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LOGs for ID: 220209112104107964

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 = 220209112104107964.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 220209112104107964.atom to be opened. Openam> File opened: 220209112104107964.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 = 4291 First residue number = 5 Last residue number = 701 Number of atoms found = 33222 Mean number per residue = 7.7 Pdbmat> Coordinate statistics: = 143.047329 +/- 29.118983 From: 68.487000 To: 215.072000 = 151.314477 +/- 25.870483 From: 82.158000 To: 220.048000 = 143.191467 +/- 28.898764 From: 64.468000 To: 215.077000 Pdbmat> Masses are all set to one. %Pdbmat-W> residue:'COA ' is not a well known amino-acid. %Pdbmat-W> residue:'BTI ' is not a well known amino-acid. %Pdbmat-W> 2 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 1.8580 % Filled. Pdbmat> 12481133 non-zero elements. Pdbmat> 1364906 atom-atom interactions. Pdbmat> Number per atom= 82.17 +/- 19.71 Maximum number = 123 Minimum number = 14 Pdbmat> Matrix trace = 2.729812E+07 Pdbmat> Larger element = 482.707 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 4291 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 = 220209112104107964.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 220209112104107964.atom to be opened. Openam> file on opening on unit 11: 220209112104107964.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 33222 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> 4291 residues. Blocpdb> 175 atoms in block 1 Block first atom: 1 Blocpdb> 183 atoms in block 2 Block first atom: 176 Blocpdb> 188 atoms in block 3 Block first atom: 359 Blocpdb> 163 atoms in block 4 Block first atom: 547 Blocpdb> 161 atoms in block 5 Block first atom: 710 Blocpdb> 159 atoms in block 6 Block first atom: 871 Blocpdb> 153 atoms in block 7 Block first atom: 1030 Blocpdb> 155 atoms in block 8 Block first atom: 1183 Blocpdb> 174 atoms in block 9 Block first atom: 1338 Blocpdb> 155 atoms in block 10 Block first atom: 1512 Blocpdb> 180 atoms in block 11 Block first atom: 1667 Blocpdb> 172 atoms in block 12 Block first atom: 1847 Blocpdb> 179 atoms in block 13 Block first atom: 2019 Blocpdb> 172 atoms in block 14 Block first atom: 2198 Blocpdb> 162 atoms in block 15 Block first atom: 2370 Blocpdb> 172 atoms in block 16 Block first atom: 2532 Blocpdb> 166 atoms in block 17 Block first atom: 2704 Blocpdb> 168 atoms in block 18 Block first atom: 2870 Blocpdb> 165 atoms in block 19 Block first atom: 3038 Blocpdb> 159 atoms in block 20 Block first atom: 3203 Blocpdb> 181 atoms in block 21 Block first atom: 3362 Blocpdb> 179 atoms in block 22 Block first atom: 3543 Blocpdb> 181 atoms in block 23 Block first atom: 3722 Blocpdb> 175 atoms in block 24 Block first atom: 3903 Blocpdb> 183 atoms in block 25 Block first atom: 4078 Blocpdb> 188 atoms in block 26 Block first atom: 4261 Blocpdb> 163 atoms in block 27 Block first atom: 4449 Blocpdb> 161 atoms in block 28 Block first atom: 4612 Blocpdb> 159 atoms in block 29 Block first atom: 4773 Blocpdb> 153 atoms in block 30 Block first atom: 4932 Blocpdb> 155 atoms in block 31 Block first atom: 5085 Blocpdb> 174 atoms in block 32 