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LOGs for ID: 22020814023233018

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 = 22020814023233018.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 22020814023233018.atom to be opened. Openam> File opened: 22020814023233018.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 = 1955 First residue number = 1 Last residue number = 478 Number of atoms found = 31395 Mean number per residue = 16.1 Pdbmat> Coordinate statistics: = 138.733186 +/- 16.856737 From: 98.232000 To: 178.045000 = 138.732576 +/- 16.876353 From: 98.892000 To: 177.382000 = 122.106963 +/- 37.262496 From: 59.869000 To: 214.977000 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 15.7968 % Filled. Pdbmat> 22192417 non-zero elements. Pdbmat> 2445298 atom-atom interactions. Pdbmat> Number per atom= 155.78 +/- 37.93 Maximum number = 228 Minimum number = 22 Pdbmat> Matrix trace = 4.890596E+07 Pdbmat> Larger element = 865.340 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 1955 non-zero elements, NRBL set to 10 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 = 22020814023233018.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 10 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 22020814023233018.atom to be opened. Openam> file on opening on unit 11: 22020814023233018.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 31395 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 10 residue(s) per block. Blocpdb> 1955 residues. Blocpdb> 196 atoms in block 1 Block first atom: 1 Blocpdb> 173 atoms in block 2 Block first atom: 197 Blocpdb> 142 atoms in block 3 Block first atom: 370 Blocpdb> 176 atoms in block 4 Block first atom: 512 Blocpdb> 157 atoms in block 5 Block first atom: 688 Blocpdb> 173 atoms in block 6 Block first atom: 845 Blocpdb> 165 atoms in block 7 Block first atom: 1018 Blocpdb> 168 atoms in block 8 Block first atom: 1183 Blocpdb> 165 atoms in block 9 Block first atom: 1351 Blocpdb> 158 atoms in block 10 Block first atom: 1516 Blocpdb> 153 atoms in block 11 Block first atom: 1674 Blocpdb> 145 atoms in block 12 Block first atom: 1827 Blocpdb> 152 atoms in block 13 Block first atom: 1972 Blocpdb> 180 atoms in block 14 Block first atom: 2124 Blocpdb> 167 atoms in block 15 Block first atom: 2304 Blocpdb> 150 atoms in block 16 Block first atom: 2471 Blocpdb> 142 atoms in block 17 Block first atom: 2621 Blocpdb> 140 atoms in block 18 Block first atom: 2763 Blocpdb> 163 atoms in block 19 Block first atom: 2903 Blocpdb> 162 atoms in block 20 Block first atom: 3066 Blocpdb> 194 atoms in block 21 Block first atom: 3228 Blocpdb> 157 atoms in block 22 Block first atom: 3422 Blocpdb> 162 atoms in block 23 Block first atom: 3579 Blocpdb> 140 atoms in block 24 Block first atom: 3741 Blocpdb> 157 atoms in block 25 Block first atom: 3881 Blocpdb> 168 atoms in block 26 Block first atom: 4038 Blocpdb> 140 atoms in block 27 Block first atom: 4206 Blocpdb> 158 atoms in block 28 Block first atom: 4346 Blocpdb> 150 atoms in block 29 Block first atom: 4504 Blocpdb> 162 atoms in block 30 Block first atom: 4654 Blocpdb> 167 atoms in block 31 Block first atom: 4816 Blocpdb> 179 atoms in block 32 Block first atom: 4983 Blocpdb> 161 atoms in block 33 Block first atom: 5162 Blocpdb> 184 atoms in block 34 Block first atom: 5323 Blocpdb> 140 atoms in block 35 Block first atom: 5507 Blocpdb> 160 atoms in block 36 Block first atom: 5647 Blocpdb> 157 atoms in block 37 Block first atom: 5807 Blocpdb> 146 atoms in block 38 Block first atom: 5964 Blocpdb> 150 atoms in block 39 Block first atom: 6110 Blocpdb> 20 atoms in block 40 Block first atom: 6260 Blocpdb> 196 atoms in block 41 Block first atom: 6280 Blocpdb> 173 atoms in block 42 Block first atom: 6476 Blocpdb> 142 atoms in block 43 Block first atom: 6649 Blocpdb> 176 atoms in block 44 Block first atom: 6791 Blocpdb> 157 atoms in block 45 Block first atom: 6967 Blocpdb> 173 atoms in block 46 Block first atom: 7124 Blocpdb> 165 atoms in block 47 Block first atom: 7297 Blocpdb> 168 atoms in block 48 Block first atom: 7462 Blocpdb> 165 atoms in block 49 Block first atom: 7630 Blocpdb> 158 atoms in block 50 Block first atom: 7795 Blocpdb> 153 atoms in block 51 Block first atom: 7953 Blocpdb> 145 atoms in block 52 