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LOGs for ID: 21030309085113446

output from eigenvector calculation:


STDOUT:
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 = 21030309085113446.atom Pdbmat> Distance cutoff = 11.00 Force constant = 10.00 Origin of mass values = CONS Pdbmat> Levelshift = 1.0E-09 PRINTing level = 2 Pdbmat> Coordinate file 21030309085113446.atom to be opened. Openam> File opened: 21030309085113446.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 = 1084 First residue number = 714 Last residue number = 713 Number of atoms found = 2872 Mean number per residue = 2.6 Pdbmat> Coordinate statistics: = 66.789871 +/- 21.612632 From: 23.516000 To: 107.610000 = 78.887118 +/- 25.456613 From: 22.333000 To: 122.435000 = 45.619462 +/- 12.219409 From: 10.857000 To: 70.360000 Pdbmat> Masses are all set to one. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> residue:'SAP2' is not a well known amino-acid. %Pdbmat-W> ........ %Pdbmat-W> 12 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 3.0250 % Filled. Pdbmat> 1122953 non-zero elements. Pdbmat> 122879 atom-atom interactions. Pdbmat> Number per atom= 85.57 +/- 50.73 Maximum number = 228 Minimum number = 7 Pdbmat> Matrix trace = 2.457580E+06 Pdbmat> Larger element = 1023.89 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 1084 non-zero elements, NRBL set to 6 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 = 21030309085113446.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 6 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 21030309085113446.atom to be opened. Openam> file on opening on unit 11: 21030309085113446.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 2872 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 6 residue(s) per block. Blocpdb> 1084 residues. Blocpdb> 900 atoms in block 1 Block first atom: 1 Blocpdb> 900 atoms in block 2 Block first atom: 901 Blocpdb> 6 atoms in block 3 Block first atom: 1801 Blocpdb> 6 atoms in block 4 Block first atom: 1807 Blocpdb> 6 atoms in block 5 Block first atom: 1813 Blocpdb> 6 atoms in block 6 Block first atom: 1819 Blocpdb> 6 atoms in block 7 Block first atom: 1825 Blocpdb> 6 atoms in block 8 Block first atom: 1831 Blocpdb> 6 atoms in block 9 Block first atom: 1837 Blocpdb> 6 atoms in block 10 Block first atom: 1843 Blocpdb> 6 atoms in block 11 Block first atom: 1849 Blocpdb> 6 atoms in block 12 Block first atom: 1855 Blocpdb> 6 atoms in block 13 Block first atom: 1861 Blocpdb> 6 atoms in block 14 Block first atom: 1867 Blocpdb> 6 atoms in block 15 Block first atom: 1873 Blocpdb> 6 atoms in block 16 Block first atom: 1879 Blocpdb> 6 atoms in block 17 Block first atom: 1885 Blocpdb> 6 atoms in block 18 Block first atom: 1891 Blocpdb> 6 atoms in block 19 Block first atom: 1897 Blocpdb> 6 atoms in block 20 Block first atom: 1903 Blocpdb> 6 atoms in block 21 Block first atom: 1909 Blocpdb> 6 atoms in block 22 Block first atom: 1915 Blocpdb> 6 atoms in block 23 Block first atom: 1921 Blocpdb> 6 atoms in block 24 Block first atom: 1927 Blocpdb> 6 atoms in block 25 Block first atom: 1933 Blocpdb> 6 atoms in block 26 Block