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***  VIRAL PROTEIN 29-JUN-20 6XM4  ***

LOGs for ID: 210621033016102353

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 = 210621033016102353.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 210621033016102353.atom to be opened. Openam> File opened: 210621033016102353.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 = 3143 First residue number = 27 Last residue number = 1147 Number of atoms found = 24544 Mean number per residue = 7.8 Pdbmat> Coordinate statistics: = 186.113364 +/- 22.517689 From: 113.734000 To: 240.143000 = 187.474916 +/- 24.219959 From: 116.888000 To: 243.984000 = 186.138137 +/- 38.104182 From: 96.165000 To: 283.163000 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 1.5671 % Filled. Pdbmat> 8828801 non-zero elements. Pdbmat> 964803 atom-atom interactions. Pdbmat> Number per atom= 78.62 +/- 19.63 Maximum number = 126 Minimum number = 12 Pdbmat> Matrix trace = 1.929606E+07 Pdbmat> Larger element = 491.178 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 3143 non-zero elements, NRBL set to 16 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 = 210621033016102353.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 16 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 210621033016102353.atom to be opened. Openam> file on opening on unit 11: 210621033016102353.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 24544 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 16 residue(s) per block. Blocpdb> 3143 residues. Blocpdb> 133 atoms in block 1 Block first atom: 1 Blocpdb> 134 atoms in block 2 Block first atom: 134 Blocpdb> 97 atoms in block 3 Block first atom: 268 Blocpdb> 124 atoms in block 4 Block first atom: 365 Blocpdb> 130 atoms in block 5 Block first atom: 489 Blocpdb> 118 atoms in block 6 Block first atom: 619 Blocpdb> 129 atoms in block 7 Block first atom: 737 Blocpdb> 119 atoms in block 8 Block first atom: 866 Blocpdb> 145 atoms in block 9 Block first atom: 985 Blocpdb> 133 atoms in block 10 Block first atom: 1130 Blocpdb> 117 atoms in block 11 Block first atom: 1263 Blocpdb> 137 atoms in block 12 Block first atom: 1380 Blocpdb> 7 atoms in block 13 Block first atom: 1517 Blocpdb> 142 atoms in block 14 Block first atom: 1524 Blocpdb> 113 atoms in block 15 Block first atom: 1666 Blocpdb> 122 atoms in block 16 Block first atom: 1779 Blocpdb> 132 atoms in block 17 Block first atom: 1901 Blocpdb> 131 atoms in block 18 Block first atom: 2033 Blocpdb> 136 atoms in block 19 Block first atom: 2164 Blocpdb> 121 atoms in block 20 Block first atom: 2300 Blocpdb> 123 atoms in block 21 Block first atom: 2421 Blocpdb> 129 atoms in block 22 Block first atom: 2544 Blocpdb> 126 atoms in block 23 Block first atom: 2673 Blocpdb> 124 atoms in block 24 Block first atom: 2799 Blocpdb> 39 atoms in block 25 Block first atom: 2923 Blocpdb> 145 atoms in block 26 Block first atom: 2962 Blocpdb> 127 atoms in block 27 Block first atom: 3107 Blocpdb> 123 atoms in block 28 Block first atom: 3234 Blocpdb> 131 atoms in block 29 Block first atom: 3357 Blocpdb> 115 atoms in block 30 Block first atom: 3488 Blocpdb> 127 atoms in block 31 Block first atom: 3603 Blocpdb> 116 atoms in block 32 Block first atom: 3730 Blocpdb> 132 atoms in block 33 Block