
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   10 (   78),  selected   10 , name T0318TS022_5_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_5_1-D2.T0318_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
 ERROR! 0 0 10 335
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     156           -
LGA    -       -      N     157           -
LGA    -       -      E     158           -
LGA    -       -      D     159           -
LGA    -       -      A     160           -
LGA    -       -      V     161           -
LGA    -       -      F     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      D     165           -
LGA    -       -      L     166           -
LGA    -       -      S     167           -
LGA    -       -      E     168           -
LGA    -       -      S     169           -
LGA    -       -      V     170           -
LGA    -       -      R     171           -
LGA    -       -      E     172           -
LGA    -       -      T     173           -
LGA    -       -      A     174           -
LGA    -       -      R     175           -
LGA    -       -      L     176           -
LGA    -       -      I     177           -
LGA    -       -      D     178           -
LGA    -       -      T     179           -
LGA    -       -      P     180           -
LGA    -       -      A     181           -
LGA    -       -      N     182           -
LGA    -       -      I     183           -
LGA    -       -      L     184           -
LGA    -       -      T     185           -
LGA    -       -      T     186           -
LGA    -       -      D     187           -
LGA    -       -      A     188           -
LGA    -       -      L     189           -
LGA    -       -      V     190           -
LGA    -       -      D     191           -
LGA    -       -      E     192           -
LGA    -       -      A     193           -
LGA    -       -      V     194           -
LGA    -       -      K     195           -
LGA    -       -      V     196           -
LGA    -       -      G     197           -
LGA    -       -      N     198           -
LGA    -       -      A     199           -
LGA    -       -      T     200           -
LGA    -       -      G     201           -
LGA    -       -      S     202           -
LGA    -       -      K     203           -
LGA    -       -      I     204           -
LGA    -       -      T     205           -
LGA    -       -      V     206           -
LGA    -       -      I     207           -
LGA    -       -      R     208           -
LGA    -       -      G     209           -
LGA    -       -      E     210           -
LGA    -       -      E     211           -
LGA    -       -      L     212           -
LGA    -       -      L     213           -
LGA    -       -      K     214           -
LGA    -       -      A     215           -
LGA    -       -      G     216           -
LGA    -       -      F     217           -
LGA    -       -      G     218           -
LGA    -       -      G     219           -
LGA    -       -      I     220           -
LGA    -       -      Y     221           -
LGA    -       -      H     222           -
LGA    -       -      V     223           -
LGA    -       -      G     224           -
LGA    -       -      K     225           -
LGA    -       -      A     226           -
LGA    -       -      G     227           -
LGA    -       -      P     228           -
LGA    -       -      T     229           -
LGA    -       -      P     230           -
LGA    -       -      P     231           -
LGA    -       -      A     232           -
LGA    -       -      F     233           -
LGA    -       -      V     234           -
LGA    -       -      V     235           -
LGA    -       -      L     236           -
LGA    -       -      S     237           -
LGA    -       -      H     238           -
LGA    -       -      E     239           -
LGA    -       -      V     240           -
LGA    -       -      P     241           -
LGA    -       -      G     242           -
LGA    -       -      S     243           -
LGA    -       -      T     244           -
LGA    -       -      E     245           -