first atom: 1939 Blocpdb> 6 atoms in block 27 Block first atom: 1945 Blocpdb> 6 atoms in block 28 Block first atom: 1951 Blocpdb> 6 atoms in block 29 Block first atom: 1957 Blocpdb> 6 atoms in block 30 Block first atom: 1963 Blocpdb> 6 atoms in block 31 Block first atom: 1969 Blocpdb> 6 atoms in block 32 Block first atom: 1975 %Blocpdb-Wn> 1 atoms in block 33 i.e., less than what is required for a rigid body. %Blocpdb-Wn> Last atom in this block is the 1981th, in residue B 603 %Blocpdb-Wn> It will be merged with next block. Blocpdb> 7 atoms in block 33 Block first atom: 1981 Blocpdb> 6 atoms in block 34 Block first atom: 1988 Blocpdb> 6 atoms in block 35 Block first atom: 1994 Blocpdb> 6 atoms in block 36 Block first atom: 2000 Blocpdb> 6 atoms in block 37 Block first atom: 2006 Blocpdb> 6 atoms in block 38 Block first atom: 2012 Blocpdb> 6 atoms in block 39 Block first atom: 2018 Blocpdb> 6 atoms in block 40 Block first atom: 2024 Blocpdb> 6 atoms in block 41 Block first atom: 2030 Blocpdb> 6 atoms in block 42 Block first atom: 2036 Blocpdb> 6 atoms in block 43 Block first atom: 2042 Blocpdb> 6 atoms in block 44 Block first atom: 2048 Blocpdb> 6 atoms in block 45 Block first atom: 2054 Blocpdb> 6 atoms in block 46 Block first atom: 2060 Blocpdb> 3 atoms in block 47 Block first atom: 2066 Blocpdb> 6 atoms in block 48 Block first atom: 2069 Blocpdb> 6 atoms in block 49 Block first atom: 2075 Blocpdb> 6 atoms in block 50 Block first atom: 2081 Blocpdb> 6 atoms in block 51 Block first atom: 2087 Blocpdb> 6 atoms in block 52 Block first atom: 2093 Blocpdb> 6 atoms in block 53 Block first atom: 2099 Blocpdb> 6 atoms in block 54 Block first atom: 2105 Blocpdb> 6 atoms in block 55 Block first atom: 2111 Blocpdb> 6 atoms in block 56 Block first atom: 2117 Blocpdb> 6 atoms in block 57 Block first atom: 2123 Blocpdb> 6 atoms in block 58 Block first atom: 2129 Blocpdb> 6 atoms in block 59 Block first atom: 2135 Blocpdb> 6 atoms in block 60 Block first atom: 2141 Blocpdb> 6 atoms in block 61 Block first atom: 2147 Blocpdb> 6 atoms in block 62 Block first atom: 2153 Blocpdb> 6 atoms in block 63 Block first atom: 2159 Blocpdb> 6 atoms in block 64 Block first atom: 2165 Blocpdb> 6 atoms in block 65 Block first atom: 2171 Blocpdb> 6 atoms in block 66 Block first atom: 2177 Blocpdb> 6 atoms in block 67 Block first atom: 2183 Blocpdb> 6 atoms in block 68 Block first atom: 2189 Blocpdb> 6 atoms in block 69 Block first atom: 2195 Blocpdb> 6 atoms in block 70 Block first atom: 2201 Blocpdb> 6 atoms in block 71 Block first atom: 2207 Blocpdb> 6 atoms in block 72 Block first atom: 2213 Blocpdb> 6 atoms in block 73 Block first atom: 2219 Blocpdb> 6 atoms in block 74 Block first atom: 2225 Blocpdb> 6 atoms in block 75 Block first atom: 2231 Blocpdb> 6 atoms in block 76 Block first atom: 2237 Blocpdb> 6 atoms in block 77 Block first atom: 2243 %Blocpdb-Wn> 1 atoms in block 78 i.e., less than what is required for a rigid body. %Blocpdb-Wn> Last atom in this block is the 2249th, in residue C 603 %Blocpdb-Wn> It will be merged with next block. Blocpdb> 7 atoms in block 78 Block first atom: 2249 Blocpdb> 6 