SimRNA (c) 2009-2024 Genesilico, ver. 3.33 PDB Replica Exchange Monte Carlo Method is SWITCHED ON 10 replicas were ordered .reading parameteres setting random seed = 1 initiating replica nr: 1 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.900 successfully initiated initiating replica nr: 2 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.950 successfully initiated initiating replica nr: 3 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.000 successfully initiated initiating replica nr: 4 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.050 successfully initiated initiating replica nr: 5 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.100 successfully initiated initiating replica nr: 6 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.150 successfully initiated initiating replica nr: 7 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.200 successfully initiated initiating replica nr: 8 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.250 successfully initiated initiating replica nr: 9 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.300 successfully initiated initiating replica nr: 10 before entireStruct->initialize(input) reading input pdb file: /home/simrnaweb/SimRNAWeb/SIMULATIONS/seq3-23573a1d/inputs/struct.pdb number of recognized chains: 1 chain 'A' contains: 253 residues chain 'A' is classfied as RNA number of RNA chain(s) to be parsed: 1 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 253 nucleotides atom position constraints swiched ON 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 DONE x_protein_frc: 0.000 x_rna_frc: 1.000 int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 1270 n_atoms_counter: 1270 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 EntireStructure::rnaStruct limitingSphereRadius : 253.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 80000 trajectory write in every 16000 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.350 successfully initiated .calculating program compiled for parallel execution of replicas in Replica Exchange MC method program can utilize maximum as many CPU cores as replicas, in this case: 10 ================================== temp. level: 1, replica: 1 ===================================== Write number: 1 Temperature: 0.900000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 2 ===================================== Write number: 1 Temperature: 0.950000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 1 Temperature: 1.000000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 4 ===================================== Write number: 1 Temperature: 1.050000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 5 ===================================== Write number: 1 Temperature: 1.100000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 6 ===================================== Write number: 1 Temperature: 1.150000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 7 ===================================== Write number: 1 Temperature: 1.200000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 8 ===================================== Write number: 1 Temperature: 1.250000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 1 Temperature: 1.300000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 1 Temperature: 1.350000 Total energy: -2971.406718 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.406718 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.406718 (E_RNA) where: Base-Base interactions energy: -1913.880 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.943 local terms energy: -1047.584286 where: bonds (distance) C4'-P energy: -213.933 bonds (distance) P-C4' energy: -220.375 flat angles C4'-P-C4' energy: -201.642 flat angles P-C4'-P energy: -160.864 tors. eta vs tors. theta energy: -250.771 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 1, replica: 1 ===================================== Write number: 2 Temperature: 0.900000 Total energy: -2974.643369 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2974.643369 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2974.643369 (E_RNA) where: Base-Base interactions energy: -1912.251 where: short stacking energy: -849.139 Base-Backbone interact. energy: -9.891 local terms energy: -1052.501160 where: bonds (distance) C4'-P energy: -216.015 bonds (distance) P-C4' energy: -220.605 flat angles C4'-P-C4' energy: -204.150 flat angles P-C4'-P energy: -160.564 tors. eta vs tors. theta energy: -251.167 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 2 ===================================== Write number: 2 Temperature: 0.950000 Total energy: -2976.367776 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2976.367776 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2976.367776 (E_RNA) where: Base-Base interactions energy: -1917.996 where: short stacking energy: -853.001 Base-Backbone interact. energy: -10.237 local terms energy: -1048.135435 where: bonds (distance) C4'-P energy: -213.751 bonds (distance) P-C4' energy: -218.913 flat angles C4'-P-C4' energy: -204.619 flat angles P-C4'-P energy: -159.182 tors. eta vs tors. theta energy: -251.670 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 2 Temperature: 1.000000 Total energy: -2980.017432 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2980.017432 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2980.017432 (E_RNA) where: Base-Base interactions energy: -1920.202 where: short stacking energy: -856.702 Base-Backbone interact. energy: -10.524 local terms energy: -1049.291642 where: bonds (distance) C4'-P energy: -214.371 bonds (distance) P-C4' energy: -219.198 flat angles C4'-P-C4' energy: -204.114 flat angles P-C4'-P energy: -160.191 tors. eta vs tors. theta energy: -251.417 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 4 ===================================== Write number: 2 Temperature: 1.050000 Total energy: -2975.630107 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2975.630107 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2975.630107 (E_RNA) where: Base-Base interactions energy: -1918.229 where: short stacking energy: -859.827 Base-Backbone interact. energy: -11.070 local terms energy: -1046.330758 where: bonds (distance) C4'-P energy: -212.711 bonds (distance) P-C4' energy: -217.238 flat angles C4'-P-C4' energy: -206.248 flat angles P-C4'-P energy: -158.356 tors. eta vs tors. theta energy: -251.777 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 5 ===================================== Write number: 2 Temperature: 1.100000 Total energy: -2972.451599 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2972.451599 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2972.451599 (E_RNA) where: Base-Base interactions energy: -1915.790 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.483 local terms energy: -1047.178163 where: bonds (distance) C4'-P energy: -214.193 bonds (distance) P-C4' energy: -218.747 flat angles C4'-P-C4' energy: -202.875 flat angles P-C4'-P energy: -160.811 tors. eta vs tors. theta energy: -250.552 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 6 ===================================== Write number: 2 Temperature: 1.150000 Total energy: -2973.438959 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2973.438959 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2973.438959 (E_RNA) where: Base-Base interactions energy: -1912.621 where: short stacking energy: -852.923 Base-Backbone interact. energy: -10.296 local terms energy: -1050.522090 where: bonds (distance) C4'-P energy: -214.496 bonds (distance) P-C4' energy: -218.765 flat angles C4'-P-C4' energy: -206.724 flat angles P-C4'-P energy: -159.109 tors. eta vs tors. theta energy: -251.429 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 7 ===================================== Write number: 2 Temperature: 1.200000 Total energy: -2972.409668 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2972.409668 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2972.409668 (E_RNA) where: Base-Base interactions energy: -1913.784 where: short stacking energy: -850.941 Base-Backbone interact. energy: -9.327 local terms energy: -1049.298485 where: bonds (distance) C4'-P energy: -214.297 bonds (distance) P-C4' energy: -219.670 flat angles C4'-P-C4' energy: -204.197 flat angles P-C4'-P energy: -159.894 tors. eta vs tors. theta energy: -251.240 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 8 ===================================== Write number: 2 Temperature: 1.250000 Total energy: -2971.193250 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2971.193250 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2971.193250 (E_RNA) where: Base-Base interactions energy: -1915.605 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.250 local terms energy: -1046.338375 where: bonds (distance) C4'-P energy: -213.460 bonds (distance) P-C4' energy: -218.747 flat angles C4'-P-C4' energy: -202.875 flat angles P-C4'-P energy: -160.726 tors. eta vs tors. theta energy: -250.530 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 2 Temperature: 1.300000 Total energy: -2973.682716 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2973.682716 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2973.682716 (E_RNA) where: Base-Base interactions energy: -1915.599 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.938 local terms energy: -1048.145668 where: bonds (distance) C4'-P energy: -215.398 bonds (distance) P-C4' energy: -219.005 flat angles C4'-P-C4' energy: -202.526 flat angles P-C4'-P energy: -160.707 tors. eta vs tors. theta energy: -250.509 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 2 Temperature: 1.350000 Total energy: -2973.819855 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2973.819855 