
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0386TS125_1u-D2
# Molecule2: number of CA atoms   81 (  636),  selected   24 , name T0386_D2.pdb
# PARAMETERS: T0386TS125_1u-D2.T0386_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       219 - 239         4.93    11.94
  LCS_AVERAGE:     20.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         1.32    14.81
  LCS_AVERAGE:     10.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       225 - 234         0.60    14.60
  LCS_AVERAGE:      7.00

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   81
LCS_GDT     N     219     N     219      4    7   20     3    3    6    7    7    7    7    7    9    9   13   14   15   18   18   20   20   20   20   20 
LCS_GDT     P     220     P     220      4    7   20     3    3    6    7    7    7    7   10   12   15   15   15   17   18   19   20   20   20   20   20 
LCS_GDT     E     221     E     221      4    7   20     3    3    6    7    7    7    7   10   13   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     I     223     I     223      4    7   20     3    4    6    7    7    7    9   10   13   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     R     224     R     224      3    7   20     3    4    6    7    7    7    9   11   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     L     225     L     225     10   13   20     7   10   11   11   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     L     226     L     226     10   13   20     7   10   11   12   13   13   13   13   14   14   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     K     227     K     227     10   13   20     7   10   11   12   13   13   13   13   14   14   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     E     228     E     228     10   13   20     7   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     F     229     F     229     10   13   20     7   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     M     230     M     230     10   13   20     7   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     H     231     H     231     10   13   20     7   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     T     232     T     232     10   13   20     7   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     M     233     M     233     10   13   20     4   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     K     234     K     234     10   13   20     4   10   11   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     N     235     N     235      4   13   20     3    4    4   12   13   13   13   13   14   14   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     T     236     T     236      4   13   20     3    6   11   12   13   13   13   13   14   14   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     G     237     G     237      3   13   20     3    3    4   12   13   13   13   13   14   15   16   16   17   18   19   20   20   20   20   20 
LCS_GDT     R     238     R     238      3    4   20     3    4    5    6    7    7    9   11   14   15   15   16   17   18   19   20   20   20   20   20 
LCS_GDT     N     239     N     239      3    4   20     0    3    5    6    7    7    9   10   13   15   15   15   17   18   19   20   20   20   20   20 
LCS_GDT     E     250     E     250      0    0    0     0    0    0    0    0    1    1    1    1    1    1    3    5    5   12   12   12   13   13   13 
LCS_GDT     G     251     G     251      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    9   10   12   12   12   13   13   13 
LCS_GDT     R     259     R     259      0    0    0     0    0    0    0    0    0    0    3    4    6    8    9   11   13   15   15   16   17   18   20 
LCS_GDT     G     260     G     260      0    0    0     0    0    0    0    0    2    2    3    4    6    8    9   10   13   15   15   16   17   18   20 
LCS_AVERAGE  LCS_A:  12.83  (   7.00   10.91   20.58 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      7     10     11     12     13     13     13     13     14     15     16     16     17     18     19     20     20     20     20     20 
GDT PERCENT_CA   8.64  12.35  13.58  14.81  16.05  16.05  16.05  16.05  17.28  18.52  19.75  19.75  20.99  22.22  23.46  24.69  24.69  24.69  24.69  24.69
GDT RMS_LOCAL    0.09   0.60   0.81   1.33   1.32   1.32   1.32   1.32   2.20   3.69   3.72   3.57   4.03   4.28   4.69   4.93   4.93   4.93   4.93   4.93
GDT RMS_ALL_CA  14.17  14.60  14.77  14.90  14.81  14.81  14.81  14.81  14.48  11.83  13.53  13.65  13.35  12.84  12.13  11.94  11.94  11.94  11.94  11.94

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         21.039
LGA    P     220      P     220         17.470
LGA    E     221      E     221         11.275
LGA    I     223      I     223         12.158
LGA    R     224      R     224          7.978
LGA    L     225      L     225          1.127
LGA    L     226      L     226          0.818
LGA    K     227      K     227          0.584
LGA    E     228      E     228          1.027
LGA    F     229      F     229          0.964
LGA    M     230      M     230          0.806
LGA    H     231      H     231          0.991
LGA    T     232      T     232          0.413
LGA    M     233      M     233          0.686
LGA    K     234      K     234          1.457
LGA    N     235      N     235          2.692
LGA    T     236      T     236          1.311
LGA    G     237      G     237          2.237
LGA    R     238      R     238          7.611
LGA    N     239      N     239         11.484
LGA    E     250      E     250         35.730
LGA    G     251      G     251         39.817
LGA    R     259      R     259         22.248
LGA    G     260      G     260         24.725

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   81    4.0     13    1.32    16.975    15.500     0.916

