
#######################################################
#                                                     #
#                        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   21 (  165),  selected   17 , name T0385TS009_1_4
# Molecule2: number of CA atoms  142 ( 1050),  selected   17 , name T0385.pdb
# PARAMETERS: T0385TS009_1_4.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       142 - 158         4.70     4.70
  LCS_AVERAGE:     11.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       154 - 158         1.34    12.81
  LCS_AVERAGE:      3.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       142 - 145         0.67    16.76
  LONGEST_CONTINUOUS_SEGMENT:     4       155 - 158         0.84    12.96
  LCS_AVERAGE:      2.44

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     T     142     T     142      4    4   17     3    4    4    7    7    9    9   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     R     143     R     143      4    4   17     3    4    6    6    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     W     144     W     144      4    4   17     3    4    5    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     N     145     N     145      4    4   17     3    4    4    4    7    7    7   10   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     R     146     R     146      3    4   17     3    5    6    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     V     147     V     147      3    4   17     3    5    6    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     L     148     L     148      3    4   17     3    3    4    5    7    7   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     G     149     G     149      3    4   17     3    5    6    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     A     150     A     150      3    4   17     3    3    3    4    7    8    9   11   12   13   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     W     151     W     151      3    4   17     3    3    4    5    7    7    8   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     P     152     P     152      3    4   17     3    5    6    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     I     153     I     153      3    4   17     3    3    3    4    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     T     154     T     154      3    5   17     3    5    6    7    7    9   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     A     155     A     155      4    5   17     3    3    4    5    5    7   10   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     A     156     A     156      4    5   17     3    3    4    5    5    6    9   11   14   14   14   15   16   16   16   16   17   17   17   17 
LCS_GDT     F     157     F     157      4    5   17     3    3    4    5    5    5    6    6    7   11   12   15   16   16   16   16   17   17   17   17 
LCS_GDT     P     158     P     158      4    5   17     3    3    4    5    5    5    6    6    6    7    7    7   10   10   16   16   17   17   17   17 
LCS_AVERAGE  LCS_A:   5.81  (   2.44    3.02   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      5      6      7      7      9     10     11     14     14     14     15     16     16     16     16     17     17     17     17 
GDT PERCENT_CA   2.11   3.52   4.23   4.93   4.93   6.34   7.04   7.75   9.86   9.86   9.86  10.56  11.27  11.27  11.27  11.27  11.97  11.97  11.97  11.97
GDT RMS_LOCAL    0.01   0.49   0.89   1.30   1.27   1.89   2.58   2.48   3.32   3.32   3.32   3.56   4.05   4.05   4.05   4.05   4.70   4.70   4.70   4.70
GDT RMS_ALL_CA  15.67   7.45   7.54   7.66   7.23   7.65   6.03   8.03   5.45   5.45   5.45   5.58   4.96   4.96   4.96   4.96   4.70   4.70   4.70   4.70

