
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0318TS174_1u-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   15 , name T0318_D1.pdb
# PARAMETERS: T0318TS174_1u-D1.T0318_D1.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:    14       142 - 155         2.99     7.79
  LCS_AVERAGE:      8.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       142 - 153         1.93     7.99
  LCS_AVERAGE:      6.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       146 - 152         0.87     8.48
  LCS_AVERAGE:      3.51

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:  154
LCS_GDT     I     141     I     141      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     R     142     R     142      5   12   14     4    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     E     143     E     143      5   12   14     4    5    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     L     144     L     144      5   12   14     4    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     N     145     N     145      5   12   14     4    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     V     146     V     146      7   12   14     4    6    7    8   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     N     147     N     147      7   12   14     3    6    7    7    9   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     I     148     I     148      7   12   14     3    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     D     149     D     149      7   12   14     3    6    7    8    9   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     V     150     V     150      7   12   14     3    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     V     151     V     151      7   12   14     4    6    7    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     C     152     C     152      7   12   14     4    6    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     D     153     D     153      4   12   14     4    4    8    9   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     K     154     K     154      4    8   14     4    4    4    8   10   12   13   13   13   13   13   13   13   14   14   14   14   14   14   14 
LCS_GDT     L     155     L     155      4    5   14     0    3    4    5    5    5    5    7    7    7    9   11   11   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   6.26  (   3.51    6.80    8.48 )

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      4      6      8      9     10     12     13     13     13     13     13     13     13     14     14     14     14     14     14     14 
GDT PERCENT_CA   2.60   3.90   5.19   5.84   6.49   7.79   8.44   8.44   8.44   8.44   8.44   8.44   8.44   9.09   9.09   9.09   9.09   9.09   9.09   9.09
GDT RMS_LOCAL    0.21   0.62   0.99   1.23   1.39   1.93   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_ALL_CA   7.84   8.93   8.03   7.99   7.97   7.99   7.84   7.84   7.84   7.84   7.84   7.84   7.84   7.79   7.79   7.79   7.79   7.79   7.79   7.79

#      Molecule1      Molecule2       DISTANCE
LGA    I     141      I     141         27.947
LGA    R     142      R     142          1.130
LGA    E     143      E     143          1.777
LGA    L     144      L     144          0.961
LGA    N     145      N     145          0.724
LGA    V     146      V     146          2.221
LGA    N     147      N     147          3.329
LGA    I     148      I     148          0.995
LGA    D     149      D     149          3.334
LGA    V     150      V     150          1.494
LGA    V     151      V     151          1.596
LGA    C     152      C     152          2.036
LGA    D     153      D     153          1.943
LGA    K     154      K     154          2.800
LGA    L     155      L     155          9.324

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  154    4.0     13    2.05     6.818     7.139     0.605

LGA_LOCAL      RMSD =  2.048  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.842  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  7.194  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.853443 * X  +   0.194406 * Y  +  -0.483571 * Z  +  76.649323
  Y_new =   0.122935 * X  +   0.826560 * Y  +   0.549260 * Z  + -22.143282
  Z_new =   0.506480 * X  +  -0.528210 * Y  +   0.681522 * Z  +  25.488716 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.659337    2.482255  [ DEG:   -37.7773    142.2227 ]
  Theta =  -0.531098   -2.610495  [ DEG:   -30.4297   -149.5703 ]
  Phi   =   0.143062   -2.998531  [ DEG:     8.1968   -171.8032 ]
 
