CNRS Nantes University US2B US2B
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***  D70GelNemo  ***

LOGs for ID: 2406061052251339624

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 = 2406061052251339624.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 2406061052251339624.atom to be opened. Openam> File opened: 2406061052251339624.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 = 1771 First residue number = 1 Last residue number = 1771 Number of atoms found = 27589 Mean number per residue = 15.6 Pdbmat> Coordinate statistics: = -0.195779 +/- 34.605735 From: -90.345000 To: 77.849000 = 7.712501 +/- 31.664728 From: -85.499000 To: 95.699000 = -13.036961 +/- 30.497226 From: -79.653000 To: 56.944000 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 -1.7727 % Filled. Pdbmat> 15417573 non-zero elements. Pdbmat> 1694941 atom-atom interactions. Pdbmat> Number per atom= 122.87 +/- 58.50 Maximum number = 268 Minimum number = 17 Pdbmat> Matrix trace = 3.389882E+07 Pdbmat> Larger element = 931.376 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 1771 non-zero elements, NRBL set to 9 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 = 2406061052251339624.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 9 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 2406061052251339624.atom to be opened. Openam> file on opening on unit 11: 2406061052251339624.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 27589 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 9 residue(s) per block. Blocpdb> 1771 residues. Blocpdb> 139 atoms in block 1 Block first atom: 1 Blocpdb> 148 atoms in block 2 Block first atom: 140 Blocpdb> 150 atoms in block 3 Block first atom: 288 Blocpdb> 141 atoms in block 4 Block first atom: 438 Blocpdb> 128 atoms in block 5 Block first atom: 579 Blocpdb> 132 atoms in block 6 Block first atom: 707 Blocpdb> 142 atoms in block 7 Block first atom: 839 Blocpdb> 135 atoms in block 8 Block first atom: 981 Blocpdb> 131 atoms in block 9 Block first atom: 1116 Blocpdb> 141 atoms in block 10 Block first atom: 1247 Blocpdb> 140 atoms in block 11 Block first atom: 1388 Blocpdb> 134 atoms in block 12 Block first atom: 1528 Blocpdb> 150 atoms in block 13 Block first atom: 1662 Blocpdb> 144 atoms in block 14 Block first atom: 1812 Blocpdb> 112 atoms in block 15 Block first atom: 1956 Blocpdb> 155 atoms in block 16 Block first atom: 2068 Blocpdb> 122 atoms in block 17 Block first atom: 2223 Blocpdb> 144 atoms in block 18 Block first atom: 2345 Blocpdb> 128 atoms in block 19 Block first atom: 2489 Blocpdb> 153 atoms in block 20 Block first atom: 2617 Blocpdb> 143 atoms in block 21 Block first atom: 2770 Blocpdb> 120 atoms in block 22 Block first atom: 2913 Blocpdb> 117 atoms in block 23 Block first atom: 3033 Blocpdb> 132 atoms in block 24 Block first atom: 3150 Blocpdb> 165 atoms in block 25 Block first atom: 3282 Blocpdb> 139 atoms in block 26 Block first atom: 3447 Blocpdb> 122 atoms in block 27 Block first atom: 3586 Blocpdb> 136 atoms in block 28 Block first atom: 3708 Blocpdb> 131 atoms in block 29 Block first atom: 3844 Blocpdb> 129 atoms in block 30 Block first atom: 3975 Blocpdb> 132 atoms in block 31 Block first atom: 4104 Blocpdb> 143 atoms in block 32 Block first atom: 4236 Blocpdb> 151 atoms in block 33 Block first atom: 4379 Blocpdb> 139 atoms in block 34 Block first atom: 4530 Blocpdb> 139 atoms in block 35 Block first atom: 4669 Blocpdb> 149 atoms in block 36 Block first atom: 4808 Blocpdb> 135 atoms in block 37 Block first atom: 4957 Blocpdb> 132 atoms in block 38 Block first atom: 5092 Blocpdb> 157 atoms in block 39 Block first atom: 5224 Blocpdb> 145 atoms in block 40 Block first atom: 5381 Blocpdb> 128 atoms in block 41 Block first atom: 5526 Blocpdb> 143 atoms in block 42 Block first atom: 5654 Blocpdb> 163 atoms in block 43 Block first atom: 5797 Blocpdb> 155 atoms in block 44 Block first atom: 5960 Blocpdb> 146 atoms in block 45 Block first atom: 6115 Blocpdb> 133 atoms in block 46 Block first atom: 6261 Blocpdb> 158 atoms in block 47 Block first atom: 6394 Blocpdb> 131 atoms in block 48 Block first atom: 6552 Blocpdb> 121 atoms in block 49 Block first atom: 6683 Blocpdb> 132 atoms in block 50 Block first atom: 6804 Blocpdb> 135 