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***  TRANSPORT PROTEIN 29-APR-11 2LCK  ***

LOGs for ID: 23011717532984182

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 = 23011717532984182.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 23011717532984182.atom to be opened. Openam> File opened: 23011717532984182.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 = 4455 First residue number = 13 Last residue number = 309 Number of atoms found = 68385 Mean number per residue = 15.4 Pdbmat> Coordinate statistics: = 15.902445 +/- 10.973133 From: -15.047000 To: 46.975000 = 20.599407 +/- 16.988874 From: -19.564000 To: 61.213000 = 23.116000 +/- 11.709327 From: -5.339000 To: 52.130000 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 ******** % Filled. Pdbmat> 521735242 non-zero elements. Pdbmat> 57934920 atom-atom interactions. Pdbmat> Number per atom= 1694.38 +/- 465.12 Maximum number = 2874 Minimum number = 144 Pdbmat> Matrix trace = 1.158698E+09 Pdbmat> Larger element = 11620.9 Pdbmat> 0 elements larger than +/- 1.0E+10 Pdbmat> Normal end. automatic determination of NRBL (NRBL = nresidues/200 + 1) 4455 non-zero elements, NRBL set to 23 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 = 23011717532984182.atom Eigenvector OUTPut file = matrix.eigenrtb Nb of VECTors required = 106 EigeNVALues chosen = LOWE Type of SUBStructuring = NONE Nb of residues per BLOck = 23 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 23011717532984182.atom to be opened. Openam> file on opening on unit 11: 23011717532984182.atom Blocpdb> Coordinate file in PDB format. Blocpdb> 68385 atoms picked in pdb file. Blocpdb> All masses set to unity. Blocpdb> Coordinate file is rewritten. Blocpdb> Substructuring: Blocpdb> 23 residue(s) per block. Blocpdb> 4455 residues. Blocpdb> 334 atoms in block 1 Block first atom: 1 Blocpdb> 346 atoms in block 2 Block first atom: 335 Blocpdb> 363 atoms in block 3 Block first atom: 681 Blocpdb> 365 atoms in block 4 Block first atom: 1044 Blocpdb> 323 atoms in block 5 Block first atom: 1409 Blocpdb> 350 atoms in block 6 Block first atom: 1732 Blocpdb> 363 atoms in block 7 Block first atom: 2082 Blocpdb> 340 atoms in block 8 Block first atom: 2445 Blocpdb> 372 atoms in block 9 Block first atom: 2785 Blocpdb> 335 atoms in block 10 Block first atom: 3157 Blocpdb> 336 atoms in block 11 Block first atom: 3492 Blocpdb> 387 atoms in block 12 Block first atom: 3828 Blocpdb> 345 atoms in block 13 Block first atom: 4215 Blocpdb> 334 atoms in block 14 Block first atom: 4560 Blocpdb> 346 atoms in block 15 Block first atom: 4894 Blocpdb> 363 atoms in block 16 Block first atom: 5240 Blocpdb> 365 atoms in block 17 Block first atom: 5603 Blocpdb> 323 atoms in block 18 Block first atom: 5968 Blocpdb> 350 atoms in block 19 Block first atom: 6291 Blocpdb> 363 atoms in block 20 Block first atom: 6641 Blocpdb> 340 atoms in block 21 Block first atom: 7004 Blocpdb> 372 atoms in block 22 Block first atom: 7344 Blocpdb> 335 atoms in block 23 Block first atom: 7716 Blocpdb> 336 atoms in block 24 Block first atom: 8051 Blocpdb> 387 atoms in block 25 Block first atom: 8387 Blocpdb> 345 atoms in block 26 Block first atom: 8774 Blocpdb> 334 atoms in block 27 Block