RNA models for: Demo1-5a837e9e (Demo1)
UGCGAGAGCG
n steps: 10 (~ n of SimRNA frames: 800, curr n of frames 800 = 100.0%) Dec. 24, 2023, 2:41 p.m.
The best score and representatives of up to five top clusters from your simulation:
- Best score Demo1-5a837e9e_sim_minE_TOTAL-000001_AA.pdb
- #1 cluster Demo1-5a837e9e_sim_thrs1.10A_clust01-000001_AA.pdb
- #2 cluster Demo1-5a837e9e_sim_thrs1.10A_clust02-000001_AA.pdb
The trajectory file for the simulation can be found here (the file might be > 1GB!).
The raw output files for each step of the pipeline can be found here
Best score model:
Demo1-5a837e9eJmol._Canvas2D (Jmol) "jmolApplet0"[x]
1st cluster representative:
Jmol._Canvas2D (Jmol) "jmolApplet1"[x]
2nd cluster representative:
Jmol._Canvas2D (Jmol) "jmolApplet2"[x]
The log of the data processing.
Job log: SimRNA (c) 2009-2024 Genesilico, ver. 3.33
Replica Exchange Monte Carlo Method is SWITCHED ON
10 replicas were ordered
.reading parameteres
setting random seed = 1
initiating replica nr: 1
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 0.900
successfully initiated
initiating replica nr: 2
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 0.950
successfully initiated
initiating replica nr: 3
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.000
successfully initiated
initiating replica nr: 4
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.050
successfully initiated
initiating replica nr: 5
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.100
successfully initiated
initiating replica nr: 6
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.150
successfully initiated
initiating replica nr: 7
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.200
successfully initiated
initiating replica nr: 8
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.250
successfully initiated
initiating replica nr: 9
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.300
successfully initiated
initiating replica nr: 10
before entireStruct->initialize(input)
file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa first_line: R
number of RNA chain(s) decalred/expected in file: /home/smoafinejad/SimRNP/test/SIMULATIONS/Demo1-5a837e9e/inputs/seq.fa: 1
curr_seq: _UGCGAGAGCG_
chainIds_rna: _A_, chainIds_protein: __
chainId: A, chainSeq: UGCGAGAGCG
RNAStructure(struct InputParam): Fraction Of One Atom Moves = 0.450000
RNAStructure(struct InputParam): Fraction Of Two Atoms Moves = 0.440000
RNAStructure(struct InputParam): Fraction Of Fragment Moves = 0.010000
RNAStructure(struct InputParam): Fraction Of Nitrogen Atom Moves = 0.100000
RNAStructure(struct InputParam): Fraction Of Rigid Rotation Moves = 0.000000
RNAStructure(struct InputParam): Fraction Of Rigid Translation Moves = 0.000000
RNA chains:
chain A contains 10 nucleotides
loading histrogram: ./data/rna/dist_PC.data.new_hist assigned_name: dist_PC.data.new_hist DONE
loading histrogram: ./data/rna/dist_CP.data.new_hist assigned_name: dist_CP.data.new_hist DONE
loading histrogram: ./data/rna/angle_PCP.data.new_hist assigned_name: angle_PCP.data.new_hist DONE
loading histrogram: ./data/rna/angle_CPC.data.new_hist assigned_name: angle_CPC.data.new_hist DONE
loading histrogram: ./data/rna/eta_theta.data.new_hist assigned_name: eta_theta.data.new_hist DONE
reweighting term eta_theta by 0.400000, default value
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
reading conformers file: ./data/rna/A_conformers
n_lines: 4766
16 15 69 34 27
46 26 156 83 35
93 127 1269 89 50
187 157 1927 88 75
51 22 67 25 32
DONE
reading conformers file: ./data/rna/C_conformers
n_lines: 5164
7 8 61 17 4
14 12 143 49 12
23 140 2110 21 24
88 101 2101 19 36
25 21 108 8 12
DONE
reading conformers file: ./data/rna/G_conformers
n_lines: 6375
11 7 79 21 50
20 17 175 54 39
42 102 2774 90 34
61 94 2314 71 100
20 22 142 15 21
DONE
reading conformers file: ./data/rna/U_conformers
n_lines: 3617
6 6 43 33 24
20 20 131 50 28
30 58 1412 30 24
64 82 1197 31 32
71 36 132 13 44
DONE
loading histrogram: ./data/rna/AA3.hist assigned_name: AA3.hist DONE
loading histrogram: ./data/rna/AC3.hist assigned_name: AC3.hist DONE
loading histrogram: ./data/rna/AG3.hist assigned_name: AG3.hist DONE
loading histrogram: ./data/rna/AU3.hist assigned_name: AU3.hist DONE
loading histrogram: ./data/rna/CA3.hist assigned_name: CA3.hist DONE
loading histrogram: ./data/rna/CC3.hist assigned_name: CC3.hist DONE
loading histrogram: ./data/rna/CG3.hist assigned_name: CG3.hist DONE
loading histrogram: ./data/rna/CU3.hist assigned_name: CU3.hist DONE
loading histrogram: ./data/rna/GA3.hist assigned_name: GA3.hist DONE
loading histrogram: ./data/rna/GC3.hist assigned_name: GC3.hist DONE
loading histrogram: ./data/rna/GG3.hist assigned_name: GG3.hist DONE
loading histrogram: ./data/rna/GU3.hist assigned_name: GU3.hist DONE
loading histrogram: ./data/rna/UA3.hist assigned_name: UA3.hist DONE
loading histrogram: ./data/rna/UC3.hist assigned_name: UC3.hist DONE
loading histrogram: ./data/rna/UG3.hist assigned_name: UG3.hist DONE
loading histrogram: ./data/rna/UU3.hist assigned_name: UU3.hist DONE
loading histrogram: ./data/rna/AU3_WW-repulsive.hist assigned_name: AU3_WW-repulsive.hist DONE
scaling: histogram AU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/CG3_WW-repulsive.hist assigned_name: CG3_WW-repulsive.hist DONE
scaling: histogram CG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GC3_WW-repulsive.hist assigned_name: GC3_WW-repulsive.hist DONE
scaling: histogram GC3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/GU3_WW-repulsive.hist assigned_name: GU3_WW-repulsive.hist DONE
scaling: histogram GU3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UA3_WW-repulsive.hist assigned_name: UA3_WW-repulsive.hist DONE
scaling: histogram UA3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/UG3_WW-repulsive.hist assigned_name: UG3_WW-repulsive.hist DONE
scaling: histogram UG3_WW-repulsive.hist was multiplied by -1.000000
loading histrogram: ./data/rna/A-C4_3.hist assigned_name: A-C4_3.hist DONE
loading histrogram: ./data/rna/C-C4_3.hist assigned_name: C-C4_3.hist DONE
loading histrogram: ./data/rna/G-C4_3.hist assigned_name: G-C4_3.hist DONE
loading histrogram: ./data/rna/U-C4_3.hist assigned_name: U-C4_3.hist DONE
loading histrogram: ./data/rna/A-P_3.hist assigned_name: A-P_3.hist DONE
loading histrogram: ./data/rna/C-P_3.hist assigned_name: C-P_3.hist DONE
loading histrogram: ./data/rna/G-P_3.hist assigned_name: G-P_3.hist DONE
loading histrogram: ./data/rna/U-P_3.hist assigned_name: U-P_3.hist DONE
loading histrogram: ./data/rna/A_3_exvol.hist assigned_name: A_3_exvol.hist DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/C_3_exvol.hist assigned_name: C_3_exvol.hist DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/G_3_exvol.hist assigned_name: G_3_exvol.hist DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/rna/U_3_exvol.hist assigned_name: U_3_exvol.hist DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
exiting function: void RNAStructure::createFromSequence(char *chainIds, char** chainSeqs)
x_protein_frc: 0.000
x_rna_frc: 1.000
int EntireStructure::calcNumberOfAtoms(): numberOfAtoms: 55
n_atoms_counter: 55
Fraction Of RNA Moves = 1.000000
Fraction Of Protein Moves = 0.000000
RNAStructure::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <---> nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <---> nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <---> nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
RNAStructure::tertiaryStrcWeight = 1.000000
EntireStructure::rnaStruct limitingSphereRadius : 10.000000 DONE
before calcCenterOfMass();
after calcCenterOfMass();
before calcTotalEnergy();
after calcTotalEnergy();
after entireStruct->initialize(input)
leaving: void SimulatedAnnealing::chooseTypeOfChain(struct InputParam input)
number of iterations = 160000
trajectory write in every 16000 iterations
after each trajectory write attempt of changing replicas will be done
replica Temperature = 1.350
successfully initiated
.calculating
program compiled for parallel execution of replicas in Replica Exchange MC method
program can utilize maximum as many CPU cores as replicas, in this case: 10
==================================
temp. level: 1, replica: 1
=====================================
Write number: 1
Temperature: 0.900000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 2
=====================================
Write number: 1
Temperature: 0.950000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 3
=====================================
Write number: 1
Temperature: 1.000000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 4
=====================================
Write number: 1
Temperature: 1.050000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 5, replica: 5
=====================================
Write number: 1
Temperature: 1.100000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 6
=====================================
Write number: 1
Temperature: 1.150000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 7, replica: 7
=====================================
Write number: 1
Temperature: 1.200000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 8
=====================================
Write number: 1
Temperature: 1.250000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 9
=====================================
Write number: 1
Temperature: 1.300000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 10
=====================================
Write number: 1
Temperature: 1.350000
Total energy: -4.231719 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -4.231719 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -35.551219 (E_RNA)
where:
Base-Base interactions energy: -0.634
where: short stacking energy: -0.634
Base-Backbone interact. energy: -0.000
local terms energy: -34.916784
where:
bonds (distance) C4'-P energy: -9.716
bonds (distance) P-C4' energy: -9.841
flat angles C4'-P-C4' energy: -7.342