LGA    -       -      H     246           -
LGA    -       -      I     247           -
LGA    -       -      A     248           -
LGA    -       -      L     249           -
LGA    -       -      V     250           -
LGA    -       -      G     251           -
LGA    -       -      K     252           -
LGA    -       -      G     253           -
LGA    -       -      V     254           -
LGA    -       -      V     255           -
LGA    -       -      Y     256           -
LGA    -       -      D     257           -
LGA    -       -      T     258           -
LGA    -       -      G     259           -
LGA    -       -      G     260           -
LGA    -       -      L     261           -
LGA    -       -      Q     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      K     266           -
LGA    -       -      T     267           -
LGA    -       -      G     268           -
LGA    -       -      M     269           -
LGA    -       -      P     270           -
LGA    -       -      N     271           -
LGA    -       -      M     272           -
LGA    -       -      K     273           -
LGA    -       -      R     274           -
LGA    -       -      D     275           -
LGA    -       -      M     276           -
LGA    -       -      G     277           -
LGA    -       -      G     278           -
LGA    -       -      A     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      M     282           -
LGA    -       -      L     283           -
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      Y     286           -
LGA    -       -      S     287           -
LGA    -       -      A     288           -
LGA    -       -      L     289           -
LGA    -       -      V     290           -
LGA    -       -      K     291           -
LGA    -       -      H     292           -
LGA    -       -      G     293           -
LGA    -       -      F     294           -
LGA    -       -      S     295           -
LGA    -       -      Q     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      H     299           -
LGA    -       -      A     300           -
LGA    -       -      C     301           -
LGA    -       -      L     302           -
LGA    -       -      C     303           -
LGA    -       -      I     304           -
LGA    -       -      V     305           -
LGA    -       -      E     306           -
LGA    -       -      N     307           -
LGA    -       -      N     308           -
LGA    -       -      V     309           -
LGA    -       -      S     310           -
LGA    -       -      P     311           -
LGA    -       -      I     312           -
LGA    -       -      A     313           -
LGA    -       -      N     314           -
LGA    -       -      K     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      D     318           -
LGA    -       -      I     319           -
LGA    -       -      I     320           -
LGA    -       -      K     321           -
LGA    -       -      M     322           -
LGA    -       -      L     323           -
LGA    -       -      S     324           -
LGA    -       -      G     325           -
LGA    -       -      K     326           -
LGA    -       -      T     327           -
LGA    -       -      V     328           -
LGA    -       -      E     329           -
LGA    -       -      I     330           -
LGA    -       -      N     331           -
LGA    -       -      N     332           -
LGA    -       -      T     333           -
LGA    -       -      D     334           -
LGA    -       -      A     335           -
LGA    -       -      E     336           -
LGA    -       -      G     337           -
LGA    -       -      R     338           -
LGA    -       -      L     339           -
LGA    -       -      I     340           -
LGA    -       -      L     341           -
LGA    -       -      A     342           -
LGA    -       -      D     343           -
LGA    -       -      G     344           -
LGA    -       -      V     345           -
LGA    -       -      F     346           -
LGA    -       -      Y     347           -
