SimRNA (c) 2009-2024 Genesilico, ver. 3.33 PDB Replica Exchange Monte Carlo Method is SWITCHED ON 7 replicas were ordered .reading parameteres setting random seed = 1 initiating replica nr: 1 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.700 successfully initiated initiating replica nr: 2 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.767 successfully initiated initiating replica nr: 3 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.833 successfully initiated initiating replica nr: 4 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.900 successfully initiated initiating replica nr: 5 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 0.967 successfully initiated initiating replica nr: 6 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.033 successfully initiated initiating replica nr: 7 before entireStruct->initialize(input) reading input pdb file: struct.pdb number of recognized chains: 1 chain '0' contains: 205 residues chain '0' 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 0 contains 205 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: 1030 n_atoms_counter: 1030 Fraction Of RNA Moves = 1.000000 Fraction Of Protein Moves = 0.000000 RNAStructure::secondStrcWeight = 1.000000 chain: 1: _...((((((((..(((((((..............(((((((...................((((((......))))))........)))))).)........(..(((.(((.....))).(.((((..(((.(((((.......))))).)).)...).))))..))).)................))))...)))))))))))_ chain: 1: _.........................((((.((((.......))))...))))((((.......................................................................................................................)))).........................._ nucl1: 65, chain1: 0, <---> nucl2: 72, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 65, chainIndex_2: 0, nuclIndex_2: 72 nucl1: 64, chain1: 0, <---> nucl2: 73, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 64, chainIndex_2: 0, nuclIndex_2: 73 nucl1: 63, chain1: 0, <---> nucl2: 74, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 63, chainIndex_2: 0, nuclIndex_2: 74 nucl1: 62, chain1: 0, <---> nucl2: 75, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 62, chainIndex_2: 0, nuclIndex_2: 75 nucl1: 61, chain1: 0, <---> nucl2: 76, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 61, chainIndex_2: 0, nuclIndex_2: 76 nucl1: 60, chain1: 0, <---> nucl2: 77, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 60, chainIndex_2: 0, nuclIndex_2: 77 nucl1: 40, chain1: 0, <---> nucl2: 86, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 40, chainIndex_2: 0, nuclIndex_2: 86 nucl1: 39, chain1: 0, <---> nucl2: 87, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 39, chainIndex_2: 0, nuclIndex_2: 87 nucl1: 38, chain1: 0, <---> nucl2: 88, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 38, chainIndex_2: 0, nuclIndex_2: 88 nucl1: 37, chain1: 0, <---> nucl2: 89, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 37, chainIndex_2: 0, nuclIndex_2: 89 nucl1: 36, chain1: 0, <---> nucl2: 90, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 36, chainIndex_2: 0, nuclIndex_2: 90 nucl1: 35, chain1: 0, <---> nucl2: 91, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 35, chainIndex_2: 0, nuclIndex_2: 91 nucl1: 34, chain1: 0, <---> nucl2: 93, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 34, chainIndex_2: 0, nuclIndex_2: 93 nucl1: 111, chain1: 0, <---> nucl2: 117, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 111, chainIndex_2: 0, nuclIndex_2: 117 nucl1: 110, chain1: 0, <---> nucl2: 118, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 110, chainIndex_2: 0, nuclIndex_2: 118 nucl1: 109, chain1: 0, <---> nucl2: 119, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 109, chainIndex_2: 0, nuclIndex_2: 119 nucl1: 137, chain1: 0, <---> nucl2: 145, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 137, chainIndex_2: 0, nuclIndex_2: 145 nucl1: 136, chain1: 0, <---> nucl2: 146, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 136, chainIndex_2: 0, nuclIndex_2: 146 nucl1: 135, chain1: 0, <---> nucl2: 147, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 135, chainIndex_2: 0, nuclIndex_2: 147 nucl1: 134, chain1: 0, <---> nucl2: 148, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 134, chainIndex_2: 0, nuclIndex_2: 148 nucl1: 133, chain1: 0, <---> nucl2: 149, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 133, chainIndex_2: 