
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0316AL257_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   27 , name T0316_D3.pdb
# PARAMETERS: T0316AL257_4-D3.T0316_D3.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:    21       288 - 308         4.97     7.60
  LCS_AVERAGE:     21.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       298 - 303         1.65    10.71
  LCS_AVERAGE:      5.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       284 - 287         0.72    18.97
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.78    17.51
  LCS_AVERAGE:      3.29

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:   90
LCS_GDT     M     284     M     284      4    5   11     3    4    4    4    4    5    5    5    6    7    7    9   17   19   19   20   22   25   25   27 
LCS_GDT     S     285     S     285      4    5   11     3    4    4    4    4    5    7    8   10   11   16   18   19   20   21   21   22   25   25   27 
LCS_GDT     T     286     T     286      4    5   11     3    4    4    4    4    5    5    5    6    7    8   10   13   18   18   19   22   25   25   27 
LCS_GDT     S     287     S     287      4    5   11     3    4    4    4    4    5    5    5    7    8    8   10   17   18   19   21   22   25   25   27 
LCS_GDT     L     288     L     288      3    5   21     3    3    5    6    7    8    9   11   12   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     E     289     E     289      3    3   21     3    3    5    6    7    8   10   11   12   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     A     290     A     290      4    4   21     1    3    5    6    7    8   10   11   12   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     S     291     S     291      4    4   21     3    3    4    4    4    5    7    7   11   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     Q     292     Q     292      4    4   21     3    3    4    4    4    5    8   10   11   14   15   18   19   19   21   21   22   25   25   27 
LCS_GDT     V     293     V     293      4    4   21     3    3    5    5    6    7   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     H     294     H     294      3    3   21     3    3    5    5    6    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     F     295     F     295      3    4   21     3    3    5    5    7    7    9   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     T     296     T     296      3    4   21     3    3    4    4    4    5    5    7    9   10   14   15   17   17   18   20   22   23   24   27 
LCS_GDT     R     297     R     297      3    4   21     3    4    4    4    6    6    8    9   11   15   15   16   17   19   20   21   22   23   24   27 
LCS_GDT     E     298     E     298      3    6   21     3    4    4    5    7    7    9   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     M     299     M     299      3    6   21     3    4    5    5    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     P     300     P     300      3    6   21     1    3    5    5    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     E     301     E     301      3    6   21     0    3    4    4    7    7    9   10   12   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     E     302     E     302      3    6   21     0    3    4    5    7    7    9   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     F     303     F     303      3    6   21     0    4    4    5    7    7    9   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     T     304     T     304      3    3   21     0    3    4    4    4    5    9   10   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     L     305     L     305      3    4   21     3    3    5    6    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     E     306     E     306      3    5   21     3    3    5    6    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     C     307     C     307      3    5   21     3    3    3    6    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     T     308     T     308      0    5   21     0    0    3    5    7    8   10   11   13   15   18   18   19   20   21   21   22   25   25   27 
