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[filename].LOG

A record of the LINUS simulation.


============================================================
LINUS version 2.4
============================================================

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