
#######################################################
#                                                     #
#                        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   17 (  137),  selected   17 , name T0385TS009_4_2
# Molecule2: number of CA atoms  142 ( 1050),  selected   17 , name T0385.pdb
# PARAMETERS: T0385TS009_4_2.T0385.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:    17       141 - 157         3.24     3.24
  LCS_AVERAGE:     11.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       151 - 157         1.40    12.23
  LCS_AVERAGE:      4.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       152 - 156         0.99    11.80
  LCS_AVERAGE:      2.86

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:  142
LCS_GDT     A     141     A     141      3    5   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     T     142     T     142      3    5   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R     143     R     143      3    5   17     3    3    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     W     144     W     144      3    5   17     3    3    4    4    6    8   10   11   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     N     145     N     145      4    5   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R     146     R     146      4    4   17     3    4    4    5    6    7   10   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V     147     V     147      4    4   17     3    4    6    6    7    7    8   10   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L     148     L     148      4    5   17     3    4    4    5   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     G     149     G     149      4    5   17     3    3    4    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     A     150     A     150      4    5   17     3    3    6    6    6    9   11   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     W     151     W     151      4    7   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     P     152     P     152      5    7   17     3    4    6    6    7    7    8   11   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     I     153     I     153      5    7   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     T     154     T     154      5    7   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     A     155     A     155      5    7   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     A     156     A     156      5    7   17     3    4    6    7   10   11   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     F     157     F     157      4    7   17     3    3    5    6    7    8   12   13   16   17   17   17   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   6.28  (   2.86    4.02   11.97 )

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      6      7     10     11     12     13     16     17     17     17     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   2.11   2.82   4.23   4.93   7.04   7.75   8.45   9.15  11.27  11.97  11.97  11.97  11.97  11.97  11.97  11.97  11.97  11.97  11.97  11.97
GDT RMS_LOCAL    0.02   0.47   1.14   1.30   1.86   2.02   2.30   2.55   3.09   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24
GDT RMS_ALL_CA  15.83   4.59  13.90   4.12   3.50   3.45   3.37   3.29   3.26   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24

#      Molecule1      Molecule2       DISTANCE
LGA    A     141      A     141          0.312
LGA    T     142      T     142          2.730
LGA    R     143      R     143          2.555
LGA    W     144      W     144          4.710
LGA    N     145      N     145          2.323
LGA    R     146      R     146          4.500
LGA    V     147      V     147          4.767
LGA    L     148      L     148          2.856
LGA    G     149      G     149          3.038
LGA    A     150      A     150          3.827
LGA    W     151      W     151          1.568
LGA    P     152      P     152          4.907
LGA    I     153      I     153          2.724
LGA    T     154      T     154          1.642