flat angles P-C4'-P energy: -8.399
tors. eta vs tors. theta energy: 0.381
Dist. restrs. and SS energy: 31.320 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 1, replica: 1
=====================================
Write number: 2
Temperature: 0.900000
Total energy: -98.487754 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.487754 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.530574 (E_RNA)
where:
Base-Base interactions energy: -64.664
where: short stacking energy: -33.546
Base-Backbone interact. energy: -0.002
local terms energy: -33.864602
where:
bonds (distance) C4'-P energy: -6.114
bonds (distance) P-C4' energy: -7.094
flat angles C4'-P-C4' energy: -7.612
flat angles P-C4'-P energy: -5.841
tors. eta vs tors. theta energy: -7.204
Dist. restrs. and SS energy: 0.043 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 2
=====================================
Write number: 2
Temperature: 0.950000
Total energy: -99.955771 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.955771 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -100.060667 (E_RNA)
where:
Base-Base interactions energy: -68.731
where: short stacking energy: -27.392
Base-Backbone interact. energy: -1.126
local terms energy: -30.203825
where:
bonds (distance) C4'-P energy: -6.201
bonds (distance) P-C4' energy: -8.796
flat angles C4'-P-C4' energy: -7.408
flat angles P-C4'-P energy: -4.073
tors. eta vs tors. theta energy: -3.726
Dist. restrs. and SS energy: 0.105 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 3
=====================================
Write number: 2
Temperature: 1.000000
Total energy: -99.808539 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.808539 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -99.808539 (E_RNA)
where:
Base-Base interactions energy: -67.540
where: short stacking energy: -27.401
Base-Backbone interact. energy: -1.423
local terms energy: -30.845307
where:
bonds (distance) C4'-P energy: -6.184
bonds (distance) P-C4' energy: -7.336
flat angles C4'-P-C4' energy: -6.151
flat angles P-C4'-P energy: -5.432
tors. eta vs tors. theta energy: -5.742
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 4
=====================================
Write number: 2
Temperature: 1.050000
Total energy: -101.758247 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.758247 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.951986 (E_RNA)
where:
Base-Base interactions energy: -67.496
where: short stacking energy: -29.680
Base-Backbone interact. energy: -0.464
local terms energy: -33.992288
where:
bonds (distance) C4'-P energy: -6.148
bonds (distance) P-C4' energy: -7.364
flat angles C4'-P-C4' energy: -8.648
flat angles P-C4'-P energy: -5.392
tors. eta vs tors. theta energy: -6.440
Dist. restrs. and SS energy: 0.194 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 5, replica: 5
=====================================
Write number: 2
Temperature: 1.100000
Total energy: -92.092654 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -92.092654 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -92.139633 (E_RNA)
where:
Base-Base interactions energy: -60.228
where: short stacking energy: -22.787
Base-Backbone interact. energy: -0.058
local terms energy: -31.854257
where:
bonds (distance) C4'-P energy: -6.805
bonds (distance) P-C4' energy: -8.302
flat angles C4'-P-C4' energy: -7.353
flat angles P-C4'-P energy: -3.510
tors. eta vs tors. theta energy: -5.885
Dist. restrs. and SS energy: 0.047 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 6
=====================================
Write number: 2
Temperature: 1.150000
Total energy: -98.574097 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.574097 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.618375 (E_RNA)
where:
Base-Base interactions energy: -64.544
where: short stacking energy: -25.280
Base-Backbone interact. energy: -0.464
local terms energy: -33.610114
where:
bonds (distance) C4'-P energy: -7.534
bonds (distance) P-C4' energy: -7.649
flat angles C4'-P-C4' energy: -7.386
flat angles P-C4'-P energy: -3.836
tors. eta vs tors. theta energy: -7.206
Dist. restrs. and SS energy: 0.044 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 7, replica: 7
=====================================
Write number: 2
Temperature: 1.200000
Total energy: -103.997716 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.997716 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.248123 (E_RNA)
where:
Base-Base interactions energy: -72.127
where: short stacking energy: -29.294
Base-Backbone interact. energy: -1.175
local terms energy: -30.945752
where:
bonds (distance) C4'-P energy: -7.438
bonds (distance) P-C4' energy: -6.780
flat angles C4'-P-C4' energy: -4.426
flat angles P-C4'-P energy: -5.017
tors. eta vs tors. theta energy: -7.284
Dist. restrs. and SS energy: 0.250 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 8
=====================================
Write number: 2
Temperature: 1.250000
Total energy: -98.495936 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.495936 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.578753 (E_RNA)
where:
Base-Base interactions energy: -63.092
where: short stacking energy: -28.062
Base-Backbone interact. energy: -0.000
local terms energy: -35.486841
where:
bonds (distance) C4'-P energy: -7.676
bonds (distance) P-C4' energy: -8.662
flat angles C4'-P-C4' energy: -6.659
flat angles P-C4'-P energy: -5.920
tors. eta vs tors. theta energy: -6.570
Dist. restrs. and SS energy: 0.083 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 9
=====================================
Write number: 2
Temperature: 1.300000
Total energy: -84.440881 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -84.440881 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -84.692213 (E_RNA)
where:
Base-Base interactions energy: -55.946
where: short stacking energy: -25.171
Base-Backbone interact. energy: -0.095
local terms energy: -28.651750
where:
bonds (distance) C4'-P energy: -4.418
bonds (distance) P-C4' energy: -9.087
flat angles C4'-P-C4' energy: -6.178
flat angles P-C4'-P energy: -5.680
tors. eta vs tors. theta energy: -3.288
Dist. restrs. and SS energy: 0.251 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 10
=====================================
Write number: 2
Temperature: 1.350000
Total energy: -74.530648 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -74.530648 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -74.746624 (E_RNA)
where:
Base-Base interactions energy: -49.803
where: short stacking energy: -18.503
Base-Backbone interact. energy: -0.499
local terms energy: -24.444027
where:
bonds (distance) C4'-P energy: -3.742
bonds (distance) P-C4' energy: -5.306
flat angles C4'-P-C4' energy: -5.586
flat angles P-C4'-P energy: -5.652
tors. eta vs tors. theta energy: -4.158
Dist. restrs. and SS energy: 0.216 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 1, replica: 1
=====================================
Write number: 3
Temperature: 0.900000
Total energy: -108.336739 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -108.336739 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -108.406201 (E_RNA)
where:
Base-Base interactions energy: -70.064
where: short stacking energy: -27.929
Base-Backbone interact. energy: -0.595
local terms energy: -37.747438
where:
bonds (distance) C4'-P energy: -8.404
bonds (distance) P-C4' energy: -7.600
flat angles C4'-P-C4' energy: -7.738
flat angles P-C4'-P energy: -4.444
tors. eta vs tors. theta energy: -9.562
Dist. restrs. and SS energy: 0.069 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 2
=====================================
Write number: 3
Temperature: 0.950000
Total energy: -103.936070 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.936070 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.021362 (E_RNA)
where:
Base-Base interactions energy: -65.107
where: short stacking energy: -26.608
Base-Backbone interact. energy: -0.437
local terms energy: -38.477773
where:
bonds (distance) C4'-P energy: -9.161
bonds (distance) P-C4' energy: -8.121
flat angles C4'-P-C4' energy: -8.332
flat angles P-C4'-P energy: -5.625
tors. eta vs tors. theta energy: -7.238
Dist. restrs. and SS energy: 0.085 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 3
=====================================
Write number: 3
Temperature: 1.000000
Total energy: -103.033538 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.033538 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.033538 (E_RNA)
where:
Base-Base interactions energy: -74.581
where: short stacking energy: -30.639
Base-Backbone interact. energy: -1.030
local terms energy: -27.423087
where:
bonds (distance) C4'-P energy: -4.720
bonds (distance) P-C4' energy: -6.171
flat angles C4'-P-C4' energy: -5.768
flat angles P-C4'-P energy: -3.490
tors. eta vs tors. theta energy: -7.275
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 5
=====================================
Write number: 3
Temperature: 1.050000
Total energy: -104.361311 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -104.361311 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.487632 (E_RNA)
where:
Base-Base interactions energy: -67.885
where: short stacking energy: -29.506
Base-Backbone interact. energy: -0.071
local terms energy: -36.531951
where:
bonds (distance) C4'-P energy: -6.673
bonds (distance) P-C4' energy: -9.124
flat angles C4'-P-C4' energy: -9.027
flat angles P-C4'-P energy: -3.851
tors. eta vs tors. theta energy: -7.857
Dist. restrs. and SS energy: 0.126 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 5, replica: 4
=====================================
Write number: 3
Temperature: 1.100000
Total energy: -100.637407 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -100.637407 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -100.694607 (E_RNA)
where:
Base-Base interactions energy: -66.450
where: short stacking energy: -26.358
Base-Backbone interact. energy: -0.009