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2973.819855 (E_RNA) where: Base-Base interactions energy: -1915.598 where: short stacking energy: -853.076 Base-Backbone interact. energy: -9.938 local terms energy: -1048.283937 where: bonds (distance) C4'-P energy: -215.398 bonds (distance) P-C4' energy: -219.005 flat angles C4'-P-C4' energy: -202.526 flat angles P-C4'-P energy: -160.845 tors. eta vs tors. theta energy: -250.509 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 1, replica: 1 ===================================== Write number: 3 Temperature: 0.900000 Total energy: -2821.215389 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2821.215389 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2821.215389 (E_RNA) where: Base-Base interactions energy: -1984.167 where: short stacking energy: -839.753 Base-Backbone interact. energy: -5.459 local terms energy: -831.589868 where: bonds (distance) C4'-P energy: -144.800 bonds (distance) P-C4' energy: -164.536 flat angles C4'-P-C4' energy: -173.809 flat angles P-C4'-P energy: -118.679 tors. eta vs tors. theta energy: -229.765 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 2 ===================================== Write number: 3 Temperature: 0.950000 Total energy: -2767.997823 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2767.997823 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2767.997823 (E_RNA) where: Base-Base interactions energy: -1919.188 where: short stacking energy: -791.915 Base-Backbone interact. energy: -6.595 local terms energy: -842.214580 where: bonds (distance) C4'-P energy: -147.912 bonds (distance) P-C4' energy: -167.015 flat angles C4'-P-C4' energy: -164.989 flat angles P-C4'-P energy: -129.696 tors. eta vs tors. theta energy: -232.604 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 3 Temperature: 1.000000 Total energy: -2734.785395 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2734.785395 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2734.785395 (E_RNA) where: Base-Base interactions energy: -1889.573 where: short stacking energy: -806.226 Base-Backbone interact. energy: -6.131 local terms energy: -839.081400 where: bonds (distance) C4'-P energy: -140.701 bonds (distance) P-C4' energy: -151.484 flat angles C4'-P-C4' energy: -176.689 flat angles P-C4'-P energy: -112.764 tors. eta vs tors. theta energy: -257.443 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 5 ===================================== Write number: 3 Temperature: 1.050000 Total energy: -2618.814546 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2618.814546 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2618.814546 (E_RNA) where: Base-Base interactions energy: -1805.451 where: short stacking energy: -785.019 Base-Backbone interact. energy: -4.223 local terms energy: -809.140208 where: bonds (distance) C4'-P energy: -156.744 bonds (distance) P-C4' energy: -121.815 flat angles C4'-P-C4' energy: -173.002 flat angles P-C4'-P energy: -115.744 tors. eta vs tors. theta energy: -241.835 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 4 ===================================== Write number: 3 Temperature: 1.100000 Total energy: -2506.489619 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2506.489619 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2506.489619 (E_RNA) where: Base-Base interactions energy: -1741.575 where: short stacking energy: -753.516 Base-Backbone interact. energy: -5.696 local terms energy: -759.218945 where: bonds (distance) C4'-P energy: -111.669 bonds (distance) P-C4' energy: -152.073 flat angles C4'-P-C4' energy: -155.084 flat angles P-C4'-P energy: -110.714 tors. eta vs tors. theta energy: -229.680 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 7 ===================================== Write number: 3 Temperature: 1.150000 Total energy: -2387.603695 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2387.603695 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2387.603695 (E_RNA) where: Base-Base interactions energy: -1668.367 where: short stacking energy: -718.527 Base-Backbone interact. energy: 0.168 local terms energy: -719.404533 where: bonds (distance) C4'-P energy: -134.003 bonds (distance) P-C4' energy: -124.846 flat angles C4'-P-C4' energy: -161.720 flat angles P-C4'-P energy: -95.506 tors. eta vs tors. theta energy: -203.330 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 6 ===================================== Write number: 3 Temperature: 1.200000 Total energy: -2357.758027 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2357.758027 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2357.758027 (E_RNA) where: Base-Base interactions energy: -1667.763 where: short stacking energy: -667.817 Base-Backbone interact. energy: -4.054 local terms energy: -685.941562 where: bonds (distance) C4'-P energy: -116.284 bonds (distance) P-C4' energy: -135.847 flat angles C4'-P-C4' energy: -147.425 flat angles P-C4'-P energy: -80.127 tors. eta vs tors. theta energy: -206.259 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 8 ===================================== Write number: 3 Temperature: 1.250000 Total energy: -2254.309303 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2254.309303 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2254.309303 (E_RNA) where: Base-Base interactions energy: -1563.409 where: short stacking energy: -667.246 Base-Backbone interact. energy: -6.382 local terms energy: -684.518393 where: bonds (distance) C4'-P energy: -115.442 bonds (distance) P-C4' energy: -125.387 flat angles C4'-P-C4' energy: -168.438 flat angles P-C4'-P energy: -91.355 tors. eta vs tors. theta energy: -183.897 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 3 Temperature: 1.300000 Total energy: -2104.890758 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2104.890758 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2104.890758 (E_RNA) where: Base-Base interactions energy: -1478.268 where: short stacking energy: -609.203 Base-Backbone interact. energy: -0.375 local terms energy: -626.247636 where: bonds (distance) C4'-P energy: -101.581 bonds (distance) P-C4' energy: -137.928 flat angles C4'-P-C4' energy: -133.299 flat angles P-C4'-P energy: -96.054 tors. eta vs tors. theta energy: -157.385 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 3 Temperature: 1.350000 Total energy: -1972.674351 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1972.674351 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1972.674351 (E_RNA) where: Base-Base interactions energy: -1355.677 where: short stacking energy: -579.604 Base-Backbone interact. energy: -5.012 local terms energy: -611.985337 where: bonds (distance) C4'-P energy: -117.545 bonds (distance) P-C4' energy: -115.036 flat angles C4'-P-C4' energy: -149.290 flat angles P-C4'-P energy: -73.972 tors. eta vs tors. theta energy: -156.143 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 1, replica: 1 ===================================== Write number: 4 Temperature: 0.900000 Total energy: -2828.197623 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2828.197623 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2828.197623 (E_RNA) where: Base-Base interactions energy: -1967.773 where: short stacking energy: -841.927 Base-Backbone interact. energy: -1.426 local terms energy: -858.998021 where: bonds (distance) C4'-P energy: -141.882 bonds (distance) P-C4' energy: -144.016 flat angles C4'-P-C4' energy: -190.729 flat angles P-C4'-P energy: -126.055 tors. eta vs tors. theta energy: -256.316 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 2 ===================================== Write number: 4 Temperature: 0.950000 Total energy: -2761.152222 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2761.152222 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2761.152222 (E_RNA) where: Base-Base interactions energy: -1904.528 where: short stacking energy: -789.841 Base-Backbone interact. energy: -4.168 local terms energy: -852.455730 where: bonds (distance) C4'-P energy: -141.589 bonds (distance) P-C4' energy: -160.610 flat angles C4'-P-C4' energy: -183.864 flat angles P-C4'-P energy: -123.320 tors. eta vs tors. theta energy: -243.072 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 4 Temperature: 1.000000 Total energy: -2712.094129 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2712.094129 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2712.094129 (E_RNA) where: Base-Base interactions energy: -1883.927 where: short stacking energy: -816.416 Base-Backbone interact. energy: -5.954 local terms energy: -822.213638 where: bonds (distance) C4'-P energy: -132.924 bonds (distance) P-C4' energy: -147.097 flat angles C4'-P-C4' energy: -178.391 flat angles P-C4'-P energy: -115.516 tors. eta vs tors. theta energy: -248.286 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 5 ===================================== Write number: 4 Temperature: 1.050000 Total energy: -2659.307488 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2659.307488 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2659.307488 (E_RNA) where: Base-Base interactions energy: -1846.274 where: short stacking energy: -778.028 Base-Backbone interact. energy: -4.108 local terms energy: -808.926102 where: bonds (distance) C4'-P energy: -133.370 bonds (distance) P-C4' energy: -161.156 flat angles C4'-P-C4' energy: -166.052 flat angles P-C4'-P energy: -107.320 tors. eta vs tors. theta energy: -241.029 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 4 ===================================== Write number: 4 Temperature: 1.100000 Total energy: -2449.731384 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2449.731384 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2449.731384 (E_RNA) where: Base-Base interactions energy: -1686.860 where: short stacking energy: -753.000 Base-Backbone interact. energy: -1.546 local terms energy: -761.325830 where: bonds (distance) C4'-P energy: -143.331 bonds (distance) P-C4' energy: -139.102 flat angles C4'-P-C4' energy: -165.844 flat angles P-C4'-P energy: -108.263 tors. eta vs tors. theta energy: -204.785 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 7 ===================================== Write number: 4 Temperature: 1.150000 Total energy: -2360.681037 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2360.681037 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2360.681037 (E_RNA) where: Base-Base interactions energy: -1648.920 where: short stacking energy: -710.654 Base-Backbone interact. energy: -1.713 local terms energy: -710.047416 where: bonds (distance) C4'-P energy: -141.265 bonds (distance) P-C4' energy: -140.488 flat angles C4'-P-C4' energy: -144.355 flat angles P-C4'-P energy: -89.883 tors. eta vs tors. theta energy: -194.056 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 6 ===================================== Write number: 4 Temperature: 1.200000 Total energy: -2400.081450 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2400.081450 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2400.081450 (E_RNA) where: Base-Base interactions energy: -1696.778 where: short stacking energy: -712.770 Base-Backbone interact. energy: -3.150 local terms energy: -700.154146 where: bonds (distance) C4'-P energy: -112.534 bonds (distance) P-C4' energy: -114.769 flat angles C4'-P-C4' energy: -150.007 flat angles P-C4'-P energy: -103.097 tors. eta vs tors. theta energy: -219.747 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 8 ===================================== Write number: 4 Temperature: 1.250000 Total energy: -2200.396837 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2200.396837 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2200.396837 (E_RNA) where: Base-Base interactions energy: -1497.511 where: short stacking energy: -635.721 Base-Backbone interact. energy: -0.786 local terms energy: -702.099987 where: bonds (distance) C4'-P energy: -108.888 bonds (distance) P-C4' energy: -156.627 flat angles C4'-P-C4' energy: -161.095 flat angles P-C4'-P energy: -89.759 tors. eta vs tors. theta energy: -185.732 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 4 Temperature: 1.300000 Total energy: -2023.471018 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2023.471018 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2023.471018 (E_RNA) where: Base-Base interactions energy: -1393.040 where: short stacking energy: -595.839 Base-Backbone interact. energy: 5.873 local terms energy: -636.303905 where: bonds (distance) C4'-P energy: -117.529 bonds (distance) P-C4' energy: -137.841 flat angles C4'-P-C4' energy: -147.317 flat angles P-C4'-P energy: -87.728 tors. eta vs tors. theta energy: -145.889 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 4 Temperature: 1.350000 Total energy: -1957.974029 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1957.974029 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1957.974029 (E_RNA) where: Base-Base interactions energy: -1370.537 where: short stacking energy: -580.945 Base-Backbone interact. energy: -3.024 local terms energy: -584.412782 where: bonds (distance) C4'-P energy: -117.789 bonds (distance) P-C4' energy: -113.786 flat angles C4'-P-C4' energy: -125.273 flat angles P-C4'-P energy: -83.029 tors. eta vs tors. theta energy: -144.536 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 1, replica: 1 ===================================== Write number: 5 Temperature: 0.900000 Total energy: -2836.720308 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2836.720308 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2836.720308 (E_RNA) where: Base-Base interactions energy: -1961.031 where: short stacking energy: -854.301 Base-Backbone interact. energy: -5.243 local terms energy: -870.445606 where: bonds (distance) C4'-P energy: -157.136 bonds (distance) P-C4' energy: -159.472 flat angles C4'-P-C4' energy: -170.315 flat angles P-C4'-P energy: -137.529 tors. eta vs tors. theta energy: -245.994 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 2 ===================================== Write number: 5 Temperature: 0.950000 Total energy: -2780.122390 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2780.122390 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2780.122390 (E_RNA) where: Base-Base interactions energy: -1935.014 where: short stacking energy: -824.091 Base-Backbone interact. energy: -2.193 local terms energy: -842.915718 where: bonds (distance) C4'-P energy: -156.970 bonds (distance) P-C4' energy: -164.775 flat angles C4'-P-C4' energy: -169.497 flat angles P-C4'-P energy: -109.698 tors. eta vs tors. theta energy: -241.976 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 5 