SimRNA (c) 2009-2024 Genesilico, ver. 3.33 .reading parameteres before entireStruct->initialize(input) file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/G-quadruplex-dde33e24/inputs/seq.fa first_line: R number of RNA chain(s) decalred/expected in file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/G-quadruplex-dde33e24/inputs/seq.fa: 1 curr_seq: _GGAGGAGGAGGA_ chainIds_rna: _A_, chainIds_protein: __ chainId: A, chainSeq: GGAGGAGGAGGA RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000 RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000 RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000 RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000 RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000 RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000 RNA chains: chain A contains 12 nucleotides loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE reweighting term eta_theta by 0.400000, default value scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000 eta-theta term was reweighted by factor 0.400000 provided by the user reading conformers file: ./data/rna/A_conformers n_lines: 4766 16 15 69 34 27 46 26 156 83 35 93 127 1269 89 50 187 157 1927 88 75 51 22 67 25 32 DONE reading conformers file: ./data/rna/C_conformers n_lines: 5164 7 8 61 17 4 14 12 143 49 12 23 140 2110 21 24 88 101 2101 19 36 25 21 108 8 12 DONE reading conformers file: ./data/rna/G_conformers n_lines: 6375 11 7 79 21 50 20 17 175 54 39 42 102 2774 90 34 61 94 2314 71 100 20 22 142 15 21 DONE reading conformers file: ./data/rna/U_conformers n_lines: 3617 6 6 43 33 24 20 20 131 50 28 30 58 1412 30 24 64 82 1197 31 32 71 36 132 13 44 DONE loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000 loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE scaling: histogram A_3_exvol.hist was multiplied by 0.100000 loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE scaling: histogram C_3_exvol.hist was multiplied by 0.100000 loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE scaling: histogram G_3_exvol.hist was multiplied by 0.100000 loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE scaling: histogram U_3_exvol.hist was multiplied by 0.100000 x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 65 n_atoms_counter: 65 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 RNAStructure::tertiaryStrcWeight = 1.000000 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2 : 2 , with interaction type: GA_SHt 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2 : 3 , with interaction type: GG_WHc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2 : 9 , with interaction type: GG_HWc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2 : 4 , with interaction type: GG_WHc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2 : 10 , with interaction type: GG_HWc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2 : 6 , with interaction type: GG_WHc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2 : 7 , with interaction type: GG_WHc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2 : 8 , with interaction type: GA_SHt 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2 : 9 , with interaction type: GG_WHc 3D structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2 : 10 , with interaction type: GG_WHc EntireStructure::rnaStruct limitingSphereRadius : 12.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) random seed = 1 number of iterations = 1600000 trajectory write in every 16000 iterations initTemp = 1.350 finalTemp = 0.900 tempStep = -2.812500e-07 DONE .calculating ===================================== Write number: 1 Temperature: 1.350000 Total energy: 2462.321270 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: 2462.321270 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -43.703332 (E_RNA) where: Base-Base interactions energy: -1.022 where: short stacking energy: -1.022 Base-Backbone interact. energy: -0.000 local terms energy: -42.680999 where: bonds (distance) C4'-P energy: -11.659 bonds (distance) P-C4' energy: -11.630 flat angles C4'-P-C4' energy: -8.811 flat angles P-C4'-P energy: -10.078 tors. eta vs tors. theta energy: -0.502 Dist. restrs. and SS energy: 2506.025 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 2 Temperature: 1.345500 Total energy: -14.482999 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -14.482999 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -53.186571 (E_RNA) where: Base-Base interactions energy: -25.642 where: short stacking energy: -10.657 Base-Backbone interact. energy: 0.379 local terms energy: -27.922949 where: bonds (distance) C4'-P energy: -6.890 bonds (distance) P-C4' energy: -10.165 flat angles C4'-P-C4' energy: -6.261 flat angles P-C4'-P energy: -1.901 tors. eta vs tors. theta energy: -2.706 Dist. restrs. and SS energy: 38.704 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 3 Temperature: 1.341000 Total energy: -44.464716 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -44.464716 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -55.023347 (E_RNA) where: Base-Base interactions energy: -29.595 where: short stacking energy: -19.867 Base-Backbone interact. energy: -0.032 local terms energy: -25.396254 where: bonds (distance) C4'-P energy: -9.387 bonds (distance) P-C4' energy: -8.411 flat angles C4'-P-C4' energy: -5.911 flat angles P-C4'-P energy: -1.543 tors. eta vs tors. theta energy: -0.144 Dist. restrs. and SS energy: 10.559 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 4 Temperature: 1.336500 Total energy: -56.293395 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -56.293395 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -65.334540 (E_RNA) where: Base-Base interactions energy: -32.558 where: short stacking energy: -19.943 Base-Backbone interact. energy: -0.328 local terms energy: -32.448039 where: bonds (distance) C4'-P energy: -9.644 bonds (distance) P-C4' energy: -11.099 flat angles C4'-P-C4' energy: -6.728 flat angles P-C4'-P energy: -1.768 tors. eta vs tors. theta energy: -3.209 Dist. restrs. and SS energy: 9.041 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 5 Temperature: 1.332000 Total energy: -48.888873 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -48.888873 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -58.396571 (E_RNA) where: Base-Base interactions energy: -30.881 where: short stacking energy: -18.849 Base-Backbone interact. energy: -0.002 local terms energy: -27.513675 where: bonds (distance) C4'-P energy: -7.336 bonds (distance) P-C4' energy: -8.840 flat angles C4'-P-C4' energy: -5.399 flat angles P-C4'-P energy: -5.195 tors. eta vs tors. theta energy: -0.743 Dist. restrs. and SS energy: 9.508 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 6 Temperature: 1.327500 Total energy: -50.420527 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -50.420527 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -56.769309 (E_RNA) where: Base-Base interactions energy: -29.509 where: short stacking energy: -17.083 Base-Backbone interact. energy: -0.001 local terms energy: -27.258905 where: bonds (distance) C4'-P energy: -9.196 bonds (distance) P-C4' energy: -9.950 flat angles C4'-P-C4' energy: -1.269 flat angles P-C4'-P energy: -5.351 tors. eta vs tors. theta energy: -1.493 Dist. restrs. and SS energy: 6.349 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 7 Temperature: 1.323000 Total energy: -51.764849 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -51.764849 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -65.320650 (E_RNA) where: Base-Base interactions energy: -32.946 where: short stacking energy: -21.961 Base-Backbone interact. energy: -0.002 local terms energy: -32.372263 where: bonds (distance) C4'-P energy: -8.676 bonds (distance) P-C4' energy: -10.320 flat angles C4'-P-C4' energy: -2.058 flat angles P-C4'-P energy: -6.199 tors. eta vs tors. theta energy: -5.119 Dist. restrs. and SS energy: 13.556 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 8 Temperature: 1.318500 Total energy: -53.499628 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -53.499628 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -64.097883 (E_RNA) where: Base-Base interactions energy: -39.002 where: short stacking energy: -22.609 Base-Backbone interact. energy: -0.000 local terms energy: -25.095327 where: bonds (distance) C4'-P energy: -5.085 bonds (distance) P-C4' energy: -8.411 flat angles C4'-P-C4' energy: -4.323 flat angles P-C4'-P energy: -3.000 tors. eta vs tors. theta energy: -4.276 Dist. restrs. and SS energy: 10.598 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 9 Temperature: 1.314000 Total energy: -48.856353 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -48.856353 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -57.438367 (E_RNA) where: Base-Base interactions energy: -32.214 where: short stacking energy: -20.666 Base-Backbone interact. energy: 0.217 local terms energy: -25.441339 where: bonds (distance) C4'-P energy: -6.455 bonds (distance) P-C4' energy: -8.217 flat angles C4'-P-C4' energy: -4.213 flat angles P-C4'-P energy: -2.272 tors. eta vs tors. theta energy: -4.283 Dist. restrs. and SS energy: 8.582 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 10 Temperature: 1.309500 Total energy: -51.774657 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -51.774657 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -60.795999 (E_RNA) where: Base-Base interactions energy: -31.720 where: short stacking energy: -18.890 Base-Backbone interact. energy: 0.757 local terms energy: -29.833060 where: bonds (distance) C4'-P energy: -6.473 bonds (distance) P-C4' energy: -9.932 flat angles C4'-P-C4' energy: -7.314 flat angles P-C4'-P energy: -3.489 tors. eta vs tors. theta energy: -2.626 Dist. restrs. and SS energy: 9.021 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 11 Temperature: 1.305000 Total energy: -63.421731 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.421731 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.341802 (E_RNA) where: Base-Base interactions energy: -40.394 where: short stacking energy: -25.473 Base-Backbone interact. energy: 1.095 local terms energy: -30.043086 where: bonds (distance) C4'-P energy: -8.910 bonds (distance) P-C4' energy: -6.245 flat angles C4'-P-C4' energy: -7.644 flat angles P-C4'-P energy: -2.997 tors. eta vs tors. theta energy: -4.246 Dist. restrs. and SS energy: 5.920 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 12 Temperature: 1.300500 Total energy: -54.906153 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -54.906153 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.149084 (E_RNA) where: Base-Base interactions energy: -38.614 where: short stacking energy: -23.332 Base-Backbone interact. energy: 0.703 local terms energy: -30.238137 where: bonds (distance) C4'-P energy: -8.401 bonds (distance) P-C4' energy: -8.531 flat angles C4'-P-C4' energy: -4.924 flat angles P-C4'-P energy: -3.323 tors. eta vs tors. theta energy: -5.059 Dist. restrs. and SS energy: 13.243 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 13 Temperature: 1.296000 Total energy: -63.083892 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.083892 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.907934 (E_RNA) where: Base-Base interactions energy: -36.593 where: short stacking energy: -20.762 Base-Backbone interact. energy: -0.002 local terms energy: -32.312692 where: bonds (distance) C4'-P energy: -9.697 bonds (distance) P-C4' energy: -9.144 flat angles C4'-P-C4' energy: -5.005 flat angles P-C4'-P energy: -0.719 tors. eta vs tors. theta energy: -7.747 Dist. restrs. and SS energy: 5.824 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 14 Temperature: 1.291500 Total energy: -55.827094 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -55.827094 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.322842 (E_RNA) where: Base-Base interactions energy: -38.529 where: short stacking energy: -23.002 Base-Backbone interact. energy: -0.194 local terms energy: -29.600330 where: bonds (distance) C4'-P energy: -5.677 bonds (distance) P-C4' energy: -8.094 flat angles C4'-P-C4' energy: -8.347 flat angles P-C4'-P energy: -4.613 tors. eta vs tors. theta energy: -2.869 Dist. restrs. and SS energy: 12.496 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 15 Temperature: 1.287000 Total energy: -56.980946 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -56.980946 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -71.264123 (E_RNA) where: Base-Base interactions energy: -40.434 where: short stacking energy: -22.577 Base-Backbone interact. energy: -0.003 local terms energy: -30.827647 where: bonds (distance) C4'-P energy: -7.267 bonds (distance) P-C4' energy: -9.905 flat angles C4'-P-C4' energy: -3.827 flat angles P-C4'-P energy: -3.032 tors. eta vs tors. theta energy: -6.796 Dist. restrs. and SS energy: 14.283 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 16 Temperature: 1.282500 Total energy: -59.470381 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -59.470381 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -67.314375 (E_RNA) where: Base-Base interactions energy: -35.058 where: short stacking energy: -23.330 Base-Backbone interact. energy: -0.017 local terms energy: -32.240318 where: bonds (distance) C4'-P energy: -7.051 bonds (distance) P-C4' energy: -5.269 flat angles C4'-P-C4' energy: -10.579 flat angles P-C4'-P energy: -3.551 tors. eta vs tors. theta energy: -5.790 Dist. restrs. and SS energy: 7.844 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 17 Temperature: 1.278000 Total energy: -62.920409 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -62.920409 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.756220 (E_RNA) where: Base-Base interactions energy: -38.719 where: short stacking energy: -23.869 Base-Backbone interact. energy: -0.004 local terms energy: -30.033030 where: bonds (distance) C4'-P energy: -4.046 bonds (distance) P-C4' energy: -9.067 flat angles C4'-P-C4' energy: -8.066 flat angles P-C4'-P energy: -4.751 tors. eta vs tors. theta energy: -4.103 Dist. restrs. and SS energy: 5.836 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 18 Temperature: 1.273500 Total energy: -54.616725 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -54.616725 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -60.588659 (E_RNA) where: Base-Base interactions energy: -28.424 where: short stacking energy: -20.514 Base-Backbone interact. energy: -0.005 local terms energy: -32.160405 where: bonds (distance) C4'-P energy: -8.216 bonds (distance) P-C4' energy: -7.610 flat angles C4'-P-C4' energy: -8.589 flat angles P-C4'-P energy: -4.874 tors. eta vs tors. theta energy: -2.873 Dist. restrs. and SS energy: 5.972 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 19 Temperature: 1.269000 Total energy: -58.071707 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.071707 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -64.771218 (E_RNA) where: Base-Base interactions energy: -35.235 where: short stacking energy: -23.311 Base-Backbone interact. energy: -0.004 local terms energy: -29.532701 where: bonds (distance) C4'-P energy: -6.269 bonds (distance) P-C4' energy: -7.099 flat angles C4'-P-C4' energy: -8.733 flat angles P-C4'-P energy: -2.753 tors. eta vs tors. theta energy: -4.677 Dist. restrs. and SS energy: 6.700 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 20 Temperature: 1.264500 Total energy: -58.328798 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.328798 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.024745 (E_RNA) where: Base-Base interactions energy: -37.013 where: short stacking energy: -25.948 Base-Backbone interact. energy: -0.002 local terms energy: -32.010035 where: bonds (distance) C4'-P energy: -6.745 bonds (distance) P-C4' energy: -5.954 flat angles C4'-P-C4' energy: -8.222 flat angles P-C4'-P energy: -6.329 tors. eta vs tors. theta energy: -4.760 Dist. restrs. and SS energy: 10.696 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 21 Temperature: 1.260000 Total energy: -53.694257 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -53.694257 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -63.126812 (E_RNA) where: Base-Base interactions energy: -40.119 where: short stacking energy: -25.718 Base-Backbone interact. energy: 0.520 local terms energy: -23.527508 where: bonds (distance) C4'-P energy: -8.144 bonds (distance) P-C4' energy: -2.649 flat angles C4'-P-C4' energy: -4.663 flat angles P-C4'-P energy: -2.689 tors. eta vs tors. theta energy: -5.382 Dist. restrs. and SS energy: 9.433 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 22 Temperature: 1.255500 Total energy: -61.838739 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.838739 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -70.492421 (E_RNA) where: Base-Base interactions energy: -40.199 where: short stacking energy: -27.170 Base-Backbone interact. energy: -0.003 local terms energy: -30.290313 where: bonds (distance) C4'-P energy: -8.286 bonds (distance) P-C4' energy: -7.230 flat angles C4'-P-C4' energy: -5.102 flat angles P-C4'-P energy: -3.124 tors. eta vs tors. theta energy: -6.548 Dist. restrs. and SS energy: 8.654 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 23 Temperature: 1.251000 Total energy: -59.678899 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -59.678899 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -67.950451 (E_RNA) where: Base-Base interactions energy: -39.734 where: short stacking energy: -27.466 Base-Backbone interact. energy: 1.810 local terms energy: -30.026664 where: bonds (distance) C4'-P energy: -6.084 bonds (distance) P-C4' energy: -5.991 flat angles C4'-P-C4' energy: -6.138 flat angles P-C4'-P energy: -5.372 tors. eta vs tors. theta energy: -6.442 Dist. restrs. and SS energy: 8.272 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 24 Temperature: 1.246500 Total energy: -49.718381 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -49.718381 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -58.132685 (E_RNA) where: Base-Base interactions energy: -32.296 where: short stacking energy: -21.228 Base-Backbone interact. energy: -0.009 local terms energy: -25.827770 where: bonds (distance) C4'-P energy: -2.440 bonds (distance) P-C4' energy: -8.886 flat angles C4'-P-C4' energy: -3.903 flat angles P-C4'-P energy: -0.879 tors. eta vs tors. theta energy: -9.720 Dist. restrs. and SS energy: 8.414 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 25 Temperature: 1.242000 Total energy: -53.481400 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -53.481400 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -67.968830 (E_RNA) where: Base-Base interactions energy: -33.061 where: short stacking energy: -23.753 Base-Backbone interact. energy: -0.012 local terms energy: -34.895737 where: bonds (distance) C4'-P energy: -10.153 bonds (distance) P-C4' energy: -7.273 flat angles C4'-P-C4' energy: -7.633 flat angles P-C4'-P energy: -4.549 tors. eta vs tors. theta energy: -5.289 Dist. restrs. and SS energy: 14.487 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 26 Temperature: 1.237500 Total energy: -53.686788 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -53.686788 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -59.516515 (E_RNA) where: Base-Base interactions energy: -28.190 where: short stacking energy: -18.981 Base-Backbone interact. energy: -0.012 local terms energy: -31.314980 where: bonds (distance) C4'-P energy: -7.226 bonds (distance) P-C4' energy: -8.389 flat angles C4'-P-C4' energy: -8.450 flat angles P-C4'-P energy: -3.070 tors. eta vs tors. theta energy: -4.180 Dist. restrs. and SS energy: 5.830 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 27 Temperature: 1.233000 Total energy: -62.229761 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -62.229761 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.007682 (E_RNA) where: Base-Base interactions energy: -34.382 where: short stacking energy: -20.457 Base-Backbone interact. energy: -0.006 local terms energy: -33.619889 where: bonds (distance) C4'-P energy: -9.821 bonds (distance) P-C4' energy: -10.419 flat angles C4'-P-C4' energy: -6.588 flat angles P-C4'-P energy: -2.300 tors. eta vs tors. theta energy: -4.491 Dist. restrs. and SS energy: 5.778 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 28 Temperature: 1.228500 Total energy: -58.468385 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.468385 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.176812 (E_RNA) where: Base-Base interactions energy: -32.950 where: short stacking energy: -22.056 Base-Backbone interact. energy: -0.009 local terms energy: -33.217926 where: bonds (distance) C4'-P energy: -7.333 bonds (distance) P-C4' energy: -8.675 flat angles C4'-P-C4' energy: -7.873 flat angles P-C4'-P energy: -2.908 tors. eta vs tors. theta energy: -6.428 Dist. restrs. and SS energy: 7.708 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 29 Temperature: 1.224000 Total energy: -57.316258 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -57.316258 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -63.717518 (E_RNA) where: Base-Base interactions energy: -32.326 where: short stacking energy: -20.638 Base-Backbone interact. energy: -0.007 local terms energy: -31.385016 where: bonds (distance) C4'-P energy: -7.684 bonds (distance) P-C4' energy: -10.423 flat angles C4'-P-C4' energy: -7.554 flat angles P-C4'-P energy: -4.781 tors. eta vs tors. theta energy: -0.944 Dist. restrs. and SS energy: 6.401 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 30 Temperature: 1.219500 Total energy: -57.892823 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -57.892823 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.110596 (E_RNA) where: Base-Base interactions energy: -35.281 where: short stacking energy: -25.978 Base-Backbone interact. energy: -0.033 local terms energy: -30.797161 where: bonds (distance) C4'-P energy: -5.860 bonds (distance) P-C4' energy: -9.144 flat angles C4'-P-C4' energy: -5.030 flat angles P-C4'-P energy: -5.731 tors. eta vs tors. theta energy: -5.032 Dist. restrs. and SS energy: 8.218 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 31 Temperature: 1.215000 Total energy: -58.225494 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.225494 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -64.709912 (E_RNA) where: Base-Base interactions energy: -35.458 where: short stacking energy: -23.668 Base-Backbone interact. energy: -0.008 local terms energy: -29.243636 where: bonds (distance) C4'-P energy: -3.603 bonds (distance) P-C4' energy: -7.959 flat angles C4'-P-C4' energy: -9.841 flat angles P-C4'-P energy: -3.824 tors. eta vs tors. theta energy: -4.017 Dist. restrs. and SS energy: 6.484 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 32 Temperature: 1.210500 Total energy: -51.853412 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -51.853412 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -63.348442 (E_RNA) where: Base-Base interactions energy: -29.725 where: short stacking energy: -17.019 Base-Backbone interact. energy: -0.002 local terms energy: -33.620863 where: bonds (distance) C4'-P energy: -7.113 bonds (distance) P-C4' energy: -10.398 flat angles C4'-P-C4' energy: -5.419 flat angles P-C4'-P energy: -2.356 tors. eta vs tors. theta energy: -8.336 Dist. restrs. and SS energy: 11.495 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 33 Temperature: 1.206000 Total energy: -52.936938 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -52.936938 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.298399 (E_RNA) where: Base-Base interactions energy: -32.633 where: short stacking energy: -23.528 Base-Backbone interact. energy: -0.006 local terms energy: -33.659610 where: bonds (distance) C4'-P energy: -7.660 bonds (distance) P-C4' energy: -10.060 flat angles C4'-P-C4' energy: -0.222 flat angles P-C4'-P energy: -5.260 tors. eta vs tors. theta energy: -10.458 Dist. restrs. and SS energy: 13.361 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 34 Temperature: 1.201500 Total energy: -61.371622 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.371622 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.751984 (E_RNA) where: Base-Base interactions energy: -32.998 where: short stacking energy: -23.837 Base-Backbone interact. energy: -0.077 local terms energy: -33.676716 where: bonds (distance) C4'-P energy: -6.095 bonds (distance) P-C4' energy: -8.098 flat angles C4'-P-C4' energy: -8.872 flat angles P-C4'-P energy: -5.157 tors. eta vs tors. theta energy: -5.455 Dist. restrs. and SS energy: 5.380 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 35 Temperature: 1.197000 Total energy: -57.550566 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -57.550566 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -64.571146 (E_RNA) where: Base-Base interactions energy: -32.175 where: short stacking energy: -19.898 Base-Backbone interact. energy: 0.164 local terms energy: -32.560038 where: bonds (distance) C4'-P energy: -6.547 bonds (distance) P-C4' energy: -10.398 flat angles C4'-P-C4' energy: -5.947 flat angles P-C4'-P energy: -5.638 tors. eta vs tors. theta energy: -4.030 Dist. restrs. and