LGA    A     155      A     155          2.510
LGA    A     156      A     156          2.225
LGA    F     157      F     157          3.660

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  142    4.0     13    2.55     7.218     7.222     0.491

LGA_LOCAL      RMSD =  2.549  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.236  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  3.236  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.579367 * X  +   0.753717 * Y  +   0.310233 * Z  +   2.916655
  Y_new =  -0.768255 * X  +   0.632123 * Y  +  -0.101020 * Z  +  40.020271
  Z_new =  -0.272245 * X  +  -0.179810 * Y  +   0.945278 * Z  +  46.505714 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.187974    2.953619  [ DEG:   -10.7701    169.2299 ]
  Theta =   0.275726    2.865867  [ DEG:    15.7979    164.2021 ]
  Phi   =  -0.924655    2.216938  [ DEG:   -52.9788    127.0212 ]
 
# 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: T0385TS009_4_2                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_4_2.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  142   4.0   13   2.55   7.222     3.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_4_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1021  N   ALA   141      22.442  20.777  17.970  1.00  0.00              
ATOM   1022  CA  ALA   141      22.104  21.954  17.179  1.00  0.00              
ATOM   1023  C   ALA   141      23.358  22.631  16.636  1.00  0.00              
ATOM   1024  O   ALA   141      24.377  22.713  17.322  1.00  0.00              
ATOM   1025  CB  ALA   141      21.175  21.576  16.035  1.00  0.00              
ATOM   1026  N   THR   142      23.275  23.116  15.401  1.00  0.00              
ATOM   1027  CA  THR   142      24.428  23.802  14.750  1.00  0.00              
ATOM   1028  C   THR   142      24.453  23.533  13.249  1.00  0.00              
ATOM   1029  O   THR   142      24.859  24.388  12.463  1.00  0.00              
ATOM   1030  CB  THR   142      24.387  25.323  14.988  1.00  0.00              
ATOM   1031  OG1 THR   142      23.259  25.651  15.808  1.00  0.00              
ATOM   1032  CG2 THR   142      25.661  25.789  15.676  1.00  0.00              
ATOM   1033  N   ARG   143      24.018  22.339  12.860  1.00  0.00              
ATOM   1034  CA  ARG   143      23.991  21.954  11.454  1.00  0.00              
ATOM   1035  C   ARG   143      23.367  23.049  10.595  1.00  0.00              
ATOM   1036  O   ARG   143      22.491  22.783   9.773  1.00  0.00              
ATOM   1037  CB  ARG   143      25.403  21.638  10.958  1.00  0.00              
ATOM   1038  CG  ARG   143      25.618  20.178  10.589  1.00  0.00              
ATOM   1039  CD  ARG   143      26.846  20.007   9.710  1.00  0.00              
ATOM   1040  NE  ARG   143      26.915  18.671   9.122  1.00  0.00              
ATOM   1041  CZ  ARG   143      26.323  18.325   7.984  1.00  0.00              
ATOM   1042  NH1 ARG   143      25.614  19.217   7.307  1.00  0.00              
ATOM   1043  NH2 ARG   143      26.442  17.086   7.526  1.00  0.00              
ATOM   1044  N   TRP   144      23.824  24.282  10.791  1.00  0.00              
ATOM   1045  CA  TRP   144      23.311  25.419  10.037  1.00  0.00              
ATOM   1046  C   TRP   144      21.821  25.264   9.750  1.00  0.00              
ATOM   1047  O   TRP   144      21.416  25.068   8.604  1.00  0.00              
ATOM   1048  CB  TRP   144      23.569  26.724  10.792  1.00  0.00              
ATOM   1049  CG  TRP   144      24.438  27.689  10.043  1.00  0.00              
ATOM   1050  CD1 TRP   144      24.168  29.000   9.780  1.00  0.00              
ATOM   1051  CD2 TRP   144      25.718  27.416   9.460  1.00  0.00              
ATOM   1052  NE1 TRP   144      25.200  29.564   9.070  1.00  0.00              
ATOM   1053  CE2 TRP   144      26.165  28.611   8.862  1.00  0.00              
ATOM   1054  CE3 TRP   144      26.529  26.280   9.389  1.00  0.00              
ATOM   1055  CZ2 TRP   144      27.387  28.701   8.197  1.00  0.00              