Temperature: 1.000000 Total energy: -2673.729101 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2673.729101 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2673.729101 (E_RNA) where: Base-Base interactions energy: -1847.795 where: short stacking energy: -824.211 Base-Backbone interact. energy: -4.614 local terms energy: -821.320169 where: bonds (distance) C4'-P energy: -141.826 bonds (distance) P-C4' energy: -160.451 flat angles C4'-P-C4' energy: -183.488 flat angles P-C4'-P energy: -109.005 tors. eta vs tors. theta energy: -226.550 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 5 ===================================== Write number: 5 Temperature: 1.050000 Total energy: -2630.904000 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2630.904000 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2630.904000 (E_RNA) where: Base-Base interactions energy: -1807.226 where: short stacking energy: -792.372 Base-Backbone interact. energy: -1.937 local terms energy: -821.741120 where: bonds (distance) C4'-P energy: -137.931 bonds (distance) P-C4' energy: -149.331 flat angles C4'-P-C4' energy: -185.309 flat angles P-C4'-P energy: -106.150 tors. eta vs tors. theta energy: -243.020 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 4 ===================================== Write number: 5 Temperature: 1.100000 Total energy: -2489.300836 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2489.300836 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2489.300836 (E_RNA) where: Base-Base interactions energy: -1730.280 where: short stacking energy: -719.998 Base-Backbone interact. energy: -2.330 local terms energy: -756.691440 where: bonds (distance) C4'-P energy: -118.337 bonds (distance) P-C4' energy: -128.339 flat angles C4'-P-C4' energy: -176.722 flat angles P-C4'-P energy: -113.405 tors. eta vs tors. theta energy: -219.889 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 7 ===================================== Write number: 5 Temperature: 1.150000 Total energy: -2423.294544 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2423.294544 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2423.294544 (E_RNA) where: Base-Base interactions energy: -1653.959 where: short stacking energy: -721.578 Base-Backbone interact. energy: -1.737 local terms energy: -767.598649 where: bonds (distance) C4'-P energy: -148.256 bonds (distance) P-C4' energy: -147.691 flat angles C4'-P-C4' energy: -154.308 flat angles P-C4'-P energy: -96.948 tors. eta vs tors. theta energy: -220.396 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 6 ===================================== Write number: 5 Temperature: 1.200000 Total energy: -2416.495680 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2416.495680 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2416.495680 (E_RNA) where: Base-Base interactions energy: -1666.432 where: short stacking energy: -706.810 Base-Backbone interact. energy: -1.216 local terms energy: -748.847353 where: bonds (distance) C4'-P energy: -135.029 bonds (distance) P-C4' energy: -143.796 flat angles C4'-P-C4' energy: -150.790 flat angles P-C4'-P energy: -90.985 tors. eta vs tors. theta energy: -228.248 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 8 ===================================== Write number: 5 Temperature: 1.250000 Total energy: -2180.197792 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2180.197792 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2180.197792 (E_RNA) where: Base-Base interactions energy: -1522.541 where: short stacking energy: -646.793 Base-Backbone interact. energy: 10.097 local terms energy: -667.753504 where: bonds (distance) C4'-P energy: -122.463 bonds (distance) P-C4' energy: -135.115 flat angles C4'-P-C4' energy: -147.211 flat angles P-C4'-P energy: -83.889 tors. eta vs tors. theta energy: -179.075 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 5 Temperature: 1.300000 Total energy: -1899.641960 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1899.641960 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1899.641960 (E_RNA) where: Base-Base interactions energy: -1280.633 where: short stacking energy: -562.674 Base-Backbone interact. energy: 3.092 local terms energy: -622.100966 where: bonds (distance) C4'-P energy: -126.785 bonds (distance) P-C4' energy: -143.305 flat angles C4'-P-C4' energy: -134.665 flat angles P-C4'-P energy: -63.159 tors. eta vs tors. theta energy: -154.187 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 5 Temperature: 1.350000 Total energy: -1943.871017 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1943.871017 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1943.871017 (E_RNA) where: Base-Base interactions energy: -1314.368 where: short stacking energy: -580.201 Base-Backbone interact. energy: -3.027 local terms energy: -626.475829 where: bonds (distance) C4'-P energy: -118.013 bonds (distance) P-C4' energy: -118.455 flat angles C4'-P-C4' energy: -129.121 flat angles P-C4'-P energy: -90.135 tors. eta vs tors. theta energy: -170.753 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 1, replica: 2 ===================================== Write number: 6 Temperature: 0.900000 Total energy: -2849.837779 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2849.837779 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2849.837779 (E_RNA) where: Base-Base interactions energy: -1973.355 where: short stacking energy: -816.585 Base-Backbone interact. energy: -10.177 local terms energy: -866.305694 where: bonds (distance) C4'-P energy: -159.403 bonds (distance) P-C4' energy: -170.174 flat angles C4'-P-C4' energy: -167.315 flat angles P-C4'-P energy: -120.631 tors. eta vs tors. theta energy: -248.783 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 2, replica: 1 ===================================== Write number: 6 Temperature: 0.950000 Total energy: -2774.952084 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2774.952084 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2774.952084 (E_RNA) where: Base-Base interactions energy: -1928.705 where: short stacking energy: -814.271 Base-Backbone interact. energy: -2.869 local terms energy: -843.378604 where: bonds (distance) C4'-P energy: -148.154 bonds (distance) P-C4' energy: -152.299 flat angles C4'-P-C4' energy: -165.937 flat angles P-C4'-P energy: -124.069 tors. eta vs tors. theta energy: -252.919 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 3, replica: 3 ===================================== Write number: 6 Temperature: 1.000000 Total energy: -2709.811173 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2709.811173 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2709.811173 (E_RNA) where: Base-Base interactions energy: -1869.410 where: short stacking energy: -798.473 Base-Backbone interact. energy: -2.653 local terms energy: -837.748280 where: bonds (distance) C4'-P energy: -140.682 bonds (distance) P-C4' energy: -155.749 flat angles C4'-P-C4' energy: -173.693 flat angles P-C4'-P energy: -112.356 tors. eta vs tors. theta energy: -255.268 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 4, replica: 5 ===================================== Write number: 6 Temperature: 1.050000 Total energy: -2638.909084 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2638.909084 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2638.909084 (E_RNA) where: Base-Base interactions energy: -1815.119 where: short stacking energy: -815.225 Base-Backbone interact. energy: -3.148 local terms energy: -820.641623 where: bonds (distance) C4'-P energy: -132.335 bonds (distance) P-C4' energy: -139.336 flat angles C4'-P-C4' energy: -175.951 flat angles P-C4'-P energy: -123.686 tors. eta vs tors. theta energy: -249.334 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 5, replica: 4 ===================================== Write number: 6 Temperature: 1.100000 Total energy: -2503.882506 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2503.882506 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2503.882506 (E_RNA) where: Base-Base interactions energy: -1719.650 where: short stacking energy: -722.171 Base-Backbone interact. energy: -1.150 local terms energy: -783.082217 where: bonds (distance) C4'-P energy: -141.962 bonds (distance) P-C4' energy: -148.990 flat angles C4'-P-C4' energy: -167.499 flat angles P-C4'-P energy: -108.596 tors. eta vs tors. theta energy: -216.036 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 6, replica: 7 ===================================== Write number: 6 Temperature: 1.150000 Total energy: -2376.040232 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2376.040232 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2376.040232 (E_RNA) where: Base-Base interactions energy: -1625.312 where: short stacking energy: -678.325 Base-Backbone interact. energy: -3.576 local terms energy: -747.152171 where: bonds (distance) C4'-P energy: -130.051 bonds (distance) P-C4' energy: -131.958 flat angles C4'-P-C4' energy: -164.260 flat angles P-C4'-P energy: -118.509 tors. eta vs tors. theta energy: -202.374 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 7, replica: 8 ===================================== Write number: 6 Temperature: 1.200000 Total energy: -2301.085979 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2301.085979 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2301.085979 (E_RNA) where: Base-Base interactions energy: -1603.488 where: short stacking energy: -700.379 Base-Backbone interact. energy: -0.237 local terms energy: -697.360497 where: bonds (distance) C4'-P energy: -129.780 bonds (distance) P-C4' energy: -119.332 flat angles C4'-P-C4' energy: -158.250 flat angles P-C4'-P energy: -95.369 tors. eta vs tors. theta energy: -194.630 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 