SS energy: 7.021 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 36 Temperature: 1.192500 Total energy: -58.178513 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.178513 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.161144 (E_RNA) where: Base-Base interactions energy: -30.718 where: short stacking energy: -22.026 Base-Backbone interact. energy: -0.074 local terms energy: -35.369437 where: bonds (distance) C4'-P energy: -9.014 bonds (distance) P-C4' energy: -10.122 flat angles C4'-P-C4' energy: -4.210 flat angles P-C4'-P energy: -6.556 tors. eta vs tors. theta energy: -5.468 Dist. restrs. and SS energy: 7.983 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 37 Temperature: 1.188000 Total energy: -55.378828 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -55.378828 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -63.983471 (E_RNA) where: Base-Base interactions energy: -30.493 where: short stacking energy: -20.393 Base-Backbone interact. energy: -0.005 local terms energy: -33.485927 where: bonds (distance) C4'-P energy: -8.231 bonds (distance) P-C4' energy: -9.865 flat angles C4'-P-C4' energy: -5.210 flat angles P-C4'-P energy: -6.556 tors. eta vs tors. theta energy: -3.624 Dist. restrs. and SS energy: 8.605 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 38 Temperature: 1.183500 Total energy: -69.215591 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.215591 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.154982 (E_RNA) where: Base-Base interactions energy: -40.053 where: short stacking energy: -23.895 Base-Backbone interact. energy: -0.026 local terms energy: -35.076728 where: bonds (distance) C4'-P energy: -7.035 bonds (distance) P-C4' energy: -10.582 flat angles C4'-P-C4' energy: -6.607 flat angles P-C4'-P energy: -5.921 tors. eta vs tors. theta energy: -4.932 Dist. restrs. and SS energy: 5.939 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 39 Temperature: 1.179000 Total energy: -59.403391 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -59.403391 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -65.362731 (E_RNA) where: Base-Base interactions energy: -34.400 where: short stacking energy: -17.108 Base-Backbone interact. energy: -0.013 local terms energy: -30.949919 where: bonds (distance) C4'-P energy: -6.633 bonds (distance) P-C4' energy: -10.144 flat angles C4'-P-C4' energy: -6.285 flat angles P-C4'-P energy: -3.519 tors. eta vs tors. theta energy: -4.369 Dist. restrs. and SS energy: 5.959 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 40 Temperature: 1.174500 Total energy: -62.946956 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -62.946956 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -70.381785 (E_RNA) where: Base-Base interactions energy: -37.724 where: short stacking energy: -26.000 Base-Backbone interact. energy: -0.002 local terms energy: -32.656556 where: bonds (distance) C4'-P energy: -8.029 bonds (distance) P-C4' energy: -5.662 flat angles C4'-P-C4' energy: -6.784 flat angles P-C4'-P energy: -5.043 tors. eta vs tors. theta energy: -7.139 Dist. restrs. and SS energy: 7.435 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 41 Temperature: 1.170000 Total energy: -60.658613 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -60.658613 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -70.266000 (E_RNA) where: Base-Base interactions energy: -36.238 where: short stacking energy: -26.807 Base-Backbone interact. energy: -0.009 local terms energy: -34.019773 where: bonds (distance) C4'-P energy: -5.880 bonds (distance) P-C4' energy: -10.162 flat angles C4'-P-C4' energy: -4.815 flat angles P-C4'-P energy: -4.639 tors. eta vs tors. theta energy: -8.525 Dist. restrs. and SS energy: 9.607 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 42 Temperature: 1.165500 Total energy: -58.360126 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.360126 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.609115 (E_RNA) where: Base-Base interactions energy: -36.022 where: short stacking energy: -26.609 Base-Backbone interact. energy: -0.005 local terms energy: -32.582050 where: bonds (distance) C4'-P energy: -7.772 bonds (distance) P-C4' energy: -8.107 flat angles C4'-P-C4' energy: -8.490 flat angles P-C4'-P energy: -2.158 tors. eta vs tors. theta energy: -6.055 Dist. restrs. and SS energy: 10.249 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 43 Temperature: 1.161000 Total energy: -59.817683 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -59.817683 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.081925 (E_RNA) where: Base-Base interactions energy: -34.687 where: short stacking energy: -22.870 Base-Backbone interact. energy: -0.024 local terms energy: -33.371160 where: bonds (distance) C4'-P energy: -7.084 bonds (distance) P-C4' energy: -6.291 flat angles C4'-P-C4' energy: -7.446 flat angles P-C4'-P energy: -6.702 tors. eta vs tors. theta energy: -5.848 Dist. restrs. and SS energy: 8.264 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 44 Temperature: 1.156500 Total energy: -63.718364 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.718364 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -74.403653 (E_RNA) where: Base-Base interactions energy: -37.504 where: short stacking energy: -22.434 Base-Backbone interact. energy: -0.015 local terms energy: -36.884178 where: bonds (distance) C4'-P energy: -9.494 bonds (distance) P-C4' energy: -9.566 flat angles C4'-P-C4' energy: -7.780 flat angles P-C4'-P energy: -5.092 tors. eta vs tors. theta energy: -4.952 Dist. restrs. and SS energy: 10.685 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 45 Temperature: 1.152000 Total energy: -61.711454 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.711454 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.535208 (E_RNA) where: Base-Base interactions energy: -29.960 where: short stacking energy: -17.461 Base-Backbone interact. energy: -0.017 local terms energy: -36.558894 where: bonds (distance) C4'-P energy: -8.500 bonds (distance) P-C4' energy: -9.803 flat angles C4'-P-C4' energy: -6.670 flat angles P-C4'-P energy: -7.914 tors. eta vs tors. theta energy: -3.673 Dist. restrs. and SS energy: 4.824 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 46 Temperature: 1.147500 Total energy: -66.726433 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -66.726433 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.609045 (E_RNA) where: Base-Base interactions energy: -38.535 where: short stacking energy: -24.362 Base-Backbone interact. energy: -0.004 local terms energy: -31.070041 where: bonds (distance) C4'-P energy: -3.588 bonds (distance) P-C4' energy: -9.041 flat angles C4'-P-C4' energy: -6.028 flat angles P-C4'-P energy: -6.032 tors. eta vs tors. theta energy: -6.381 Dist. restrs. and SS energy: 2.883 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 47 Temperature: 1.143000 Total energy: -57.492073 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -57.492073 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -67.554206 (E_RNA) where: Base-Base interactions energy: -36.746 where: short stacking energy: -26.622 Base-Backbone interact. energy: -0.521 local terms energy: -30.287438 where: bonds (distance) C4'-P energy: -1.529 bonds (distance) P-C4' energy: -8.389 flat angles C4'-P-C4' energy: -8.593 flat angles P-C4'-P energy: -5.201 tors. eta vs tors. theta energy: -6.576 Dist. restrs. and SS energy: 10.062 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 48 Temperature: 1.138500 Total energy: -58.323420 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -58.323420 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -62.964360 (E_RNA) where: Base-Base interactions energy: -36.173 where: short stacking energy: -23.673 Base-Backbone interact. energy: -0.330 local terms energy: -26.461240 where: bonds (distance) C4'-P energy: -8.137 bonds (distance) P-C4' energy: -6.876 flat angles C4'-P-C4' energy: -2.296 flat angles P-C4'-P energy: -5.305 tors. eta vs tors. theta energy: -3.848 Dist. restrs. and SS energy: 4.641 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 49 Temperature: 1.134000 Total energy: -68.622603 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.622603 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.698229 (E_RNA) where: Base-Base interactions energy: -40.917 where: short stacking energy: -23.642 Base-Backbone