#      Molecule1      Molecule2       DISTANCE
LGA    T     142      T     142          2.844
LGA    R     143      R     143          3.162
LGA    W     144      W     144          3.227
LGA    N     145      N     145          6.745
LGA    R     146      R     146          1.970
LGA    V     147      V     147          0.949
LGA    L     148      L     148          4.745
LGA    G     149      G     149          1.465
LGA    A     150      A     150          3.969
LGA    W     151      W     151          3.853
LGA    P     152      P     152          0.778
LGA    I     153      I     153          2.338
LGA    T     154      T     154          1.841
LGA    A     155      A     155          8.191
LGA    A     156      A     156         10.531
LGA    F     157      F     157         16.826
LGA    P     158      P     158         22.326

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  142    4.0     11    2.48     6.866     6.288     0.426

LGA_LOCAL      RMSD =  2.481  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.055  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  4.699  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.161816 * X  +  -0.965946 * Y  +  -0.201901 * Z  +   6.317906
  Y_new =  -0.703616 * X  +  -0.256389 * Y  +   0.662713 * Z  + -21.269545
  Z_new =  -0.691910 * X  +   0.034823 * Y  +  -0.721143 * Z  +  -8.310599 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.093341   -0.048251  [ DEG:   177.2354     -2.7646 ]
  Theta =   0.764132    2.377461  [ DEG:    43.7815    136.2185 ]
  Phi   =  -1.344750    1.796843  [ DEG:   -77.0485    102.9515 ]
 
# 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_1_4                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_4.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  142   4.0   11   2.48   6.288     4.70
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_4
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1026  N   THR   142      25.362  27.436  14.810  1.00  0.00              
ATOM   1027  CA  THR   142      24.244  26.952  13.950  1.00  0.00              
ATOM   1028  C   THR   142      24.027  25.453  14.120  1.00  0.00              
ATOM   1029  O   THR   142      23.659  24.758  13.173  1.00  0.00              
ATOM   1030  CB  THR   142      22.930  27.691  14.263  1.00  0.00              
ATOM   1031  OG1 THR   142      23.162  28.675  15.279  1.00  0.00              
ATOM   1032  CG2 THR   142      22.393  28.375  13.015  1.00  0.00              
ATOM   1033  N   ARG   143      24.257  24.961  15.333  1.00  0.00              
ATOM   1034  CA  ARG   143      24.087  23.544  15.630  1.00  0.00              
ATOM   1035  C   ARG   143      24.184  22.699  14.364  1.00  0.00              
ATOM   1036  O   ARG   143      23.207  22.549  13.631  1.00  0.00              
ATOM   1037  CB  ARG   143      25.128  23.081  16.652  1.00  0.00              
ATOM   1038  CG  ARG   143      24.534  22.520  17.933  1.00  0.00              
ATOM   1039  CD  ARG   143      25.617  22.000  18.863  1.00  0.00              
ATOM   1040  NE  ARG   143      25.098  21.025  19.817  1.00  0.00              
ATOM   1041  CZ  ARG   143      25.207  19.708  19.674  1.00  0.00              
ATOM   1042  NH1 ARG   143      25.821  19.206  18.612  1.00  0.00              
ATOM   1043  NH2 ARG   143      24.703  18.897  20.594  1.00  0.00              
ATOM   1044  N   TRP   144      25.368  22.151  14.113  1.00  0.00              
ATOM   1045  CA  TRP   144      25.594  21.321  12.936  1.00  0.00              
ATOM   1046  C   TRP   144      25.466  22.137  11.653  1.00  0.00              
ATOM   1047  O   TRP   144      24.847  21.696  10.685  1.00  0.00              
ATOM   1048  CB  TRP   144      26.973  20.661  13.004  1.00  0.00              
ATOM   1049  CG  TRP   144      27.110  19.468  12.108  1.00  0.00              