8, replica: 6 ===================================== Write number: 6 Temperature: 1.250000 Total energy: -2310.691080 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -2310.691080 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -2310.691080 (E_RNA) where: Base-Base interactions energy: -1619.863 where: short stacking energy: -666.992 Base-Backbone interact. energy: 0.635 local terms energy: -691.463004 where: bonds (distance) C4'-P energy: -125.441 bonds (distance) P-C4' energy: -107.996 flat angles C4'-P-C4' energy: -151.615 flat angles P-C4'-P energy: -94.485 tors. eta vs tors. theta energy: -211.926 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 9, replica: 9 ===================================== Write number: 6 Temperature: 1.300000 Total energy: -1856.739862 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1856.739862 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1856.739862 (E_RNA) where: Base-Base interactions energy: -1248.238 where: short stacking energy: -505.815 Base-Backbone interact. energy: -1.967 local terms energy: -606.535071 where: bonds (distance) C4'-P energy: -117.553 bonds (distance) P-C4' energy: -123.693 flat angles C4'-P-C4' energy: -133.735 flat angles P-C4'-P energy: -87.003 tors. eta vs tors. theta energy: -144.552 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) ================================== temp. level: 10, replica: 10 ===================================== Write number: 6 Temperature: 1.350000 Total energy: -1691.783178 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1691.783178 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1691.783178 (E_RNA) where: Base-Base interactions energy: -1133.538 where: short stacking energy: -515.073 Base-Backbone interact. energy: -6.014 local terms energy: -552.231596 where: bonds (distance) C4'-P energy: -103.220 bonds (distance) P-C4' energy: -123.612 flat angles C4'-P-C4' energy: -111.731 flat angles P-C4'-P energy: -88.406 tors. eta vs tors. theta energy: -125.262 Dist. restrs. and SS energy: 0.000 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) replica 2 ended at temp. level: 1, temp: 0.900000 for this replica: moves confirmed at first: 1036408 moves confirmed later: 1086515 all moves confirmed: 2122923 percent of confirmed moves: 26.536538 current total energy: -2707.069523 recalc. total energy: -2707.069523 replica 1 ended at temp. level: 2, temp: 0.950000 for this replica: moves confirmed at first: 1020979 moves confirmed later: 1069319 all moves confirmed: 2090298 percent of confirmed moves: 26.128725 current total energy: -2675.610181 recalc. total energy: -2675.610181 replica 3 ended at temp. level: 3, temp: 1.000000 for this replica: moves confirmed at first: 1080354 moves confirmed later: 1149980 all moves confirmed: 2230334 percent of confirmed moves: 27.879175 current total energy: -2600.015019 recalc. total energy: -2600.015019 replica 5 ended at temp. level: 4, temp: 1.050000 for this replica: moves confirmed at first: 1143071 moves confirmed later: 1222983 all moves confirmed: 2366054 percent of confirmed moves: 29.575675 current total energy: -2497.729665 recalc. total energy: -2497.729665 replica 4 ended at temp. level: 5, temp: 1.100000 for this replica: moves confirmed at first: 1208076 moves confirmed later: 1305432 all moves confirmed: 2513508 percent of confirmed moves: 31.418850 current total energy: -2417.958728 recalc. total energy: -2417.958728 replica 7 ended at temp. level: 6, temp: 1.150000 for this replica: moves confirmed at first: 1302076 moves confirmed later: 1421923 all moves confirmed: 2723999 percent of confirmed moves: 34.049988 current total energy: -2274.416881 recalc. total energy: -2274.416881 replica 8 ended at temp. level: 7, temp: 1.200000 for this replica: moves confirmed at first: 1422551 moves confirmed later: 1572050 all moves confirmed: 2994601 percent of confirmed moves: 37.432513 current total energy: -2220.182348 recalc. total energy: -2220.182348 replica 6 ended at temp. level: 8, temp: 1.250000 for this replica: moves confirmed at first: 1283132 moves confirmed later: 1405768 all moves confirmed: 2688900 percent of confirmed moves: 33.611250 current total energy: -2103.360118 recalc. total energy: -2103.360118 replica 9 ended at temp. level: 9, temp: 1.300000 for this replica: moves confirmed at first: 1617719 moves confirmed later: 1819981 all moves confirmed: 3437700 percent of confirmed moves: 42.971250 current total energy: -1641.833577 recalc. total energy: -1641.833577 replica 10 ended at temp. level: 10, temp: 1.350000 for this replica: moves confirmed at first: 1693142 moves confirmed later: 1926983 all moves confirmed: 3620125 percent of confirmed moves: 45.251562 current total energy: -1513.304843 recalc. total energy: -1513.304843 out arg RESULTS//1/seq3-23573a1d_01 Time of doing 80000 iterations: 551.667 seconds