SimRNAweb2.0


SimRNA (Demo1)

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 top five clusters of your simulation:

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:

Demo1-5a837e9e

1st cluster representative:

2nd cluster representative:

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