interact. energy: -0.423 local terms energy: -35.357815 where: bonds (distance) C4'-P energy: -9.875 bonds (distance) P-C4' energy: -9.982 flat angles C4'-P-C4' energy: -9.288 flat angles P-C4'-P energy: -3.235 tors. eta vs tors. theta energy: -2.978 Dist. restrs. and SS energy: 8.076 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 50 Temperature: 1.129500 Total energy: -60.621182 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -60.621182 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.437029 (E_RNA) where: Base-Base interactions energy: -31.156 where: short stacking energy: -18.485 Base-Backbone interact. energy: -0.231 local terms energy: -37.050518 where: bonds (distance) C4'-P energy: -9.937 bonds (distance) P-C4' energy: -9.506 flat angles C4'-P-C4' energy: -7.186 flat angles P-C4'-P energy: -5.875 tors. eta vs tors. theta energy: -4.547 Dist. restrs. and SS energy: 7.816 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 51 Temperature: 1.125000 Total energy: -64.538073 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -64.538073 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.738853 (E_RNA) where: Base-Base interactions energy: -35.890 where: short stacking energy: -20.136 Base-Backbone interact. energy: 0.304 local terms energy: -34.153041 where: bonds (distance) C4'-P energy: -8.144 bonds (distance) P-C4' energy: -8.668 flat angles C4'-P-C4' energy: -8.359 flat angles P-C4'-P energy: -5.242 tors. eta vs tors. theta energy: -3.740 Dist. restrs. and SS energy: 5.201 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 52 Temperature: 1.120500 Total energy: -64.848113 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -64.848113 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.435997 (E_RNA) where: Base-Base interactions energy: -39.996 where: short stacking energy: -23.509 Base-Backbone interact. energy: -0.006 local terms energy: -29.434242 where: bonds (distance) C4'-P energy: -8.003 bonds (distance) P-C4' energy: -9.067 flat angles C4'-P-C4' energy: -6.245 flat angles P-C4'-P energy: -1.835 tors. eta vs tors. theta energy: -4.284 Dist. restrs. and SS energy: 4.588 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 53 Temperature: 1.116000 Total energy: -61.024159 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.024159 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.564513 (E_RNA) where: Base-Base interactions energy: -36.109 where: short stacking energy: -23.001 Base-Backbone interact. energy: -0.098 local terms energy: -32.357506 where: bonds (distance) C4'-P energy: -6.551 bonds (distance) P-C4' energy: -9.116 flat angles C4'-P-C4' energy: -8.324 flat angles P-C4'-P energy: -5.061 tors. eta vs tors. theta energy: -3.306 Dist. restrs. and SS energy: 7.540 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 54 Temperature: 1.111500 Total energy: -70.419385 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.419385 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.562906 (E_RNA) where: Base-Base interactions energy: -38.434 where: short stacking energy: -23.184 Base-Backbone interact. energy: -0.029 local terms energy: -37.100024 where: bonds (distance) C4'-P energy: -8.632 bonds (distance) P-C4' energy: -9.975 flat angles C4'-P-C4' energy: -8.401 flat angles P-C4'-P energy: -5.490 tors. eta vs tors. theta energy: -4.602 Dist. restrs. and SS energy: 5.144 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 55 Temperature: 1.107000 Total energy: -63.473290 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.473290 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.335598 (E_RNA) where: Base-Base interactions energy: -37.587 where: short stacking energy: -24.634 Base-Backbone interact. energy: -0.700 local terms energy: -31.048526 where: bonds (distance) C4'-P energy: -8.632 bonds (distance) P-C4' energy: -5.631 flat angles C4'-P-C4' energy: -7.147 flat angles P-C4'-P energy: -4.892 tors. eta vs tors. theta energy: -4.746 Dist. restrs. and SS energy: 5.862 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 56 Temperature: 1.102500 Total energy: -63.282490 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.282490 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -69.944103 (E_RNA) where: Base-Base interactions energy: -41.942 where: short stacking energy: -22.028 Base-Backbone interact. energy: -0.025 local terms energy: -27.976795 where: bonds (distance) C4'-P energy: -4.375 bonds (distance) P-C4' energy: -9.432 flat angles C4'-P-C4' energy: -6.131 flat angles P-C4'-P energy: -2.887 tors. eta vs tors. theta energy: -5.152 Dist. restrs. and SS energy: 6.662 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 57 Temperature: 1.098000 Total energy: -63.958155 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.958155 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -70.413351 (E_RNA) where: Base-Base interactions energy: -35.623 where: short stacking energy: -26.452 Base-Backbone interact. energy: 0.758 local terms energy: -35.548787 where: bonds (distance) C4'-P energy: -8.501 bonds (distance) P-C4' energy: -10.084 flat angles C4'-P-C4' energy: -6.176 flat angles P-C4'-P energy: -6.651 tors. eta vs tors. theta energy: -4.136 Dist. restrs. and SS energy: 6.455 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 58 Temperature: 1.093500 Total energy: -61.448341 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.448341 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.195992 (E_RNA) where: Base-Base interactions energy: -37.922 where: short stacking energy: -22.095 Base-Backbone interact. energy: 0.277 local terms energy: -30.550380 where: bonds (distance) C4'-P energy: -8.782 bonds (distance) P-C4' energy: -8.632 flat angles C4'-P-C4' energy: -5.479 flat angles P-C4'-P energy: -4.626 tors. eta vs tors. theta energy: -3.031 Dist. restrs. and SS energy: 6.748 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 59 Temperature: 1.089000 Total energy: -61.529422 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -61.529422 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.602351 (E_RNA) where: Base-Base interactions energy: -36.864 where: short stacking energy: -23.706 Base-Backbone interact. energy: -0.036 local terms energy: -31.701970 where: bonds (distance) C4'-P energy: -8.969 bonds (distance) P-C4' energy: -6.982 flat angles C4'-P-C4' energy: -6.025 flat angles P-C4'-P energy: -4.924 tors. eta vs tors. theta energy: -4.802 Dist. restrs. and SS energy: 7.073 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 60 Temperature: 1.084500 Total energy: -68.120934 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.120934 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -73.781115 (E_RNA) where: Base-Base interactions energy: -39.307 where: short stacking energy: -24.609 Base-Backbone interact. energy: -0.006 local terms energy: -34.468635 where: bonds (distance) C4'-P energy: -7.543 bonds (distance) P-C4' energy: -7.032 flat angles C4'-P-C4' energy: -9.568 flat angles P-C4'-P energy: -3.648 tors. eta vs tors. theta energy: -6.677 Dist. restrs. and SS energy: 5.660 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 61 Temperature: 1.080000 Total energy: -65.056373 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -65.056373 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -70.128787 (E_RNA) where: Base-Base interactions energy: -37.096 where: short stacking energy: -24.236 Base-Backbone interact. energy: -0.006 local terms energy: -33.026875 where: bonds (distance) C4'-P energy: -7.800 bonds (distance) P-C4' energy: -9.453 flat angles C4'-P-C4' energy: -7.740 flat angles P-C4'-P energy: -2.895 tors. eta vs tors. theta energy: -5.138 Dist. restrs. and SS energy: 5.072 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 62 Temperature: 1.075500 Total energy: -69.638288 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.638288 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.988227 (E_RNA) where: Base-Base interactions energy: -38.147 where: short stacking energy: -25.615 Base-Backbone interact. energy: -0.053 local terms energy: -37.788036 where: bonds (distance) C4'-P energy: -8.547 bonds (distance) P-C4' energy: -9.239 flat angles C4'-P-C4' energy: -8.608 flat angles P-C4'-P energy: -4.264 tors. eta vs tors. theta energy: -7.131 Dist. restrs. and SS energy: 6.350 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 63 Temperature: 1.071000 Total energy: -69.350109 