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logfile1
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Using parameters from /home/rpagan/Desktop/nuneutralrobustness/scwrl4_lin//Scwrl4.ini
<Timing tag = "Loading_PDB_file" duration = "0.000" />
Using rotamer library: /home/rpagan/Desktop/nuneutralrobustness/scwrl4_lin/bbDepRotLib.bin
Caution! Flexible subrotamers are disabled (Rigid Rotamer Model has been forced)
Residue A 1 is being treated as N-terminal
<Timing tag = "Adding_residues" duration = "0.000" />
Sequence file has been loaded
---------------
"sgknvwwamilsmniqyvvvmfiicfcscqpivsvintqyhpamvfglincdhsgr"
---------------
Warning! In the provided sequence file, the position 0 reads as 's' which mismatches the MET A 1 in the input PDB file.
9 MET rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 1 reads as 'g' which mismatches the THR A 2 in the input PDB file.
1 THR rotamers derived from the rotamer library will be used
Incomplete LYS sidechain at A 3 in the input PDB file.
26 LYS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 3 reads as 'n' which mismatches the GLN A 4 in the input PDB file.
19 GLN rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 4 reads as 'v' which mismatches the GLU A 5 in the input PDB file.
3 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 5 reads as 'w' which mismatches the LYS A 6 in the input PDB file.
16 LYS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 6 reads as 'w' which mismatches the THR A 7 in the input PDB file.
17 THR rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 8 reads as 'm' which mismatches the LEU A 9 in the input PDB file.
12 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 9 reads as 'i' which mismatches the ASN A 10 in the input PDB file.
4 ASN rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 10 reads as 'l' which mismatches the MET A 11 in the input PDB file.
3 MET rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 11 reads as 's' which mismatches the ALA A 12 in the input PDB file.
9 ALA rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 12 reads as 'm' which mismatches the ARG A 13 in the input PDB file.
12 ARG rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 13 reads as 'n' which mismatches the PHE A 14 in the input PDB file.
20 PHE rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 15 reads as 'q' which mismatches the ARG A 16 in the input PDB file.
42 ARG rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 16 reads as 'y' which mismatches the SER A 17 in the input PDB file.
16 SER rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 17 reads as 'v' which mismatches the GLN A 18 in the input PDB file.
2 GLN rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 18 reads as 'v' which mismatches the THR A 19 in the input PDB file.
3 THR rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 19 reads as 'v' which mismatches the LEU A 20 in the input PDB file.
3 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 20 reads as 'm' which mismatches the THR A 21 in the input PDB file.
12 THR rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 21 reads as 'f' which mismatches the LEU A 22 in the input PDB file.
9 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 22 reads as 'i' which mismatches the LEU A 23 in the input PDB file.
4 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 23 reads as 'i' which mismatches the GLU A 24 in the input PDB file.
4 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 24 reads as 'c' which mismatches the LYS A 25 in the input PDB file.
3 LYS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 25 reads as 'f' which mismatches the LEU A 26 in the input PDB file.
10 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 26 reads as 'c' which mismatches the ASN A 27 in the input PDB file.
2 ASN rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 27 reads as 's' which mismatches the GLU A 28 in the input PDB file.
9 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 28 reads as 'c' which mismatches the LEU A 29 in the input PDB file.
2 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 29 reads as 'q' which mismatches the ASP A 30 in the input PDB file.
23 ASP rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 30 reads as 'p' which mismatches the ALA A 31 in the input PDB file.
2 ALA rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 31 reads as 'i' which mismatches the ASP A 32 in the input PDB file.
2 ASP rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 32 reads as 'v' which mismatches the GLU A 33 in the input PDB file.
3 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 33 reads as 's' which mismatches the GLN A 34 in the input PDB file.
9 GLN rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 34 reads as 'v' which mismatches the ALA A 35 in the input PDB file.
2 ALA rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 35 reads as 'i' which mismatches the ASP A 36 in the input PDB file.