first atom: 9119 Blocpdb> 346 atoms in block 28 Block first atom: 9453 Blocpdb> 363 atoms in block 29 Block first atom: 9799 Blocpdb> 365 atoms in block 30 Block first atom: 10162 Blocpdb> 323 atoms in block 31 Block first atom: 10527 Blocpdb> 350 atoms in block 32 Block first atom: 10850 Blocpdb> 363 atoms in block 33 Block first atom: 11200 Blocpdb> 340 atoms in block 34 Block first atom: 11563 Blocpdb> 372 atoms in block 35 Block first atom: 11903 Blocpdb> 335 atoms in block 36 Block first atom: 12275 Blocpdb> 336 atoms in block 37 Block first atom: 12610 Blocpdb> 387 atoms in block 38 Block first atom: 12946 Blocpdb> 345 atoms in block 39 Block first atom: 13333 Blocpdb> 334 atoms in block 40 Block first atom: 13678 Blocpdb> 346 atoms in block 41 Block first atom: 14012 Blocpdb> 363 atoms in block 42 Block first atom: 14358 Blocpdb> 365 atoms in block 43 Block first atom: 14721 Blocpdb> 323 atoms in block 44 Block first atom: 15086 Blocpdb> 350 atoms in block 45 Block first atom: 15409 Blocpdb> 363 atoms in block 46 Block first atom: 15759 Blocpdb> 340 atoms in block 47 Block first atom: 16122 Blocpdb> 372 atoms in block 48 Block first atom: 16462 Blocpdb> 335 atoms in block 49 Block first atom: 16834 Blocpdb> 336 atoms in block 50 Block first atom: 17169 Blocpdb> 387 atoms in block 51 Block first atom: 17505 Blocpdb> 345 atoms in block 52 Block first atom: 17892 Blocpdb> 334 atoms in block 53 Block first atom: 18237 Blocpdb> 346 atoms in block 54 Block first atom: 18571 Blocpdb> 363 atoms in block 55 Block first atom: 18917 Blocpdb> 365 atoms in block 56 Block first atom: 19280 Blocpdb> 323 atoms in block 57 Block first atom: 19645 Blocpdb> 350 atoms in block 58 Block first atom: 19968 Blocpdb> 363 atoms in block 59 Block first atom: 20318 Blocpdb> 340 atoms in block 60 Block first atom: 20681 Blocpdb> 372 atoms in block 61 Block first atom: 21021 Blocpdb> 335 atoms in block 62 Block first atom: 21393 Blocpdb> 336 atoms in block 63 Block first atom: 21728 Blocpdb> 387 atoms in block 64 Block first atom: 22064 Blocpdb> 345 atoms in block 65 Block first atom: 22451 Blocpdb> 334 atoms in block 66 Block first atom: 22796 Blocpdb> 346 atoms in block 67 Block first atom: 23130 Blocpdb> 363 atoms in block 68 Block first atom: 23476 Blocpdb> 365 atoms in block 69 Block first atom: 23839 Blocpdb> 323 atoms in block 70 Block first atom: 24204 Blocpdb> 350 atoms in block 71 Block first atom: 24527 Blocpdb> 363 atoms in block 72 Block first atom: 24877 Blocpdb> 340 atoms in block 73 Block first atom: 25240 Blocpdb> 372 atoms in block 74 Block first atom: 25580 Blocpdb> 335 atoms in block 75 Block first atom: 25952 Blocpdb> 336 atoms in block 76 Block first atom: 26287 Blocpdb> 387 atoms in block 77 Block first atom: 26623 Blocpdb> 345 atoms in block 78 Block first atom: 27010 Blocpdb> 334 atoms in block 79 Block first atom: 27355 Blocpdb> 346 atoms in block 80 Block first atom: 27689 Blocpdb> 363 atoms in block 81 Block first atom: 28035 Blocpdb> 365 atoms in block 82 Block first atom: 28398 Blocpdb> 323 atoms in block 83 Block first atom: 28763 Blocpdb> 350 atoms in block 84 Block first atom: 29086 Blocpdb> 363 atoms in block 85 Block first atom: 29436 Blocpdb> 340 atoms in block 