first atom: 3846 Blocpdb> 123 atoms in block 34 Block first atom: 3978 Blocpdb> 107 atoms in block 35 Block first atom: 4101 Blocpdb> 123 atoms in block 36 Block first atom: 4208 Blocpdb> 131 atoms in block 37 Block first atom: 4331 Blocpdb> 112 atoms in block 38 Block first atom: 4462 Blocpdb> 118 atoms in block 39 Block first atom: 4574 Blocpdb> 45 atoms in block 40 Block first atom: 4692 Blocpdb> 115 atoms in block 41 Block first atom: 4737 Blocpdb> 121 atoms in block 42 Block first atom: 4852 Blocpdb> 116 atoms in block 43 Block first atom: 4973 Blocpdb> 117 atoms in block 44 Block first atom: 5089 Blocpdb> 127 atoms in block 45 Block first atom: 5206 Blocpdb> 124 atoms in block 46 Block first atom: 5333 Blocpdb> 130 atoms in block 47 Block first atom: 5457 Blocpdb> 126 atoms in block 48 Block first atom: 5587 Blocpdb> 102 atoms in block 49 Block first atom: 5713 Blocpdb> 120 atoms in block 50 Block first atom: 5815 Blocpdb> 117 atoms in block 51 Block first atom: 5935 Blocpdb> 112 atoms in block 52 Block first atom: 6052 Blocpdb> 125 atoms in block 53 Block first atom: 6164 Blocpdb> 136 atoms in block 54 Block first atom: 6289 Blocpdb> 106 atoms in block 55 Block first atom: 6425 Blocpdb> 120 atoms in block 56 Block first atom: 6531 Blocpdb> 115 atoms in block 57 Block first atom: 6651 Blocpdb> 126 atoms in block 58 Block first atom: 6766 Blocpdb> 131 atoms in block 59 Block first atom: 6892 Blocpdb> 122 atoms in block 60 Block first atom: 7023 Blocpdb> 116 atoms in block 61 Block first atom: 7145 Blocpdb> 124 atoms in block 62 Block first atom: 7261 Blocpdb> 127 atoms in block 63 Block first atom: 7385 Blocpdb> 119 atoms in block 64 Block first atom: 7512 Blocpdb> 134 atoms in block 65 Block first atom: 7631 Blocpdb> 136 atoms in block 66 Block first atom: 7765 Blocpdb> 114 atoms in block 67 Block first atom: 7901 Blocpdb> 89 atoms in block 68 Block first atom: 8015 Blocpdb> 133 atoms in block 69 Block first atom: 8104 Blocpdb> 134 atoms in block 70 Block first atom: 8237 Blocpdb> 97 atoms in block 71 Block first atom: 8371 Blocpdb> 124 atoms in block 72 Block first atom: 8468 Blocpdb> 130 atoms in block 73 Block first atom: 8592 Blocpdb> 118 atoms in block 74 Block first atom: 8722 Blocpdb> 129 atoms in block 75 Block first atom: 8840 Blocpdb> 110 atoms in block 76 Block first atom: 8969 Blocpdb> 145 atoms in block 77 Block first atom: 9079 Blocpdb> 133 atoms in block 78 Block first atom: 9224 Blocpdb> 117 atoms in block 79 Block first atom: 9357 Blocpdb> 137 atoms in block 80 Block first atom: 9474 Blocpdb> 14 atoms in block 81 Block first atom: 9611 Blocpdb> 145 atoms in block 82 Block first atom: 9625 Blocpdb> 113 atoms in block 83 Block first atom: 9770 Blocpdb> 122 atoms in block 84 Block first atom: 9883 Blocpdb> 135 atoms in block 85 Block first atom: 10005 Blocpdb> 125 atoms in block 86 Block first atom: 10140 Blocpdb> 139 atoms in block 87 Block first atom: 10265 Blocpdb> 120 atoms in block 88 Block first atom: 10404 Blocpdb> 127 atoms in block 89 Block first atom: 10524 Blocpdb> 129 atoms in block 90 Block first atom: 10651 Blocpdb> 124 atoms in block 91 Block first atom: 10780 Blocpdb> 123 atoms in block 92 Block first atom: 10904 Blocpdb> 136 atoms in block 93 Block first atom: 11027 Blocpdb> 135 atoms in