LCS_GDT     D     350     D     350      0    5   19     0    0    3    4    6    7    7    9   10   13   15   18   19   20   21   21   22   25   25   27 
LCS_GDT     G     351     G     351      0    5   19     1    2    3    4    5    5    5    7    9   10   11   11   14   16   18   20   20   25   25   27 
LCS_AVERAGE  LCS_A:  10.01  (   3.29    5.23   21.52 )

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      3      4      5      6      7      8     10     11     13     15     18     18     19     20     21     21     22     25     25     27 
GDT PERCENT_CA   3.33   4.44   5.56   6.67   7.78   8.89  11.11  12.22  14.44  16.67  20.00  20.00  21.11  22.22  23.33  23.33  24.44  27.78  27.78  30.00
GDT RMS_LOCAL    0.02   0.67   1.17   1.34   1.56   1.96   2.63   2.79   3.14   3.63   4.12   4.12   4.27   4.67   4.82   4.82   5.15   5.98   5.98   6.52
GDT RMS_ALL_CA  24.19  19.11   7.50   7.46   7.37   7.23   7.07   7.07   8.57   9.01   7.22   7.22   7.35   6.72   6.79   6.79   6.71   6.63   6.63   6.52

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         10.835
LGA    S     285      S     285          7.907
LGA    T     286      T     286         12.106
LGA    S     287      S     287          9.564
LGA    L     288      L     288          3.537
LGA    E     289      E     289          1.789
LGA    A     290      A     290          1.672
LGA    S     291      S     291          5.126
LGA    Q     292      Q     292          7.986
LGA    V     293      V     293          3.922
LGA    H     294      H     294          3.469
LGA    F     295      F     295          5.001
LGA    T     296      T     296         10.356
LGA    R     297      R     297          8.975
LGA    E     298      E     298          5.535
LGA    M     299      M     299          3.631
LGA    P     300      P     300          3.066
LGA    E     301      E     301          8.393
LGA    E     302      E     302          7.637
LGA    F     303      F     303          7.645
LGA    T     304      T     304          6.732
LGA    L     305      L     305          1.574
LGA    E     306      E     306          0.999
LGA    C     307      C     307          2.297
LGA    T     308      T     308          2.918
LGA    D     350      D     350          9.007
LGA    G     351      G     351         14.070

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   90    4.0     11    2.79    11.667    10.634     0.380

LGA_LOCAL      RMSD =  2.792  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.068  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  6.520  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.411627 * X  +  -0.737552 * Y  +  -0.535332 * Z  + 125.210426
  Y_new =   0.183801 * X  +  -0.642518 * Y  +   0.743900 * Z  + -26.420481
  Z_new =  -0.892626 * X  +   0.207815 * Y  +   0.400041 * Z  + -44.576469 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.479113   -2.662479  [ DEG:    27.4512   -152.5488 ]
  Theta =   1.103136    2.038456  [ DEG:    63.2051    116.7949 ]
  Phi   =   2.721634   -0.419959  [ DEG:   155.9381    -24.0619 ]
 
# 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: T0316AL257_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL257_4-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   90   4.0   11   2.79  10.634     6.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL257_4-D3
REMARK Aligment from pdb entry: 1ct9_A
ATOM    997  N   MET   284      27.243   5.229  -5.887  1.00  0.00              
ATOM    998  CA  MET   284      27.685   5.018  -7.276  1.00  0.00              
ATOM    999  C   MET   284      28.886   5.886  -7.707  1.00  0.00              
ATOM   1000  O   MET   284      29.373   5.816  -8.837  1.00  0.00              
ATOM   1001  N   SER   285      29.331   6.751  -6.811  1.00  0.00              
ATOM   1002  CA  SER   285      30.434   7.650  -7.073  1.00  0.00              
ATOM   1003  C   SER   285      31.221   7.761  -5.799  1.00  0.00              
