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[filename].LOG
A record of the LINUS simulation.
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LINUS version 2.3
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Simulation starting time: Wed Apr 14 09:52:43 2004
Input PDB Filename: ala.pdb
Molecule POLYALA
Number of Residues: 11
Number of Atoms : 69
----- Simulation Parameters -----
Number of Cycles: 500
Structure Save Frequency: 10
Random Generator Seeds at Start: (4137497295.0, 3761194588.0, 3762611522.0, 2003469299.0, 621661198.0, 4231236562.0)
Beta for run: 2
Number of trials: 1
----- Bump Check Information -----
Total Number of Bumps = 0
----- Contact Score Information -----
Contact probe size: 2.8
Total possible number of contacts: 25
------ Contact Score Listing -----
1 ALA CB 3 ALA CB Distance = 6.795 Score = 0.000
2 ALA CB 4 ALA CB Distance = 6.795 Score = 0.000
3 ALA CB 5 ALA CB Distance = 6.796 Score = 0.000
4 ALA CB 6 ALA CB Distance = 6.796 Score = 0.000
5 ALA CB 7 ALA CB Distance = 6.796 Score = 0.000
6 ALA CB 8 ALA CB Distance = 6.796 Score = 0.000
7 ALA CB 9 ALA CB Distance = 6.796 Score = 0.000
Total Contact Score = -0.00111561
----- Hydrogen Bond Score Information -----
Hydrogen Bond Distance: 3
Hydrogen Bond Torsion: 130
Hydrogen Bond Probe Size: 1.5
Hydrogen Bond Score:
Short: 0.6
Long: 1
------ Hydrogen Bond Score Listing -----
Total Hydrogen Bond Score = 0.000
Total Energy of Initial Structure = -0.00111561
HBond Minimum Window Size: 2
HBond Maximum Window Size: 6
Contact Minimum Window Size: 2
Contact Maximum Window Size: 6
----- Sampling Weights at Start of Run -----
RESIDUE HELIX SHEET TURN1 TURN2 COIL PII
0 ACE 0.200 0.200 0.100 0.100 0.200 0.200
1 ALA 0.200 0.200 0.100 0.100 0.200 0.200
2 ALA 0.200 0.200 0.100 0.100 0.200 0.200
3 ALA 0.200 0.200 0.100 0.100 0.200 0.200
4 ALA 0.200 0.200 0.100 0.100 0.200 0.200
5 ALA 0.200 0.200 0.100 0.100 0.200 0.200
6 ALA 0.200 0.200 0.100 0.100 0.200 0.200
7 ALA 0.200 0.200 0.100 0.100 0.200 0.200
8 ALA 0.200 0.200 0.100 0.100 0.200 0.200
9 ALA 0.200 0.200 0.100 0.100 0.200 0.200
10 NME 0.200 0.200 0.100 0.100 0.200 0.200
Simulation Finished at: Wed Apr 14 09:52:45 2004
Number of Structures Accepted: 504
Number of Structures Rejected by Sterics: 1474
Total Number of Structures Rejected: 2996
Best Score: -5.93433
Final Score: -3.89311
Random Generator Seeds at End: (3742073636.0, 3489762168.0, 811740156.0, 2135120641.0, 3537347582.0, 4145701928.0)
----- Bump Check Information -----
0 ACE O 4 ALA H Minimum = 2.025 Actual = 1.94075
3 ALA O 7 ALA H Minimum = 2.016 Actual = 1.86658
4 ALA O 8 ALA H Minimum = 2.016 Actual = 1.80424
6 ALA O 9 ALA H Minimum = 2.016 Actual = 1.89252
Total Number of Bumps = 4
----- Contact Score Information -----
Contact probe size: 2.8
Total possible number of contacts: 25
------ Contact Score Listing -----
1 ALA CB 4 ALA CB Distance = 5.895 Score = 0.032
2 ALA CB 5 ALA CB Distance = 5.796 Score = 0.036
3 ALA CB 6 ALA CB Distance = 6.196 Score = 0.022
3 ALA CB 7 ALA CB Distance = 5.521 Score = 0.046
4 ALA CB 7 ALA CB Distance = 5.730 Score = 0.038
4 ALA CB 8 ALA CB Distance = 5.703 Score = 0.039
5 ALA CB 8 ALA CB Distance = 6.091 Score = 0.025
6 ALA CB 9 ALA CB Distance = 5.650 Score = 0.041
Total Contact Score = -0.279228
----- Hydrogen Bond Score Information -----
Hydrogen Bond Distance: 3
Hydrogen Bond Torsion: 130
Hydrogen Bond Probe Size: 1.5
Hydrogen Bond Score:
Short: 0.6
Long: 1
------ Hydrogen Bond Score Listing -----
5 ALA N 2 ALA O Distance = 3.213 Score = 0.515
6 ALA N 2 ALA O Distance = 3.405 Score = 0.438
7 ALA N 3 ALA O Distance = 2.791 Score = 0.600
8 ALA N 4 ALA O Distance = 2.756 Score = 0.600
9 ALA N 6 ALA O Distance = 2.658 Score = 0.600
Total Hydrogen Bond Score = -2.753
Total Energy of Initial Structure = -3.03207
----- Sampling Weights at Start of Run -----
----- Move Type Details ----
Residue Helix Sheet Turn1 Turn2 Coil PII
Accepted Rejected Accepted Rejected Accepted Rejected Accepted Rejected Accepted Rejected Accepted Rejected
0 ACE 0 0 0 0 0 0 0 0 0 0 0 0
1 ALA 0 0 0 0 0 0 0 0 0 0 0 0
2 ALA 66 47 18 79 10 38 2 43 9 83 16 80
3 ALA 42 54 6 91 5 56 3 32 6 84 12 83
4 ALA 41 72 5 114 3 48 4 44 1 91 4 98
5 ALA 39 54 1 85 3 35 2 43 2 104 4 99
6 ALA 40 50 1 95 2 47 3 54 2 108 4 94
7 ALA 41 56 5 101 2 39 5 58 4 96 7 92
8 ALA 52 47 6 89 5 52 9 35 5 108 7 118
9 ALA 0 0 0 0 0 0 0 0 0 0 0 0
10 NME 0 0 0 0 0 0 0 0 0 0 0 0
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