block 94 Block first atom: 11163 Blocpdb> 113 atoms in block 95 Block first atom: 11298 Blocpdb> 132 atoms in block 96 Block first atom: 11411 Blocpdb> 137 atoms in block 97 Block first atom: 11543 Blocpdb> 114 atoms in block 98 Block first atom: 11680 Blocpdb> 117 atoms in block 99 Block first atom: 11794 Blocpdb> 137 atoms in block 100 Block first atom: 11911 Blocpdb> 122 atoms in block 101 Block first atom: 12048 Blocpdb> 111 atoms in block 102 Block first atom: 12170 Blocpdb> 120 atoms in block 103 Block first atom: 12281 Blocpdb> 117 atoms in block 104 Block first atom: 12401 Blocpdb> 129 atoms in block 105 Block first atom: 12518 Blocpdb> 122 atoms in block 106 Block first atom: 12647 Blocpdb> 81 atoms in block 107 Block first atom: 12769 Blocpdb> 115 atoms in block 108 Block first atom: 12850 Blocpdb> 121 atoms in block 109 Block first atom: 12965 Blocpdb> 116 atoms in block 110 Block first atom: 13086 Blocpdb> 117 atoms in block 111 Block first atom: 13202 Blocpdb> 127 atoms in block 112 Block first atom: 13319 Blocpdb> 124 atoms in block 113 Block first atom: 13446 Blocpdb> 130 atoms in block 114 Block first atom: 13570 Blocpdb> 126 atoms in block 115 Block first atom: 13700 Blocpdb> 124 atoms in block 116 Block first atom: 13826 Blocpdb> 124 atoms in block 117 Block first atom: 13950 Blocpdb> 120 atoms in block 118 Block first atom: 14074 Blocpdb> 117 atoms in block 119 Block first atom: 14194 Blocpdb> 112 atoms in block 120 Block first atom: 14311 Blocpdb> 125 atoms in block 121 Block first atom: 14423 Blocpdb> 136 atoms in block 122 Block first atom: 14548 Blocpdb> 106 atoms in block 123 Block first atom: 14684 Blocpdb> 120 atoms in block 124 Block first atom: 14790 Blocpdb> 115 atoms in block 125 Block first atom: 14910 Blocpdb> 126 atoms in block 126 Block first atom: 15025 Blocpdb> 131 atoms in block 127 Block first atom: 15151 Blocpdb> 122 atoms in block 128 Block first atom: 15282 Blocpdb> 116 atoms in block 129 Block first atom: 15404 Blocpdb> 124 atoms in block 130 Block first atom: 15520 Blocpdb> 127 atoms in block 131 Block first atom: 15644 Blocpdb> 119 atoms in block 132 Block first atom: 15771 Blocpdb> 134 atoms in block 133 Block first atom: 15890 Blocpdb> 136 atoms in block 134 Block first atom: 16024 Blocpdb> 114 atoms in block 135 Block first atom: 16160 Blocpdb> 89 atoms in block 136 Block first atom: 16274 Blocpdb> 133 atoms in block 137 Block first atom: 16363 Blocpdb> 134 atoms in block 138 Block first atom: 16496 Blocpdb> 97 atoms in block 139 Block first atom: 16630 Blocpdb> 124 atoms in block 140 Block first atom: 16727 Blocpdb> 130 atoms in block 141 Block first atom: 16851 Blocpdb> 118 atoms in block 142 Block first atom: 16981 Blocpdb> 129 atoms in block 143 Block first atom: 17099 Blocpdb> 110 atoms in block 144 Block first atom: 17228 Blocpdb> 145 atoms in block 145 Block first atom: 17338 Blocpdb> 133 atoms in block 146 Block first atom: 17483 Blocpdb> 117 atoms in block 147 Block first atom: 17616 Blocpdb> 137 atoms in block 148 Block first atom: 17733 Blocpdb> 14 atoms in block 149 Block first atom: 17870 Blocpdb> 142 atoms in block 150 Block first atom: 17884 Blocpdb> 113 atoms in block 151 Block first atom: 18026 Blocpdb> 122 atoms in block 152 Block first atom: 18139 Blocpdb> 132 