LGA_LOCAL      RMSD =  1.319  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.814  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 10.216  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.481188 * X  +  -0.196346 * Y  +   0.854345 * Z  +  26.269806
  Y_new =  -0.683436 * X  +   0.526305 * Y  +   0.505884 * Z  +  72.120590
  Z_new =  -0.548975 * X  +  -0.827316 * Y  +   0.119062 * Z  +  79.830666 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.427864    1.713728  [ DEG:   -81.8106     98.1894 ]
  Theta =   0.581137    2.560456  [ DEG:    33.2967    146.7033 ]
  Phi   =  -0.957343    2.184250  [ DEG:   -54.8517    125.1483 ]
 
# 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: T0386TS125_1u-D2                              
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS125_1u-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   81   4.0   13   1.32  15.500    10.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS125_1u-D2
PFRMAT   TS
TARGET   T0386
MODEL    1  UNREFINED
PARENT   2f6sa   
ATOM   1249  N   ASN   219      12.479  70.595  88.055    1.00  0.50
ATOM   1250  CA  ASN   219      11.313  69.734  87.860    1.00  0.50
ATOM   1251  C   ASN   219      11.645  68.291  88.202    1.00  0.50
ATOM   1252  O   ASN   219      12.777  67.838  87.968    1.00  0.50
ATOM   1255  N   PRO   220      10.654  67.580  88.749    1.00  0.50
ATOM   1256  CA  PRO   220      10.743  66.133  88.991    1.00  0.50
ATOM   1257  C   PRO   220      10.450  65.307  87.737    1.00  0.50
ATOM   1258  O   PRO   220      10.706  64.109  87.699    1.00  0.50
ATOM   1261  N   GLU   221       9.934  65.969  86.713    1.00  0.50
ATOM   1262  CA  GLU   221       9.540  65.316  85.486    1.00  0.50
ATOM   1263  C   GLU   221      10.729  65.081  84.552    1.00  0.50
ATOM   1264  O   GLU   221      10.780  65.598  83.430    1.00  0.50
ATOM   1269  N   ILE   223      11.669  64.269  85.012    1.00  0.50
ATOM   1270  CA  ILE   223      12.993  64.203  84.391    1.00  0.50
ATOM   1271  C   ILE   223      13.029  63.443  83.071    1.00  0.50
ATOM   1272  O   ILE   223      14.070  63.395  82.404    1.00  0.50
ATOM   1276  N   ARG   224      11.902  62.840  82.707    1.00  0.50
ATOM   1277  CA  ARG   224      11.877  61.894  81.604    1.00  0.50
ATOM   1278  C   ARG   224      10.944  62.284  80.468    1.00  0.50
ATOM   1279  O   ARG   224      10.997  61.675  79.400    1.00  0.50
ATOM   1284  N   LEU   225      10.088  63.281  80.696    1.00  0.50
ATOM   1285  CA  LEU   225       9.205  63.769  79.649    1.00  0.50
ATOM   1286  C   LEU   225      10.001  64.335  78.451    1.00  0.50
ATOM   1287  O   LEU   225      10.707  65.356  78.593    1.00  0.50
ATOM   1292  N   LEU   226       9.907  63.682  77.264    1.00  0.50
ATOM   1293  CA  LEU   226      10.798  64.205  76.213    1.00  0.50
ATOM   1294  C   LEU   226      10.334  65.569  75.653    1.00  0.50
ATOM   1295  O   LEU   226      11.178  66.325  75.155    1.00  0.50
ATOM   1299  N   LYS   227       9.041  65.902  75.769    1.00  0.50
ATOM   1300  CA  LYS   227       8.582  67.258  75.403    1.00  0.50
ATOM   1301  C   LYS   227       9.290  68.321  76.267    1.00  0.50
ATOM   1302  O   LYS   227       9.873  69.285  75.745    1.00  0.50
ATOM   1307  N   GLU   228       9.250  68.118  77.585    1.00  0.50
ATOM   1308  CA  GLU   228       9.933  68.973  78.552    1.00  0.50
ATOM   1309  C   GLU   228      11.431  69.091  78.237    1.00  0.50
ATOM   1310  O   GLU   228      12.001  70.177  78.290    1.00  0.50
ATOM   1314  N   PHE   229      12.044  67.964  77.893    1.00  0.50
ATOM   1315  CA  PHE   229      13.465  67.910  77.618    1.00  0.50
ATOM   1316  C   PHE   229      13.817  68.666  76.336    1.00  0.50
ATOM   1317  O   PHE   229      14.801  69.403  76.297    1.00  0.50