# 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: T0318TS174_1u-D1                              
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS174_1u-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  154   4.0   13   2.05   7.139     7.19
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS174_1u-D1
PFRMAT TS
TARGET T0318
MODEL 1  UNREFINED
PARENT 1lcp_A 
ATOM   1089  N   ILE   141      24.404  35.004  11.395  1.00  1.00
ATOM   1090  CA  ILE   141      25.025  34.234  12.467  1.00  1.00
ATOM   1091  C   ILE   141      26.026  33.275  11.818  1.00  1.00
ATOM   1092  O   ILE   141      25.661  32.528  10.901  1.00  1.00
ATOM   1093  CB  ILE   141      23.944  33.435  13.174  1.00  1.00
ATOM   1094  CG1 ILE   141      24.636  32.711  14.322  1.00  1.00
ATOM   1095  CG2 ILE   141      23.312  32.400  12.256  1.00  1.00
ATOM   1096  CD1 ILE   141      25.186  33.624  15.417  1.00  1.00
ATOM   1097  N   ARG   142      37.302  56.780  12.346  1.00  1.00
ATOM   1098  CA  ARG   142      35.895  56.951  11.975  1.00  1.00
ATOM   1099  C   ARG   142      35.392  55.671  11.330  1.00  1.00
ATOM   1100  O   ARG   142      34.219  55.327  11.453  1.00  1.00
ATOM   1101  CB  ARG   142      35.719  58.065  10.943  1.00  1.00
ATOM   1102  CG  ARG   142      34.366  58.245  10.669  1.00  1.00
ATOM   1103  CD  ARG   142      33.622  58.744  11.902  1.00  1.00
ATOM   1104  NE  ARG   142      32.329  58.940  11.723  1.00  1.00
ATOM   1105  CZ  ARG   142      31.392  57.980  11.832  1.00  1.00
ATOM   1106  NH1 ARG   142      30.119  58.292  11.630  1.00  1.00
ATOM   1107  NH2 ARG   142      32.007  56.677  12.177  1.00  1.00
ATOM   1108  N   GLU   143      36.259  55.013  10.573  1.00  1.00
ATOM   1109  CA  GLU   143      35.892  53.788   9.886  1.00  1.00
ATOM   1110  C   GLU   143      36.429  52.570  10.610  1.00  1.00
ATOM   1111  O   GLU   143      37.642  52.414  10.799  1.00  1.00
ATOM   1112  CB  GLU   143      36.352  53.855   8.437  1.00  1.00
ATOM   1113  CG  GLU   143      35.653  54.914   7.621  1.00  1.00
ATOM   1114  CD  GLU   143      36.318  56.269   7.724  1.00  1.00
ATOM   1115  OE1 GLU   143      37.283  56.480   8.386  1.00  1.00
ATOM   1116  OE2 GLU   143      35.693  57.174   7.000  1.00  1.00
ATOM   1117  N   LEU   144      35.510  51.707  11.025  1.00  1.00
ATOM   1118  CA  LEU   144      35.874  50.520  11.780  1.00  1.00
ATOM   1119  C   LEU   144      35.188  49.271  11.261  1.00  1.00
ATOM   1120  O   LEU   144      34.079  49.346  10.724  1.00  1.00
ATOM   1121  CB  LEU   144      35.466  50.716  13.239  1.00  1.00
ATOM   1122  CG  LEU   144      35.887  49.530  14.113  1.00  1.00
ATOM   1123  CD1 LEU   144      37.384  49.335  14.250  1.00  1.00
ATOM   1124  CD2 LEU   144      35.193  49.713  15.477  1.00  1.00
ATOM   1125  N   ASN   145      35.824  48.121  11.474  1.00  1.00
ATOM   1126  CA  ASN   145      35.259  46.844  11.067  1.00  1.00
ATOM   1127  C   ASN   145      34.073  46.571  11.990  1.00  1.00
ATOM   1128  O   ASN   145      33.933  47.204  13.038  1.00  1.00
ATOM   1129  CB  ASN   145      36.299  45.721  11.200  1.00  1.00
ATOM   1130  CG  ASN   145      36.737  45.565  12.651  1.00  1.00
ATOM   1131  OD1 ASN   145      37.086  46.534  13.315  1.00  1.00
ATOM   1132  ND2 ASN   145      36.700  44.329  13.117  1.00  1.00
ATOM   1133  N   VAL   146      33.210  45.648  11.589  1.00  1.00
ATOM   1134  CA  VAL   146      32.037  45.288  12.385  1.00  1.00
ATOM   1135  C   VAL   146      32.484  44.651  13.698  1.00  1.00
ATOM   1136  O   VAL   146      33.437  43.865  13.710  1.00  1.00
ATOM   1137  CB  VAL   146      31.144  44.285  11.600  1.00  1.00
ATOM   1138  CG1 VAL   146      29.985  43.800  12.443  1.00  1.00
ATOM   1139  CG2 VAL   146      30.625  44.935  10.326  1.00  1.00
ATOM   1140  N   ASN   147      31.825  45.002  14.802  1.00  1.00
ATOM   1141  CA  ASN   147      32.167  44.419  16.102  1.00  1.00
ATOM   1142  C   ASN   147      31.623  42.991  16.150  1.00  1.00
ATOM   1143  O   ASN   147      30.422  42.774  15.978  1.00  1.00
ATOM   1144  CB  ASN   147      31.573  45.239  17.272  1.00  1.00
ATOM   1145  CG  ASN   147      32.041  44.727  18.632  1.00  1.00
