
#######################################################
#                                                     #
#                        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   25 (  124),  selected   25 , name T0386TS239_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   25 , name T0386_D2.pdb
# PARAMETERS: T0386TS239_2-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:    22       219 - 240         4.78     7.50
  LCS_AVERAGE:     26.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       219 - 231         1.82    12.43
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         1.79     9.34
  LCS_AVERAGE:     13.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       226 - 234         0.69    10.01
  LCS_AVERAGE:      7.85

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      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     P     220     P     220      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     E     221     E     221      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     K     222     K     222      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     I     223     I     223      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     R     224     R     224      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     L     225     L     225      7   13   22     7    8    8   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     L     226     L     226      9   13   22     6    9    9   10   12   13   15   16   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     K     227     K     227      9   13   22     6    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     E     228     E     228      9   13   22     6    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     F     229     F     229      9   13   22     6    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     M     230     M     230      9   13   22     6    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     H     231     H     231      9   13   22     6    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     T     232     T     232      9   13   22     4    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     M     233     M     233      9   13   22     4    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     K     234     K     234      9   13   22     4    9    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     N     235     N     235      4   13   22     3    4    4    7   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     T     236     T     236      4   13   22     3    4    9   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     237     G     237      3   13   22     3    3    3   10   12   13   15   17   19   19   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     R     238     R     238      3    4   22     3    3    3    4    5    6    8   11   15   18   20   20   20   21   21   22   22   22   22   22 
LCS_GDT     N     239     N     239      3    4   22     3    3    3    4    4    6    8    8   10   11   14   18   18   21   21   22   22   22   22   22 
LCS_GDT     V     240     V     240      3    4   22     3    3    3    4    4    6    8    8   10   11   12   14   16   19   21   22   22   22   22   22 
LCS_GDT     N     241     N     241      3    4   15     1    3    3    4    4    6    8    8   10   11   12   12   12   13   15   16   16   17   18   19 
LCS_GDT     D     242     D     242      3    4   15     1    3    3    3    4    6    8    8   10   11   12   14   15   15   16   16   17   19   21   22 
LCS_GDT     R     243     R     243      3    3   15     0    3    3    3    4    6    8    8   10   11   12   12   12   13   14   16   16   17   18   18 