ATOM   1004  O   SER   285      30.710   7.445  -4.699  1.00  0.00              
ATOM   1005  N   THR   286      32.462   8.214  -5.996  1.00  0.00              
ATOM   1006  CA  THR   286      33.426   8.386  -4.927  1.00  0.00              
ATOM   1007  C   THR   286      32.972   9.388  -3.867  1.00  0.00              
ATOM   1008  O   THR   286      33.208   9.131  -2.671  1.00  0.00              
ATOM   1009  N   SER   287      32.311  10.487  -4.331  1.00  0.00              
ATOM   1010  CA  SER   287      31.757  11.523  -3.470  1.00  0.00              
ATOM   1011  C   SER   287      30.625  10.933  -2.641  1.00  0.00              
ATOM   1012  O   SER   287      30.654  11.054  -1.433  1.00  0.00              
ATOM   1013  N   LEU   288      29.700  10.230  -3.313  1.00  0.00              
ATOM   1014  CA  LEU   288      28.592   9.552  -2.637  1.00  0.00              
ATOM   1015  C   LEU   288      29.106   8.623  -1.591  1.00  0.00              
ATOM   1016  O   LEU   288      28.616   8.568  -0.465  1.00  0.00              
ATOM   1017  N   GLU   289      30.142   7.896  -1.976  1.00  0.00              
ATOM   1018  CA  GLU   289      30.761   6.957  -1.084  1.00  0.00              
ATOM   1019  C   GLU   289      31.363   7.617   0.154  1.00  0.00              
ATOM   1020  O   GLU   289      31.237   7.118   1.281  1.00  0.00              
ATOM   1021  N   ALA   290      32.048   8.732  -0.070  1.00  0.00              
ATOM   1022  CA  ALA   290      32.684   9.520   0.990  1.00  0.00              
ATOM   1023  C   ALA   290      31.660   9.922   2.064  1.00  0.00              
ATOM   1024  O   ALA   290      31.820   9.710   3.265  1.00  0.00              
ATOM   1025  N   SER   291      30.592  10.553   1.582  1.00  0.00              
ATOM   1026  CA  SER   291      29.515  11.020   2.408  1.00  0.00              
ATOM   1027  C   SER   291      28.799   9.859   3.072  1.00  0.00              
ATOM   1028  O   SER   291      28.463   9.915   4.259  1.00  0.00              
ATOM   1029  N   GLN   292      28.537   8.804   2.324  1.00  0.00              
ATOM   1030  CA  GLN   292      27.853   7.648   2.899  1.00  0.00              
ATOM   1031  C   GLN   292      28.668   7.044   4.050  1.00  0.00              
ATOM   1032  O   GLN   292      28.165   6.627   5.109  1.00  0.00              
ATOM   1033  N   VAL   293      29.970   6.963   3.836  1.00  0.00              
ATOM   1034  CA  VAL   293      30.848   6.392   4.838  1.00  0.00              
ATOM   1035  C   VAL   293      30.771   7.173   6.148  1.00  0.00              
ATOM   1036  O   VAL   293      30.759   6.622   7.251  1.00  0.00              
ATOM   1037  N   HIS   294      30.758   8.502   6.072  1.00  0.00              
ATOM   1038  CA  HIS   294      30.661   9.298   7.305  1.00  0.00              
ATOM   1039  C   HIS   294      29.311   9.115   7.972  1.00  0.00              
ATOM   1040  O   HIS   294      29.221   8.893   9.178  1.00  0.00              
ATOM   1041  N   PHE   295      28.302   9.176   7.116  1.00  0.00              
ATOM   1042  CA  PHE   295      26.942   9.007   7.536  1.00  0.00              
ATOM   1043  C   PHE   295      26.799   7.755   8.373  1.00  0.00              
ATOM   1044  O   PHE   295      26.365   7.795   9.538  1.00  0.00              
ATOM   1045  N   THR   296      27.144   6.631   7.741  1.00  0.00              
ATOM   1046  CA  THR   296      26.998   5.324   8.396  1.00  0.00              
ATOM   1047  C   THR   296      27.775   5.328   9.660  1.00  0.00              
ATOM   1048  O   THR   296      27.369   4.846  10.718  1.00  0.00              
ATOM   1049  N   ARG   297      28.891   5.944   9.551  1.00  0.00              
ATOM   1050  CA  ARG   297      29.715   6.010  10.704  1.00  0.00              
ATOM   1051  C   ARG   297      29.041   6.733  11.853  1.00  0.00              
ATOM   1052  O   ARG   297      29.246   6.428  13.019  1.00  0.00              
ATOM   1053  N   GLU   298      28.223   7.706  11.520  1.00  0.00              
ATOM   1054  CA  GLU   298      27.571   8.492  12.550  1.00  0.00              