ATOM   1146  OD1 ASN   147      31.526  43.742  19.148  1.00  1.00
ATOM   1147  ND2 ASN   147      33.026  45.412  19.176  1.00  1.00
ATOM   1148  N   ILE   148      32.501  42.022  16.369  1.00  1.00
ATOM   1149  CA  ILE   148      32.080  40.623  16.408  1.00  1.00
ATOM   1150  C   ILE   148      31.979  40.056  17.819  1.00  1.00
ATOM   1151  O   ILE   148      32.892  40.204  18.632  1.00  1.00
ATOM   1152  CB  ILE   148      33.023  39.709  15.557  1.00  1.00
ATOM   1153  CG1 ILE   148      33.081  40.191  14.115  1.00  1.00
ATOM   1154  CG2 ILE   148      32.496  38.280  15.578  1.00  1.00
ATOM   1155  CD1 ILE   148      31.731  40.224  13.391  1.00  1.00
ATOM   1156  N   ASP   149      30.866  39.391  18.102  1.00  1.00
ATOM   1157  CA  ASP   149      30.664  38.763  19.397  1.00  1.00
ATOM   1158  C   ASP   149      30.855  37.251  19.240  1.00  1.00
ATOM   1159  O   ASP   149      30.007  36.569  18.649  1.00  1.00
ATOM   1160  CB  ASP   149      29.261  39.068  19.935  1.00  1.00
ATOM   1161  CG  ASP   149      29.035  38.492  21.326  1.00  1.00
ATOM   1162  OD1 ASP   149      29.569  38.793  22.296  1.00  1.00
ATOM   1163  OD2 ASP   149      28.108  37.588  21.281  1.00  1.00
ATOM   1164  N   VAL   150      32.006  36.756  19.701  1.00  1.00
ATOM   1165  CA  VAL   150      32.349  35.330  19.650  1.00  1.00
ATOM   1166  C   VAL   150      31.929  34.596  20.932  1.00  1.00
ATOM   1167  O   VAL   150      32.175  35.081  22.045  1.00  1.00
ATOM   1168  CB  VAL   150      33.862  35.157  19.415  1.00  1.00
ATOM   1169  CG1 VAL   150      34.309  35.784  18.109  1.00  1.00
ATOM   1170  CG2 VAL   150      34.193  33.681  19.454  1.00  1.00
ATOM   1171  N   VAL   151      31.305  33.428  20.775  1.00  1.00
ATOM   1172  CA  VAL   151      30.856  32.619  21.912  1.00  1.00
ATOM   1173  C   VAL   151      31.088  31.127  21.649  1.00  1.00
ATOM   1174  O   VAL   151      31.210  30.706  20.499  1.00  1.00
ATOM   1175  CB  VAL   151      29.362  32.858  22.188  1.00  1.00
ATOM   1176  CG1 VAL   151      28.493  32.426  21.023  1.00  1.00
ATOM   1177  CG2 VAL   151      29.149  34.316  22.524  1.00  1.00
ATOM   1178  N   CYS   152      31.178  30.338  22.716  1.00  1.00
ATOM   1179  CA  CYS   152      31.360  28.893  22.597  1.00  1.00
ATOM   1180  C   CYS   152      30.206  28.214  21.841  1.00  1.00
ATOM   1181  O   CYS   152      29.040  28.560  22.046  1.00  1.00
ATOM   1182  CB  CYS   152      31.443  28.263  23.998  1.00  1.00
ATOM   1183  SG  CYS   152      31.764  26.468  23.812  1.00  1.00
ATOM   1184  N   ASP   153      30.540  27.286  20.946  1.00  1.00
ATOM   1185  CA  ASP   153      29.532  26.509  20.233  1.00  1.00
ATOM   1186  C   ASP   153      29.286  25.291  21.142  1.00  1.00
ATOM   1187  O   ASP   153      30.192  24.493  21.394  1.00  1.00
ATOM   1188  CB  ASP   153      30.058  26.051  18.870  1.00  1.00
ATOM   1189  CG  ASP   153      29.009  25.301  18.060  1.00  1.00
ATOM   1190  OD1 ASP   153      28.029  25.721  17.638  1.00  1.00
ATOM   1191  OD2 ASP   153      29.387  24.074  17.884  1.00  1.00
ATOM   1192  N   LYS   154      28.079  25.180  21.672  1.00  1.00
ATOM   1193  CA  LYS   154      27.762  24.081  22.563  1.00  1.00
ATOM   1194  C   LYS   154      27.723  24.577  24.000  1.00  1.00
ATOM   1195  O   LYS   154      27.954  25.760  24.276  1.00  1.00
ATOM   1196  CB  LYS   154      27.187  23.090  23.000  1.00  1.00
ATOM   1197  CG  LYS   154      26.867  22.089  23.913  1.00  1.00
ATOM   1198  CD  LYS   154      25.693  21.249  23.402  1.00  1.00
ATOM   1199  CE  LYS   154      25.338  20.151  24.411  1.00  1.00
ATOM   1200  NZ  LYS   154      24.201  19.331  23.922  1.00  1.00
ATOM   1201  N   LEU   155      27.474  23.662  24.928  1.00  1.00
ATOM   1202  CA  LEU   155      27.366  24.015  26.336  1.00  1.00
ATOM   1203  C   LEU   155      28.196  23.161  27.284  1.00  1.00
ATOM   1204  O   LEU   155      28.026  23.261  28.497  1.00  1.00
ATOM   1205  CB  LEU   155      25.905  23.894  26.749  1.00  1.00
ATOM   1206  CG  LEU   155      25.286  22.499  26.676  1.00  1.00
ATOM   1207  CD1 LEU   155      25.687  21.556  27.805  1.00  1.00
ATOM   1208  CD2 LEU   155      23.755  22.681  26.584  1.00  1.00
TER
END