atoms in block 153 Block first atom: 18261 Blocpdb> 131 atoms in block 154 Block first atom: 18393 Blocpdb> 136 atoms in block 155 Block first atom: 18524 Blocpdb> 121 atoms in block 156 Block first atom: 18660 Blocpdb> 123 atoms in block 157 Block first atom: 18781 Blocpdb> 129 atoms in block 158 Block first atom: 18904 Blocpdb> 126 atoms in block 159 Block first atom: 19033 Blocpdb> 124 atoms in block 160 Block first atom: 19159 Blocpdb> 39 atoms in block 161 Block first atom: 19283 Blocpdb> 145 atoms in block 162 Block first atom: 19322 Blocpdb> 127 atoms in block 163 Block first atom: 19467 Blocpdb> 123 atoms in block 164 Block first atom: 19594 Blocpdb> 131 atoms in block 165 Block first atom: 19717 Blocpdb> 115 atoms in block 166 Block first atom: 19848 Blocpdb> 127 atoms in block 167 Block first atom: 19963 Blocpdb> 116 atoms in block 168 Block first atom: 20090 Blocpdb> 132 atoms in block 169 Block first atom: 20206 Blocpdb> 123 atoms in block 170 Block first atom: 20338 Blocpdb> 107 atoms in block 171 Block first atom: 20461 Blocpdb> 123 atoms in block 172 Block first atom: 20568 Blocpdb> 131 atoms in block 173 Block first atom: 20691 Blocpdb> 112 atoms in block 174 Block first atom: 20822 Blocpdb> 118 atoms in block 175 Block first atom: 20934 Blocpdb> 45 atoms in block 176 Block first atom: 21052 Blocpdb> 115 atoms in block 177 Block first atom: 21097 Blocpdb> 121 atoms in block 178 Block first atom: 21212 Blocpdb> 116 atoms in block 179 Block first atom: 21333 Blocpdb> 117 atoms in block 180 Block first atom: 21449 Blocpdb> 127 atoms in block 181 Block first atom: 21566 Blocpdb> 124 atoms in block 182 Block first atom: 21693 Blocpdb> 130 atoms in block 183 Block first atom: 21817 Blocpdb> 126 atoms in block 184 Block first atom: 21947 Blocpdb> 124 atoms in block 185 Block first atom: 22073 Blocpdb> 75 atoms in block 186 Block first atom: 22197 Blocpdb> 119 atoms in block 187 Block first atom: 22272 Blocpdb> 117 atoms in block 188 Block first atom: 22391 Blocpdb> 115 atoms in block 189 Block first atom: 22508 Blocpdb> 124 atoms in block 190 Block first atom: 22623 Blocpdb> 130 atoms in block 191 Block first atom: 22747 Blocpdb> 107 atoms in block 192 Block first atom: 22877 Blocpdb> 123 atoms in block 193 Block first atom: 22984 Blocpdb> 116 atoms in block 194 Block first atom: 23107 Blocpdb> 126 atoms in block 195 Block first atom: 23223 Blocpdb> 131 atoms in block 196 Block first atom: 23349 Blocpdb> 116 atoms in block 197 Block first atom: 23480 Blocpdb> 125 atoms in block 198 Block first atom: 23596 Blocpdb> 122 atoms in block 199 Block first atom: 23721 Blocpdb> 127 atoms in block 200 Block first atom: 23843 Blocpdb> 120 atoms in block 201 Block first atom: 23970 Blocpdb> 132 atoms in block 202 Block first atom: 24090 Blocpdb> 138 atoms in block 203 Block first atom: 24222 Blocpdb> 115 atoms in block 204 Block first atom: 24360 Blocpdb> 70 atoms in block 205 Block first atom: 24474 Blocpdb> 205 blocks. Blocpdb> At most, 145 atoms in each of them. Blocpdb> At least, 7 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: 32219146 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 0m0.145s user 0m0.092s sys 0m0.044s




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Last modification: October 18th, 2018.