LCS_AVERAGE  LCS_A:  15.77  (   7.85   13.33   26.12 )

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      9      9     10     12     13     15     17     19     19     20     20     20     21     21     22     22     22     22     22 
GDT PERCENT_CA   8.64  11.11  11.11  12.35  14.81  16.05  18.52  20.99  23.46  23.46  24.69  24.69  24.69  25.93  25.93  27.16  27.16  27.16  27.16  27.16
GDT RMS_LOCAL    0.31   0.69   0.69   1.01   1.45   1.82   2.28   2.84   3.06   3.06   3.41   3.41   3.41   4.21   4.21   4.78   4.78   4.78   4.78   4.78
GDT RMS_ALL_CA  14.43  10.01  10.01   9.83   9.65  12.43  10.73   9.17   9.42   9.42   8.98   8.98   8.98   8.20   8.20   7.50   7.50   7.50   7.50   7.50

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          2.999
LGA    P     220      P     220          3.933
LGA    E     221      E     221          2.953
LGA    K     222      K     222          0.932
LGA    I     223      I     223          2.168
LGA    R     224      R     224          0.849
LGA    L     225      L     225          1.980
LGA    L     226      L     226          4.974
LGA    K     227      K     227          4.334
LGA    E     228      E     228          3.733
LGA    F     229      F     229          3.739
LGA    M     230      M     230          3.192
LGA    H     231      H     231          2.280
LGA    T     232      T     232          1.137
LGA    M     233      M     233          0.935
LGA    K     234      K     234          1.940
LGA    N     235      N     235          3.840
LGA    T     236      T     236          3.900
LGA    G     237      G     237          3.885
LGA    R     238      R     238          8.056
LGA    N     239      N     239         13.635
LGA    V     240      V     240         15.837
LGA    N     241      N     241         21.627
LGA    D     242      D     242         21.347
LGA    R     243      R     243         23.795

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   81    4.0     17    2.83    17.901    17.228     0.581

LGA_LOCAL      RMSD =  2.827  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.322  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  6.861  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.081052 * X  +   0.132620 * Y  +  -0.987847 * Z  +  62.183163
  Y_new =   0.662532 * X  +   0.733282 * Y  +   0.152804 * Z  +  39.238960
  Z_new =   0.744636 * X  +  -0.666866 * Y  +  -0.028431 * Z  +  69.100769 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.613405    1.528188  [ DEG:   -92.4413     87.5587 ]
  Theta =  -0.839989   -2.301604  [ DEG:   -48.1278   -131.8722 ]
  Phi   =   1.449065   -1.692528  [ DEG:    83.0253    -96.9747 ]
 
# 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: T0386TS239_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   81   4.0   17   2.83  17.228     6.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 1gz5_A
ATOM    991  N   ASN   219       2.875  54.903  78.513  1.00  9.99
ATOM    992  CA  ASN   219       2.417  55.834  77.505  1.00  9.99
ATOM    993  C   ASN   219       2.402  57.200  78.099  1.00  9.99
ATOM    994  O   ASN   219       2.824  58.143  77.467  1.00  9.99
ATOM    995  CB  ASN   219       1.043  55.480  76.952  1.00  9.99
ATOM    996  N   PRO   220       1.997  57.309  79.341  1.00  9.99
ATOM    997  CA  PRO   220       1.949  58.629  79.920  1.00  9.99
ATOM    998  C   PRO   220       3.367  59.233  80.037  1.00  9.99
ATOM    999  O   PRO   220       3.599  60.396  79.666  1.00  9.99
ATOM   1000  CB  PRO   220       1.083  58.652  81.205  1.00  9.99
ATOM   1001  N   GLU   221       4.315  58.441  80.500  1.00  9.99
ATOM   1002  CA  GLU   221       5.718  58.892  80.578  1.00  9.99