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.350109 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -74.483163 (E_RNA) where: Base-Base interactions energy: -37.160 where: short stacking energy: -23.829 Base-Backbone interact. energy: -0.013 local terms energy: -37.309904 where: bonds (distance) C4'-P energy: -10.347 bonds (distance) P-C4' energy: -8.609 flat angles C4'-P-C4' energy: -9.046 flat angles P-C4'-P energy: -5.217 tors. eta vs tors. theta energy: -4.090 Dist. restrs. and SS energy: 5.133 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 64 Temperature: 1.066500 Total energy: -69.123087 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.123087 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -73.012954 (E_RNA) where: Base-Base interactions energy: -43.415 where: short stacking energy: -23.354 Base-Backbone interact. energy: -0.181 local terms energy: -29.416320 where: bonds (distance) C4'-P energy: -6.390 bonds (distance) P-C4' energy: -9.147 flat angles C4'-P-C4' energy: -4.431 flat angles P-C4'-P energy: -3.742 tors. eta vs tors. theta energy: -5.706 Dist. restrs. and SS energy: 3.890 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 65 Temperature: 1.062000 Total energy: -70.814032 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.814032 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.968902 (E_RNA) where: Base-Base interactions energy: -39.100 where: short stacking energy: -25.543 Base-Backbone interact. energy: -0.222 local terms energy: -37.647008 where: bonds (distance) C4'-P energy: -9.668 bonds (distance) P-C4' energy: -10.423 flat angles C4'-P-C4' energy: -6.180 flat angles P-C4'-P energy: -5.566 tors. eta vs tors. theta energy: -5.810 Dist. restrs. and SS energy: 6.155 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 66 Temperature: 1.057500 Total energy: -68.222720 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.222720 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -77.382451 (E_RNA) where: Base-Base interactions energy: -39.818 where: short stacking energy: -21.888 Base-Backbone interact. energy: -0.002 local terms energy: -37.561935 where: bonds (distance) C4'-P energy: -8.551 bonds (distance) P-C4' energy: -10.867 flat angles C4'-P-C4' energy: -7.511 flat angles P-C4'-P energy: -5.142 tors. eta vs tors. theta energy: -5.492 Dist. restrs. and SS energy: 9.160 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 67 Temperature: 1.053000 Total energy: -67.000716 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -67.000716 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.990544 (E_RNA) where: Base-Base interactions energy: -46.398 where: short stacking energy: -25.206 Base-Backbone interact. energy: -0.259 local terms energy: -29.333821 where: bonds (distance) C4'-P energy: -1.986 bonds (distance) P-C4' energy: -9.545 flat angles C4'-P-C4' energy: -5.875 flat angles P-C4'-P energy: -5.715 tors. eta vs tors. theta energy: -6.213 Dist. restrs. and SS energy: 8.990 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 68 Temperature: 1.048500 Total energy: -60.302888 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -60.302888 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.715215 (E_RNA) where: Base-Base interactions energy: -37.015 where: short stacking energy: -26.881 Base-Backbone interact. energy: -0.015 local terms energy: -31.684817 where: bonds (distance) C4'-P energy: -7.111 bonds (distance) P-C4' energy: -6.433 flat angles C4'-P-C4' energy: -8.744 flat angles P-C4'-P energy: -2.492 tors. eta vs tors. theta energy: -6.905 Dist. restrs. and SS energy: 8.412 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 69 Temperature: 1.044000 Total energy: -65.683280 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -65.683280 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -71.575136 (E_RNA) where: Base-Base interactions energy: -35.933 where: short stacking energy: -21.187 Base-Backbone interact. energy: -0.489 local terms energy: -35.153337 where: bonds (distance) C4'-P energy: -10.169 bonds (distance) P-C4' energy: -10.659 flat angles C4'-P-C4' energy: -4.996 flat angles P-C4'-P energy: -5.651 tors. eta vs tors. theta energy: -3.679 Dist. restrs. and SS energy: 5.892 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 70 Temperature: 1.039500 Total energy: -72.498463 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -72.498463 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.129342 (E_RNA) where: Base-Base interactions energy: -40.254 where: short stacking energy: -21.469 Base-Backbone interact. energy: -0.012 local terms energy: -34.863085 where: bonds (distance) C4'-P energy: -8.376 bonds (distance) P-C4' energy: -10.101 flat angles C4'-P-C4' energy: -5.414 flat angles P-C4'-P energy: -6.112 tors. eta vs tors. theta energy: -4.860 Dist. restrs. and SS energy: 2.631 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 71 Temperature: 1.035000 Total energy: -63.180139 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.180139 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -67.218658 (E_RNA) where: Base-Base interactions energy: -35.965 where: short stacking energy: -21.864 Base-Backbone interact. energy: -0.023 local terms energy: -31.231042 where: bonds (distance) C4'-P energy: -8.099 bonds (distance) P-C4' energy: -9.143 flat angles C4'-P-C4' energy: -8.448 flat angles P-C4'-P energy: -3.027 tors. eta vs tors. theta energy: -2.515 Dist. restrs. and SS energy: 4.039 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 72 Temperature: 1.030500 Total energy: -63.599242 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -63.599242 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -66.627446 (E_RNA) where: Base-Base interactions energy: -40.494 where: short stacking energy: -23.892 Base-Backbone interact. energy: -0.004 local terms energy: -26.129783 where: bonds (distance) C4'-P energy: -4.883 bonds (distance) P-C4' energy: -8.512 flat angles C4'-P-C4' energy: -4.587 flat angles P-C4'-P energy: -4.080 tors. eta vs tors. theta energy: -4.068 Dist. restrs. and SS energy: 3.028 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 73 Temperature: 1.026000 Total energy: -73.058705 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.058705 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -85.230160 (E_RNA) where: Base-Base interactions energy: -45.775 where: short stacking energy: -29.019 Base-Backbone interact. energy: -0.003 local terms energy: -39.451950 where: bonds (distance) C4'-P energy: -7.635 bonds (distance) P-C4' energy: -10.419 flat angles C4'-P-C4' energy: -7.443 flat angles P-C4'-P energy: -5.731 tors. eta vs tors. theta energy: -8.223 Dist. restrs. and SS energy: 12.171 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 74 Temperature: 1.021500 Total energy: -66.351810 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -66.351810 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.834328 (E_RNA) where: Base-Base interactions energy: -39.046 where: short stacking energy: -22.830 Base-Backbone interact. energy: -0.012 local terms energy: -33.776381 where: bonds (distance) C4'-P energy: -9.381 bonds (distance) P-C4' energy: -9.147 flat angles C4'-P-C4' energy: -6.035 flat angles P-C4'-P energy: -4.396 tors. eta vs tors. theta energy: -4.817 Dist. restrs. and SS energy: 6.483 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 75 Temperature: 1.017000 Total energy: -68.007391 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.007391 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.895550 (E_RNA) where: Base-Base interactions energy: -38.866 where: short stacking energy: -24.307 Base-Backbone interact. energy: -0.005 local terms energy: -34.024728 where: bonds (distance) C4'-P energy: -8.103 bonds (distance) P-C4' energy: -9.821 flat angles C4'-P-C4' energy: -8.237 flat angles P-C4'-P energy: -4.227 tors. eta vs tors. theta energy: -3.638 Dist. restrs. and SS energy: 4.888 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 76 Temperature: 1.012500 Total energy: -66.701707 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -66.701707 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -74.895126 (E_RNA) where: Base-Base interactions energy: -36.875 where: short stacking energy: -24.398 Base-Backbone interact. energy: -0.016 local terms energy: -38.003465 where: bonds (distance) C4'-P energy: -8.339 bonds (distance) P-C4' energy: -9.699 flat