ATOM   1056  CZ3 TRP   144      27.740  26.372   8.731  1.00  0.00              
ATOM   1057  CH2 TRP   144      28.161  27.574   8.141  1.00  0.00              
ATOM   1058  N   ASN   145      21.010  25.354  10.798  1.00  0.00              
ATOM   1059  CA  ASN   145      19.564  25.225  10.662  1.00  0.00              
ATOM   1060  C   ASN   145      19.162  23.776  10.408  1.00  0.00              
ATOM   1061  O   ASN   145      18.120  23.506   9.809  1.00  0.00              
ATOM   1062  CB  ASN   145      18.858  25.756  11.911  1.00  0.00              
ATOM   1063  CG  ASN   145      17.357  25.873  11.726  1.00  0.00              
ATOM   1064  OD1 ASN   145      16.755  26.883  12.090  1.00  0.00              
ATOM   1065  ND2 ASN   145      16.750  24.837  11.159  1.00  0.00              
ATOM   1066  N   ARG   146      19.994  22.847  10.867  1.00  0.00              
ATOM   1067  CA  ARG   146      19.727  21.424  10.690  1.00  0.00              
ATOM   1068  C   ARG   146      19.254  21.123   9.272  1.00  0.00              
ATOM   1069  O   ARG   146      19.986  20.538   8.474  1.00  0.00              
ATOM   1070  CB  ARG   146      20.974  20.600  11.015  1.00  0.00              
ATOM   1071  CG  ARG   146      21.154  20.302  12.494  1.00  0.00              
ATOM   1072  CD  ARG   146      22.516  19.687  12.772  1.00  0.00              
ATOM   1073  NE  ARG   146      22.969  19.956  14.134  1.00  0.00              
ATOM   1074  CZ  ARG   146      22.351  19.522  15.227  1.00  0.00              
ATOM   1075  NH1 ARG   146      21.247  18.795  15.119  1.00  0.00              
ATOM   1076  NH2 ARG   146      22.837  19.817  16.425  1.00  0.00              
ATOM   1077  N   VAL   147      18.026  21.529   8.964  1.00  0.00              
ATOM   1078  CA  VAL   147      17.442  21.299   7.612  1.00  0.00              
ATOM   1079  C   VAL   147      18.411  21.720   6.513  1.00  0.00              
ATOM   1080  O   VAL   147      17.995  22.135   5.430  1.00  0.00              
ATOM   1081  CB  VAL   147      17.059  19.822   7.406  1.00  0.00              
ATOM   1082  CG1 VAL   147      15.564  19.688   7.158  1.00  0.00              
ATOM   1083  CG2 VAL   147      17.484  18.989   8.606  1.00  0.00              
ATOM   1084  N   LEU   148      19.704  21.612   6.797  1.00  0.00              
ATOM   1085  CA  LEU   148      20.735  21.982   5.834  1.00  0.00              
ATOM   1086  C   LEU   148      20.203  22.987   4.817  1.00  0.00              
ATOM   1087  O   LEU   148      19.949  22.641   3.664  1.00  0.00              
ATOM   1088  CB  LEU   148      21.958  22.556   6.552  1.00  0.00              
ATOM   1089  CG  LEU   148      21.773  23.919   7.224  1.00  0.00              
ATOM   1090  CD1 LEU   148      20.404  24.497   6.897  1.00  0.00              
ATOM   1091  CD2 LEU   148      22.877  24.877   6.809  1.00  0.00              
ATOM   1092  N   GLY   149      20.040  24.232   5.253  1.00  0.00              
ATOM   1093  CA  GLY   149      19.539  25.265   4.365  1.00  0.00              
ATOM   1094  C   GLY   149      18.123  24.994   3.899  1.00  0.00              
ATOM   1095  O   GLY   149      17.846  24.980   2.700  1.00  0.00              
ATOM   1096  N   ALA   150      17.219  24.776   4.849  1.00  0.00              
ATOM   1097  CA  ALA   150      15.823  24.502   4.530  1.00  0.00              
ATOM   1098  C   ALA   150      15.684  23.225   3.710  1.00  0.00              
ATOM   1099  O   ALA   150      14.751  22.447   3.909  1.00  0.00              
ATOM   1100  CB  ALA   150      14.999  24.401   5.804  1.00  0.00              
ATOM   1101  N   TRP   151      16.618  23.013   2.790  1.00  0.00              
ATOM   1102  CA  TRP   151      16.601  21.829   1.939  1.00  0.00              
ATOM   1103  C   TRP   151      16.343  20.567   2.755  1.00  0.00              
ATOM   1104  O   TRP   151      16.535  19.449   2.276  1.00  0.00              
ATOM   1105  CB  TRP   151      15.544  21.972   0.842  1.00  0.00              
ATOM   1106  CG  TRP   151      15.950  22.899  -0.263  1.00  0.00              