86 Block first atom: 29799 Blocpdb> 372 atoms in block 87 Block first atom: 30139 Blocpdb> 335 atoms in block 88 Block first atom: 30511 Blocpdb> 336 atoms in block 89 Block first atom: 30846 Blocpdb> 387 atoms in block 90 Block first atom: 31182 Blocpdb> 345 atoms in block 91 Block first atom: 31569 Blocpdb> 334 atoms in block 92 Block first atom: 31914 Blocpdb> 346 atoms in block 93 Block first atom: 32248 Blocpdb> 363 atoms in block 94 Block first atom: 32594 Blocpdb> 365 atoms in block 95 Block first atom: 32957 Blocpdb> 323 atoms in block 96 Block first atom: 33322 Blocpdb> 350 atoms in block 97 Block first atom: 33645 Blocpdb> 363 atoms in block 98 Block first atom: 33995 Blocpdb> 340 atoms in block 99 Block first atom: 34358 Blocpdb> 372 atoms in block 100 Block first atom: 34698 Blocpdb> 335 atoms in block 101 Block first atom: 35070 Blocpdb> 336 atoms in block 102 Block first atom: 35405 Blocpdb> 387 atoms in block 103 Block first atom: 35741 Blocpdb> 345 atoms in block 104 Block first atom: 36128 Blocpdb> 334 atoms in block 105 Block first atom: 36473 Blocpdb> 346 atoms in block 106 Block first atom: 36807 Blocpdb> 363 atoms in block 107 Block first atom: 37153 Blocpdb> 365 atoms in block 108 Block first atom: 37516 Blocpdb> 323 atoms in block 109 Block first atom: 37881 Blocpdb> 350 atoms in block 110 Block first atom: 38204 Blocpdb> 363 atoms in block 111 Block first atom: 38554 Blocpdb> 340 atoms in block 112 Block first atom: 38917 Blocpdb> 372 atoms in block 113 Block first atom: 39257 Blocpdb> 335 atoms in block 114 Block first atom: 39629 Blocpdb> 336 atoms in block 115 Block first atom: 39964 Blocpdb> 387 atoms in block 116 Block first atom: 40300 Blocpdb> 345 atoms in block 117 Block first atom: 40687 Blocpdb> 334 atoms in block 118 Block first atom: 41032 Blocpdb> 346 atoms in block 119 Block first atom: 41366 Blocpdb> 363 atoms in block 120 Block first atom: 41712 Blocpdb> 365 atoms in block 121 Block first atom: 42075 Blocpdb> 323 atoms in block 122 Block first atom: 42440 Blocpdb> 350 atoms in block 123 Block first atom: 42763 Blocpdb> 363 atoms in block 124 Block first atom: 43113 Blocpdb> 340 atoms in block 125 Block first atom: 43476 Blocpdb> 372 atoms in block 126 Block first atom: 43816 Blocpdb> 335 atoms in block 127 Block first atom: 44188 Blocpdb> 336 atoms in block 128 Block first atom: 44523 Blocpdb> 387 atoms in block 129 Block first atom: 44859 Blocpdb> 345 atoms in block 130 Block first atom: 45246 Blocpdb> 334 atoms in block 131 Block first atom: 45591 Blocpdb> 346 atoms in block 132 Block first atom: 45925 Blocpdb> 363 atoms in block 133 Block first atom: 46271 Blocpdb> 365 atoms in block 134 Block first atom: 46634 Blocpdb> 323 atoms in block 135 Block first atom: 46999 Blocpdb> 350 atoms in block 136 Block first atom: 47322 Blocpdb> 363 atoms in block 137 Block first atom: 47672 Blocpdb> 340 atoms in block 138 Block first atom: 48035 Blocpdb> 372 atoms in block 139 Block first atom: 48375 Blocpdb> 335 atoms in block 140 Block first atom: 48747 Blocpdb> 336 atoms in block 141 Block first atom: 49082 Blocpdb> 387 atoms in block 142 Block first atom: 49418 Blocpdb> 345 atoms in block 143 Block first atom: 49805 Blocpdb> 334 atoms in