Block first atom: 5240 Blocpdb> 155 atoms in block 33 Block first atom: 5414 Blocpdb> 180 atoms in block 34 Block first atom: 5569 Blocpdb> 172 atoms in block 35 Block first atom: 5749 Blocpdb> 179 atoms in block 36 Block first atom: 5921 Blocpdb> 172 atoms in block 37 Block first atom: 6100 Blocpdb> 162 atoms in block 38 Block first atom: 6272 Blocpdb> 172 atoms in block 39 Block first atom: 6434 Blocpdb> 166 atoms in block 40 Block first atom: 6606 Blocpdb> 168 atoms in block 41 Block first atom: 6772 Blocpdb> 165 atoms in block 42 Block first atom: 6940 Blocpdb> 159 atoms in block 43 Block first atom: 7105 Blocpdb> 181 atoms in block 44 Block first atom: 7264 Blocpdb> 179 atoms in block 45 Block first atom: 7445 Blocpdb> 181 atoms in block 46 Block first atom: 7624 Blocpdb> 175 atoms in block 47 Block first atom: 7805 Blocpdb> 183 atoms in block 48 Block first atom: 7980 Blocpdb> 188 atoms in block 49 Block first atom: 8163 Blocpdb> 163 atoms in block 50 Block first atom: 8351 Blocpdb> 161 atoms in block 51 Block first atom: 8514 Blocpdb> 159 atoms in block 52 Block first atom: 8675 Blocpdb> 153 atoms in block 53 Block first atom: 8834 Blocpdb> 155 atoms in block 54 Block first atom: 8987 Blocpdb> 174 atoms in block 55 Block first atom: 9142 Blocpdb> 155 atoms in block 56 Block first atom: 9316 Blocpdb> 180 atoms in block 57 Block first atom: 9471 Blocpdb> 172 atoms in block 58 Block first atom: 9651 Blocpdb> 179 atoms in block 59 Block first atom: 9823 Blocpdb> 172 atoms in block 60 Block first atom: 10002 Blocpdb> 162 atoms in block 61 Block first atom: 10174 Blocpdb> 172 atoms in block 62 Block first atom: 10336 Blocpdb> 166 atoms in block 63 Block first atom: 10508 Blocpdb> 168 atoms in block 64 Block first atom: 10674 Blocpdb> 165 atoms in block 65 Block first atom: 10842 Blocpdb> 159 atoms in block 66 Block first atom: 11007 Blocpdb> 181 atoms in block 67 Block first atom: 11166 Blocpdb> 179 atoms in block 68 Block first atom: 11347 Blocpdb> 181 atoms in block 69 Block first atom: 11526 Blocpdb> 175 atoms in block 70 Block first atom: 11707 Blocpdb> 183 atoms in block 71 Block first atom: 11882 Blocpdb> 188 atoms in block 72 Block first atom: 12065 Blocpdb> 163 atoms in block 73 Block first atom: 12253 Blocpdb> 161 atoms in block 74 Block first atom: 12416 Blocpdb> 159 atoms in block 75 Block first atom: 12577 Blocpdb> 153 atoms in block 76 Block first atom: 12736 Blocpdb> 155 atoms in block 77 Block first atom: 12889 Blocpdb> 174 atoms in block 78 Block first atom: 13044 Blocpdb> 155 atoms in block 79 Block first atom: 13218 Blocpdb> 180 atoms in block 80 Block first atom: 13373 Blocpdb> 172 atoms in block 81 Block first atom: 13553 Blocpdb> 179 atoms in block 82 Block first atom: 13725 Blocpdb> 172 atoms in block 83 Block first atom: 13904 Blocpdb> 162 atoms in block 84 Block first atom: 14076 Blocpdb> 172 atoms in block 85 Block first atom: 14238 Blocpdb> 166 atoms in block 86 Block first atom: 14410 Blocpdb> 168 atoms in block 87 Block first atom: 14576 Blocpdb> 165 atoms in block 88 Block first atom: 14744 Blocpdb> 159 atoms in block 89 Block first atom: 14909 Blocpdb> 181 atoms in block 90 Block first atom: 15068 Blocpdb> 179 atoms in block 91 Block first