LGA    -       -      A     348           -
LGA    -       -      K     349           -
LGA    -       -      E     350           -
LGA    -       -      T     351           -
LGA    -       -      L     352           -
LGA    -       -      K     353           -
LGA    -       -      A     354           -
LGA    -       -      T     355           -
LGA    -       -      T     356           -
LGA    -       -      I     357           -
LGA    -       -      F     358           -
LGA    -       -      D     359           -
LGA    -       -      M     360           -
LGA    -       -      A     361           -
LGA    -       -      T     362           -
LGA    -       -      L     363           -
LGA    -       -      T     364           -
LGA    -       -      G     365           -
LGA    -       -      A     366           -
LGA    -       -      Q     367           -
LGA    -       -      A     368           -
LGA    -       -      W     369           -
LGA    -       -      L     370           -
LGA    -       -      S     371           -
LGA    -       -      G     372           -
LGA    -       -      R     373           -
LGA    -       -      L     374           -
LGA    -       -      H     375           -
LGA    -       -      G     376           -
LGA    -       -      A     377           -
LGA    -       -      A     378           -
LGA    -       -      M     379           -
LGA    -       -      T     380           -
LGA    T     156      N     381          0.459
LGA    N     157      D     382          0.606
LGA    E     158      E     383          1.444
LGA    D     159      Q     384          2.072
LGA    -       -      L     385           -
LGA    -       -      E     386           -
LGA    A     160      N     387          1.073
LGA    V     161      E     388          1.750
LGA    -       -      I     389           -
LGA    -       -      I     390           -
LGA    F     162      K     391          1.616
LGA    L     163      A     392          0.483
LGA    -       -      G     393           -
LGA    -       -      K     394           -
LGA    T     164      A     395          1.469
LGA    D     165      S     396          1.549
LGA    -       -      G     397           -
LGA    -       -      D     398           -
LGA    -       -      L     399           -
LGA    -       -      V     400           -
LGA    -       -      A     401           -
LGA    -       -      P     402           -
LGA    -       -      M     403           -
LGA    -       -      L     404           -
LGA    -       -      F     405           -
LGA    -       -      A     406           -
LGA    -       -      P     407           -
LGA    -       -      D     408           -
LGA    -       -      L     409           -
LGA    -       -      F     410           -
LGA    -       -      F     411           -
LGA    -       -      G     412           -
LGA    -       -      D     413           -
LGA    -       -      L     414           -
LGA    -       -      K     415           -
LGA    -       -      S     416           -
LGA    -       -      S     417           -
LGA    -       -      I     418           -
LGA    -       -      A     419           -
LGA    -       -      D     420           -
LGA    -       -      M     421           -
LGA    -       -      K     422           -
LGA    -       -      N     423           -
LGA    -       -      S     424           -
LGA    -       -      N     425           -
LGA    -       -      L     426           -
LGA    -       -      G     427           -
LGA    -       -      K     428           -
LGA    -       -      M     429           -
LGA    -       -      D     430           -
LGA    -       -      G     431           -
LGA    -       -      P     432           -
LGA    -       -      P     433           -
LGA    -       -      S     434           -
LGA    -       -      A     435           -
LGA    -       -      V     436           -
LGA    -       -      A     437           -
LGA    -       -      G     438           -
LGA    -       -      L     439           -
LGA    -       -      L     440           -
LGA    -       -      I     441           -