2 ASP rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 36 reads as 'n' which mismatches the ILE A 37 in the input PDB file.
18 ILE rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 37 reads as 't' which mismatches the CYS A 38 in the input PDB file.
6 CYS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 38 reads as 'q' which mismatches the GLU A 39 in the input PDB file.
46 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 39 reads as 'y' which mismatches the SER A 40 in the input PDB file.
20 SER rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 40 reads as 'h' which mismatches the LEU A 41 in the input PDB file.
36 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 41 reads as 'p' which mismatches the HIS A 42 in the input PDB file.
2 HIS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 42 reads as 'a' which mismatches the ASP A 43 in the input PDB file.
1 ASP rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 43 reads as 'm' which mismatches the HIS A 44 in the input PDB file.
13 HIS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 44 reads as 'v' which mismatches the ALA A 45 in the input PDB file.
2 ALA rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 45 reads as 'f' which mismatches the ASP A 46 in the input PDB file.
9 ASP rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 46 reads as 'g' which mismatches the GLU A 47 in the input PDB file.
1 GLU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 48 reads as 'i' which mismatches the TYR A 49 in the input PDB file.
2 TYR rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 49 reads as 'n' which mismatches the ARG A 50 in the input PDB file.
19 ARG rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 50 reads as 'c' which mismatches the SER A 51 in the input PDB file.
2 SER rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 51 reads as 'd' which mismatches the CYS A 52 in the input PDB file.
11 CYS rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 52 reads as 'h' which mismatches the LEU A 53 in the input PDB file.
42 LEU rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 53 reads as 's' which mismatches the ALA A 54 in the input PDB file.
9 ALA rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 54 reads as 'g' which mismatches the ARG A 55 in the input PDB file.
1 ARG rotamers derived from the rotamer library will be used
Warning! In the provided sequence file, the position 55 reads as 'r' which mismatches the PHE A 56 in the input PDB file.
21 PHE rotamers derived from the rotamer library will be used
<Timing tag = "Building_Atoms_Sets" duration = "0.000" />
<Timing tag = "Building_Flexible_Subrotamers" duration = "0.000" />
<Timing tag = "Computing_Symmetry_Operators" duration = "0.000" />
<Timing tag = "Updating_Self_Energies" duration = "0.010" />
<Timing tag = "Computing_Active_Rotamers" duration = "0.000" />
<Timing tag = "Resolving_Disulfide_Bonds" duration = "0.000" />
Total number of subrotamer interactions = 5829
<Timing tag = "Updating_Pairwise_Energies" duration = "0.010" />
<Timing tag = "Normalizing_Atoms_Sets" duration = "0.000" />
<Timing tag = "Computing_Interaction_Graph" duration = "0.020" />
<Timing tag = "Building_Atoms_Sets" duration = "0.000" />
<Timing tag = "Building_Flexible_Subrotamers" duration = "0.000" />
<Timing tag = "Computing_Symmetry_Operators" duration = "0.000" />
<Timing tag = "Updating_Self_Energies" duration = "0.010" />
<Timing tag = "Computing_Active_Rotamers" duration = "0.000" />
<Timing tag = "Resolving_Disulfide_Bonds" duration = "0.000" />
Total number of subrotamer interactions = 0
<Timing tag = "Updating_Pairwise_Energies" duration = "0.000" />
<Timing tag = "Normalizing_Atoms_Sets" duration = "0.000" />
Running Goldstein's DEE (version G)
:::::::::::::::::::::::::::::::::::
Initial number of residues - 47
Initial number of rotamers - 499
77 redundant edges eliminated
Isolated residues removed - 5
round 1:
10 redundant edges eliminated
Isolated residues removed - 23
Rotamers eliminated - 386
round 2:
2 redundant edges eliminated
Isolated residues removed - 4
Rotamers eliminated - 20
round 3:
0 redundant edges eliminated
Isolated residues removed - 0
Rotamers eliminated - 1
round 4:
0 redundant edges eliminated
Isolated residues removed - 0
Rotamers eliminated - 0
Energy accumulated during DEE = 185.41
<Timing tag = "DEE" duration = "0.000" />
Searching for clusters... 4 clusters found
Processing cluster of 3 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 3e+1
1 : -> 37 39
0( 1 ) : 39 -> 38
ArtPts = 0 MaxDegree = 1 MaxBag = 1 AvgBag = 2
===============================
Launching bottom-to-top process
Combinations:
in intersections - 3
in exclusions - 63.2
total to search - 18
Maximal size of a key is 3 elements
Processing nodes .