atom: 15249 Blocpdb> 181 atoms in block 92 Block first atom: 15428 Blocpdb> 175 atoms in block 93 Block first atom: 15609 Blocpdb> 183 atoms in block 94 Block first atom: 15784 Blocpdb> 188 atoms in block 95 Block first atom: 15967 Blocpdb> 163 atoms in block 96 Block first atom: 16155 Blocpdb> 161 atoms in block 97 Block first atom: 16318 Blocpdb> 159 atoms in block 98 Block first atom: 16479 Blocpdb> 153 atoms in block 99 Block first atom: 16638 Blocpdb> 155 atoms in block 100 Block first atom: 16791 Blocpdb> 174 atoms in block 101 Block first atom: 16946 Blocpdb> 155 atoms in block 102 Block first atom: 17120 Blocpdb> 180 atoms in block 103 Block first atom: 17275 Blocpdb> 172 atoms in block 104 Block first atom: 17455 Blocpdb> 179 atoms in block 105 Block first atom: 17627 Blocpdb> 172 atoms in block 106 Block first atom: 17806 Blocpdb> 162 atoms in block 107 Block first atom: 17978 Blocpdb> 172 atoms in block 108 Block first atom: 18140 Blocpdb> 166 atoms in block 109 Block first atom: 18312 Blocpdb> 168 atoms in block 110 Block first atom: 18478 Blocpdb> 165 atoms in block 111 Block first atom: 18646 Blocpdb> 159 atoms in block 112 Block first atom: 18811 Blocpdb> 181 atoms in block 113 Block first atom: 18970 Blocpdb> 179 atoms in block 114 Block first atom: 19151 Blocpdb> 181 atoms in block 115 Block first atom: 19330 Blocpdb> 175 atoms in block 116 Block first atom: 19511 Blocpdb> 183 atoms in block 117 Block first atom: 19686 Blocpdb> 188 atoms in block 118 Block first atom: 19869 Blocpdb> 163 atoms in block 119 Block first atom: 20057 Blocpdb> 161 atoms in block 120 Block first atom: 20220 Blocpdb> 159 atoms in block 121 Block first atom: 20381 Blocpdb> 153 atoms in block 122 Block first atom: 20540 Blocpdb> 155 atoms in block 123 Block first atom: 20693 Blocpdb> 174 atoms in block 124 Block first atom: 20848 Blocpdb> 155 atoms in block 125 Block first atom: 21022 Blocpdb> 180 atoms in block 126 Block first atom: 21177 Blocpdb> 172 atoms in block 127 Block first atom: 21357 Blocpdb> 179 atoms in block 128 Block first atom: 21529 Blocpdb> 172 atoms in block 129 Block first atom: 21708 Blocpdb> 162 atoms in block 130 Block first atom: 21880 Blocpdb> 172 atoms in block 131 Block first atom: 22042 Blocpdb> 166 atoms in block 132 Block first atom: 22214 Blocpdb> 168 atoms in block 133 Block first atom: 22380 Blocpdb> 165 atoms in block 134 Block first atom: 22548 Blocpdb> 159 atoms in block 135 Block first atom: 22713 Blocpdb> 181 atoms in block 136 Block first atom: 22872 Blocpdb> 179 atoms in block 137 Block first atom: 23053 Blocpdb> 181 atoms in block 138 Block first atom: 23232 Blocpdb> 159 atoms in block 139 Block first atom: 23413 Blocpdb> 183 atoms in block 140 Block first atom: 23572 Blocpdb> 63 atoms in block 141 Block first atom: 23755 Blocpdb> 159 atoms in block 142 Block first atom: 23818 Blocpdb> 161 atoms in block 143 Block first atom: 23977 Blocpdb> 164 atoms in block 144 Block first atom: 24138 Blocpdb> 166 atoms in block 145 Block first atom: 24302 Blocpdb> 166 atoms in block 146 Block first atom: 24468 Blocpdb> 172 atoms in block 147 Block first atom: 24634 Blocpdb> 152 atoms in block 148 Block first atom: 24806 Blocpdb> 20 atoms in block 149 Block