local terms energy: -34.235591
where:
bonds (distance) C4'-P energy: -7.647
bonds (distance) P-C4' energy: -7.717
flat angles C4'-P-C4' energy: -7.844
flat angles P-C4'-P energy: -3.907
tors. eta vs tors. theta energy: -7.121
Dist. restrs. and SS energy: 0.057 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 7
=====================================
Write number: 3
Temperature: 1.150000
Total energy: -102.823955 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -102.823955 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -102.937182 (E_RNA)
where:
Base-Base interactions energy: -65.128
where: short stacking energy: -26.169
Base-Backbone interact. energy: -1.702
local terms energy: -36.107090
where:
bonds (distance) C4'-P energy: -8.929
bonds (distance) P-C4' energy: -8.855
flat angles C4'-P-C4' energy: -4.642
flat angles P-C4'-P energy: -5.906
tors. eta vs tors. theta energy: -7.776
Dist. restrs. and SS energy: 0.113 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 7, replica: 6
=====================================
Write number: 3
Temperature: 1.200000
Total energy: -99.297114 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.297114 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -99.455131 (E_RNA)
where:
Base-Base interactions energy: -65.065
where: short stacking energy: -29.695
Base-Backbone interact. energy: -0.148
local terms energy: -34.242608
where:
bonds (distance) C4'-P energy: -8.495
bonds (distance) P-C4' energy: -7.880
flat angles C4'-P-C4' energy: -8.692
flat angles P-C4'-P energy: -4.112
tors. eta vs tors. theta energy: -5.064
Dist. restrs. and SS energy: 0.158 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 8
=====================================
Write number: 3
Temperature: 1.250000
Total energy: -98.870001 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.870001 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.963465 (E_RNA)
where:
Base-Base interactions energy: -64.785
where: short stacking energy: -26.137
Base-Backbone interact. energy: -0.011
local terms energy: -34.167292
where:
bonds (distance) C4'-P energy: -4.855
bonds (distance) P-C4' energy: -7.358
flat angles C4'-P-C4' energy: -7.798
flat angles P-C4'-P energy: -6.816
tors. eta vs tors. theta energy: -7.340
Dist. restrs. and SS energy: 0.093 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 9
=====================================
Write number: 3
Temperature: 1.300000
Total energy: -82.238361 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -82.238361 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -82.682929 (E_RNA)
where:
Base-Base interactions energy: -52.206
where: short stacking energy: -23.478
Base-Backbone interact. energy: -0.033
local terms energy: -30.443259
where:
bonds (distance) C4'-P energy: -7.356
bonds (distance) P-C4' energy: -8.047
flat angles C4'-P-C4' energy: -5.976
flat angles P-C4'-P energy: -4.245
tors. eta vs tors. theta energy: -4.818
Dist. restrs. and SS energy: 0.445 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 10
=====================================
Write number: 3
Temperature: 1.350000
Total energy: -79.545879 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -79.545879 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -80.307924 (E_RNA)
where:
Base-Base interactions energy: -52.751
where: short stacking energy: -17.974
Base-Backbone interact. energy: -0.476
local terms energy: -27.080632
where:
bonds (distance) C4'-P energy: -4.367
bonds (distance) P-C4' energy: -7.978
flat angles C4'-P-C4' energy: -7.193
flat angles P-C4'-P energy: -5.001
tors. eta vs tors. theta energy: -2.542
Dist. restrs. and SS energy: 0.762 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 1, replica: 1
=====================================
Write number: 4
Temperature: 0.900000
Total energy: -111.674573 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -111.674573 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -111.684749 (E_RNA)
where:
Base-Base interactions energy: -72.904
where: short stacking energy: -29.544
Base-Backbone interact. energy: -1.707
local terms energy: -37.073196
where:
bonds (distance) C4'-P energy: -6.569
bonds (distance) P-C4' energy: -8.401
flat angles C4'-P-C4' energy: -7.236
flat angles P-C4'-P energy: -6.640
tors. eta vs tors. theta energy: -8.226
Dist. restrs. and SS energy: 0.010 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 2
=====================================
Write number: 4
Temperature: 0.950000
Total energy: -101.702030 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.702030 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.711147 (E_RNA)
where:
Base-Base interactions energy: -64.746
where: short stacking energy: -24.830
Base-Backbone interact. energy: 0.468
local terms energy: -37.433113
where:
bonds (distance) C4'-P energy: -8.118
bonds (distance) P-C4' energy: -8.376
flat angles C4'-P-C4' energy: -6.984
flat angles P-C4'-P energy: -6.037
tors. eta vs tors. theta energy: -7.919
Dist. restrs. and SS energy: 0.009 (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: 5
=====================================
Write number: 4
Temperature: 1.000000
Total energy: -106.236415 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -106.236415 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -106.236415 (E_RNA)
where:
Base-Base interactions energy: -70.656
where: short stacking energy: -30.624
Base-Backbone interact. energy: -1.267
local terms energy: -34.313227
where:
bonds (distance) C4'-P energy: -7.960
bonds (distance) P-C4' energy: -8.640
flat angles C4'-P-C4' energy: -7.726
flat angles P-C4'-P energy: -2.687
tors. eta vs tors. theta energy: -7.300
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 3
=====================================
Write number: 4
Temperature: 1.050000
Total energy: -105.099356 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -105.099356 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -105.139518 (E_RNA)
where:
Base-Base interactions energy: -68.911
where: short stacking energy: -28.272
Base-Backbone interact. energy: -0.707
local terms energy: -35.521760
where:
bonds (distance) C4'-P energy: -6.043
bonds (distance) P-C4' energy: -8.208
flat angles C4'-P-C4' energy: -7.513
flat angles P-C4'-P energy: -6.669
tors. eta vs tors. theta energy: -7.089
Dist. restrs. and SS energy: 0.040 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 5, replica: 4
=====================================
Write number: 4
Temperature: 1.100000
Total energy: -101.230613 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.230613 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.243805 (E_RNA)
where:
Base-Base interactions energy: -63.327
where: short stacking energy: -27.319
Base-Backbone interact. energy: -0.054
local terms energy: -37.862635
where:
bonds (distance) C4'-P energy: -8.681
bonds (distance) P-C4' energy: -8.837
flat angles C4'-P-C4' energy: -7.047
flat angles P-C4'-P energy: -6.695
tors. eta vs tors. theta energy: -6.603
Dist. restrs. and SS energy: 0.013 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 7
=====================================
Write number: 4
Temperature: 1.150000
Total energy: -104.024842 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -104.024842 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.064189 (E_RNA)
where:
Base-Base interactions energy: -69.209
where: short stacking energy: -26.745
Base-Backbone interact. energy: -0.063
local terms energy: -34.792768
where:
bonds (distance) C4'-P energy: -8.317
bonds (distance) P-C4' energy: -8.444
flat angles C4'-P-C4' energy: -6.332
flat angles P-C4'-P energy: -3.342
tors. eta vs tors. theta energy: -8.357
Dist. restrs. and SS energy: 0.039 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 7, replica: 8
=====================================
Write number: 4
Temperature: 1.200000
Total energy: -94.852526 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -94.852526 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -94.950871 (E_RNA)
where:
Base-Base interactions energy: -63.890
where: short stacking energy: -25.383
Base-Backbone interact. energy: -1.106
local terms energy: -29.955030
where:
bonds (distance) C4'-P energy: -4.277
bonds (distance) P-C4' energy: -8.891
flat angles C4'-P-C4' energy: -5.989
flat angles P-C4'-P energy: -4.597
tors. eta vs tors. theta energy: -6.202
Dist. restrs. and SS energy: 0.098 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 6
=====================================
Write number: 4
Temperature: 1.250000
Total energy: -97.565352 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -97.565352 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -97.565352 (E_RNA)
where:
Base-Base interactions energy: -63.229
where: short stacking energy: -23.316
Base-Backbone interact. energy: -1.458
local terms energy: -32.878105
where:
bonds (distance) C4'-P energy: -8.283
bonds (distance) P-C4' energy: -4.258
flat angles C4'-P-C4' energy: -8.729
flat angles P-C4'-P energy: -4.596
tors. eta vs tors. theta energy: -7.012
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 10
=====================================
Write number: 4
Temperature: 1.300000
Total energy: -88.190884 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -88.190884 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -88.190884 (E_RNA)
where:
Base-Base interactions energy: -60.524
where: short stacking energy: -22.246
Base-Backbone interact. energy: -1.556
local terms energy: -26.111040
where:
bonds (distance) C4'-P energy: -3.345
bonds (distance) P-C4' energy: -7.861
flat angles C4'-P-C4' energy: -5.888
flat angles P-C4'-P energy: -5.270
tors. eta vs tors. theta energy: -3.747
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 4
Temperature: 1.350000
Total energy: -89.294378 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -89.294378 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -89.327029 (E_RNA)
where:
Base-Base interactions energy: -58.168