ATOM   1322  N   MET   230      12.997  68.504  75.304    1.00  0.50
ATOM   1323  CA  MET   230      13.205  69.199  74.037    1.00  0.50
ATOM   1324  C   MET   230      13.023  70.715  74.197    1.00  0.50
ATOM   1325  O   MET   230      13.846  71.486  73.705    1.00  0.50
ATOM   1330  N   HIS   231      11.967  71.132  74.895    1.00  0.50
ATOM   1331  CA  HIS   231      11.790  72.541  75.245    1.00  0.50
ATOM   1332  C   HIS   231      13.010  73.101  75.970    1.00  0.50
ATOM   1333  O   HIS   231      13.453  74.217  75.685    1.00  0.50
ATOM   1339  N   THR   232      13.556  72.309  76.887    1.00  0.50
ATOM   1340  CA  THR   232      14.753  72.661  77.608    1.00  0.50
ATOM   1341  C   THR   232      15.950  72.866  76.701    1.00  0.50
ATOM   1342  O   THR   232      16.658  73.884  76.806    1.00  0.50
ATOM   1343  N   MET   233      16.188  71.914  75.804    1.00  0.50
ATOM   1344  CA  MET   233      17.365  71.982  74.949    1.00  0.50
ATOM   1345  C   MET   233      17.228  73.082  73.911    1.00  0.50
ATOM   1346  O   MET   233      18.207  73.722  73.572    1.00  0.50
ATOM   1351  N   LYS   234      16.010  73.318  73.424    1.00  0.50
ATOM   1352  CA  LYS   234      15.752  74.415  72.507    1.00  0.50
ATOM   1353  C   LYS   234      16.141  75.739  73.178    1.00  0.50
ATOM   1354  O   LYS   234      16.721  76.611  72.546    1.00  0.50
ATOM   1358  N   ASN   235      15.839  75.885  74.462    1.00  0.50
ATOM   1359  CA  ASN   235      16.159  77.110  75.170    1.00  0.50
ATOM   1360  C   ASN   235      17.667  77.225  75.365    1.00  0.50
ATOM   1361  O   ASN   235      18.240  78.311  75.210    1.00  0.50
ATOM   1367  N   THR   236      18.309  76.097  75.681    1.00  0.50
ATOM   1368  CA  THR   236      19.748  76.060  75.822    1.00  0.50
ATOM   1369  C   THR   236      20.416  76.611  74.553    1.00  0.50
ATOM   1370  O   THR   236      21.337  77.424  74.634    1.00  0.50
ATOM   1373  N   GLY   237      19.944  76.168  73.386    1.00  0.50
ATOM   1374  CA  GLY   237      20.474  76.645  72.102    1.00  0.50
ATOM   1375  C   GLY   237      20.109  78.101  71.838    1.00  0.50
ATOM   1376  O   GLY   237      20.870  78.843  71.204    1.00  0.50
ATOM   1385  N   ARG   238      18.951  78.506  72.351    1.00  0.50
ATOM   1386  CA  ARG   238      18.540  79.884  72.269    1.00  0.50
ATOM   1387  C   ARG   238      19.480  80.813  73.035    1.00  0.50
ATOM   1388  O   ARG   238      19.660  81.967  72.634    1.00  0.50
ATOM   1397  N   ASN   239      20.072  80.306  74.129    1.00  0.50
ATOM   1398  CA  ASN   239      20.983  81.084  74.962    1.00  0.50
ATOM   1399  C   ASN   239      22.212  81.491  74.146    1.00  0.50
ATOM   1400  O   ASN   239      22.842  82.499  74.434    1.00  0.50
ATOM   1409  N   GLU   250      22.549  80.669  73.150    1.00  0.50
ATOM   1410  CA  GLU   250      23.690  80.884  72.287    1.00  0.50
ATOM   1411  C   GLU   250      23.331  81.702  71.039    1.00  0.50
ATOM   1412  O   GLU   250      24.175  81.883  70.159    1.00  0.50
ATOM   1418  N   GLY   251      22.084  82.184  70.956    1.00  0.50
ATOM   1419  CA  GLY   251      21.638  83.018  69.834    1.00  0.50
ATOM   1420  C   GLY   251      20.900  82.324  68.694    1.00  0.50
ATOM   1421  O   GLY   251      20.698  82.916  67.629    1.00  0.50
ATOM   1422  N   ARG   259      20.497  81.070  68.893    1.00  0.50
ATOM   1423  CA  ARG   259      19.698  80.365  67.887    1.00  0.50
ATOM   1424  C   ARG   259      18.212  80.665  68.083    1.00  0.50
ATOM   1425  O   ARG   259      17.641  80.329  69.123    1.00  0.50
ATOM   1430  N   GLY   260      17.591  81.295  67.081    1.00  0.50
ATOM   1431  CA  GLY   260      16.221  81.809  67.206    1.00  0.50
ATOM   1432  C   GLY   260      15.231  81.089  66.309    1.00  0.50
ATOM   1433  O   GLY   260      14.847  79.946  66.581    1.00  0.50
TER
END