ATOM   1003  C   GLU   221       6.303  59.367  79.239  1.00  9.99
ATOM   1004  O   GLU   221       7.026  60.365  79.197  1.00  9.99
ATOM   1005  CB  GLU   221       6.643  57.790  81.097  1.00  9.99
ATOM   1006  N   LYS   222       5.982  58.678  78.156  1.00  9.99
ATOM   1007  CA  LYS   222       6.490  59.100  76.854  1.00  9.99
ATOM   1008  C   LYS   222       5.699  60.239  76.186  1.00  9.99
ATOM   1009  O   LYS   222       6.237  60.927  75.336  1.00  9.99
ATOM   1010  CB  LYS   222       6.691  57.889  75.870  1.00  9.99
ATOM   1011  N   ILE   223       4.432  60.427  76.580  1.00  9.99
ATOM   1012  CA  ILE   223       3.661  61.560  76.147  1.00  9.99
ATOM   1013  C   ILE   223       4.188  62.816  76.845  1.00  9.99
ATOM   1014  O   ILE   223       4.319  63.876  76.208  1.00  9.99
ATOM   1015  CB  ILE   223       2.118  61.353  76.388  1.00  9.99
ATOM   1016  N   ARG   224       4.493  62.708  78.138  1.00  9.99
ATOM   1017  CA  ARG   224       4.965  63.880  78.872  1.00  9.99
ATOM   1018  C   ARG   224       6.342  64.236  78.385  1.00  9.99
ATOM   1019  O   ARG   224       6.682  65.403  78.338  1.00  9.99
ATOM   1020  CB  ARG   224       4.988  63.707  80.402  1.00  9.99
ATOM   1021  N   LEU   225       7.127  63.240  78.002  1.00  9.99
ATOM   1022  CA  LEU   225       8.460  63.487  77.497  1.00  9.99
ATOM   1023  C   LEU   225       8.641  63.145  75.996  1.00  9.99
ATOM   1024  O   LEU   225       9.479  62.337  75.599  1.00  9.99
ATOM   1025  CB  LEU   225       9.504  62.824  78.377  1.00  9.99
ATOM   1026  N   LEU   226       9.313  64.091  72.000  1.00  9.99
ATOM   1027  CA  LEU   226      10.397  64.750  71.260  1.00  9.99
ATOM   1028  C   LEU   226      10.249  66.293  71.283  1.00  9.99
ATOM   1029  O   LEU   226      11.232  67.044  71.310  1.00  9.99
ATOM   1030  CB  LEU   226      10.541  64.215  69.772  1.00  9.99
ATOM   1031  N   LYS   227       9.021  66.780  71.286  1.00  9.99
ATOM   1032  CA  LYS   227       8.825  68.236  71.407  1.00  9.99
ATOM   1033  C   LYS   227       9.316  68.829  72.735  1.00  9.99
ATOM   1034  O   LYS   227       9.935  69.886  72.762  1.00  9.99
ATOM   1035  CB  LYS   227       7.382  68.646  71.176  1.00  9.99
ATOM   1036  N   GLU   228       9.068  68.123  73.829  1.00  9.99
ATOM   1037  CA  GLU   228       9.689  68.452  75.130  1.00  9.99
ATOM   1038  C   GLU   228      11.237  68.452  75.147  1.00  9.99
ATOM   1039  O   GLU   228      11.837  69.401  75.679  1.00  9.99
ATOM   1040  CB  GLU   228       9.146  67.533  76.221  1.00  9.99
ATOM   1041  N   PHE   229      11.845  67.409  74.566  1.00  9.99
ATOM   1042  CA  PHE   229      13.303  67.278  74.431  1.00  9.99
ATOM   1043  C   PHE   229      13.909  68.546  73.813  1.00  9.99
ATOM   1044  O   PHE   229      14.696  69.260  74.419  1.00  9.99
ATOM   1045  CB  PHE   229      13.607  66.073  73.545  1.00  9.99
ATOM   1046  N   MET   230      13.461  68.822  72.608  1.00  9.99
ATOM   1047  CA  MET   230      13.826  69.959  71.798  1.00  9.99
ATOM   1048  C   MET   230      13.630  71.298  72.541  1.00  9.99
ATOM   1049  O   MET   230      14.506  72.157  72.582  1.00  9.99
ATOM   1050  CB  MET   230      12.879  69.856  70.590  1.00  9.99
ATOM   1051  N   HIS   231      12.465  71.460  73.132  1.00  9.99
ATOM   1052  CA  HIS   231      12.166  72.650  73.921  1.00  9.99
ATOM   1053  C   HIS   231      13.112  72.895  75.093  1.00  9.99
ATOM   1054  O   HIS   231      13.605  74.011  75.271  1.00  9.99
ATOM   1055  CB  HIS   231      10.762  72.551  74.487  1.00  9.99
ATOM   1056  N   THR   232      13.349  71.846  75.890  1.00  9.99
ATOM   1057  CA  THR   232      14.225  71.926  77.075  1.00  9.99
ATOM   1058  C   THR   232      15.649  72.242  76.704  1.00  9.99