Block first atom: 8106 Blocpdb> 152 atoms in block 53 Block first atom: 8251 Blocpdb> 180 atoms in block 54 Block first atom: 8403 Blocpdb> 167 atoms in block 55 Block first atom: 8583 Blocpdb> 150 atoms in block 56 Block first atom: 8750 Blocpdb> 142 atoms in block 57 Block first atom: 8900 Blocpdb> 140 atoms in block 58 Block first atom: 9042 Blocpdb> 163 atoms in block 59 Block first atom: 9182 Blocpdb> 162 atoms in block 60 Block first atom: 9345 Blocpdb> 194 atoms in block 61 Block first atom: 9507 Blocpdb> 157 atoms in block 62 Block first atom: 9701 Blocpdb> 162 atoms in block 63 Block first atom: 9858 Blocpdb> 140 atoms in block 64 Block first atom: 10020 Blocpdb> 157 atoms in block 65 Block first atom: 10160 Blocpdb> 168 atoms in block 66 Block first atom: 10317 Blocpdb> 140 atoms in block 67 Block first atom: 10485 Blocpdb> 158 atoms in block 68 Block first atom: 10625 Blocpdb> 150 atoms in block 69 Block first atom: 10783 Blocpdb> 162 atoms in block 70 Block first atom: 10933 Blocpdb> 167 atoms in block 71 Block first atom: 11095 Blocpdb> 179 atoms in block 72 Block first atom: 11262 Blocpdb> 161 atoms in block 73 Block first atom: 11441 Blocpdb> 184 atoms in block 74 Block first atom: 11602 Blocpdb> 140 atoms in block 75 Block first atom: 11786 Blocpdb> 160 atoms in block 76 Block first atom: 11926 Blocpdb> 157 atoms in block 77 Block first atom: 12086 Blocpdb> 146 atoms in block 78 Block first atom: 12243 Blocpdb> 150 atoms in block 79 Block first atom: 12389 Blocpdb> 20 atoms in block 80 Block first atom: 12539 Blocpdb> 196 atoms in block 81 Block first atom: 12559 Blocpdb> 173 atoms in block 82 Block first atom: 12755 Blocpdb> 142 atoms in block 83 Block first atom: 12928 Blocpdb> 176 atoms in block 84 Block first atom: 13070 Blocpdb> 157 atoms in block 85 Block first atom: 13246 Blocpdb> 173 atoms in block 86 Block first atom: 13403 Blocpdb> 165 atoms in block 87 Block first atom: 13576 Blocpdb> 168 atoms in block 88 Block first atom: 13741 Blocpdb> 165 atoms in block 89 Block first atom: 13909 Blocpdb> 158 atoms in block 90 Block first atom: 14074 Blocpdb> 153 atoms in block 91 Block first atom: 14232 Blocpdb> 145 atoms in block 92 Block first atom: 14385 Blocpdb> 152 atoms in block 93 Block first atom: 14530 Blocpdb> 180 atoms in block 94 Block first atom: 14682 Blocpdb> 167 atoms in block 95 Block first atom: 14862 Blocpdb> 150 atoms in block 96 Block first atom: 15029 Blocpdb> 142 atoms in block 97 Block first atom: 15179 Blocpdb> 140 atoms in block 98 Block first atom: 15321 Blocpdb> 163 atoms in block 99 Block first atom: 15461 Blocpdb> 162 atoms in block 100 Block first atom: 15624 Blocpdb> 194 atoms in block 101 Block first atom: 15786 Blocpdb> 157 atoms in block 102 Block first atom: 15980 Blocpdb> 162 atoms in block 103 Block first atom: 16137 Blocpdb> 140 atoms in block 104 Block first atom: 16299 Blocpdb> 157 atoms in block 105 Block first atom: 16439 Blocpdb> 168 atoms in block 106 Block first atom: 16596 Blocpdb> 140 atoms in block 107 Block first atom: 16764 Blocpdb> 158 atoms in block 108 Block first atom: 16904 Blocpdb> 150 atoms in block 109 Block first atom: 17062 Blocpdb> 162 atoms in block 110 Block first atom: 17212 Blocpdb> 167 atoms in block 111 Block first atom: 17374 Blocpdb> 179 atoms in block 112 Block first atom: 17541 Blocpdb> 161 atoms in block 113 Block first atom: 17720 Blocpdb> 184 atoms in block 114 Block first atom: 17881 Blocpdb> 140 atoms in block 115 Block first atom: 18065 Blocpdb> 160 atoms in block 116 Block first atom: 18205 Blocpdb> 157 atoms in block 117 Block first atom: 18365 Blocpdb> 146 atoms in block 118 Block first atom: 18522 Blocpdb> 150 atoms in block 119 Block first atom: 18668 Blocpdb> 20 atoms in block 120 Block first atom: 18818 Blocpdb> 196 atoms in block 121 Block first atom: 18838 Blocpdb> 173 atoms in block 122 Block first atom: 19034 Blocpdb> 142 atoms in block 123 Block first atom: 19207 Blocpdb> 176 atoms in block 124 Block first atom: 19349 Blocpdb> 157 atoms in block 125 Block first atom: 19525 Blocpdb> 173 atoms in block 126 Block first atom: 19682 Blocpdb> 165 atoms in block 127 Block first atom: 19855 Blocpdb> 168 atoms in block 128 Block first atom: 20020 Blocpdb> 165 atoms in block 129 Block first atom: 