0, nuclIndex_2: 149 nucl1: 131, chain1: 0, <---> nucl2: 151, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 131, chainIndex_2: 0, nuclIndex_2: 151 nucl1: 130, chain1: 0, <---> nucl2: 152, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 130, chainIndex_2: 0, nuclIndex_2: 152 nucl1: 129, chain1: 0, <---> nucl2: 154, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 129, chainIndex_2: 0, nuclIndex_2: 154 nucl1: 126, chain1: 0, <---> nucl2: 158, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 126, chainIndex_2: 0, nuclIndex_2: 158 nucl1: 125, chain1: 0, <---> nucl2: 160, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 125, chainIndex_2: 0, nuclIndex_2: 160 nucl1: 124, chain1: 0, <---> nucl2: 161, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 124, chainIndex_2: 0, nuclIndex_2: 161 nucl1: 123, chain1: 0, <---> nucl2: 162, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 123, chainIndex_2: 0, nuclIndex_2: 162 nucl1: 121, chain1: 0, <---> nucl2: 163, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 121, chainIndex_2: 0, nuclIndex_2: 163 nucl1: 107, chain1: 0, <---> nucl2: 166, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 107, chainIndex_2: 0, nuclIndex_2: 166 nucl1: 106, chain1: 0, <---> nucl2: 167, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 106, chainIndex_2: 0, nuclIndex_2: 167 nucl1: 105, chain1: 0, <---> nucl2: 168, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 105, chainIndex_2: 0, nuclIndex_2: 168 nucl1: 102, chain1: 0, <---> nucl2: 170, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 102, chainIndex_2: 0, nuclIndex_2: 170 nucl1: 19, chain1: 0, <---> nucl2: 187, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 19, chainIndex_2: 0, nuclIndex_2: 187 nucl1: 18, chain1: 0, <---> nucl2: 188, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 18, chainIndex_2: 0, nuclIndex_2: 188 nucl1: 17, chain1: 0, <---> nucl2: 189, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 17, chainIndex_2: 0, nuclIndex_2: 189 nucl1: 16, chain1: 0, <---> nucl2: 190, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 16, chainIndex_2: 0, nuclIndex_2: 190 nucl1: 15, chain1: 0, <---> nucl2: 194, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 15, chainIndex_2: 0, nuclIndex_2: 194 nucl1: 14, chain1: 0, <---> nucl2: 195, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 14, chainIndex_2: 0, nuclIndex_2: 195 nucl1: 13, chain1: 0, <---> nucl2: 196, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 13, chainIndex_2: 0, nuclIndex_2: 196 nucl1: 10, chain1: 0, <---> nucl2: 197, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 10, chainIndex_2: 0, nuclIndex_2: 197 nucl1: 9, chain1: 0, <---> nucl2: 198, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 9, chainIndex_2: 0, nuclIndex_2: 198 nucl1: 8, chain1: 0, <---> nucl2: 199, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 8, chainIndex_2: 0, nuclIndex_2: 199 nucl1: 7, chain1: 0, <---> nucl2: 200, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 7, chainIndex_2: 0, nuclIndex_2: 200 nucl1: 6, chain1: 0, <---> nucl2: 201, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 6, chainIndex_2: 0, nuclIndex_2: 201 nucl1: 5, chain1: 0, <---> nucl2: 202, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 5, chainIndex_2: 0, nuclIndex_2: 202 nucl1: 4, chain1: 0, <---> nucl2: 203, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 4, chainIndex_2: 0, nuclIndex_2: 203 nucl1: 3, chain1: 0, <---> nucl2: 204, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 3, chainIndex_2: 0, nuclIndex_2: 204 nucl1: 33, chain1: 0, <---> nucl2: 41, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 33, chainIndex_2: 0, nuclIndex_2: 41 nucl1: 32, chain1: 0, <---> nucl2: 42, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 32, chainIndex_2: 0, nuclIndex_2: 42 nucl1: 31, chain1: 0, <---> nucl2: 43, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 31, chainIndex_2: 0, nuclIndex_2: 43 nucl1: 30, chain1: 0, <---> nucl2: 44, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 30, chainIndex_2: 0, nuclIndex_2: 44 nucl1: 28, chain1: 0, <---> nucl2: 48, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 28, chainIndex_2: 0, nuclIndex_2: 48 nucl1: 27, chain1: 0, <---> nucl2: 49, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 27, chainIndex_2: 0, nuclIndex_2: 49 nucl1: 26, chain1: 0, <---> nucl2: 50, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 26, chainIndex_2: 0, nuclIndex_2: 50 nucl1: 25, chain1: 0, <---> nucl2: 51, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 25, chainIndex_2: 0, nuclIndex_2: 51 nucl1: 55, chain1: 0, <---> nucl2: 175, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 55, chainIndex_2: 0, nuclIndex_2: 175 nucl1: 54, chain1: 0, <---> nucl2: 176, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 54, chainIndex_2: 0, nuclIndex_2: 176 nucl1: 53, chain1: 0, <---> nucl2: 177, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 53, chainIndex_2: 0, nuclIndex_2: 177 nucl1: 52, chain1: 0, <---> nucl2: 178, chain2: 0 secondary structure restraint added: chainIndex_1: 0, nuclIndex_1: 52, chainIndex_2: 0, nuclIndex_2: 178 RNAStructure::tertiaryStrcWeight = 1.000000 EntireStructure::rnaStruct limitingSphereRadius : 205.000000 DONE before calcCenterOfMass(); after calcCenterOfMass(); before calcTotalEnergy(); after calcTotalEnergy(); after entireStruct->initialize(input) leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input) number of iterations = 1 trajectory write in every 1 iterations after each trajectory write attempt of changing replicas will be done replica Temperature = 1.100 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: 7 ================================== temp. level: 1, replica: 1 ===================================== Write number: 1 Temperature: 0.700000 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 0.766667 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 0.833333 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 0.900000 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 0.966667 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 1.033333 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 1.100000 Total energy: -1839.966072 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1839.966072 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1888.206081 (E_RNA) where: Base-Base interactions energy: -1281.310 where: short stacking energy: -499.809 Base-Backbone interact. energy: 22.465 local terms energy: -629.361055 where: bonds (distance) C4'-P energy: -148.073 bonds (distance) P-C4' energy: -146.261 flat angles C4'-P-C4' energy: -142.044 flat angles P-C4'-P energy: -67.243 tors. eta vs tors. theta energy: -125.740 Dist. restrs. and SS energy: 48.240 (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: 0.700000 Total energy: -1859.583801 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1859.583801 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1906.986466 (E_RNA) where: Base-Base interactions energy: -1297.749 where: short stacking energy: -510.656 Base-Backbone interact. energy: 22.977 local terms energy: -632.213496 where: bonds (distance) C4'-P energy: -145.244 bonds (distance) P-C4' energy: -148.217 flat angles C4'-P-C4' energy: -142.215 flat angles P-C4'-P energy: -72.571 tors. eta vs tors. theta energy: -126.900 Dist. restrs. and SS energy: 47.403 (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: 0.766667 Total energy: -1855.167161 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1855.167161 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1902.961693 (E_RNA) where: Base-Base interactions energy: -1297.779 where: short stacking energy: -507.554 Base-Backbone interact. energy: 22.827 local terms energy: -628.009694 where: bonds (distance) C4'-P energy: -145.671 bonds (distance) P-C4' energy: -145.484 flat angles C4'-P-C4' energy: -140.892 flat angles P-C4'-P energy: -72.876 tors. eta vs tors. theta energy: -126.020 Dist. restrs. and SS energy: 47.795 (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: 0.833333 Total energy: -1856.166587 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1856.166587 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1903.961468 (E_RNA) where: Base-Base interactions energy: -1294.853 where: short stacking energy: -508.368 Base-Backbone interact. energy: 22.787 local terms energy: -631.895302 where: bonds (distance) C4'-P energy: -144.643 bonds (distance) P-C4' energy: -145.883 flat angles C4'-P-C4' energy: -144.323 flat angles P-C4'-P energy: -73.588 tors. eta vs tors. theta energy: -126.392 Dist. restrs. and SS energy: 47.795 (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: 0.900000 Total energy: -1852.042005 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1852.042005 