ATOM   1050  CD1 TRP   144      28.161  18.598  12.056  1.00  0.00              
ATOM   1051  CD2 TRP   144      26.163  19.011  11.134  1.00  0.00              
ATOM   1052  NE1 TRP   144      27.929  17.628  11.112  1.00  0.00              
ATOM   1053  CE2 TRP   144      26.708  17.860  10.532  1.00  0.00              
ATOM   1054  CE3 TRP   144      24.910  19.465  10.715  1.00  0.00              
ATOM   1055  CZ2 TRP   144      26.041  17.155   9.530  1.00  0.00              
ATOM   1056  CZ3 TRP   144      24.250  18.764   9.722  1.00  0.00              
ATOM   1057  CH2 TRP   144      24.815  17.621   9.139  1.00  0.00              
ATOM   1058  N   ASN   145      26.054  23.328  11.654  1.00  0.00              
ATOM   1059  CA  ASN   145      26.006  24.208  10.492  1.00  0.00              
ATOM   1060  C   ASN   145      24.581  24.354   9.970  1.00  0.00              
ATOM   1061  O   ASN   145      24.368  24.623   8.787  1.00  0.00              
ATOM   1062  CB  ASN   145      26.585  25.582  10.835  1.00  0.00              
ATOM   1063  CG  ASN   145      27.648  26.029   9.852  1.00  0.00              
ATOM   1064  OD1 ASN   145      28.272  27.074  10.030  1.00  0.00              
ATOM   1065  ND2 ASN   145      27.857  25.234   8.808  1.00  0.00              
ATOM   1066  N   ARG   146      23.610  24.175  10.859  1.00  0.00              
ATOM   1067  CA  ARG   146      22.203  24.288  10.489  1.00  0.00              
ATOM   1068  C   ARG   146      21.885  23.436   9.265  1.00  0.00              
ATOM   1069  O   ARG   146      20.769  23.468   8.747  1.00  0.00              
ATOM   1070  CB  ARG   146      21.308  23.881  11.661  1.00  0.00              
ATOM   1071  CG  ARG   146      21.180  24.941  12.742  1.00  0.00              
ATOM   1072  CD  ARG   146      20.375  24.429  13.926  1.00  0.00              
ATOM   1073  NE  ARG   146      20.802  25.038  15.182  1.00  0.00              
ATOM   1074  CZ  ARG   146      20.659  26.327  15.474  1.00  0.00              
ATOM   1075  NH1 ARG   146      20.097  27.147  14.597  1.00  0.00              
ATOM   1076  NH2 ARG   146      21.079  26.792  16.643  1.00  0.00              
ATOM   1077  N   VAL   147      22.872  22.673   8.808  1.00  0.00              
ATOM   1078  CA  VAL   147      22.696  21.792   7.619  1.00  0.00              
ATOM   1079  C   VAL   147      21.761  22.427   6.595  1.00  0.00              
ATOM   1080  O   VAL   147      20.878  21.763   6.052  1.00  0.00              
ATOM   1081  CB  VAL   147      24.045  21.479   6.943  1.00  0.00              
ATOM   1082  CG1 VAL   147      24.346  19.990   7.020  1.00  0.00              
ATOM   1083  CG2 VAL   147      25.161  22.290   7.581  1.00  0.00              
ATOM   1084  N   LEU   148      21.961  23.715   6.338  1.00  0.00              
ATOM   1085  CA  LEU   148      21.136  24.442   5.380  1.00  0.00              
ATOM   1086  C   LEU   148      19.681  23.991   5.452  1.00  0.00              
ATOM   1087  O   LEU   148      19.034  23.785   4.425  1.00  0.00              
ATOM   1088  CB  LEU   148      21.232  25.949   5.626  1.00  0.00              
ATOM   1089  CG  LEU   148      20.885  26.429   7.036  1.00  0.00              
ATOM   1090  CD1 LEU   148      20.087  25.372   7.783  1.00  0.00              
ATOM   1091  CD2 LEU   148      20.124  27.745   6.984  1.00  0.00              
ATOM   1092  N   GLY   149      19.173  23.839   6.669  1.00  0.00              
ATOM   1093  CA  GLY   149      17.797  23.413   6.849  1.00  0.00              
ATOM   1094  C   GLY   149      17.327  22.491   5.742  1.00  0.00              
ATOM   1095  O   GLY   149      16.142  22.457   5.410  1.00  0.00              
ATOM   1096  N   ALA   150      18.257  21.737   5.165  1.00  0.00              