ATOM   1107  CD1 TRP   151      15.572  22.826  -1.573  1.00  0.00              
ATOM   1108  CD2 TRP   151      16.810  24.040  -0.156  1.00  0.00              
ATOM   1109  NE1 TRP   151      16.144  23.850  -2.290  1.00  0.00              
ATOM   1110  CE2 TRP   151      16.909  24.610  -1.441  1.00  0.00              
ATOM   1111  CE3 TRP   151      17.505  24.634   0.902  1.00  0.00              
ATOM   1112  CZ2 TRP   151      17.676  25.745  -1.697  1.00  0.00              
ATOM   1113  CZ3 TRP   151      18.265  25.758   0.646  1.00  0.00              
ATOM   1114  CH2 TRP   151      18.346  26.305  -0.644  1.00  0.00              
ATOM   1115  N   PRO   152      15.900  20.736   4.009  1.00  0.00              
ATOM   1116  CA  PRO   152      15.611  19.610   4.903  1.00  0.00              
ATOM   1117  C   PRO   152      14.636  18.622   4.272  1.00  0.00              
ATOM   1118  O   PRO   152      14.481  17.498   4.749  1.00  0.00              
ATOM   1119  CB  PRO   152      16.982  18.954   5.083  1.00  0.00              
ATOM   1120  CG  PRO   152      17.085  17.987   3.952  1.00  0.00              
ATOM   1121  CD  PRO   152      15.648  22.039   4.648  1.00  0.00              
ATOM   1122  N   ILE   153      13.980  19.050   3.198  1.00  0.00              
ATOM   1123  CA  ILE   153      12.996  18.185   2.485  1.00  0.00              
ATOM   1124  C   ILE   153      11.765  17.925   3.346  1.00  0.00              
ATOM   1125  O   ILE   153      11.879  17.557   4.515  1.00  0.00              
ATOM   1126  CB  ILE   153      12.555  18.814   1.152  1.00  0.00              
ATOM   1127  CG2 ILE   153      13.667  19.679   0.577  1.00  0.00              
ATOM   1128  CG1 ILE   153      11.278  19.634   1.345  1.00  0.00              
ATOM   1129  CD1 ILE   153      11.116  20.758   0.345  1.00  0.00              
ATOM   1130  N   THR   154      10.588  18.119   2.759  1.00  0.00              
ATOM   1131  CA  THR   154       9.305  17.901   3.487  1.00  0.00              
ATOM   1132  C   THR   154       8.265  18.946   3.098  1.00  0.00              
ATOM   1133  O   THR   154       8.595  19.969   2.497  1.00  0.00              
ATOM   1134  CB  THR   154       8.733  16.496   3.216  1.00  0.00              
ATOM   1135  OG1 THR   154       9.124  16.063   1.906  1.00  0.00              
ATOM   1136  CG2 THR   154       9.248  15.504   4.246  1.00  0.00              
ATOM   1137  N   ALA   155       7.010  18.682   3.444  1.00  0.00              
ATOM   1138  CA  ALA   155       5.921  19.600   3.131  1.00  0.00              
ATOM   1139  C   ALA   155       4.578  18.876   3.116  1.00  0.00              
ATOM   1140  O   ALA   155       3.818  18.979   2.153  1.00  0.00              
ATOM   1141  CB  ALA   155       5.887  20.744   4.133  1.00  0.00              
ATOM   1142  N   ALA   156       4.293  18.144   4.188  1.00  0.00              
ATOM   1143  CA  ALA   156       3.043  17.402   4.299  1.00  0.00              
ATOM   1144  C   ALA   156       2.644  16.790   2.961  1.00  0.00              
ATOM   1145  O   ALA   156       1.820  17.345   2.235  1.00  0.00              
ATOM   1146  CB  ALA   156       3.163  16.317   5.358  1.00  0.00              
ATOM   1147  N   PHE   157       3.234  15.643   2.641  1.00  0.00              
ATOM   1148  CA  PHE   157       2.942  14.953   1.391  1.00  0.00              
ATOM   1149  C   PHE   157       4.203  14.775   0.552  1.00  0.00              
ATOM   1150  O   PHE   157       5.216  15.437   0.777  1.00  0.00              
ATOM   1151  CB  PHE   157       2.297  13.593   1.667  1.00  0.00              
ATOM   1152  CG  PHE   157       2.590  12.559   0.618  1.00  0.00              
ATOM   1153  CD1 PHE   157       3.556  11.591   0.831  1.00  0.00              
ATOM   1154  CD2 PHE   157       1.901  12.554  -0.582  1.00  0.00              
ATOM   1155  CE1 PHE   157       3.826  10.639  -0.134  1.00  0.00              
ATOM   1156  CE2 PHE   157       2.171  11.603  -1.547  1.00  0.00              
ATOM   1157  CZ  PHE   157       3.129  10.648  -1.327  1.00  0.00              
TER
END
