximum allowed is LIWORK= 5000000 %Diagrtb-Er> IRWKMX up to: 444808099 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 0m0.246s user 0m0.244s sys 0m0.000s




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Last modification: October 18th, 2018.