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1898.930462 (E_RNA) where: Base-Base interactions energy: -1287.216 where: short stacking energy: -507.084 Base-Backbone interact. energy: 22.766 local terms energy: -634.480053 where: bonds (distance) C4'-P energy: -146.234 bonds (distance) P-C4' energy: -146.840 flat angles C4'-P-C4' energy: -141.631 flat angles P-C4'-P energy: -72.485 tors. eta vs tors. theta energy: -127.291 Dist. restrs. and SS energy: 46.888 (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: 0.966667 Total energy: -1855.460225 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1855.460225 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1902.081422 (E_RNA) where: Base-Base interactions energy: -1277.250 where: short stacking energy: -492.767 Base-Backbone interact. energy: 21.138 local terms energy: -645.969125 where: bonds (distance) C4'-P energy: -147.765 bonds (distance) P-C4' energy: -157.498 flat angles C4'-P-C4' energy: -144.305 flat angles P-C4'-P energy: -71.670 tors. eta vs tors. theta energy: -127.665 Dist. restrs. and SS energy: 46.621 (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: 1.033333 Total energy: -1846.482066 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1846.482066 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1893.735064 (E_RNA) where: Base-Base interactions energy: -1287.575 where: short stacking energy: -505.335 Base-Backbone interact. energy: 23.031 local terms energy: -629.191155 where: bonds (distance) C4'-P energy: -146.465 bonds (distance) P-C4' energy: -146.752 flat angles C4'-P-C4' energy: -141.126 flat angles P-C4'-P energy: -71.901 tors. eta vs tors. theta energy: -125.880 Dist. restrs. and SS energy: 47.253 (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: 1.100000 Total energy: -1847.448208 (ES_TOTAL = E_TOTAL + S_TOTAL) where: RNA energy: -1847.448208 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA) where: Molecular energy: -1894.698738 (E_RNA) where: Base-Base interactions energy: -1289.471 where: short stacking energy: -508.683 Base-Backbone interact. energy: 23.257 local terms energy: -628.485075 where: bonds (distance) C4'-P energy: -144.043 bonds (distance) P-C4' energy: -148.020 flat angles C4'-P-C4' energy: -141.694 flat angles P-C4'-P energy: -70.851 tors. eta vs tors. theta energy: -126.810 Dist. restrs. and SS energy: 47.251 (S_DIST_RNA) chem. prob. restrs. energy: 0.000 (S_CHEM_RNA) Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA) replica 1 ended at temp. level: 1, temp: 0.700000 for this replica: moves confirmed at first: 21 moves confirmed later: 13 all moves confirmed: 34 percent of confirmed moves: 34.000000 current total energy: -1859.583801 recalc. total energy: -1859.583801 replica 3 ended at temp. level: 2, temp: 0.766667 for this replica: moves confirmed at first: 20 moves confirmed later: 13 all moves confirmed: 33 percent of confirmed moves: 33.000000 current total energy: -1856.166587 recalc. total energy: -1856.166587 replica 2 ended at temp. level: 3, temp: 0.833333 for this replica: moves confirmed at first: 22 moves confirmed later: 12 all moves confirmed: 34 percent of confirmed moves: 34.000000 current total energy: -1854.784537 recalc. total energy: -1854.784537 replica 5 ended at temp. level: 4, temp: 0.900000 for this replica: moves confirmed at first: 20 moves confirmed later: 12 all moves confirmed: 32 percent of confirmed moves: 32.000000 current total energy: -1851.171141 recalc. total energy: -1851.171141 replica 4 ended at temp. level: 5, temp: 0.966667 for this replica: moves confirmed at first: 18 moves confirmed later: 12 all moves confirmed: 30 percent of confirmed moves: 30.000000 current total energy: -1851.477965 recalc. total energy: -1851.477965 replica 7 ended at temp. level: 6, temp: 1.033333 for this replica: moves confirmed at first: 15 moves confirmed later: 13 all moves confirmed: 28 percent of confirmed moves: 28.000000 current total energy: -1844.133290 recalc. total energy: -1844.133290 replica 6 ended at temp. level: 7, temp: 1.100000 for this replica: moves confirmed at first: 18 moves confirmed later: 13 all moves confirmed: 31 percent of confirmed moves: 31.000000 current total energy: -1844.498313 recalc. total energy: -1844.498313 out arg RESULTS//1/R1242a-79c94447_01 Time of doing 1 iterations: 0.084 seconds