ATOM   1059  O   THR   232      16.275  73.121  77.326  1.00  9.99
ATOM   1060  CB  THR   232      14.178  70.642  77.895  1.00  9.99
ATOM   1061  N   MET   233      16.136  71.566  75.664  1.00  9.99
ATOM   1062  CA  MET   233      17.494  71.802  75.218  1.00  9.99
ATOM   1063  C   MET   233      17.696  73.235  74.688  1.00  9.99
ATOM   1064  O   MET   233      18.611  73.938  75.109  1.00  9.99
ATOM   1065  CB  MET   233      17.941  70.764  74.188  1.00  9.99
ATOM   1066  N   LYS   234      16.836  73.655  73.767  1.00  9.99
ATOM   1067  CA  LYS   234      16.969  74.960  73.159  1.00  9.99
ATOM   1068  C   LYS   234      16.804  76.042  74.240  1.00  9.99
ATOM   1069  O   LYS   234      17.559  77.013  74.289  1.00  9.99
ATOM   1070  CB  LYS   234      15.915  75.164  72.019  1.00  9.99
ATOM   1071  N   ASN   235      15.818  75.865  75.110  1.00  9.99
ATOM   1072  CA  ASN   235      15.602  76.828  76.188  1.00  9.99
ATOM   1073  C   ASN   235      16.805  76.933  77.115  1.00  9.99
ATOM   1074  O   ASN   235      17.193  78.030  77.467  1.00  9.99
ATOM   1075  CB  ASN   235      14.325  76.495  76.962  1.00  9.99
ATOM   1076  N   THR   236      17.402  75.784  77.480  1.00  9.99
ATOM   1077  CA  THR   236      18.603  75.774  78.315  1.00  9.99
ATOM   1078  C   THR   236      19.768  76.459  77.613  1.00  9.99
ATOM   1079  O   THR   236      20.478  77.246  78.225  1.00  9.99
ATOM   1080  CB  THR   236      18.979  74.352  78.723  1.00  9.99
ATOM   1081  N   GLY   237      19.950  76.157  76.329  1.00  9.99
ATOM   1082  CA  GLY   237      20.975  76.801  75.504  1.00  9.99
ATOM   1083  C   GLY   237      20.782  78.335  75.374  1.00  9.99
ATOM   1084  O   GLY   237      21.731  79.114  75.500  1.00  9.99
ATOM   1085  N   ARG   238      19.548  78.760  75.120  1.00  9.99
ATOM   1086  CA  ARG   238      19.252  80.169  74.900  1.00  9.99
ATOM   1087  C   ARG   238      19.493  80.931  76.174  1.00  9.99
ATOM   1088  O   ARG   238      19.697  82.120  76.137  1.00  9.99
ATOM   1089  CB  ARG   238      17.804  80.365  74.467  1.00  9.99
ATOM   1090  N   ASN   239      19.484  80.218  77.299  1.00  9.99
ATOM   1091  CA  ASN   239      19.632  80.822  78.634  1.00  9.99
ATOM   1092  C   ASN   239      21.088  81.146  79.001  1.00  9.99
ATOM   1093  O   ASN   239      21.325  81.908  79.938  1.00  9.99
ATOM   1094  CB  ASN   239      19.037  79.885  79.686  1.00  9.99
ATOM   1095  N   VAL   240      22.065  80.547  78.298  1.00  9.99
ATOM   1096  CA  VAL   240      23.451  80.865  78.647  1.00  9.99
ATOM   1097  C   VAL   240      23.975  82.094  77.881  1.00  9.99
ATOM   1098  O   VAL   240      23.597  82.332  76.714  1.00  9.99
ATOM   1099  CB  VAL   240      24.413  79.600  78.701  1.00  9.99
ATOM   1100  N   ASN   241      24.794  82.903  78.555  1.00  9.99
ATOM   1101  CA  ASN   241      25.423  84.024  77.882  1.00  9.99
ATOM   1102  C   ASN   241      26.664  83.538  77.143  1.00  9.99
ATOM   1103  O   ASN   241      27.508  82.872  77.731  1.00  9.99
ATOM   1104  CB  ASN   241      25.776  85.200  78.863  1.00  9.99
ATOM   1105  N   ASP   242      26.793  83.899  75.866  1.00  9.99
ATOM   1106  CA  ASP   242      27.959  83.512  75.058  1.00  9.99
ATOM   1107  C   ASP   242      29.254  84.278  75.465  1.00  9.99
ATOM   1108  O   ASP   242      29.173  85.364  76.079  1.00  9.99
ATOM   1109  CB  ASP   242      27.531  83.922  73.635  1.00  9.99
ATOM   1110  N   ARG   243      30.414  83.704  75.119  1.00  9.99
ATOM   1111  CA  ARG   243      31.722  84.236  75.524  1.00  9.99
ATOM   1112  C   ARG   243      31.988  85.613  74.920  1.00  9.99
ATOM   1113  O   ARG   243      31.612  85.855  73.757  1.00  9.99
ATOM   1114  CB  ARG   243      32.834  83.259  75.121  1.00  9.99
TER
END