<Timing tag = "Bottom_To_Top" duration = "0.000" />
<Trace tag = "Deciding_on_the_root_node" >
Number of combinations = 1.2e+1
<Timing tag = "Deciding_on_the_root_node" duration = "0.000" />
</Trace>
<Trace tag = "Top_To_Bottom" >
<Timing tag = "Top_To_Bottom" duration = "0.000" />
</Trace>
Energy of this cluster = 14.5173
Processing cluster of 4 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 1.9e+1
2 : -> 35 23
1( 2 ) : 35 -> 20
0( 1 ) : 20 -> 36
ArtPts = 0 MaxDegree = 2 MaxBag = 1 AvgBag = 2
===============================
Launching bottom-to-top process
Combinations:
in intersections - 5
in exclusions - 63.2
total to search - 15
Maximal size of a key is 3 elements
Processing nodes ..
<Timing tag = "Bottom_To_Top" duration = "0.000" />
<Trace tag = "Deciding_on_the_root_node" >
Number of combinations = 4
<Timing tag = "Deciding_on_the_root_node" duration = "0.000" />
</Trace>
<Trace tag = "Top_To_Bottom" >
<Timing tag = "Top_To_Bottom" duration = "0.000" />
</Trace>
Energy of this cluster = 29.7607
Processing cluster of 6 vertices
Redundant nodes eliminated : 2
Tree-decomposition has been built. Width+1 = 2
Total combinations to search = 5.4e+1
3 : -> 5 7 8
2( 3 ) : 7 -> 11
1( 2 ) : 11 -> 14
0( 1 ) : 14 -> 18
ArtPts = 0 MaxDegree = 2 MaxBag = 2 AvgBag = 2.25
===============================
Launching bottom-to-top process
Combinations:
in intersections - 11
in exclusions - 103.2
total to search - 30
Maximal size of a key is 6 elements
Processing nodes ...
<Timing tag = "Bottom_To_Top" duration = "0.000" />
<Trace tag = "Deciding_on_the_root_node" >
Number of combinations = 2.4e+1
<Timing tag = "Deciding_on_the_root_node" duration = "0.000" />
</Trace>
<Trace tag = "Top_To_Bottom" >
<Timing tag = "Top_To_Bottom" duration = "0.000" />
</Trace>
Energy of this cluster = 16.2193
Processing cluster of 2 vertices
Redundant nodes eliminated : 1
Tree-decomposition has been built. Width+1 = 1
Total combinations to search = 6
0 : -> 6 9
ArtPts = 0 MaxDegree = 0 MaxBag = 1 AvgBag = 2
<Trace tag = "Deciding_on_the_root_node" >
Number of combinations = 6
<Timing tag = "Deciding_on_the_root_node" duration = "0.000" />
</Trace>
<Trace tag = "Top_To_Bottom" >
<Timing tag = "Top_To_Bottom" duration = "0.000" />
</Trace>
Energy of this cluster = 6.34351
Total minimal energy of the graph = 252.251
<Timing tag = "Combinatorial_Search" duration = "0.000" />
<Timing tag = "Deriving_Optimum" duration = "0.010" />
<Timing tag = "Saving_to_PDB_file" duration = "0.000" />
Deleting workspace.
<Timing tag = "Scwrl4_Execution" duration = "0.040" />