LGA    -       -      G     442           -
LGA    -       -      A     443           -
LGA    -       -      H     444           -
LGA    -       -      I     445           -
LGA    -       -      G     446           -
LGA    -       -      F     447           -
LGA    -       -      G     448           -
LGA    -       -      E     449           -
LGA    -       -      G     450           -
LGA    -       -      L     451           -
LGA    -       -      R     452           -
LGA    -       -      W     453           -
LGA    -       -      L     454           -
LGA    -       -      H     455           -
LGA    -       -      L     456           -
LGA    -       -      D     457           -
LGA    -       -      I     458           -
LGA    -       -      A     459           -
LGA    -       -      A     460           -
LGA    -       -      P     461           -
LGA    -       -      A     462           -
LGA    -       -      E     463           -
LGA    -       -      V     464           -
LGA    -       -      G     465           -
LGA    -       -      D     466           -
LGA    -       -      R     467           -
LGA    -       -      G     468           -
LGA    -       -      T     469           -
LGA    -       -      G     470           -
LGA    -       -      Y     471           -
LGA    -       -      G     472           -
LGA    -       -      P     473           -
LGA    -       -      A     474           -
LGA    -       -      L     475           -
LGA    -       -      F     476           -
LGA    -       -      S     477           -
LGA    -       -      T     478           -
LGA    -       -      L     479           -
LGA    -       -      L     480           -
LGA    -       -      G     481           -
LGA    -       -      K     482           -
LGA    -       -      Y     483           -
LGA    -       -      T     484           -
LGA    -       -      S     485           -
LGA    -       -      V     486           -
LGA    -       -      P     487           -
LGA    -       -      M     488           -
LGA    -       -      L     489           -
LGA    -       -      K     490           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  335    5.0     10    1.36    10.00      2.846     0.684

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.381358 * X  +  -0.225739 * Y  +   0.896442 * Z  +  26.500273
  Y_new =  -0.237777 * X  +   0.961052 * Y  +   0.140855 * Z  +   9.228550
  Z_new =  -0.893324 * X  +  -0.159437 * Y  +  -0.420181 * Z  +  67.845795 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.778927    0.362665  [ DEG:  -159.2208     20.7792 ]
  Theta =   1.104688    2.036904  [ DEG:    63.2940    116.7060 ]
  Phi   =  -2.584072    0.557521  [ DEG:  -148.0564     31.9436 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0318TS022_5_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_5_1-D2.T0318_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  335   5.0   10   1.36   10.00   2.846
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1urh_A
ATOM   1201  N   THR   156      -7.481  40.211  20.150  1.00  0.00
ATOM   1202  CA  THR   156      -7.425  39.185  21.158  1.00  0.00
ATOM   1203  C   THR   156      -6.539  38.061  20.719  1.00  0.00
ATOM   1204  O   THR   156      -6.433  37.764  19.530  1.00  0.00
ATOM   1205  CB  THR   156      -8.820  38.601  21.447  1.00  0.00
ATOM   1206  OG1 THR   156      -8.738  37.676  22.538  1.00  0.00
ATOM   1207  CG2 THR   156      -9.357  37.873  20.224  1.00  0.00
ATOM   1208  N   ASN   157      -5.868  37.424  21.704  1.00  0.00
ATOM   1209  CA  ASN   157      -5.033  36.266  21.546  1.00  0.00
ATOM   1210  C   ASN   157      -4.828  35.703  22.917  1.00  0.00
ATOM   1211  O   ASN   157      -5.162  36.347  23.912  1.00  0.00
ATOM   1212  CB  ASN   157      -3.692  36.653  20.920  1.00  0.00
ATOM   1213  CG  ASN   157      -3.079  35.527  20.111  1.00  0.00
ATOM   1214  OD1 ASN   157      -3.464  34.367  20.254  1.00  0.00
ATOM   1215  ND2 ASN   157      -2.122  35.867  19.256  1.00  0.00
ATOM   1216  N   GLU   158      -4.285  34.474  23.019  1.00  0.00