20188 Blocpdb> 158 atoms in block 130 Block first atom: 20353 Blocpdb> 153 atoms in block 131 Block first atom: 20511 Blocpdb> 145 atoms in block 132 Block first atom: 20664 Blocpdb> 152 atoms in block 133 Block first atom: 20809 Blocpdb> 180 atoms in block 134 Block first atom: 20961 Blocpdb> 167 atoms in block 135 Block first atom: 21141 Blocpdb> 150 atoms in block 136 Block first atom: 21308 Blocpdb> 142 atoms in block 137 Block first atom: 21458 Blocpdb> 140 atoms in block 138 Block first atom: 21600 Blocpdb> 163 atoms in block 139 Block first atom: 21740 Blocpdb> 162 atoms in block 140 Block first atom: 21903 Blocpdb> 194 atoms in block 141 Block first atom: 22065 Blocpdb> 157 atoms in block 142 Block first atom: 22259 Blocpdb> 162 atoms in block 143 Block first atom: 22416 Blocpdb> 140 atoms in block 144 Block first atom: 22578 Blocpdb> 157 atoms in block 145 Block first atom: 22718 Blocpdb> 168 atoms in block 146 Block first atom: 22875 Blocpdb> 140 atoms in block 147 Block first atom: 23043 Blocpdb> 158 atoms in block 148 Block first atom: 23183 Blocpdb> 150 atoms in block 149 Block first atom: 23341 Blocpdb> 162 atoms in block 150 Block first atom: 23491 Blocpdb> 167 atoms in block 151 Block first atom: 23653 Blocpdb> 179 atoms in block 152 Block first atom: 23820 Blocpdb> 161 atoms in block 153 Block first atom: 23999 Blocpdb> 184 atoms in block 154 Block first atom: 24160 Blocpdb> 140 atoms in block 155 Block first atom: 24344 Blocpdb> 160 atoms in block 156 Block first atom: 24484 Blocpdb> 157 atoms in block 157 Block first atom: 24644 Blocpdb> 146 atoms in block 158 Block first atom: 24801 Blocpdb> 150 atoms in block 159 Block first atom: 24947 Blocpdb> 20 atoms in block 160 Block first atom: 25097 Blocpdb> 196 atoms in block 161 Block first atom: 25117 Blocpdb> 173 atoms in block 162 Block first atom: 25313 Blocpdb> 142 atoms in block 163 Block first atom: 25486 Blocpdb> 176 atoms in block 164 Block first atom: 25628 Blocpdb> 157 atoms in block 165 Block first atom: 25804 Blocpdb> 173 atoms in block 166 Block first atom: 25961 Blocpdb> 165 atoms in block 167 Block first atom: 26134 Blocpdb> 168 atoms in block 168 Block first atom: 26299 Blocpdb> 165 atoms in block 169 Block first atom: 26467 Blocpdb> 158 atoms in block 170 Block first atom: 26632 Blocpdb> 153 atoms in block 171 Block first atom: 26790 Blocpdb> 145 atoms in block 172 Block first atom: 26943 Blocpdb> 152 atoms in block 173 Block first atom: 27088 Blocpdb> 180 atoms in block 174 Block first atom: 27240 Blocpdb> 167 atoms in block 175 Block first atom: 27420 Blocpdb> 150 atoms in block 176 Block first atom: 27587 Blocpdb> 142 atoms in block 177 Block first atom: 27737 Blocpdb> 140 atoms in block 178 Block first atom: 27879 Blocpdb> 163 atoms in block 179 Block first atom: 28019 Blocpdb> 162 atoms in block 180 Block first atom: 28182 Blocpdb> 194 atoms in block 181 Block first atom: 28344 Blocpdb> 157 atoms in block 182 Block first atom: 28538 Blocpdb> 162 atoms in block 183 Block first atom: 28695 Blocpdb> 140 atoms in block 184 Block first atom: 28857 Blocpdb> 157 atoms in block 185 Block first atom: 28997 Blocpdb> 168 atoms in block 186 Block first atom: 29154 Blocpdb> 140 atoms in block 187 Block first atom: 29322 Blocpdb> 158 atoms in block 188 Block first atom: 29462 Blocpdb> 150 atoms in block 189 Block first atom: 29620 Blocpdb> 162 atoms in block 190 Block first atom: 29770 Blocpdb> 167 atoms in block 191 Block first atom: 29932 Blocpdb> 179 atoms in block 192 Block first atom: 30099 Blocpdb> 161 atoms in block 193 Block first atom: 30278 Blocpdb> 184 atoms in block 194 Block first atom: 30439 Blocpdb> 140 atoms in block 195 Block first atom: 30623 Blocpdb> 160 atoms in block 196 Block first atom: 30763 Blocpdb> 157 atoms in block 197 Block first atom: 30923 Blocpdb> 146 atoms in block 198 Block first atom: 31080 Blocpdb> 150 atoms in block 199 Block first atom: 31226 Blocpdb> 20 atoms in block 200 Block first atom: 31375 Blocpdb> 200 blocks. Blocpdb> At most, 196 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: 55726525 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 0m0.191s user 0m0.188s sys 0m0.000s




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Last modification: October 18th, 2018.