where: short stacking energy: -24.311
Base-Backbone interact. energy: 0.487
local terms energy: -31.646971
where:
bonds (distance) C4'-P energy: -5.589
bonds (distance) P-C4' energy: -6.904
flat angles C4'-P-C4' energy: -7.657
flat angles P-C4'-P energy: -6.215
tors. eta vs tors. theta energy: -5.282
Dist. restrs. and SS energy: 0.033 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 1, replica: 1
=====================================
Write number: 5
Temperature: 0.900000
Total energy: -109.054293 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -109.054293 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -109.054293 (E_RNA)
where:
Base-Base interactions energy: -71.480
where: short stacking energy: -29.908
Base-Backbone interact. energy: -0.180
local terms energy: -37.395089
where:
bonds (distance) C4'-P energy: -6.541
bonds (distance) P-C4' energy: -9.581
flat angles C4'-P-C4' energy: -7.736
flat angles P-C4'-P energy: -6.393
tors. eta vs tors. theta energy: -7.145
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 5
=====================================
Write number: 5
Temperature: 0.950000
Total energy: -103.645969 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.645969 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.693275 (E_RNA)
where:
Base-Base interactions energy: -70.027
where: short stacking energy: -29.405
Base-Backbone interact. energy: -0.513
local terms energy: -33.153897
where:
bonds (distance) C4'-P energy: -7.820
bonds (distance) P-C4' energy: -7.594
flat angles C4'-P-C4' energy: -7.839
flat angles P-C4'-P energy: -3.201
tors. eta vs tors. theta energy: -6.700
Dist. restrs. and SS energy: 0.047 (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: 2
=====================================
Write number: 5
Temperature: 1.000000
Total energy: -101.771034 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.771034 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.787177 (E_RNA)
where:
Base-Base interactions energy: -65.506
where: short stacking energy: -28.487
Base-Backbone interact. energy: -0.406
local terms energy: -35.874476
where:
bonds (distance) C4'-P energy: -4.890
bonds (distance) P-C4' energy: -8.796
flat angles C4'-P-C4' energy: -7.400
flat angles P-C4'-P energy: -7.035
tors. eta vs tors. theta energy: -7.755
Dist. restrs. and SS energy: 0.016 (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: 5
Temperature: 1.050000
Total energy: -103.355366 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.355366 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.368093 (E_RNA)
where:
Base-Base interactions energy: -67.817
where: short stacking energy: -26.409
Base-Backbone interact. energy: -0.722
local terms energy: -34.829061
where:
bonds (distance) C4'-P energy: -6.620
bonds (distance) P-C4' energy: -9.327
flat angles C4'-P-C4' energy: -6.553
flat angles P-C4'-P energy: -4.856
tors. eta vs tors. theta energy: -7.473
Dist. restrs. and SS energy: 0.013 (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: 3
=====================================
Write number: 5
Temperature: 1.100000
Total energy: -99.831342 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.831342 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -99.893813 (E_RNA)
where:
Base-Base interactions energy: -68.624
where: short stacking energy: -28.853
Base-Backbone interact. energy: 0.244
local terms energy: -31.513542
where:
bonds (distance) C4'-P energy: -6.876
bonds (distance) P-C4' energy: -8.017
flat angles C4'-P-C4' energy: -7.957
flat angles P-C4'-P energy: -2.961
tors. eta vs tors. theta energy: -5.702
Dist. restrs. and SS energy: 0.062 (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: 8
=====================================
Write number: 5
Temperature: 1.150000
Total energy: -102.601861 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -102.601861 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -102.661394 (E_RNA)
where:
Base-Base interactions energy: -66.798
where: short stacking energy: -23.304
Base-Backbone interact. energy: -1.203
local terms energy: -34.660630
where:
bonds (distance) C4'-P energy: -8.813
bonds (distance) P-C4' energy: -8.404
flat angles C4'-P-C4' energy: -7.950
flat angles P-C4'-P energy: -3.455
tors. eta vs tors. theta energy: -6.039
Dist. restrs. and SS energy: 0.060 (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: 5
Temperature: 1.200000
Total energy: -97.680145 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -97.680145 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -97.885498 (E_RNA)
where:
Base-Base interactions energy: -63.181
where: short stacking energy: -27.988
Base-Backbone interact. energy: -0.001
local terms energy: -34.703797
where:
bonds (distance) C4'-P energy: -5.596
bonds (distance) P-C4' energy: -8.379
flat angles C4'-P-C4' energy: -5.377
flat angles P-C4'-P energy: -7.778
tors. eta vs tors. theta energy: -7.573
Dist. restrs. and SS energy: 0.205 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 10
=====================================
Write number: 5
Temperature: 1.250000
Total energy: -97.060160 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -97.060160 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -97.070729 (E_RNA)
where:
Base-Base interactions energy: -60.857
where: short stacking energy: -23.231
Base-Backbone interact. energy: -0.076
local terms energy: -36.138157
where:
bonds (distance) C4'-P energy: -8.040
bonds (distance) P-C4' energy: -8.211
flat angles C4'-P-C4' energy: -7.730
flat angles P-C4'-P energy: -4.787
tors. eta vs tors. theta energy: -7.370
Dist. restrs. and SS energy: 0.011 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 6
=====================================
Write number: 5
Temperature: 1.300000
Total energy: -91.512521 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -91.512521 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -91.695012 (E_RNA)
where:
Base-Base interactions energy: -61.167
where: short stacking energy: -20.950
Base-Backbone interact. energy: -0.117
local terms energy: -30.411144
where:
bonds (distance) C4'-P energy: -8.520
bonds (distance) P-C4' energy: -7.665
flat angles C4'-P-C4' energy: -6.099
flat angles P-C4'-P energy: -3.425
tors. eta vs tors. theta energy: -4.703
Dist. restrs. and SS energy: 0.182 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 5
Temperature: 1.350000
Total energy: -97.075556 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -97.075556 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -97.091088 (E_RNA)
where:
Base-Base interactions energy: -67.744
where: short stacking energy: -29.776
Base-Backbone interact. energy: -1.334
local terms energy: -28.013318
where:
bonds (distance) C4'-P energy: -6.370
bonds (distance) P-C4' energy: -5.318
flat angles C4'-P-C4' energy: -5.750
flat angles P-C4'-P energy: -4.515
tors. eta vs tors. theta energy: -6.061
Dist. restrs. and SS energy: 0.016 (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: 5
=====================================
Write number: 6
Temperature: 0.900000
Total energy: -107.621446 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -107.621446 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -107.635358 (E_RNA)
where:
Base-Base interactions energy: -70.295
where: short stacking energy: -30.249
Base-Backbone interact. energy: -1.075
local terms energy: -36.265781
where:
bonds (distance) C4'-P energy: -8.023
bonds (distance) P-C4' energy: -6.864
flat angles C4'-P-C4' energy: -7.710
flat angles P-C4'-P energy: -5.685
tors. eta vs tors. theta energy: -7.984
Dist. restrs. and SS energy: 0.014 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 1
=====================================
Write number: 6
Temperature: 0.950000
Total energy: -103.528433 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.528433 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.528433 (E_RNA)
where:
Base-Base interactions energy: -72.737
where: short stacking energy: -29.670
Base-Backbone interact. energy: -0.001
local terms energy: -30.790004
where:
bonds (distance) C4'-P energy: -7.041
bonds (distance) P-C4' energy: -8.883
flat angles C4'-P-C4' energy: -6.599
flat angles P-C4'-P energy: -1.707
tors. eta vs tors. theta energy: -6.559
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 4
=====================================
Write number: 6
Temperature: 1.000000
Total energy: -104.720220 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -104.720220 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.720220 (E_RNA)
where:
Base-Base interactions energy: -68.539
where: short stacking energy: -28.217
Base-Backbone interact. energy: -1.015
local terms energy: -35.165814
where:
bonds (distance) C4'-P energy: -7.206
bonds (distance) P-C4' energy: -7.351
flat angles C4'-P-C4' energy: -6.926
flat angles P-C4'-P energy: -6.082
tors. eta vs tors. theta energy: -7.600
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 2
=====================================
Write number: 6
Temperature: 1.050000
Total energy: -103.195586 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.195586 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.195586 (E_RNA)
where:
Base-Base interactions energy: -69.622
where: short stacking energy: -25.492
Base-Backbone interact. energy: -2.032
local terms energy: -31.540952
where:
bonds (distance) C4'-P energy: -8.697
bonds (distance) P-C4' energy: -6.653
flat angles C4'-P-C4' energy: -3.220
flat angles P-C4'-P energy: -4.879
tors. eta vs tors. theta energy: -8.091
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 5, replica: 8
=====================================
Write number: 6
Temperature: 1.100000
Total energy: -102.893793 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -102.893793 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.033517 (E_RNA)
where:
Base-Base interactions energy: -69.755
where: short stacking energy: -29.884
Base-Backbone interact. energy: -0.535
local terms energy: -32.743535
where:
bonds (distance) C4'-P energy: -5.945
bonds (distance) P-C4' energy: -7.358
flat angles C4'-P-C4' energy: -6.046
flat angles P-C4'-P energy: -6.228
tors. eta vs tors. theta energy: -7.167
Dist. restrs. and SS energy: 0.140 (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: 3
=====================================
Write number: 6
Temperature: 1.150000
Total energy: -96.456319 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -96.456319 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -96.456319 (E_RNA)
where:
Base-Base interactions energy: -62.484
where: short stacking energy: -23.963
Base-Backbone interact. energy: 0.679
local terms energy: -34.651133
where:
bonds (distance) C4'-P energy: -6.537
bonds (distance) P-C4' energy: -8.644
flat angles C4'-P-C4' energy: -7.186
flat angles P-C4'-P energy: -6.186
tors. eta vs tors. theta energy: -6.099
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 7, replica: 10
=====================================
Write number: 6
Temperature: 1.200000
Total energy: -93.514339 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -93.514339 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -93.610129 (E_RNA)
where:
Base-Base interactions energy: -60.330
where: short stacking energy: -23.407
Base-Backbone interact. energy: -0.373
local terms energy: -32.906703
where:
bonds (distance) C4'-P energy: -5.331
bonds (distance) P-C4' energy: -8.045
flat angles C4'-P-C4' energy: -7.294
flat angles P-C4'-P energy: -6.143
tors. eta vs tors. theta energy: -6.094
Dist. restrs. and SS energy: 0.096 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 7
=====================================
Write number: 6
Temperature: 1.250000
Total energy: -83.754794 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -83.754794 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -83.997720 (E_RNA)
where:
Base-Base interactions energy: -58.677
where: short stacking energy: -19.826
Base-Backbone interact. energy: -0.617
local terms energy: -24.703454
where:
bonds (distance) C4'-P energy: -5.304
bonds (distance) P-C4' energy: -6.660
flat angles C4'-P-C4' energy: -7.466
flat angles P-C4'-P energy: -3.521
tors. eta vs tors. theta energy: -1.753
Dist. restrs. and SS energy: 0.243 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 6
=====================================
Write number: 6
Temperature: 1.300000
Total energy: -85.770781 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -85.770781 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -85.821231 (E_RNA)
where:
Base-Base interactions energy: -59.195
where: short stacking energy: -29.403
Base-Backbone interact. energy: -0.024
local terms energy: -26.602217
where:
bonds (distance) C4'-P energy: -1.808
bonds (distance) P-C4' energy: -4.628
flat angles C4'-P-C4' energy: -8.969
flat angles P-C4'-P energy: -5.409
tors. eta vs tors. theta energy: -5.788
Dist. restrs. and SS energy: 0.050 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 6
Temperature: 1.350000
Total energy: -90.254360 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -90.254360 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -90.356849 (E_RNA)
where:
Base-Base interactions energy: -59.731
where: short stacking energy: -19.151
Base-Backbone interact. energy: -0.003
local terms energy: -30.623059
where:
bonds (distance) C4'-P energy: -4.980
bonds (distance) P-C4' energy: -8.284
flat angles C4'-P-C4' energy: -7.024
flat angles P-C4'-P energy: -4.163
tors. eta vs tors. theta energy: -6.171
Dist. restrs. and SS energy: 0.102 (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: 5
=====================================
Write number: 7
Temperature: 0.900000
Total energy: -107.471556 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -107.471556 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -107.517705 (E_RNA)
where:
Base-Base interactions energy: -70.121
where: short stacking energy: -29.633
Base-Backbone interact. energy: -1.473
local terms energy: -35.923947
where:
bonds (distance) C4'-P energy: -8.102
bonds (distance) P-C4' energy: -9.066
flat angles C4'-P-C4' energy: -9.106
flat angles P-C4'-P energy: -2.324
tors. eta vs tors. theta energy: -7.326
Dist. restrs. and SS energy: 0.046 (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: 4
=====================================
Write number: 7
Temperature: 0.950000
Total energy: -107.723626 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -107.723626 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -107.723626 (E_RNA)
where:
Base-Base interactions energy: -70.606
where: short stacking energy: -29.876
Base-Backbone interact. energy: -0.092
local terms energy: -37.025179
where:
bonds (distance) C4'-P energy: -7.774
bonds (distance) P-C4' energy: -7.095
flat angles C4'-P-C4' energy: -9.170
flat angles P-C4'-P energy: -4.259
tors. eta vs tors. theta energy: -8.727
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 1
=====================================
Write number: 7
Temperature: 1.000000
Total energy: -105.428518 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -105.428518 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -105.428518 (E_RNA)
where:
Base-Base interactions energy: -70.605
where: short stacking energy: -27.975
Base-Backbone interact. energy: -0.633
local terms energy: -34.190139
where:
bonds (distance) C4'-P energy: -7.862
bonds (distance) P-C4' energy: -5.480
flat angles C4'-P-C4' energy: -7.815
flat angles P-C4'-P energy: -5.146
tors. eta vs tors. theta energy: -7.887
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 8
=====================================
Write number: 7
Temperature: 1.050000
Total energy: -106.101767 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -106.101767 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -106.117707 (E_RNA)
where:
Base-Base interactions energy: -70.610
where: short stacking energy: -29.658
Base-Backbone interact. energy: -1.509
local terms energy: -33.998877
where:
bonds (distance) C4'-P energy: -7.472
bonds (distance) P-C4' energy: -9.109
flat angles C4'-P-C4' energy: -5.743
flat angles P-C4'-P energy: -4.162
tors. eta vs tors. theta energy: -7.513
Dist. restrs. and SS energy: 0.016 (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: 2
=====================================
Write number: 7
Temperature: 1.100000
Total energy: -101.269180 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.269180 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.277564 (E_RNA)
where:
Base-Base interactions energy: -67.383
where: short stacking energy: -25.763
Base-Backbone interact. energy: -0.330
local terms energy: -33.564557
where:
bonds (distance) C4'-P energy: -7.322
bonds (distance) P-C4' energy: -7.877
flat angles C4'-P-C4' energy: -6.132
flat angles P-C4'-P energy: -3.677
tors. eta vs tors. theta energy: -8.557
Dist. restrs. and SS energy: 0.008 (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: 10
=====================================
Write number: 7
Temperature: 1.150000
Total energy: -92.539373 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -92.539373 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -92.797478 (E_RNA)
where:
Base-Base interactions energy: -60.377
where: short stacking energy: -25.950
Base-Backbone interact. energy: -0.958
local terms energy: -31.462131
where:
bonds (distance) C4'-P energy: -5.448
bonds (distance) P-C4' energy: -6.327
flat angles C4'-P-C4' energy: -6.286
flat angles P-C4'-P energy: -7.173
tors. eta vs tors. theta energy: -6.228
Dist. restrs. and SS energy: 0.258 (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: 3
=====================================
Write number: 7
Temperature: 1.200000
Total energy: -98.866224 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.866224 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.891653 (E_RNA)
where:
Base-Base interactions energy: -64.144
where: short stacking energy: -25.003
Base-Backbone interact. energy: -0.241
local terms energy: -34.507133
where:
bonds (distance) C4'-P energy: -5.633
bonds (distance) P-C4' energy: -8.597
flat angles C4'-P-C4' energy: -8.024
flat angles P-C4'-P energy: -4.938
tors. eta vs tors. theta energy: -7.315
Dist. restrs. and SS energy: 0.025 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 6
=====================================
Write number: 7
Temperature: 1.250000
Total energy: -94.495374 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -94.495374 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -94.544281 (E_RNA)
where:
Base-Base interactions energy: -56.814
where: short stacking energy: -20.790
Base-Backbone interact. energy: -1.576
local terms energy: -36.154624
where:
bonds (distance) C4'-P energy: -7.845
bonds (distance) P-C4' energy: -8.866
flat angles C4'-P-C4' energy: -4.071
flat angles P-C4'-P energy: -7.242
tors. eta vs tors. theta energy: -8.130
Dist. restrs. and SS energy: 0.049 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 7
=====================================
Write number: 7
Temperature: 1.300000
Total energy: -88.581365 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -88.581365 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -88.618202 (E_RNA)
where:
Base-Base interactions energy: -59.868
where: short stacking energy: -22.655
Base-Backbone interact. energy: -0.007
local terms energy: -28.743507
where:
bonds (distance) C4'-P energy: -5.418
bonds (distance) P-C4' energy: -5.677
flat angles C4'-P-C4' energy: -7.700
flat angles P-C4'-P energy: -2.255
tors. eta vs tors. theta energy: -7.693
Dist. restrs. and SS energy: 0.037 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 7
Temperature: 1.350000
Total energy: -60.957641 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -60.957641 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -61.657828 (E_RNA)
where:
Base-Base interactions energy: -34.828
where: short stacking energy: -13.677
Base-Backbone interact. energy: -0.426
local terms energy: -26.403577
where:
bonds (distance) C4'-P energy: -4.437
bonds (distance) P-C4' energy: -6.181
flat angles C4'-P-C4' energy: -6.878
flat angles P-C4'-P energy: -4.067
tors. eta vs tors. theta energy: -4.841
Dist. restrs. and SS energy: 0.700 (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: 4
=====================================
Write number: 8
Temperature: 0.900000
Total energy: -108.960057 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -108.960057 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -109.009139 (E_RNA)
where:
Base-Base interactions energy: -74.501
where: short stacking energy: -30.567
Base-Backbone interact. energy: 0.915
local terms energy: -35.423634
where:
bonds (distance) C4'-P energy: -7.684
bonds (distance) P-C4' energy: -8.312
flat angles C4'-P-C4' energy: -4.597
flat angles P-C4'-P energy: -5.665
tors. eta vs tors. theta energy: -9.166
Dist. restrs. and SS energy: 0.049 (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: 5
=====================================
Write number: 8
Temperature: 0.950000
Total energy: -110.329849 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -110.329849 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -110.350992 (E_RNA)
where:
Base-Base interactions energy: -72.243
where: short stacking energy: -29.745
Base-Backbone interact. energy: -0.691
local terms energy: -37.417130
where:
bonds (distance) C4'-P energy: -6.346
bonds (distance) P-C4' energy: -8.615
flat angles C4'-P-C4' energy: -8.987
flat angles P-C4'-P energy: -4.528
tors. eta vs tors. theta energy: -8.940
Dist. restrs. and SS energy: 0.021 (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: 8
=====================================
Write number: 8
Temperature: 1.000000
Total energy: -103.769527 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.769527 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.769527 (E_RNA)
where:
Base-Base interactions energy: -71.764
where: short stacking energy: -28.608
Base-Backbone interact. energy: -0.004
local terms energy: -32.000791
where:
bonds (distance) C4'-P energy: -7.592
bonds (distance) P-C4' energy: -7.128
flat angles C4'-P-C4' energy: -5.689
flat angles P-C4'-P energy: -6.598
tors. eta vs tors. theta energy: -4.993
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 1
=====================================
Write number: 8
Temperature: 1.050000
Total energy: -101.714266 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.714266 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.735766 (E_RNA)
where:
Base-Base interactions energy: -67.538
where: short stacking energy: -26.248
Base-Backbone interact. energy: -0.659
local terms energy: -33.539491
where:
bonds (distance) C4'-P energy: -8.503
bonds (distance) P-C4' energy: -7.330
flat angles C4'-P-C4' energy: -6.371
flat angles P-C4'-P energy: -3.990
tors. eta vs tors. theta energy: -7.346
Dist. restrs. and SS energy: 0.022 (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: 2
=====================================
Write number: 8
Temperature: 1.100000
Total energy: -102.652003 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -102.652003 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -102.844252 (E_RNA)
where:
Base-Base interactions energy: -67.442
where: short stacking energy: -25.380
Base-Backbone interact. energy: -0.001
local terms energy: -35.402037
where:
bonds (distance) C4'-P energy: -7.020
bonds (distance) P-C4' energy: -8.507
flat angles C4'-P-C4' energy: -6.225
flat angles P-C4'-P energy: -6.017
tors. eta vs tors. theta energy: -7.633
Dist. restrs. and SS energy: 0.192 (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: 10
=====================================
Write number: 8
Temperature: 1.150000
Total energy: -88.237026 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -88.237026 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -88.634566 (E_RNA)
where:
Base-Base interactions energy: -57.983
where: short stacking energy: -21.443
Base-Backbone interact. energy: -0.466
local terms energy: -30.186005
where:
bonds (distance) C4'-P energy: -5.664
bonds (distance) P-C4' energy: -9.032
flat angles C4'-P-C4' energy: -8.301
flat angles P-C4'-P energy: -1.708
tors. eta vs tors. theta energy: -5.481
Dist. restrs. and SS energy: 0.398 (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: 3
=====================================
Write number: 8
Temperature: 1.200000
Total energy: -101.005081 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.005081 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.065075 (E_RNA)
where:
Base-Base interactions energy: -70.620
where: short stacking energy: -30.395
Base-Backbone interact. energy: -1.204
local terms energy: -29.241033
where:
bonds (distance) C4'-P energy: -5.307
bonds (distance) P-C4' energy: -5.762
flat angles C4'-P-C4' energy: -4.114
flat angles P-C4'-P energy: -5.942
tors. eta vs tors. theta energy: -8.116
Dist. restrs. and SS energy: 0.060 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 6
=====================================
Write number: 8
Temperature: 1.250000
Total energy: -99.515866 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.515866 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -99.515866 (E_RNA)
where:
Base-Base interactions energy: -63.704
where: short stacking energy: -25.630
Base-Backbone interact. energy: -0.014
local terms energy: -35.798050
where:
bonds (distance) C4'-P energy: -8.743
bonds (distance) P-C4' energy: -8.171
flat angles C4'-P-C4' energy: -6.582
flat angles P-C4'-P energy: -5.326
tors. eta vs tors. theta energy: -6.976
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 7
=====================================
Write number: 8
Temperature: 1.300000
Total energy: -55.342943 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -55.342943 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -59.656932 (E_RNA)
where:
Base-Base interactions energy: -27.398
where: short stacking energy: -15.170
Base-Backbone interact. energy: -0.059
local terms energy: -32.199448
where:
bonds (distance) C4'-P energy: -8.449
bonds (distance) P-C4' energy: -9.292
flat angles C4'-P-C4' energy: -6.716
flat angles P-C4'-P energy: -5.836
tors. eta vs tors. theta energy: -1.907
Dist. restrs. and SS energy: 4.314 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 8
Temperature: 1.350000
Total energy: -95.457842 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -95.457842 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -95.478291 (E_RNA)
where:
Base-Base interactions energy: -63.686
where: short stacking energy: -24.824
Base-Backbone interact. energy: -1.272
local terms energy: -30.520633
where:
bonds (distance) C4'-P energy: -6.152
bonds (distance) P-C4' energy: -7.812
flat angles C4'-P-C4' energy: -7.205
flat angles P-C4'-P energy: -4.787
tors. eta vs tors. theta energy: -4.566
Dist. restrs. and SS energy: 0.020 (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: 4
=====================================
Write number: 9
Temperature: 0.900000
Total energy: -109.959237 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -109.959237 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -109.959237 (E_RNA)
where:
Base-Base interactions energy: -72.318
where: short stacking energy: -28.081
Base-Backbone interact. energy: -1.220
local terms energy: -36.421849
where:
bonds (distance) C4'-P energy: -7.115
bonds (distance) P-C4' energy: -8.830
flat angles C4'-P-C4' energy: -7.410
flat angles P-C4'-P energy: -5.146
tors. eta vs tors. theta energy: -7.921
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 8
=====================================
Write number: 9
Temperature: 0.950000
Total energy: -108.822229 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -108.822229 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -108.822551 (E_RNA)
where:
Base-Base interactions energy: -71.286
where: short stacking energy: -29.697
Base-Backbone interact. energy: -0.258
local terms energy: -37.278474
where:
bonds (distance) C4'-P energy: -7.542
bonds (distance) P-C4' energy: -7.883
flat angles C4'-P-C4' energy: -6.584
flat angles P-C4'-P energy: -6.089
tors. eta vs tors. theta energy: -9.180
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 5
=====================================
Write number: 9
Temperature: 1.000000
Total energy: -101.006379 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.006379 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.041223 (E_RNA)
where:
Base-Base interactions energy: -69.029
where: short stacking energy: -28.160
Base-Backbone interact. energy: -0.375
local terms energy: -31.637023
where:
bonds (distance) C4'-P energy: -8.565
bonds (distance) P-C4' energy: -6.057
flat angles C4'-P-C4' energy: -8.226
flat angles P-C4'-P energy: -1.567
tors. eta vs tors. theta energy: -7.222
Dist. restrs. and SS energy: 0.035 (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: 2
=====================================
Write number: 9
Temperature: 1.050000
Total energy: -101.433437 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.433437 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.460544 (E_RNA)
where:
Base-Base interactions energy: -67.335
where: short stacking energy: -25.883
Base-Backbone interact. energy: -0.022
local terms energy: -34.103633
where:
bonds (distance) C4'-P energy: -7.580
bonds (distance) P-C4' energy: -9.087
flat angles C4'-P-C4' energy: -7.083
flat angles P-C4'-P energy: -2.923
tors. eta vs tors. theta energy: -7.431
Dist. restrs. and SS energy: 0.027 (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: 1
=====================================
Write number: 9
Temperature: 1.100000
Total energy: -106.177010 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -106.177010 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -106.183152 (E_RNA)
where:
Base-Base interactions energy: -67.485
where: short stacking energy: -26.133
Base-Backbone interact. energy: -0.356
local terms energy: -38.342280