ATOM   1097  CA  ALA   150      17.934  20.808   4.088  1.00  0.00              
ATOM   1098  C   ALA   150      16.714  21.279   3.302  1.00  0.00              
ATOM   1099  O   ALA   150      16.405  20.745   2.238  1.00  0.00              
ATOM   1100  CB  ALA   150      19.124  20.641   3.157  1.00  0.00              
ATOM   1101  N   TRP   151      16.024  22.283   3.836  1.00  0.00              
ATOM   1102  CA  TRP   151      14.838  22.827   3.186  1.00  0.00              
ATOM   1103  C   TRP   151      14.599  22.168   1.832  1.00  0.00              
ATOM   1104  O   TRP   151      13.808  22.649   1.021  1.00  0.00              
ATOM   1105  CB  TRP   151      13.610  22.652   4.081  1.00  0.00              
ATOM   1106  CG  TRP   151      12.970  23.946   4.483  1.00  0.00              
ATOM   1107  CD1 TRP   151      11.934  24.112   5.355  1.00  0.00              
ATOM   1108  CD2 TRP   151      13.326  25.257   4.027  1.00  0.00              
ATOM   1109  NE1 TRP   151      11.621  25.445   5.472  1.00  0.00              
ATOM   1110  CE2 TRP   151      12.463  26.169   4.665  1.00  0.00              
ATOM   1111  CE3 TRP   151      14.291  25.747   3.141  1.00  0.00              
ATOM   1112  CZ2 TRP   151      12.535  27.544   4.447  1.00  0.00              
ATOM   1113  CZ3 TRP   151      14.360  27.110   2.926  1.00  0.00              
ATOM   1114  CH2 TRP   151      13.488  27.996   3.575  1.00  0.00              
ATOM   1115  N   PRO   152      15.288  21.047   1.573  1.00  0.00              
ATOM   1116  CA  PRO   152      15.155  20.311   0.312  1.00  0.00              
ATOM   1117  C   PRO   152      13.698  19.994  -0.008  1.00  0.00              
ATOM   1118  O   PRO   152      13.406  19.239  -0.934  1.00  0.00              
ATOM   1119  CB  PRO   152      15.718  21.291  -0.719  1.00  0.00              
ATOM   1120  CG  PRO   152      15.373  22.639  -0.181  1.00  0.00              
ATOM   1121  CD  PRO   152      16.249  20.414   2.494  1.00  0.00              
ATOM   1122  N   ILE   153      12.788  20.575   0.766  1.00  0.00              
ATOM   1123  CA  ILE   153      11.327  20.351   0.563  1.00  0.00              
ATOM   1124  C   ILE   153      10.946  18.905   0.860  1.00  0.00              
ATOM   1125  O   ILE   153      10.580  18.151  -0.041  1.00  0.00              
ATOM   1126  CB  ILE   153      10.484  21.287   1.447  1.00  0.00              
ATOM   1127  CG2 ILE   153      10.652  22.734   1.004  1.00  0.00              
ATOM   1128  CG1 ILE   153      10.872  21.125   2.919  1.00  0.00              
ATOM   1129  CD1 ILE   153       9.916  21.797   3.880  1.00  0.00              
ATOM   1130  N   THR   154      11.032  18.525   2.132  1.00  0.00              
ATOM   1131  CA  THR   154      10.688  17.139   2.560  1.00  0.00              
ATOM   1132  C   THR   154      11.863  16.190   2.352  1.00  0.00              
ATOM   1133  O   THR   154      11.699  15.088   1.829  1.00  0.00              
ATOM   1134  CB  THR   154      10.260  17.095   4.039  1.00  0.00              
ATOM   1135  OG1 THR   154      10.652  18.311   4.688  1.00  0.00              
ATOM   1136  CG2 THR   154       8.752  16.929   4.152  1.00  0.00              
ATOM   1137  N   ALA   155      13.049  16.625   2.766  1.00  0.00              
ATOM   1138  CA  ALA   155      14.254  15.815   2.627  1.00  0.00              
ATOM   1139  C   ALA   155      14.203  14.965   1.361  1.00  0.00              
ATOM   1140  O   ALA   155      15.097  14.157   1.109  1.00  0.00              
ATOM   1141  CB  ALA   155      15.489  16.702   2.613  1.00  0.00              
ATOM   1142  N   ALA   156      13.152  15.152   0.570  1.00  0.00              
ATOM   1143  CA  ALA   156      12.983  14.403  -0.668  1.00  0.00              