atoms in block 79 Block first atom: 2256 Blocpdb> 6 atoms in block 80 Block first atom: 2262 Blocpdb> 6 atoms in block 81 Block first atom: 2268 Blocpdb> 6 atoms in block 82 Block first atom: 2274 Blocpdb> 6 atoms in block 83 Block first atom: 2280 Blocpdb> 6 atoms in block 84 Block first atom: 2286 Blocpdb> 6 atoms in block 85 Block first atom: 2292 Blocpdb> 6 atoms in block 86 Block first atom: 2298 Blocpdb> 6 atoms in block 87 Block first atom: 2304 Blocpdb> 6 atoms in block 88 Block first atom: 2310 Blocpdb> 6 atoms in block 89 Block first atom: 2316 Blocpdb> 6 atoms in block 90 Block first atom: 2322 Blocpdb> 6 atoms in block 91 Block first atom: 2328 Blocpdb> 3 atoms in block 92 Block first atom: 2334 Blocpdb> 6 atoms in block 93 Block first atom: 2337 Blocpdb> 6 atoms in block 94 Block first atom: 2343 Blocpdb> 6 atoms in block 95 Block first atom: 2349 Blocpdb> 6 atoms in block 96 Block first atom: 2355 Blocpdb> 6 atoms in block 97 Block first atom: 2361 Blocpdb> 6 atoms in block 98 Block first atom: 2367 Blocpdb> 6 atoms in block 99 Block first atom: 2373 Blocpdb> 6 atoms in block 100 Block first atom: 2379 Blocpdb> 6 atoms in block 101 Block first atom: 2385 Blocpdb> 6 atoms in block 102 Block first atom: 2391 Blocpdb> 6 atoms in block 103 Block first atom: 2397 Blocpdb> 6 atoms in block 104 Block first atom: 2403 Blocpdb> 6 atoms in block 105 Block first atom: 2409 Blocpdb> 6 atoms in block 106 Block first atom: 2415 Blocpdb> 6 atoms in block 107 Block first atom: 2421 Blocpdb> 6 atoms in block 108 Block first atom: 2427 Blocpdb> 6 atoms in block 109 Block first atom: 2433 Blocpdb> 6 atoms in block 110 Block first atom: 2439 Blocpdb> 6 atoms in block 111 Block first atom: 2445 Blocpdb> 6 atoms in block 112 Block first atom: 2451 Blocpdb> 6 atoms in block 113 Block first atom: 2457 Blocpdb> 6 atoms in block 114 Block first atom: 2463 Blocpdb> 6 atoms in block 115 Block first atom: 2469 Blocpdb> 6 atoms in block 116 Block first atom: 2475 Blocpdb> 6 atoms in block 117 Block first atom: 2481 Blocpdb> 6 atoms in block 118 Block first atom: 2487 Blocpdb> 6 atoms in block 119 Block first atom: 2493 Blocpdb> 6 atoms in block 120 Block first atom: 2499 Blocpdb> 6 atoms in block 121 Block first atom: 2505 Blocpdb> 6 atoms in block 122 Block first atom: 2511 %Blocpdb-Wn> 1 atoms in block 123 i.e., less than what is required for a rigid body. %Blocpdb-Wn> Last atom in this block is the 2517th, in residue D 603 %Blocpdb-Wn> It will be merged with next block. Blocpdb> 7 atoms in block 123 Block first atom: 2517 Blocpdb> 6 atoms in block 124 Block first atom: 2524 Blocpdb> 6 atoms in block 125 Block first atom: 2530 Blocpdb> 6 atoms in block 126 Block first atom: 2536 Blocpdb> 6 atoms in block 127 Block first atom: 2542 Blocpdb> 6 atoms in block 128 Block first atom: 2548 Blocpdb> 6 atoms in block 129 Block first atom: 2554 Blocpdb> 6 atoms in block 130 Block first atom: 2560 Blocpdb> 6 atoms in block 131 Block first atom: 2566 Blocpdb> 6 atoms in block 132 Block first atom: 2572 Blocpdb> 6 atoms in block 133 Block first atom: 2578 Blocpdb> 6 atoms in block 134 Block first atom: 2584 