rosetta.gcc -l pdb_list -design -fixbb -chain_inc -sqc redesign >&log130&
Native Redesign Same Fraction designed correctly ln[(#same/#native)/(#design/#total)]
-----------------------------------------------------------------------------------------------
VAL 303 284 142 0.47 2.01
ILE 203 266 99 0.49 2.11
LEU 329 465 171 0.52 1.62
MET 76 75 12 0.16 2.25
PHE 167 194 65 0.39 2.20
GLY 366 342 286 0.78 2.33
ALA 404 290 133 0.33 1.63
PRO 192 332 153 0.80 2.38
TRP 55 58 16 0.29 3.12
TYR 161 186 36 0.22 1.69
SER 274 172 54 0.20 1.64
THR 289 168 46 0.16 1.45
ASN 201 222 42 0.21 1.44
GLN 147 245 14 0.10 0.56
ASP 333 223 63 0.19 1.34
GLU 298 279 35 0.12 0.64
ARG 149 176 18 0.12 1.13
LYS 320 304 46 0.14 0.76
HIS 81 67 8 0.10 1.89
CYS 157 157 157 1.00 3.36
For total residue = 4505 ,the identity for all positions is 0.33.
The distribution of each residue in different enviroment states (*Nat:Native *Des:Redesign) :
% Buried % Boundary % Surface
(Nat Des change) (Nat Des change) (Nat Des change)
------------------------------------------------------------------------------
VAL 0.56 0.58 0.01 0.27 0.24 -0.03 0.16 0.18 0.02
ILE 0.60 0.50 -0.10 0.28 0.32 0.04 0.13 0.19 0.06
LEU 0.54 0.33 -0.21 0.33 0.36 0.02 0.12 0.31 0.19
MET 0.50 0.57 0.07 0.32 0.31 -0.01 0.18 0.12 -0.06
PHE 0.65 0.51 -0.14 0.27 0.32 0.06 0.08 0.16 0.09
GLY 0.22 0.22 0.00 0.37 0.39 0.02 0.41 0.38 -0.02
ALA 0.36 0.65 0.29 0.30 0.29 -0.02 0.34 0.07 -0.27
PRO 0.18 0.13 -0.04 0.24 0.27 0.03 0.58 0.60 0.02
TRP 0.65 0.38 -0.28 0.20 0.40 0.20 0.15 0.22 0.08
TYR 0.63 0.30 -0.33 0.27 0.37 0.10 0.10 0.33 0.23
SER 0.18 0.28 0.10 0.30 0.35 0.05 0.53 0.37 -0.15
THR 0.22 0.23 0.01 0.45 0.35 -0.10 0.33 0.42 0.09
ASN 0.18 0.11 -0.07 0.40 0.18 -0.21 0.42 0.71 0.28
GLN 0.15 0.11 -0.04 0.45 0.31 -0.14 0.40 0.59 0.19
ASP 0.13 0.21 0.08 0.29 0.27 -0.01 0.59 0.52 -0.07
GLU 0.09 0.18 0.09 0.36 0.39 0.03 0.56 0.43 -0.12
ARG 0.17 0.21 0.04 0.39 0.49 0.11 0.44 0.30 -0.15
LYS 0.13 0.18 0.06 0.40 0.45 0.05 0.47 0.36 -0.11
HIS 0.32 0.63 0.31 0.35 0.28 -0.06 0.33 0.09 -0.24
CYS 0.71 0.71 0.00 0.20 0.20 0.00 0.09 0.09 0.00
The probabilities for all residues in buried, boundary and surface states :
% Buried % Boundary % Surface
(Nat Des change) (Nat Des change) (Nat Des change)
------------------------------------------------------------------------------
VAL 0.12 0.11 -0.00 0.06 0.05 -0.01 0.03 0.03 0.00
ILE 0.08 0.09 0.01 0.04 0.06 0.02 0.02 0.03 0.02
LEU 0.12 0.11 -0.02 0.07 0.11 0.04 0.03 0.09 0.07
MET 0.03 0.03 0.00 0.02 0.02 -0.00 0.01 0.01 -0.00