ATOM   1055  C   GLU   298      26.259   7.917  12.996  1.00  0.00              
ATOM   1056  O   GLU   298      25.849   8.119  14.137  1.00  0.00              
ATOM   1057  N   MET   299      25.578   7.251  12.068  1.00  0.00              
ATOM   1058  CA  MET   299      24.268   6.694  12.343  1.00  0.00              
ATOM   1059  C   MET   299      24.243   5.240  11.945  1.00  0.00              
ATOM   1060  O   MET   299      23.680   4.865  10.909  1.00  0.00              
ATOM   1061  N   PRO   300      24.942   4.458  12.753  1.00  0.00              
ATOM   1062  CA  PRO   300      25.146   3.033  12.568  1.00  0.00              
ATOM   1063  C   PRO   300      23.886   2.156  12.454  1.00  0.00              
ATOM   1064  O   PRO   300      23.928   0.945  12.613  1.00  0.00              
ATOM   1065  N   GLU   301      22.739   2.736  12.208  1.00  0.00              
ATOM   1066  CA  GLU   301      21.550   1.922  12.175  1.00  0.00              
ATOM   1067  C   GLU   301      20.945   1.809  10.808  1.00  0.00              
ATOM   1068  O   GLU   301      20.695   2.803  10.139  1.00  0.00              
ATOM   1069  N   GLU   302      20.717   0.573  10.387  1.00  0.00              
ATOM   1070  CA  GLU   302      20.165   0.324   9.078  1.00  0.00              
ATOM   1071  C   GLU   302      18.982   1.178   8.658  1.00  0.00              
ATOM   1072  O   GLU   302      18.985   1.719   7.552  1.00  0.00              
ATOM   1073  N   PHE   303      17.936   1.297   9.488  1.00  0.00              
ATOM   1074  CA  PHE   303      16.805   2.070   9.054  1.00  0.00              
ATOM   1075  C   PHE   303      17.185   3.570   8.847  1.00  0.00              
ATOM   1076  O   PHE   303      16.494   4.324   8.178  1.00  0.00              
ATOM   1077  N   THR   304      18.276   4.034   9.485  1.00  0.00              
ATOM   1078  CA  THR   304      18.679   5.431   9.300  1.00  0.00              
ATOM   1079  C   THR   304      18.925   5.685   7.837  1.00  0.00              
ATOM   1080  O   THR   304      18.401   6.629   7.255  1.00  0.00              
ATOM   1081  N   LEU   305      19.748   4.807   7.242  1.00  0.00              
ATOM   1082  CA  LEU   305      20.134   4.901   5.846  1.00  0.00              
ATOM   1083  C   LEU   305      18.925   4.874   4.966  1.00  0.00              
ATOM   1084  O   LEU   305      18.886   5.440   3.868  1.00  0.00              
ATOM   1085  N   GLU   306      17.908   4.197   5.485  1.00  0.00              
ATOM   1086  CA  GLU   306      16.665   4.017   4.746  1.00  0.00              
ATOM   1087  C   GLU   306      15.726   5.188   4.734  1.00  0.00              
ATOM   1088  O   GLU   306      14.796   5.214   3.919  1.00  0.00              
ATOM   1089  N   CYS   307      15.964   6.131   5.640  1.00  0.00              
ATOM   1090  CA  CYS   307      15.158   7.335   5.694  1.00  0.00              
ATOM   1091  C   CYS   307      15.565   8.239   4.550  1.00  0.00              
ATOM   1092  O   CYS   307      14.807   9.121   4.137  1.00  0.00              
ATOM   1093  N   THR   308      16.830   8.041   4.120  1.00  0.00              
ATOM   1094  CA  THR   308      17.463   8.788   3.031  1.00  0.00              
ATOM   1095  C   THR   308      16.972   8.220   1.709  1.00  0.00              
ATOM   1096  O   THR   308      17.271   7.081   1.389  1.00  0.00              
ATOM   1097  N   ASP   350      16.184   9.030   0.982  1.00  0.00              
ATOM   1098  CA  ASP   350      15.581   8.673  -0.299  1.00  0.00              
ATOM   1099  C   ASP   350      16.543   8.191  -1.397  1.00  0.00              
ATOM   1100  O   ASP   350      17.435   8.941  -1.829  1.00  0.00              
ATOM   1101  N   GLY   351      16.314   6.937  -1.856  1.00  0.00              
ATOM   1102  CA  GLY   351      17.103   6.284  -2.897  1.00  0.00              
ATOM   1103  C   GLY   351      16.744   6.794  -4.293  1.00  0.00              
ATOM   1104  O   GLY   351      15.954   6.190  -5.015  1.00  0.00              
END