ATOM   1144  C   ALA   156      14.204  13.538  -0.962  1.00  0.00              
ATOM   1145  O   ALA   156      14.363  13.027  -2.071  1.00  0.00              
ATOM   1146  CB  ALA   156      11.732  13.539  -0.599  1.00  0.00              
ATOM   1147  N   PHE   157      15.064  13.380   0.038  1.00  0.00              
ATOM   1148  CA  PHE   157      16.272  12.578  -0.110  1.00  0.00              
ATOM   1149  C   PHE   157      16.987  12.894  -1.419  1.00  0.00              
ATOM   1150  O   PHE   157      16.786  12.223  -2.432  1.00  0.00              
ATOM   1151  CB  PHE   157      17.215  12.805   1.074  1.00  0.00              
ATOM   1152  CG  PHE   157      18.360  11.834   1.132  1.00  0.00              
ATOM   1153  CD1 PHE   157      19.351  11.851   0.166  1.00  0.00              
ATOM   1154  CD2 PHE   157      18.445  10.903   2.153  1.00  0.00              
ATOM   1155  CE1 PHE   157      20.404  10.957   0.221  1.00  0.00              
ATOM   1156  CE2 PHE   157      19.498  10.010   2.207  1.00  0.00              
ATOM   1157  CZ  PHE   157      20.475  10.034   1.247  1.00  0.00              
ATOM   1158  N   PRO   158      17.839  13.930  -1.410  1.00  0.00              
ATOM   1159  CA  PRO   158      18.591  14.344  -2.598  1.00  0.00              
ATOM   1160  C   PRO   158      18.147  13.583  -3.843  1.00  0.00              
ATOM   1161  O   PRO   158      18.693  13.780  -4.930  1.00  0.00              
ATOM   1162  CB  PRO   158      18.235  15.826  -2.733  1.00  0.00              
ATOM   1163  CG  PRO   158      18.315  16.356  -1.340  1.00  0.00              
ATOM   1164  CD  PRO   158      18.129  14.775  -0.239  1.00  0.00              
ATOM   1165  N   GLY   159      17.156  12.714  -3.678  1.00  0.00              
ATOM   1166  CA  GLY   159      16.658  11.939  -4.798  1.00  0.00              
ATOM   1167  C   GLY   159      17.014  12.558  -6.135  1.00  0.00              
ATOM   1168  O   GLY   159      16.815  11.948  -7.186  1.00  0.00              
ATOM   1169  N   GLY   160      17.544  13.777  -6.100  1.00  0.00              
ATOM   1170  CA  GLY   160      17.918  14.455  -7.327  1.00  0.00              
ATOM   1171  C   GLY   160      18.116  13.495  -8.484  1.00  0.00              
ATOM   1172  O   GLY   160      17.220  12.723  -8.823  1.00  0.00              
ATOM   1173  N   ASP   161      19.297  13.541  -9.094  1.00  0.00              
ATOM   1174  CA  ASP   161      19.610  12.669 -10.220  1.00  0.00              
ATOM   1175  C   ASP   161      18.674  11.468 -10.265  1.00  0.00              
ATOM   1176  O   ASP   161      17.561  11.515  -9.739  1.00  0.00              
ATOM   1177  CB  ASP   161      19.535  13.446 -11.536  1.00  0.00              
ATOM   1178  CG  ASP   161      18.164  14.043 -11.782  1.00  0.00              
ATOM   1179  OD1 ASP   161      17.161  13.318 -11.612  1.00  0.00              
ATOM   1180  OD2 ASP   161      18.092  15.236 -12.145  1.00  0.00              
ATOM   1181  N   GLU   162      19.131  10.391 -10.897  1.00  0.00              
ATOM   1182  CA  GLU   162      18.334   9.175 -11.012  1.00  0.00              
ATOM   1183  C   GLU   162      19.123   8.062 -11.694  1.00  0.00              
ATOM   1184  O   GLU   162      18.588   6.934 -11.739  1.00  0.00              
ATOM   1185  CB  GLU   162      17.857   8.714  -9.634  1.00  0.00              
ATOM   1186  CG  GLU   162      16.372   8.922  -9.389  1.00  0.00              
ATOM   1187  CD  GLU   162      15.837   8.047  -8.273  1.00  0.00              
ATOM   1188  OE1 GLU   162      16.195   8.292  -7.102  1.00  0.00              
ATOM   1189  OE2 GLU   162      15.059   7.116  -8.569  1.00  0.00              
ATOM   1190  OXT GLU   162      20.245   8.362 -12.155  1.00  0.00              
TER
END