atoms in block 51 Block first atom: 6936 Blocpdb> 144 atoms in block 52 Block first atom: 7071 Blocpdb> 138 atoms in block 53 Block first atom: 7215 Blocpdb> 156 atoms in block 54 Block first atom: 7353 Blocpdb> 138 atoms in block 55 Block first atom: 7509 Blocpdb> 165 atoms in block 56 Block first atom: 7647 Blocpdb> 122 atoms in block 57 Block first atom: 7812 Blocpdb> 149 atoms in block 58 Block first atom: 7934 Blocpdb> 126 atoms in block 59 Block first atom: 8083 Blocpdb> 167 atoms in block 60 Block first atom: 8209 Blocpdb> 157 atoms in block 61 Block first atom: 8376 Blocpdb> 144 atoms in block 62 Block first atom: 8533 Blocpdb> 154 atoms in block 63 Block first atom: 8677 Blocpdb> 160 atoms in block 64 Block first atom: 8831 Blocpdb> 148 atoms in block 65 Block first atom: 8991 Blocpdb> 139 atoms in block 66 Block first atom: 9139 Blocpdb> 160 atoms in block 67 Block first atom: 9278 Blocpdb> 124 atoms in block 68 Block first atom: 9438 Blocpdb> 134 atoms in block 69 Block first atom: 9562 Blocpdb> 125 atoms in block 70 Block first atom: 9696 Blocpdb> 166 atoms in block 71 Block first atom: 9821 Blocpdb> 143 atoms in block 72 Block first atom: 9987 Blocpdb> 167 atoms in block 73 Block first atom: 10130 Blocpdb> 158 atoms in block 74 Block first atom: 10297 Blocpdb> 126 atoms in block 75 Block first atom: 10455 Blocpdb> 153 atoms in block 76 Block first atom: 10581 Blocpdb> 147 atoms in block 77 Block first atom: 10734 Blocpdb> 128 atoms in block 78 Block first atom: 10881 Blocpdb> 152 atoms in block 79 Block first atom: 11009 Blocpdb> 151 atoms in block 80 Block first atom: 11161 Blocpdb> 158 atoms in block 81 Block first atom: 11312 Blocpdb> 153 atoms in block 82 Block first atom: 11470 Blocpdb> 149 atoms in block 83 Block first atom: 11623 Blocpdb> 143 atoms in block 84 Block first atom: 11772 Blocpdb> 143 atoms in block 85 Block first atom: 11915 Blocpdb> 156 atoms in block 86 Block first atom: 12058 Blocpdb> 125 atoms in block 87 Block first atom: 12214 Blocpdb> 154 atoms in block 88 Block first atom: 12339 Blocpdb> 148 atoms in block 89 Block first atom: 12493 Blocpdb> 132 atoms in block 90 Block first atom: 12641 Blocpdb> 153 atoms in block 91 Block first atom: 12773 Blocpdb> 140 atoms in block 92 Block first atom: 12926 Blocpdb> 145 atoms in block 93 Block first atom: 13066 Blocpdb> 146 atoms in block 94 Block first atom: 13211 Blocpdb> 151 atoms in block 95 Block first atom: 13357 Blocpdb> 117 atoms in block 96 Block first atom: 13508 Blocpdb> 118 atoms in block 97 Block first atom: 13625 Blocpdb> 141 atoms in block 98 Block first atom: 13743 Blocpdb> 136 atoms in block 99 Block first atom: 13884 Blocpdb> 140 atoms in block 100 Block first atom: 14020 Blocpdb> 177 atoms in block 101 Block first atom: 14160 Blocpdb> 157 atoms in block 102 Block first atom: 14337 Blocpdb> 155 atoms in block 103 Block first atom: 14494 Blocpdb> 138 atoms in block 104 Block first atom: 14649 Blocpdb> 167 atoms in block 105 Block first atom: 14787 Blocpdb> 150 atoms in block 106 Block first atom: 14954 Blocpdb> 141 atoms in block 107 Block first atom: 15104 Blocpdb> 154 atoms in block 108 Block first atom: 15245 Blocpdb> 164 atoms in block 109 Block first atom: 15399 Blocpdb> 156 atoms in block 110 Block first atom: 15563 Blocpdb> 141 atoms in block 111 Block first atom: 15719 Blocpdb> 159 atoms in block 112 Block first atom: 15860 Blocpdb> 140 atoms in block 113 Block first atom: 16019 Blocpdb> 146 atoms in block 114 Block first atom: 16159 Blocpdb> 150 atoms in block 115 Block first atom: 16305 Blocpdb> 141 atoms in block 116 Block first atom: 16455 Blocpdb> 146 atoms in block 117 Block first atom: 16596 Blocpdb> 163 atoms in block 118 Block first atom: 16742 Blocpdb> 138 atoms in block 119 Block first atom: 16905 Blocpdb> 127 atoms in block 120 Block first atom: 17043 Blocpdb> 133 atoms in block 121 Block first atom: 17170 Blocpdb> 129 atoms in block 122 Block first atom: 17303 Blocpdb> 119 atoms in block 123 Block first atom: 17432 Blocpdb> 111 atoms in block 124 Block first atom: 17551 Blocpdb> 137 atoms in block 125 Block first atom: 17662 Blocpdb> 118 atoms in block 126 Block first atom: 17799 Blocpdb> 157 atoms in block 127 Block first atom: 17917 Blocpdb> 169 atoms in block 128 