where:
bonds (distance) C4'-P energy: -7.712
bonds (distance) P-C4' energy: -8.284
flat angles C4'-P-C4' energy: -9.049
flat angles P-C4'-P energy: -5.014
tors. eta vs tors. theta energy: -8.284
Dist. restrs. and SS energy: 0.006 (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: 3
=====================================
Write number: 9
Temperature: 1.150000
Total energy: -98.018650 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -98.018650 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -98.082377 (E_RNA)
where:
Base-Base interactions energy: -62.877
where: short stacking energy: -22.075
Base-Backbone interact. energy: -0.553
local terms energy: -34.651840
where:
bonds (distance) C4'-P energy: -7.302
bonds (distance) P-C4' energy: -9.581
flat angles C4'-P-C4' energy: -6.177
flat angles P-C4'-P energy: -5.400
tors. eta vs tors. theta energy: -6.191
Dist. restrs. and SS energy: 0.064 (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: 10
=====================================
Write number: 9
Temperature: 1.200000
Total energy: -96.036011 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -96.036011 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -96.036011 (E_RNA)
where:
Base-Base interactions energy: -68.612
where: short stacking energy: -28.921
Base-Backbone interact. energy: -0.179
local terms energy: -27.244715
where:
bonds (distance) C4'-P energy: -3.681
bonds (distance) P-C4' energy: -8.253
flat angles C4'-P-C4' energy: -4.234
flat angles P-C4'-P energy: -4.874
tors. eta vs tors. theta energy: -6.204
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 7
=====================================
Write number: 9
Temperature: 1.250000
Total energy: -101.164493 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -101.164493 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -101.173934 (E_RNA)
where:
Base-Base interactions energy: -63.918
where: short stacking energy: -31.184
Base-Backbone interact. energy: -0.210
local terms energy: -37.046308
where:
bonds (distance) C4'-P energy: -5.705
bonds (distance) P-C4' energy: -9.807
flat angles C4'-P-C4' energy: -8.232
flat angles P-C4'-P energy: -3.867
tors. eta vs tors. theta energy: -9.435
Dist. restrs. and SS energy: 0.009 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 6
=====================================
Write number: 9
Temperature: 1.300000
Total energy: -99.968235 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.968235 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -100.015074 (E_RNA)
where:
Base-Base interactions energy: -63.643
where: short stacking energy: -27.134
Base-Backbone interact. energy: -0.285
local terms energy: -36.087385
where:
bonds (distance) C4'-P energy: -7.526
bonds (distance) P-C4' energy: -8.376
flat angles C4'-P-C4' energy: -7.690
flat angles P-C4'-P energy: -7.194
tors. eta vs tors. theta energy: -5.303
Dist. restrs. and SS energy: 0.047 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 9
Temperature: 1.350000
Total energy: -78.392107 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -78.392107 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -78.470941 (E_RNA)
where:
Base-Base interactions energy: -54.965
where: short stacking energy: -25.424
Base-Backbone interact. energy: -0.005
local terms energy: -23.501700
where:
bonds (distance) C4'-P energy: -2.761
bonds (distance) P-C4' energy: -7.498
flat angles C4'-P-C4' energy: -6.057
flat angles P-C4'-P energy: -0.965
tors. eta vs tors. theta energy: -6.220
Dist. restrs. and SS energy: 0.079 (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: 8
=====================================
Write number: 10
Temperature: 0.900000
Total energy: -106.572195 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -106.572195 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -106.572195 (E_RNA)
where:
Base-Base interactions energy: -72.145
where: short stacking energy: -28.899
Base-Backbone interact. energy: -0.824
local terms energy: -33.603049
where:
bonds (distance) C4'-P energy: -6.793
bonds (distance) P-C4' energy: -7.591
flat angles C4'-P-C4' energy: -7.990
flat angles P-C4'-P energy: -3.359
tors. eta vs tors. theta energy: -7.871
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 4
=====================================
Write number: 10
Temperature: 0.950000
Total energy: -114.108045 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -114.108045 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -114.118598 (E_RNA)
where:
Base-Base interactions energy: -75.644
where: short stacking energy: -32.840
Base-Backbone interact. energy: -0.000
local terms energy: -38.474071
where:
bonds (distance) C4'-P energy: -8.387
bonds (distance) P-C4' energy: -9.045
flat angles C4'-P-C4' energy: -6.118
flat angles P-C4'-P energy: -5.111
tors. eta vs tors. theta energy: -9.813
Dist. restrs. and SS energy: 0.011 (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: 2
=====================================
Write number: 10
Temperature: 1.000000
Total energy: -103.838541 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.838541 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.849698 (E_RNA)
where:
Base-Base interactions energy: -67.852
where: short stacking energy: -29.518
Base-Backbone interact. energy: -0.170
local terms energy: -35.827600
where:
bonds (distance) C4'-P energy: -8.697
bonds (distance) P-C4' energy: -7.326
flat angles C4'-P-C4' energy: -8.765
flat angles P-C4'-P energy: -5.034
tors. eta vs tors. theta energy: -6.006
Dist. restrs. and SS energy: 0.011 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 4, replica: 5
=====================================
Write number: 10
Temperature: 1.050000
Total energy: -106.145435 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -106.145435 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -106.156165 (E_RNA)
where:
Base-Base interactions energy: -69.481
where: short stacking energy: -28.846
Base-Backbone interact. energy: 0.438
local terms energy: -37.112832
where:
bonds (distance) C4'-P energy: -7.588
bonds (distance) P-C4' energy: -8.630
flat angles C4'-P-C4' energy: -6.084
flat angles P-C4'-P energy: -7.053
tors. eta vs tors. theta energy: -7.758
Dist. restrs. and SS energy: 0.011 (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: 3
=====================================
Write number: 10
Temperature: 1.100000
Total energy: -103.503883 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -103.503883 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -103.503883 (E_RNA)
where:
Base-Base interactions energy: -69.890
where: short stacking energy: -28.782
Base-Backbone interact. energy: -0.776
local terms energy: -32.837747
where:
bonds (distance) C4'-P energy: -5.625
bonds (distance) P-C4' energy: -7.326
flat angles C4'-P-C4' energy: -7.855
flat angles P-C4'-P energy: -5.629
tors. eta vs tors. theta energy: -6.402
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 1
=====================================
Write number: 10
Temperature: 1.150000
Total energy: -100.015911 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -100.015911 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -100.022019 (E_RNA)
where:
Base-Base interactions energy: -67.161
where: short stacking energy: -25.917
Base-Backbone interact. energy: -0.780
local terms energy: -32.080544
where:
bonds (distance) C4'-P energy: -6.673
bonds (distance) P-C4' energy: -8.873
flat angles C4'-P-C4' energy: -6.689
flat angles P-C4'-P energy: -3.585
tors. eta vs tors. theta energy: -6.261
Dist. restrs. and SS energy: 0.006 (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: 10
Temperature: 1.200000
Total energy: -93.069453 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -93.069453 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -93.406264 (E_RNA)
where:
Base-Base interactions energy: -58.386
where: short stacking energy: -24.738
Base-Backbone interact. energy: -0.028
local terms energy: -34.992398
where:
bonds (distance) C4'-P energy: -7.107
bonds (distance) P-C4' energy: -9.348
flat angles C4'-P-C4' energy: -6.302
flat angles P-C4'-P energy: -6.295
tors. eta vs tors. theta energy: -5.940
Dist. restrs. and SS energy: 0.337 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 10
=====================================
Write number: 10
Temperature: 1.250000
Total energy: -96.468098 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -96.468098 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -96.470891 (E_RNA)
where:
Base-Base interactions energy: -66.706
where: short stacking energy: -26.780
Base-Backbone interact. energy: -0.105
local terms energy: -29.660346
where:
bonds (distance) C4'-P energy: -6.044
bonds (distance) P-C4' energy: -7.297
flat angles C4'-P-C4' energy: -6.439
flat angles P-C4'-P energy: -2.288
tors. eta vs tors. theta energy: -7.592
Dist. restrs. and SS energy: 0.003 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 6
=====================================
Write number: 10
Temperature: 1.300000
Total energy: -95.097110 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -95.097110 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -95.180169 (E_RNA)
where:
Base-Base interactions energy: -63.609
where: short stacking energy: -23.738
Base-Backbone interact. energy: -0.708
local terms energy: -30.863022
where:
bonds (distance) C4'-P energy: -3.531
bonds (distance) P-C4' energy: -8.171
flat angles C4'-P-C4' energy: -5.104
flat angles P-C4'-P energy: -5.429
tors. eta vs tors. theta energy: -8.628
Dist. restrs. and SS energy: 0.083 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 10
Temperature: 1.350000
Total energy: -89.377259 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -89.377259 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -89.546280 (E_RNA)
where:
Base-Base interactions energy: -60.545
where: short stacking energy: -22.132
Base-Backbone interact. energy: 1.396
local terms energy: -30.397034
where:
bonds (distance) C4'-P energy: -7.853