first atom: 24958 Blocpdb> 159 atoms in block 150 Block first atom: 24978 Blocpdb> 181 atoms in block 151 Block first atom: 25137 Blocpdb> 169 atoms in block 152 Block first atom: 25318 Blocpdb> 169 atoms in block 153 Block first atom: 25487 Blocpdb> 159 atoms in block 154 Block first atom: 25656 Blocpdb> 167 atoms in block 155 Block first atom: 25815 Blocpdb> 157 atoms in block 156 Block first atom: 25982 Blocpdb> 163 atoms in block 157 Block first atom: 26139 Blocpdb> 167 atoms in block 158 Block first atom: 26302 Blocpdb> 90 atoms in block 159 Block first atom: 26469 Blocpdb> 163 atoms in block 160 Block first atom: 26559 Blocpdb> 177 atoms in block 161 Block first atom: 26722 Blocpdb> 170 atoms in block 162 Block first atom: 26899 Blocpdb> 160 atoms in block 163 Block first atom: 27069 Blocpdb> 163 atoms in block 164 Block first atom: 27229 Blocpdb> 170 atoms in block 165 Block first atom: 27392 Blocpdb> 158 atoms in block 166 Block first atom: 27562 Blocpdb> 165 atoms in block 167 Block first atom: 27720 Blocpdb> 160 atoms in block 168 Block first atom: 27885 Blocpdb> 63 atoms in block 169 Block first atom: 28045 Blocpdb> 159 atoms in block 170 Block first atom: 28108 Blocpdb> 181 atoms in block 171 Block first atom: 28267 Blocpdb> 169 atoms in block 172 Block first atom: 28448 Blocpdb> 169 atoms in block 173 Block first atom: 28617 Blocpdb> 159 atoms in block 174 Block first atom: 28786 Blocpdb> 167 atoms in block 175 Block first atom: 28945 Blocpdb> 157 atoms in block 176 Block first atom: 29112 Blocpdb> 163 atoms in block 177 Block first atom: 29269 Blocpdb> 167 atoms in block 178 Block first atom: 29432 Blocpdb> 90 atoms in block 179 Block first atom: 29599 Blocpdb> 160 atoms in block 180 Block first atom: 29689 Blocpdb> 184 atoms in block 181 Block first atom: 29849 Blocpdb> 165 atoms in block 182 Block first atom: 30033 Blocpdb> 168 atoms in block 183 Block first atom: 30198 Blocpdb> 162 atoms in block 184 Block first atom: 30366 Blocpdb> 166 atoms in block 185 Block first atom: 30528 Blocpdb> 158 atoms in block 186 Block first atom: 30694 Blocpdb> 163 atoms in block 187 Block first atom: 30852 Blocpdb> 166 atoms in block 188 Block first atom: 31015 Blocpdb> 82 atoms in block 189 Block first atom: 31181 Blocpdb> 159 atoms in block 190 Block first atom: 31263 Blocpdb> 181 atoms in block 191 Block first atom: 31422 Blocpdb> 169 atoms in block 192 Block first atom: 31603 Blocpdb> 169 atoms in block 193 Block first atom: 31772 Blocpdb> 159 atoms in block 194 Block first atom: 31941 Blocpdb> 167 atoms in block 195 Block first atom: 32100 Blocpdb> 157 atoms in block 196 Block first atom: 32267 Blocpdb> 163 atoms in block 197 Block first atom: 32424 Blocpdb> 167 atoms in block 198 Block first atom: 32587 Blocpdb> 90 atoms in block 199 Block first atom: 32754 Blocpdb> 288 atoms in block 200 Block first atom: 32844 Blocpdb> 91 atoms in block 201 Block first atom: 33131 Blocpdb> 201 blocks. Blocpdb> At most, 288 atoms in each of them. Blocpdb> At least, 20 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: 86857921 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 0m0.188s user 0m0.184s 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: October 18th, 2018.