Block first atom: 18074 Blocpdb> 132 atoms in block 129 Block first atom: 18243 Blocpdb> 145 atoms in block 130 Block first atom: 18375 Blocpdb> 133 atoms in block 131 Block first atom: 18520 Blocpdb> 121 atoms in block 132 Block first atom: 18653 Blocpdb> 115 atoms in block 133 Block first atom: 18774 Blocpdb> 117 atoms in block 134 Block first atom: 18889 Blocpdb> 131 atoms in block 135 Block first atom: 19006 Blocpdb> 147 atoms in block 136 Block first atom: 19137 Blocpdb> 147 atoms in block 137 Block first atom: 19284 Blocpdb> 145 atoms in block 138 Block first atom: 19431 Blocpdb> 132 atoms in block 139 Block first atom: 19576 Blocpdb> 155 atoms in block 140 Block first atom: 19708 Blocpdb> 150 atoms in block 141 Block first atom: 19863 Blocpdb> 154 atoms in block 142 Block first atom: 20013 Blocpdb> 126 atoms in block 143 Block first atom: 20167 Blocpdb> 136 atoms in block 144 Block first atom: 20293 Blocpdb> 108 atoms in block 145 Block first atom: 20429 Blocpdb> 148 atoms in block 146 Block first atom: 20537 Blocpdb> 132 atoms in block 147 Block first atom: 20685 Blocpdb> 149 atoms in block 148 Block first atom: 20817 Blocpdb> 126 atoms in block 149 Block first atom: 20966 Blocpdb> 144 atoms in block 150 Block first atom: 21092 Blocpdb> 146 atoms in block 151 Block first atom: 21236 Blocpdb> 125 atoms in block 152 Block first atom: 21382 Blocpdb> 142 atoms in block 153 Block first atom: 21507 Blocpdb> 147 atoms in block 154 Block first atom: 21649 Blocpdb> 155 atoms in block 155 Block first atom: 21796 Blocpdb> 111 atoms in block 156 Block first atom: 21951 Blocpdb> 128 atoms in block 157 Block first atom: 22062 Blocpdb> 130 atoms in block 158 Block first atom: 22190 Blocpdb> 116 atoms in block 159 Block first atom: 22320 Blocpdb> 136 atoms in block 160 Block first atom: 22436 Blocpdb> 138 atoms in block 161 Block first atom: 22572 Blocpdb> 156 atoms in block 162 Block first atom: 22710 Blocpdb> 114 atoms in block 163 Block first atom: 22866 Blocpdb> 125 atoms in block 164 Block first atom: 22980 Blocpdb> 133 atoms in block 165 Block first atom: 23105 Blocpdb> 132 atoms in block 166 Block first atom: 23238 Blocpdb> 144 atoms in block 167 Block first atom: 23370 Blocpdb> 143 atoms in block 168 Block first atom: 23514 Blocpdb> 154 atoms in block 169 Block first atom: 23657 Blocpdb> 116 atoms in block 170 Block first atom: 23811 Blocpdb> 137 atoms in block 171 Block first atom: 23927 Blocpdb> 146 atoms in block 172 Block first atom: 24064 Blocpdb> 147 atoms in block 173 Block first atom: 24210 Blocpdb> 144 atoms in block 174 Block first atom: 24357 Blocpdb> 151 atoms in block 175 Block first atom: 24501 Blocpdb> 138 atoms in block 176 Block first atom: 24652 Blocpdb> 118 atoms in block 177 Block first atom: 24790 Blocpdb> 132 atoms in block 178 Block first atom: 24908 Blocpdb> 134 atoms in block 179 Block first atom: 25040 Blocpdb> 135 atoms in block 180 Block first atom: 25174 Blocpdb> 132 atoms in block 181 Block first atom: 25309 Blocpdb> 127 atoms in block 182 Block first atom: 25441 Blocpdb> 141 atoms in block 183 Block first atom: 25568 Blocpdb> 133 atoms in block 184 Block first atom: 25709 Blocpdb> 125 atoms in block 185 Block first atom: 25842 Blocpdb> 143 atoms in block 186 Block first atom: 25967 Blocpdb> 140 atoms in block 187 Block first atom: 26110 Blocpdb> 120 atoms in block 188 Block first atom: 26250 Blocpdb> 140 atoms in block 189 Block first atom: 26370 Blocpdb> 139 atoms in block 190 Block first atom: 26510 Blocpdb> 139 atoms in block 191 Block first atom: 26649 Blocpdb> 135 atoms in block 192 Block first atom: 26788 Blocpdb> 157 atoms in block 193 Block first atom: 26923 Blocpdb> 152 atoms in block 194 Block first atom: 27080 Blocpdb> 133 atoms in block 195 Block first atom: 27232 Blocpdb> 106 atoms in block 196 Block first atom: 27365 Blocpdb> 119 atoms in block 197 Block first atom: 27470 Blocpdb> 197 blocks. Blocpdb> At most, 177 atoms in each of them. Blocpdb> At least, 106 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: 44231239 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 0m0.135s user 0m0.135s sys 0m0.000s




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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: April 25th, 2023.