block 144 Block first atom: 50150 Blocpdb> 346 atoms in block 145 Block first atom: 50484 Blocpdb> 363 atoms in block 146 Block first atom: 50830 Blocpdb> 365 atoms in block 147 Block first atom: 51193 Blocpdb> 323 atoms in block 148 Block first atom: 51558 Blocpdb> 350 atoms in block 149 Block first atom: 51881 Blocpdb> 363 atoms in block 150 Block first atom: 52231 Blocpdb> 340 atoms in block 151 Block first atom: 52594 Blocpdb> 372 atoms in block 152 Block first atom: 52934 Blocpdb> 335 atoms in block 153 Block first atom: 53306 Blocpdb> 336 atoms in block 154 Block first atom: 53641 Blocpdb> 387 atoms in block 155 Block first atom: 53977 Blocpdb> 345 atoms in block 156 Block first atom: 54364 Blocpdb> 334 atoms in block 157 Block first atom: 54709 Blocpdb> 346 atoms in block 158 Block first atom: 55043 Blocpdb> 363 atoms in block 159 Block first atom: 55389 Blocpdb> 365 atoms in block 160 Block first atom: 55752 Blocpdb> 323 atoms in block 161 Block first atom: 56117 Blocpdb> 350 atoms in block 162 Block first atom: 56440 Blocpdb> 363 atoms in block 163 Block first atom: 56790 Blocpdb> 340 atoms in block 164 Block first atom: 57153 Blocpdb> 372 atoms in block 165 Block first atom: 57493 Blocpdb> 335 atoms in block 166 Block first atom: 57865 Blocpdb> 336 atoms in block 167 Block first atom: 58200 Blocpdb> 387 atoms in block 168 Block first atom: 58536 Blocpdb> 345 atoms in block 169 Block first atom: 58923 Blocpdb> 334 atoms in block 170 Block first atom: 59268 Blocpdb> 346 atoms in block 171 Block first atom: 59602 Blocpdb> 363 atoms in block 172 Block first atom: 59948 Blocpdb> 365 atoms in block 173 Block first atom: 60311 Blocpdb> 323 atoms in block 174 Block first atom: 60676 Blocpdb> 350 atoms in block 175 Block first atom: 60999 Blocpdb> 363 atoms in block 176 Block first atom: 61349 Blocpdb> 340 atoms in block 177 Block first atom: 61712 Blocpdb> 372 atoms in block 178 Block first atom: 62052 Blocpdb> 335 atoms in block 179 Block first atom: 62424 Blocpdb> 336 atoms in block 180 Block first atom: 62759 Blocpdb> 387 atoms in block 181 Block first atom: 63095 Blocpdb> 345 atoms in block 182 Block first atom: 63482 Blocpdb> 334 atoms in block 183 Block first atom: 63827 Blocpdb> 346 atoms in block 184 Block first atom: 64161 Blocpdb> 363 atoms in block 185 Block first atom: 64507 Blocpdb> 365 atoms in block 186 Block first atom: 64870 Blocpdb> 323 atoms in block 187 Block first atom: 65235 Blocpdb> 350 atoms in block 188 Block first atom: 65558 Blocpdb> 363 atoms in block 189 Block first atom: 65908 Blocpdb> 340 atoms in block 190 Block first atom: 66271 Blocpdb> 372 atoms in block 191 Block first atom: 66611 Blocpdb> 335 atoms in block 192 Block first atom: 66983 Blocpdb> 336 atoms in block 193 Block first atom: 67318 Blocpdb> 387 atoms in block 194 Block first atom: 67654 Blocpdb> 345 atoms in block 195 Block first atom: 68040 Blocpdb> 195 blocks. Blocpdb> At most, 387 atoms in each of them. Blocpdb> At least, 323 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: 239532877 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 0m0.332s user 0m0.328s sys 0m0.000s




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Last modification: October 18th, 2018.