Blocpdb> 6 atoms in block 135 Block first atom: 2590 Blocpdb> 6 atoms in block 136 Block first atom: 2596 Blocpdb> 3 atoms in block 137 Block first atom: 2602 Blocpdb> 6 atoms in block 138 Block first atom: 2605 Blocpdb> 6 atoms in block 139 Block first atom: 2611 Blocpdb> 6 atoms in block 140 Block first atom: 2617 Blocpdb> 6 atoms in block 141 Block first atom: 2623 Blocpdb> 6 atoms in block 142 Block first atom: 2629 Blocpdb> 6 atoms in block 143 Block first atom: 2635 Blocpdb> 6 atoms in block 144 Block first atom: 2641 Blocpdb> 6 atoms in block 145 Block first atom: 2647 Blocpdb> 6 atoms in block 146 Block first atom: 2653 Blocpdb> 6 atoms in block 147 Block first atom: 2659 Blocpdb> 6 atoms in block 148 Block first atom: 2665 Blocpdb> 6 atoms in block 149 Block first atom: 2671 Blocpdb> 6 atoms in block 150 Block first atom: 2677 Blocpdb> 6 atoms in block 151 Block first atom: 2683 Blocpdb> 6 atoms in block 152 Block first atom: 2689 Blocpdb> 6 atoms in block 153 Block first atom: 2695 Blocpdb> 6 atoms in block 154 Block first atom: 2701 Blocpdb> 6 atoms in block 155 Block first atom: 2707 Blocpdb> 6 atoms in block 156 Block first atom: 2713 Blocpdb> 6 atoms in block 157 Block first atom: 2719 Blocpdb> 6 atoms in block 158 Block first atom: 2725 Blocpdb> 6 atoms in block 159 Block first atom: 2731 Blocpdb> 6 atoms in block 160 Block first atom: 2737 Blocpdb> 6 atoms in block 161 Block first atom: 2743 Blocpdb> 6 atoms in block 162 Block first atom: 2749 Blocpdb> 6 atoms in block 163 Block first atom: 2755 Blocpdb> 6 atoms in block 164 Block first atom: 2761 Blocpdb> 6 atoms in block 165 Block first atom: 2767 Blocpdb> 6 atoms in block 166 Block first atom: 2773 Blocpdb> 6 atoms in block 167 Block first atom: 2779 %Blocpdb-Wn> 1 atoms in block 168 i.e., less than what is required for a rigid body. %Blocpdb-Wn> Last atom in this block is the 2785th, in residue E 603 %Blocpdb-Wn> It will be merged with next block. Blocpdb> 7 atoms in block 168 Block first atom: 2785 Blocpdb> 6 atoms in block 169 Block first atom: 2792 Blocpdb> 6 atoms in block 170 Block first atom: 2798 Blocpdb> 6 atoms in block 171 Block first atom: 2804 Blocpdb> 6 atoms in block 172 Block first atom: 2810 Blocpdb> 6 atoms in block 173 Block first atom: 2816 Blocpdb> 6 atoms in block 174 Block first atom: 2822 Blocpdb> 6 atoms in block 175 Block first atom: 2828 Blocpdb> 6 atoms in block 176 Block first atom: 2834 Blocpdb> 6 atoms in block 177 Block first atom: 2840 Blocpdb> 6 atoms in block 178 Block first atom: 2846 Blocpdb> 6 atoms in block 179 Block first atom: 2852 Blocpdb> 6 atoms in block 180 Block first atom: 2858 Blocpdb> 6 atoms in block 181 Block first atom: 2864 Blocpdb> 3 atoms in block 182 Block first atom: 2869 Blocpdb> 182 blocks. Blocpdb> At most, 900 atoms in each of them. Blocpdb> At least, 3 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: 14680001 Maximum allowed is LIWORK= 5000000 %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 0m0.036s user 0m0.012s sys 0m0.024s




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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.