% ALIGN_CLEAN, R.B. Russell, 1995
% Searching for domain descriptors...
%   2 domain descriptions read in
/disk3/pdb/pdb1csp.ent 1csp { ALL 
   0.53847    0.80016   -0.26409       -16.88881  
  -0.46688    0.02246   -0.88401        14.33235  
  -0.70145    0.59934    0.38570        -2.88944  }
/disk3/pdb/pdb1chp.ent 1chpd { CHAIN D 
  -0.72579   -0.54488   -0.41988        77.11722  
   0.68692   -0.54305   -0.48291         8.25322  
   0.03511   -0.63894    0.76845       -18.41870  }
% Reading block file...
Blocfile read: Length: 108
% Searching for STAMP data...
%   268459416 STAMP fields found: T P A G 
% Block file contains 5 sequences; the alignment length is 108
% Cleaning up allowing continuous segments of 3 or greater...
%  Cleaning done.
% The final alignment length is 107
% The alignment:
>1csp    (cluster A) sequence
>1chpd    (cluster B) sequence
>space  
>1csp_dssp  (cluster A) secondary structure from DSSP
>1chpd_dssp   (cluster B) secondary structure from DSSP
#T  -- '1' = equivalenced residues 

#P  -- averaged Pij

#A  -- distance between averaged CA atoms in angtroms

#G  -- Pij' value

*
 T  -
 P  -
 Q  -
 N  S
 I  H
 T  H
 D  H
 L  H
 C  H
 A  T
 E  T
 Y  S
 H  T
 N  T
 T  E
 Q  E
 I  E
 H  E
 T  E
 L  E
MN -E
LD EE
EK E-  0    0.21300    2.28780    2.33000 
GI E-  0    0.38700    1.67406    4.07000 
KF E-  0    0.23800    2.25053    2.58000 
VS EE  0    0.09900    2.36039    1.19000 
KY EE  0    0.35600    1.00504    3.76000 
WT EE  1    0.82000    1.25493    8.40000 
FE EE  1    0.72200    1.43249    7.42000 
NS EE
 L  -
 A  S
SD TT
EK TT
KR T-  0    0.00300    2.49572    0.23000 
GE T-  0    0.15400    2.09763    1.74000 
FM EE  1    0.62400    1.10544    6.44000 
GA EE  1    0.87100    1.12749    8.91000 
FI EE  1    0.90400    0.61313    9.24000 
II EE  1    0.88400    1.05263    9.04000 
ET EE  1    0.83300    1.17875    8.53000 
VF --  1    0.76100    1.33575    7.81000 
EK TT  1    0.63900    1.67439    6.59000 
GN TT  1    0.71400    1.31344    7.34000 
QG SS  0    0.40100    1.82628    4.21000 
DA --  0    0.41600    1.72281    4.36000 
DT -E  1    0.66100    1.34527    6.81000 
VF EE  1    0.83300    0.98301    8.53000 
FQ EE  1    0.81700    1.25631    8.37000 
VV E-
 E  -
 V  -
 P  -
 G  -
 S  T
 Q  T
 H  S
 I  -
 D  H
 S  H
 Q  H
HK EH
FK GH  0    0.02700    2.68310    0.47000 
SA GH  0    0.17700    2.09293    1.97000 
AI GH  0    0.37600    2.07811    3.96000 
I  B 
Q  - 
G  S 
E  S 
GE SH  0    0.01400    2.81401    0.34000 
FR SH  0    0.19300    2.32440    2.13000 
KM -H  0    0.25000    2.34756    2.70000 
TK -H
 D  H
 T  H
 L  H
 R  H
LI -H
EA -H  0    0.02300    2.84543    0.43000 
EY TH  0    0.12000    2.51080    1.40000 
GL TH  0    0.33500    1.94625    3.55000 
QT -H  0    0.16600    2.36074    1.86000 
AE ET
 A  -
 K  -
 V  E
VE EE
SK EE  0    0.08200    2.40234    1.02000 
FL EE  1    0.46000    1.69445    4.80000 
EC EE  1    0.64500    1.58342    6.65000 
IV EE  1    0.58700    1.65970    6.07000 
VW EE  1    0.57500    1.57541    5.95000 
E  E 
GN ET  0    0.40400    1.98605    4.24000 
NN TT  1    0.56900    1.74855    5.89000 
RK TS  1    0.48000    1.82861    5.00000 
 T  S
GP ES  0    0.06000    2.47918    0.80000 
PH EE  0    0.36300    1.38056    3.83000 
QA EE  1    0.81700    1.10859    8.37000 
AI EE  1    0.86900    1.19292    8.89000 
AA EE  1    0.80100    1.30410    8.21000 
NA EE  1    0.63400    1.17546    6.54000 
VI EE  0    0.32600    1.99652    3.46000 
TS EE  0    0.16500    2.47388    1.85000 
KM EE  0    0.06700    2.77508    0.87000 
EA -E  0    0.06300    2.78415    0.83000 
*