bonds (distance) P-C4' energy: -8.668
flat angles C4'-P-C4' energy: -5.075
flat angles P-C4'-P energy: -5.954
tors. eta vs tors. theta energy: -2.846
Dist. restrs. and SS energy: 0.169 (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: 8
=====================================
Write number: 11
Temperature: 0.900000
Total energy: -107.797136 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -107.797136 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -107.797136 (E_RNA)
where:
Base-Base interactions energy: -71.408
where: short stacking energy: -34.471
Base-Backbone interact. energy: -1.908
local terms energy: -34.480964
where:
bonds (distance) C4'-P energy: -7.120
bonds (distance) P-C4' energy: -7.910
flat angles C4'-P-C4' energy: -6.957
flat angles P-C4'-P energy: -3.907
tors. eta vs tors. theta energy: -8.586
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 2, replica: 2
=====================================
Write number: 11
Temperature: 0.950000
Total energy: -109.245979 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -109.245979 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -109.245979 (E_RNA)
where:
Base-Base interactions energy: -70.083
where: short stacking energy: -32.395
Base-Backbone interact. energy: -1.854
local terms energy: -37.309140
where:
bonds (distance) C4'-P energy: -7.439
bonds (distance) P-C4' energy: -7.646
flat angles C4'-P-C4' energy: -7.684
flat angles P-C4'-P energy: -5.349
tors. eta vs tors. theta energy: -9.191
Dist. restrs. and SS energy: 0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 3, replica: 4
=====================================
Write number: 11
Temperature: 1.000000
Total energy: -104.428614 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -104.428614 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -104.463053 (E_RNA)
where:
Base-Base interactions energy: -67.401
where: short stacking energy: -27.506
Base-Backbone interact. energy: -0.709
local terms energy: -36.353423
where:
bonds (distance) C4'-P energy: -9.028
bonds (distance) P-C4' energy: -8.407
flat angles C4'-P-C4' energy: -8.482
flat angles P-C4'-P energy: -4.563
tors. eta vs tors. theta energy: -5.873
Dist. restrs. and SS energy: 0.034 (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: 3
=====================================
Write number: 11
Temperature: 1.050000
Total energy: -99.309097 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -99.309097 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -99.379252 (E_RNA)
where:
Base-Base interactions energy: -69.248
where: short stacking energy: -28.336
Base-Backbone interact. energy: -0.105
local terms energy: -30.026422
where:
bonds (distance) C4'-P energy: -6.733
bonds (distance) P-C4' energy: -5.110
flat angles C4'-P-C4' energy: -8.583
flat angles P-C4'-P energy: -1.938
tors. eta vs tors. theta energy: -7.663
Dist. restrs. and SS energy: 0.070 (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: 11
Temperature: 1.100000
Total energy: -102.648409 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -102.648409 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -102.648409 (E_RNA)
where:
Base-Base interactions energy: -69.376
where: short stacking energy: -27.613
Base-Backbone interact. energy: -0.002
local terms energy: -33.271173
where:
bonds (distance) C4'-P energy: -5.279
bonds (distance) P-C4' energy: -7.910
flat angles C4'-P-C4' energy: -9.058
flat angles P-C4'-P energy: -6.235
tors. eta vs tors. theta energy: -4.789
Dist. restrs. and SS energy: -0.000 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 6, replica: 7
=====================================
Write number: 11
Temperature: 1.150000
Total energy: -100.816282 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -100.816282 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -100.851168 (E_RNA)
where:
Base-Base interactions energy: -67.644
where: short stacking energy: -27.691
Base-Backbone interact. energy: -0.723
local terms energy: -32.484431
where:
bonds (distance) C4'-P energy: -3.907
bonds (distance) P-C4' energy: -8.858
flat angles C4'-P-C4' energy: -8.139
flat angles P-C4'-P energy: -4.603
tors. eta vs tors. theta energy: -6.977
Dist. restrs. and SS energy: 0.035 (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: 1
=====================================
Write number: 11
Temperature: 1.200000
Total energy: -93.388443 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -93.388443 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -93.427544 (E_RNA)
where:
Base-Base interactions energy: -60.129
where: short stacking energy: -23.811
Base-Backbone interact. energy: -0.471
local terms energy: -32.827577
where:
bonds (distance) C4'-P energy: -5.965
bonds (distance) P-C4' energy: -8.566
flat angles C4'-P-C4' energy: -6.878
flat angles P-C4'-P energy: -5.717
tors. eta vs tors. theta energy: -5.702
Dist. restrs. and SS energy: 0.039 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 8, replica: 6
=====================================
Write number: 11
Temperature: 1.250000
Total energy: -93.113506 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -93.113506 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -93.149995 (E_RNA)
where:
Base-Base interactions energy: -63.045
where: short stacking energy: -27.020
Base-Backbone interact. energy: -0.001
local terms energy: -30.104275
where:
bonds (distance) C4'-P energy: -5.804
bonds (distance) P-C4' energy: -5.951
flat angles C4'-P-C4' energy: -8.539
flat angles P-C4'-P energy: -2.258
tors. eta vs tors. theta energy: -7.553
Dist. restrs. and SS energy: 0.036 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 9, replica: 10
=====================================
Write number: 11
Temperature: 1.300000
Total energy: -97.421234 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -97.421234 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -97.422420 (E_RNA)
where:
Base-Base interactions energy: -60.596
where: short stacking energy: -25.399
Base-Backbone interact. energy: -0.021
local terms energy: -36.805153
where:
bonds (distance) C4'-P energy: -8.309
bonds (distance) P-C4' energy: -8.665
flat angles C4'-P-C4' energy: -7.835
flat angles P-C4'-P energy: -5.351
tors. eta vs tors. theta energy: -6.645
Dist. restrs. and SS energy: 0.001 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
==================================
temp. level: 10, replica: 9
=====================================
Write number: 11
Temperature: 1.350000
Total energy: -93.557508 (ES_TOTAL = E_TOTAL + S_TOTAL)
where:
RNA energy: -93.557508 (E_RNA + S_DIST_RNA + S_LIMSPR_RNA)
where:
Molecular energy: -93.565622 (E_RNA)
where:
Base-Base interactions energy: -63.645
where: short stacking energy: -28.393
Base-Backbone interact. energy: -0.200
local terms energy: -29.720815
where:
bonds (distance) C4'-P energy: -6.955
bonds (distance) P-C4' energy: -7.527
flat angles C4'-P-C4' energy: -4.648
flat angles P-C4'-P energy: -3.214
tors. eta vs tors. theta energy: -7.377
Dist. restrs. and SS energy: 0.008 (S_DIST_RNA)
chem. prob. restrs. energy: 0.000 (S_CHEM_RNA)
Limit. sphere exceed penalty: 0.000 (S_LIMSPR_RNA)
replica 8 ended at temp. level: 1, temp: 0.900000
for this replica:
moves confirmed at first: 126758
moves confirmed later: 143212
all moves confirmed: 269970
percent of confirmed moves: 1.687312
current total energy: -87.691666
recalc. total energy: -87.691666
replica 2 ended at temp. level: 2, temp: 0.950000
for this replica:
moves confirmed at first: 124577
moves confirmed later: 140381
all moves confirmed: 264958
percent of confirmed moves: 1.655987
current total energy: -81.024480
recalc. total energy: -81.024480
replica 3 ended at temp. level: 3, temp: 1.000000
for this replica:
moves confirmed at first: 130108
moves confirmed later: 146155
all moves confirmed: 276263
percent of confirmed moves: 1.726644
current total energy: -80.757177
recalc. total energy: -80.757177
replica 4 ended at temp. level: 4, temp: 1.050000
for this replica:
moves confirmed at first: 123582
moves confirmed later: 138521
all moves confirmed: 262103
percent of confirmed moves: 1.638144
current total energy: -87.199188
recalc. total energy: -87.199188
replica 7 ended at temp. level: 5, temp: 1.100000
for this replica:
moves confirmed at first: 154537
moves confirmed later: 173413
all moves confirmed: 327950
percent of confirmed moves: 2.049688
current total energy: -70.966487
recalc. total energy: -70.966487
replica 5 ended at temp. level: 6, temp: 1.150000
for this replica:
moves confirmed at first: 119442
moves confirmed later: 131096
all moves confirmed: 250538
percent of confirmed moves: 1.565862
current total energy: -76.134079
recalc. total energy: -76.134079
replica 6 ended at temp. level: 7, temp: 1.200000
for this replica:
moves confirmed at first: 144653
moves confirmed later: 164261
all moves confirmed: 308914
percent of confirmed moves: 1.930713
current total energy: -73.631276
recalc. total energy: -73.631276
replica 1 ended at temp. level: 8, temp: 1.250000
for this replica:
moves confirmed at first: 127041
moves confirmed later: 139183
all moves confirmed: 266224
percent of confirmed moves: 1.663900
current total energy: -66.663107
recalc. total energy: -66.663107
replica 9 ended at temp. level: 9, temp: 1.300000
for this replica:
moves confirmed at first: 175870
moves confirmed later: 197769
all moves confirmed: 373639
percent of confirmed moves: 2.335244
current total energy: -55.627179
recalc. total energy: -55.627179
replica 10 ended at temp. level: 10, temp: 1.350000
for this replica:
moves confirmed at first: 156938
moves confirmed later: 176681
all moves confirmed: 333619
percent of confirmed moves: 2.085119
current total energy: -68.521863
recalc. total energy: -68.521863
Time of doing 160000 iterations: 28.728 seconds
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Naeim @ IIMCB Genesilico group | magnus @ Harvard
Naeim @ IIMCB Genesilico group | magnus @ Harvard