angles C4'-P-C4' energy: -7.686 flat angles P-C4'-P energy: -6.980 tors. eta vs tors. theta energy: -5.300 Dist. restrs. and SS energy: 8.193 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 77 Temperature: 1.008000 Total energy: -70.171333 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.171333 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -73.142892 (E_RNA) where: Base-Base interactions energy: -38.471 where: short stacking energy: -23.433 Base-Backbone interact. energy: -0.011 local terms energy: -34.660383 where: bonds (distance) C4'-P energy: -7.258 bonds (distance) P-C4' energy: -6.982 flat angles C4'-P-C4' energy: -8.395 flat angles P-C4'-P energy: -6.027 tors. eta vs tors. theta energy: -5.998 Dist. restrs. and SS energy: 2.972 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 78 Temperature: 1.003500 Total energy: -70.715633 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.715633 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -77.572799 (E_RNA) where: Base-Base interactions energy: -38.868 where: short stacking energy: -24.655 Base-Backbone interact. energy: -0.007 local terms energy: -38.697463 where: bonds (distance) C4'-P energy: -8.890 bonds (distance) P-C4' energy: -10.358 flat angles C4'-P-C4' energy: -9.416 flat angles P-C4'-P energy: -4.102 tors. eta vs tors. theta energy: -5.932 Dist. restrs. and SS energy: 6.857 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 79 Temperature: 0.999000 Total energy: -73.532206 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.532206 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -79.866459 (E_RNA) where: Base-Base interactions energy: -40.665 where: short stacking energy: -24.589 Base-Backbone interact. energy: -0.533 local terms energy: -38.669054 where: bonds (distance) C4'-P energy: -8.712 bonds (distance) P-C4' energy: -11.360 flat angles C4'-P-C4' energy: -7.085 flat angles P-C4'-P energy: -6.050 tors. eta vs tors. theta energy: -5.462 Dist. restrs. and SS energy: 6.334 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 80 Temperature: 0.994500 Total energy: -68.935894 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.935894 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -71.982083 (E_RNA) where: Base-Base interactions energy: -35.519 where: short stacking energy: -21.751 Base-Backbone interact. energy: -0.043 local terms energy: -36.419507 where: bonds (distance) C4'-P energy: -9.373 bonds (distance) P-C4' energy: -9.895 flat angles C4'-P-C4' energy: -7.927 flat angles P-C4'-P energy: -4.711 tors. eta vs tors. theta energy: -4.513 Dist. restrs. and SS energy: 3.046 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 81 Temperature: 0.990000 Total energy: -71.848736 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -71.848736 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.975080 (E_RNA) where: Base-Base interactions energy: -42.778 where: short stacking energy: -23.821 Base-Backbone interact. energy: -0.144 local terms energy: -33.053875 where: bonds (distance) C4'-P energy: -6.220 bonds (distance) P-C4' energy: -10.094 flat angles C4'-P-C4' energy: -8.894 flat angles P-C4'-P energy: -4.257 tors. eta vs tors. theta energy: -3.589 Dist. restrs. and SS energy: 4.126 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 82 Temperature: 0.985500 Total energy: -69.624169 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.624169 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -74.981171 (E_RNA) where: Base-Base interactions energy: -39.794 where: short stacking energy: -26.047 Base-Backbone interact. energy: -0.012 local terms energy: -35.175339 where: bonds (distance) C4'-P energy: -5.258 bonds (distance) P-C4' energy: -8.668 flat angles C4'-P-C4' energy: -10.265 flat angles P-C4'-P energy: -6.596 tors. eta vs tors. theta energy: -4.388 Dist. restrs. and SS energy: 5.357 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 83 Temperature: 0.981000 Total energy: -68.973677 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.973677 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.077752 (E_RNA) where: Base-Base interactions energy: -39.383 where: short stacking energy: -23.684 Base-Backbone interact. energy: -0.029 local terms energy: -32.665631 where: bonds (distance) C4'-P energy: -8.091 bonds (distance) P-C4' energy: -8.504 flat angles C4'-P-C4' energy: -6.766 flat angles P-C4'-P energy: -5.548 tors. eta vs tors. theta energy: -3.756 Dist. restrs. and SS energy: 3.104 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 84 Temperature: 0.976500 Total energy: -70.064064 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.064064 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.583030 (E_RNA) where: Base-Base interactions energy: -42.919 where: short stacking energy: -24.164 Base-Backbone interact. energy: -0.010 local terms energy: -32.654187 where: bonds (distance) C4'-P energy: -7.362 bonds (distance) P-C4' energy: -11.367 flat angles C4'-P-C4' energy: -3.964 flat angles P-C4'-P energy: -4.958 tors. eta vs tors. theta energy: -5.003 Dist. restrs. and SS energy: 5.519 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 85 Temperature: 0.972000 Total energy: -72.606821 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -72.606821 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.439385 (E_RNA) where: Base-Base interactions energy: -40.165 where: short stacking energy: -23.965 Base-Backbone interact. energy: -0.007 local terms energy: -35.267105 where: bonds (distance) C4'-P energy: -8.099 bonds (distance) P-C4' energy: -9.724 flat angles C4'-P-C4' energy: -7.462 flat angles P-C4'-P energy: -6.349 tors. eta vs tors. theta energy: -3.634 Dist. restrs. and SS energy: 2.833 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 86 Temperature: 0.967500 Total energy: -64.554147 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -64.554147 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -68.649427 (E_RNA) where: Base-Base interactions energy: -37.243 where: short stacking energy: -19.678 Base-Backbone interact. energy: -0.421 local terms energy: -30.985957 where: bonds (distance) C4'-P energy: -8.898 bonds (distance) P-C4' energy: -8.830 flat angles C4'-P-C4' energy: -7.916 flat angles P-C4'-P energy: -4.032 tors. eta vs tors. theta energy: -1.311 Dist. restrs. and SS energy: 4.095 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 87 Temperature: 0.963000 Total energy: -65.246399 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -65.246399 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.441957 (E_RNA) where: Base-Base interactions energy: -37.404 where: short stacking energy: -21.492 Base-Backbone interact. energy: -0.008 local terms energy: -35.029988 where: bonds (distance) C4'-P energy: -8.430 bonds (distance) P-C4' energy: -11.099 flat angles C4'-P-C4' energy: -8.081 flat angles P-C4'-P energy: -5.208 tors. eta vs tors. theta energy: -2.211 Dist. restrs. and SS energy: 7.196 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 88 Temperature: 0.958500 Total energy: -66.391942 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -66.391942 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.859961 (E_RNA) where: Base-Base interactions energy: -39.232 where: short stacking energy: -25.259 Base-Backbone interact. energy: -0.007 local terms energy: -33.620342 where: bonds (distance) C4'-P energy: -9.751 bonds (distance) P-C4' energy: -7.583 flat angles C4'-P-C4' energy: -5.415 flat angles P-C4'-P energy: -5.728 tors. eta vs tors. theta energy: -5.143 Dist. restrs. and SS energy: 6.468 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 89 Temperature: 0.954000 Total energy: -70.796484 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.796484 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.202971 (E_RNA) where: Base-Base interactions energy: -40.454 where: short stacking energy: -24.328 Base-Backbone interact. energy: -0.629 local terms energy: -34.119952 where: bonds (distance) C4'-P energy: -5.773 bonds (distance) P-C4' energy: -9.531 flat angles C4'-P-C4' energy: -8.008 flat angles P-C4'-P energy: -5.310 tors. eta vs tors. theta energy: -5.497 Dist. restrs. and SS energy: 4.406 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 90 Temperature: 0.949500 Total energy: -68.048996 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -68.048996 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.009831 (E_RNA) where: Base-Base interactions energy: -38.241 where: short stacking energy: -24.745 Base-Backbone interact. energy: -0.013 local terms energy: -36.755157 where: bonds (distance) C4'-P energy: -9.999 bonds (distance) P-C4' energy: -10.155 flat angles C4'-P-C4' energy: -9.957 flat angles P-C4'-P energy: -3.344 tors. eta vs tors. theta energy: -3.299 Dist. restrs. and SS energy: 6.961 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 91 Temperature: 0.945000 Total energy: -70.442427 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.442427 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -75.528752 (E_RNA) where: Base-Base interactions energy: -43.297 where: short stacking energy: -24.809 Base-Backbone interact. energy: 0.150 local terms energy: -32.381409 where: bonds (distance) C4'-P energy: -8.588 bonds (distance) P-C4' energy: -9.796 flat angles C4'-P-C4' energy: -5.413 flat angles P-C4'-P energy: -6.018 tors. eta vs tors. theta energy: -2.566 Dist. restrs. and SS energy: 5.086 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 92 Temperature: 0.940500 Total energy: -73.306079 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.306079 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -80.091295 (E_RNA) where: Base-Base interactions energy: -40.597 where: short stacking energy: -23.922 Base-Backbone interact. energy: -0.008 local terms energy: -39.486586 where: bonds (distance) C4'-P energy: -10.206 bonds (distance) P-C4' energy: -10.197 flat angles C4'-P-C4' energy: -9.650 flat angles P-C4'-P energy: -5.446 tors. eta vs tors. theta energy: -3.987 Dist. restrs. and SS energy: 6.785 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 93 Temperature: 0.936000 Total energy: -69.882112 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.882112 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -73.731204 (E_RNA) where: Base-Base interactions energy: -37.173 where: short stacking energy: -24.987 Base-Backbone interact. energy: -0.004 local terms energy: -36.553979 where: bonds (distance) C4'-P energy: -6.439 bonds (distance) P-C4' energy: -10.444 flat angles C4'-P-C4' energy: -6.413 flat angles P-C4'-P energy: -7.982 tors. eta vs tors. theta energy: -5.276 Dist. restrs. and SS energy: 3.849 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 94 Temperature: 0.931500 Total energy: -70.656696 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -70.656696 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.631739 (E_RNA) where: Base-Base interactions energy: -38.868 where: short stacking energy: -23.959 Base-Backbone interact. energy: -0.005 local terms energy: -37.758461 where: bonds (distance) C4'-P energy: -10.115 bonds (distance) P-C4' energy: -11.607 flat angles C4'-P-C4' energy: -6.574 flat angles P-C4'-P energy: -4.763 tors. eta vs tors. theta energy: -4.701 Dist. restrs. and SS energy: 5.975 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 95 Temperature: 0.927000 Total energy: -69.966620 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.966620 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -72.365657 (E_RNA) where: Base-Base interactions energy: -40.647 where: short stacking energy: -22.177 Base-Backbone interact. energy: -0.004 local terms energy: -31.714406 where: bonds (distance) C4'-P energy: -9.635 bonds (distance) P-C4' energy: -9.954 flat angles C4'-P-C4' energy: -8.299 flat angles P-C4'-P energy: -0.421 tors. eta vs tors. theta energy: -3.405 Dist. restrs. and SS energy: 2.399 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 96 Temperature: 0.922500 Total energy: -69.582993 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -69.582993 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.794593 (E_RNA) where: Base-Base interactions energy: -38.189 where: short stacking energy: -24.128 Base-Backbone interact. energy: -0.032 local terms energy: -38.573079 where: bonds (distance) C4'-P energy: -8.531 bonds (distance) P-C4' energy: -11.106 flat angles C4'-P-C4' energy: -7.795 flat angles P-C4'-P energy: -5.053 tors. eta vs tors. theta energy: -6.088 Dist. restrs. and SS energy: 7.212 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 97 Temperature: 0.918000 Total energy: -73.677064 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.677064 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -79.710763 (E_RNA) where: Base-Base interactions energy: -40.795 where: short stacking energy: -28.446 Base-Backbone interact. energy: -0.046 local terms energy: -38.870442 where: bonds (distance) C4'-P energy: -9.539 bonds (distance) P-C4' energy: -8.858 flat angles C4'-P-C4' energy: -5.344 flat angles P-C4'-P energy: -7.025 tors. eta vs tors. theta energy: -8.104 Dist. restrs. and SS energy: 6.034 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 98 Temperature: 0.913500 Total energy: -75.081442 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -75.081442 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -78.646799 (E_RNA) where: Base-Base interactions energy: -48.487 where: short stacking energy: -24.186 Base-Backbone interact. energy: -0.132 local terms energy: -30.028060 where: bonds (distance) C4'-P energy: -8.351 bonds (distance) P-C4' energy: -7.318 flat angles C4'-P-C4' energy: -6.607 flat angles P-C4'-P energy: -1.330 tors. eta vs tors. theta energy: -6.422 Dist. restrs. and SS energy: 3.565 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 99 Temperature: 0.909000 Total energy: -73.224554 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.224554 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.427076 (E_RNA) where: Base-Base interactions energy: -42.797 where: short stacking energy: -21.309 Base-Backbone interact. energy: -0.003 local terms energy: -33.626533 where: bonds (distance) C4'-P energy: -9.097 bonds (distance) P-C4' energy: -8.021 flat angles C4'-P-C4' energy: -6.111 flat angles P-C4'-P energy: -4.638 tors. eta vs tors. theta energy: -5.760 Dist. restrs. and SS energy: 3.203 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 100 Temperature: 0.904500 Total energy: -73.705012 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.705012 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -78.909101 (E_RNA) where: Base-Base interactions energy: -42.684 where: short stacking energy: -25.246 Base-Backbone interact. energy: -0.010 local terms energy: -36.215578 where: bonds (distance) C4'-P energy: -9.283 bonds (distance) P-C4' energy: -10.419 flat angles C4'-P-C4' energy: -6.020 flat angles P-C4'-P energy: -5.536 tors. eta vs tors. theta energy: -4.958 Dist. restrs. and SS energy: 5.204 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ===================================== Write number: 101 Temperature: 0.900000 Total energy: -73.873823 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -73.873823 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -76.727258 (E_RNA) where: Base-Base interactions energy: -38.762 where: short stacking energy: -22.949 Base-Backbone interact. energy: -0.087 local terms energy: -37.879147 where: bonds (distance) C4'-P energy: -8.981 bonds (distance) P-C4' energy: -9.377 flat angles C4'-P-C4' energy: -7.413 flat angles P-C4'-P energy: -5.810 tors. eta vs tors. theta energy: -6.299 Dist. restrs. and SS energy: 2.853 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) .writing output current total energy: -53.629675 recalc. total energy: -53.629675 numberOfNucleotides: 12 initial temperature kT: 1.350000 moves confirmed at first: 895594 moves confirmed later: 1069265 all moves confirmed: 1964859 percent of confirmed moves: 1.228037 out arg RESULTS//1/G-quadruplex-dde33e24_01 nucl1: 0, chain1: A, <---> nucl2: 2, chain2: A type of interaction: GA_SHt nucl1: 0, chain1: A, <---> nucl2: 3, chain2: A type of interaction: GG_WHc nucl1: 0, chain1: A, <---> nucl2: 9, chain2: A type of interaction: GG_HWc nucl1: 1, chain1: A, <---> nucl2: 4, chain2: A type of interaction: GG_WHc nucl1: 1, chain1: A, <---> nucl2: 10, chain2: A type of interaction: GG_HWc nucl1: 3, chain1: A, <---> nucl2: 6, chain2: A type of interaction: GG_WHc nucl1: 4, chain1: A, <---> nucl2: 7, chain2: A type of interaction: GG_WHc nucl1: 6, chain1: A, <---> nucl2: 8, chain2: A type of interaction: GA_SHt nucl1: 6, chain1: A, <---> nucl2: 9, chain2: A type of interaction: GG_WHc nucl1: 7, chain1: A, <---> nucl2: 10, chain2: A type of interaction: GG_WHc Time of doing 1600000 iterations: 223.528 seconds