ATOM   1217  CA  GLU   158      -4.153  33.890  24.323  1.00  0.00
ATOM   1218  C   GLU   158      -2.812  33.238  24.455  1.00  0.00
ATOM   1219  O   GLU   158      -2.109  33.026  23.469  1.00  0.00
ATOM   1220  CB  GLU   158      -5.238  32.835  24.550  1.00  0.00
ATOM   1221  CG  GLU   158      -5.142  31.637  23.620  1.00  0.00
ATOM   1222  CD  GLU   158      -6.286  30.660  23.810  1.00  0.00
ATOM   1223  OE1 GLU   158      -7.158  30.924  24.663  1.00  0.00
ATOM   1224  OE2 GLU   158      -6.310  29.629  23.104  1.00  0.00
ATOM   1225  N   ASP   159      -2.423  32.938  25.714  1.00  0.00
ATOM   1226  CA  ASP   159      -1.185  32.278  26.026  1.00  0.00
ATOM   1227  C   ASP   159      -0.099  33.302  26.119  1.00  0.00
ATOM   1228  O   ASP   159      -0.171  34.362  25.500  1.00  0.00
ATOM   1229  CB  ASP   159      -0.829  31.263  24.937  1.00  0.00
ATOM   1230  CG  ASP   159      -1.734  30.047  24.957  1.00  0.00
ATOM   1231  OD1 ASP   159      -2.474  29.873  25.947  1.00  0.00
ATOM   1232  OD2 ASP   159      -1.702  29.268  23.981  1.00  0.00
ATOM   1233  N   ALA   160       0.935  33.007  26.933  1.00  0.00
ATOM   1234  CA  ALA   160       2.026  33.918  27.123  1.00  0.00
ATOM   1235  C   ALA   160       2.828  33.956  25.867  1.00  0.00
ATOM   1236  O   ALA   160       2.846  32.997  25.096  1.00  0.00
ATOM   1237  CB  ALA   160       2.906  33.458  28.276  1.00  0.00
ATOM   1238  N   VAL   161       3.503  35.096  25.621  1.00  0.00
ATOM   1239  CA  VAL   161       4.300  35.211  24.439  1.00  0.00
ATOM   1240  C   VAL   161       5.719  35.307  24.874  1.00  0.00
ATOM   1241  O   VAL   161       6.055  36.065  25.783  1.00  0.00
ATOM   1242  CB  VAL   161       3.923  36.462  23.623  1.00  0.00
ATOM   1243  CG1 VAL   161       4.816  36.588  22.398  1.00  0.00
ATOM   1244  CG2 VAL   161       2.477  36.378  23.158  1.00  0.00
ATOM   1245  N   PHE   162       6.600  34.515  24.240  1.00  0.00
ATOM   1246  CA  PHE   162       7.967  34.560  24.646  1.00  0.00
ATOM   1247  C   PHE   162       8.794  34.954  23.473  1.00  0.00
ATOM   1248  O   PHE   162       8.772  34.304  22.429  1.00  0.00
ATOM   1249  CB  PHE   162       8.421  33.190  25.153  1.00  0.00
ATOM   1250  CG  PHE   162       7.705  32.734  26.392  1.00  0.00
ATOM   1251  CD1 PHE   162       6.548  31.980  26.302  1.00  0.00
ATOM   1252  CD2 PHE   162       8.188  33.060  27.648  1.00  0.00
ATOM   1253  CE1 PHE   162       5.888  31.562  27.442  1.00  0.00
ATOM   1254  CE2 PHE   162       7.528  32.640  28.788  1.00  0.00
ATOM   1255  CZ  PHE   162       6.384  31.894  28.689  1.00  0.00
ATOM   1256  N   LEU   163       9.536  36.064  23.621  1.00  0.00
ATOM   1257  CA  LEU   163      10.457  36.461  22.603  1.00  0.00
ATOM   1258  C   LEU   163      11.780  36.458  23.284  1.00  0.00
ATOM   1259  O   LEU   163      11.895  36.911  24.421  1.00  0.00
ATOM   1260  CB  LEU   163      10.102  37.851  22.072  1.00  0.00
ATOM   1261  CG  LEU   163       8.717  38.001  21.438  1.00  0.00
ATOM   1262  CD1 LEU   163       8.447  39.453  21.073  1.00  0.00
ATOM   1263  CD2 LEU   163       8.614  37.166  20.170  1.00  0.00
ATOM   1264  N   THR   164      12.816  35.915  22.625  1.00  0.00
ATOM   1265  CA  THR   164      14.095  35.908  23.265  1.00  0.00
ATOM   1266  C   THR   164      14.711  37.232  22.981  1.00  0.00
ATOM   1267  O   THR   164      14.129  38.046  22.268  1.00  0.00
ATOM   1268  CB  THR   164      14.992  34.780  22.724  1.00  0.00
ATOM   1269  OG1 THR   164      15.252  34.999  21.331  1.00  0.00
ATOM   1270  CG2 THR   164      14.309  33.431  22.890  1.00  0.00
ATOM   1271  N   ASP   165      15.895  37.495  23.564  1.00  0.00
ATOM   1272  CA  ASP   165      16.552  38.745  23.326  1.00  0.00
ATOM   1273  C   ASP   165      16.696  38.892  21.816  1.00  0.00
ATOM   1274  O   ASP   165      16.146  39.878  21.258  1.00  0.00
ATOM   1275  CB  ASP   165      17.930  38.762  23.993  1.00  0.00
ATOM   1276  CG  ASP   165      18.566  40.138  23.977  1.00  0.00
ATOM   1277  OD1 ASP   165      17.891  41.101  23.559  1.00  0.00
ATOM   1278  OD2 ASP   165      19.742  40.253  24.384  1.00  0.00
TER
END