PHE 0.07 0.07 -0.01 0.03 0.04 0.01 0.01 0.02 0.01
GLY 0.05 0.05 -0.00 0.09 0.09 -0.00 0.10 0.08 -0.01
ALA 0.10 0.13 0.03 0.08 0.06 -0.03 0.09 0.01 -0.07
PRO 0.02 0.03 0.01 0.03 0.06 0.03 0.07 0.13 0.06
TRP 0.02 0.02 -0.01 0.01 0.02 0.01 0.01 0.01 0.00
TYR 0.07 0.04 -0.03 0.03 0.05 0.02 0.01 0.04 0.03
SER 0.03 0.03 -0.00 0.05 0.04 -0.01 0.09 0.04 -0.05
THR 0.04 0.03 -0.02 0.09 0.04 -0.05 0.06 0.05 -0.02
ASN 0.02 0.02 -0.01 0.05 0.03 -0.03 0.05 0.10 0.05
GLN 0.02 0.02 0.00 0.04 0.05 0.01 0.04 0.09 0.05
ASP 0.03 0.03 0.00 0.06 0.04 -0.02 0.13 0.07 -0.05
GLU 0.02 0.03 0.02 0.07 0.07 0.00 0.11 0.08 -0.03
ARG 0.02 0.03 0.01 0.04 0.06 0.02 0.04 0.03 -0.01
LYS 0.03 0.04 0.01 0.09 0.09 0.01 0.10 0.07 -0.03
HIS 0.02 0.03 0.01 0.02 0.01 -0.01 0.02 0.00 -0.01
CYS 0.08 0.08 0.00 0.02 0.02 0.00 0.01 0.01 0.00
The fraction of redesigned correctly for the following groups are:
1. hydrophobic non-polar amino acids(VAL,ILE,LEU,MET,PHE,GLY,ALA,PRO,TRP,TYR) = 0.49
2. polar uncharged amino acid except CYS (SER,THR,ASN,GLN) = 0.17
3. negative charged amino acid(ASP,GLU) = 0.16
4. positive charged amino acid(ARG,LYS,HIS) = 0.13
The distribution of amino acid in each group are :
Native Redesign
hydrophobic non-polar 0.52 0.57
polar uncharged 0.21 0.19
negative charged 0.15 0.12
positive charged 0.13 0.13
Nat\Des VAL ILE LEU MET PHE GLY ALA PRO TRP TYR SER THR ASN GLN ASP GLU ARG LYS HIS CYS
VAL 142 47 15 7 2 1 13 8 3 6 4 14 1 6 4 11 9 9 1 0
ILE 39 99 17 2 2 0 3 4 1 1 2 5 1 5 6 5 2 7 2 0
LEU 7 25 171 9 12 4 9 4 3 4 1 6 7 4 6 20 13 20 4 0
MET 5 3 14 12 2 3 5 0 0 1 2 3 1 6 2 4 5 7 1 0
PHE 2 5 7 6 65 4 8 3 6 20 3 3 1 0 7 2 6 4 15 0
GLY 0 1 5 0 2 286 11 2 1 0 7 3 11 7 9 9 9 2 1 0
ALA 6 7 19 4 7 12 133 30 2 8 25 9 16 33 18 33 13 27 2 0
PRO 1 0 3 0 1 1 5 153 0 1 4 0 3 6 8 3 1 2 0 0
TRP 0 3 5 1 3 1 2 0 16 8 1 3 2 1 1 1 2 2 3 0
TYR 5 1 7 3 44 3 11 2 5 36 4 4 0 8 1 3 4 10 10 0
SER 2 2 18 4 6 3 22 27 2 13 54 13 20 18 18 18 13 17 4 0
THR 24 26 20 5 5 3 16 12 3 22 17 46 6 22 7 25 15 14 1 0
ASN 6 7 20 0 2 8 10 5 3 11 5 4 42 5 25 13 8 25 2 0
GLN 6 6 20 4 5 3 9 4 3 1 2 6 10 14 8 21 4 20 1 0
ASP 13 10 22 1 6 4 5 26 2 10 15 14 46 29 63 27 11 27 2 0
GLU 15 8 37 6 8 1 12 17 3 15 5 13 21 26 14 35 19 41 2 0
ARG 5 3 13 5 5 0 2 10 2 7 6 8 6 13 8 19 18 16 3 0
LYS 5 11 43 6 10 4 8 22 2 17 12 11 21 38 11 27 21 46 5 0
HIS 1 2 9 0 7 1 6 3 1 5 3 3 7 4 7 3 3 8 8 0
CYS 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 157
Nat\Des hydrophobic polar negatative positive
hydrophobic 1688 222 153 193
polar 368 284 135 124
negative 221 169 139 102
positive 215 132 75 128