
#######################################################
#                                                     #
#                        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   10 (   78),  selected   10 , name T0318TS268_5_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_5_1-D2.T0318_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:     9       156 - 164         4.98     5.65
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       156 - 159         1.63     8.78
  LCS_AVERAGE:      1.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       156 - 158         0.23    10.50
  LONGEST_CONTINUOUS_SEGMENT:     3       157 - 159         0.92     9.11
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.89    10.49
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.77     7.49
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.93     8.44
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.63    11.03
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.60    10.77
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.99    11.52
  LCS_AVERAGE:      0.90

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:  335
LCS_GDT     T     156     T     156      3    4    9     3    3    3    3    4    4    4    4    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     N     157     N     157      3    4    9     3    3    3    3    4    4    4    4    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     E     158     E     158      3    4    9     3    3    3    3    4    4    4    4    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     D     159     D     159      3    4    9     0    3    3    3    4    4    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     A     160     A     160      3    3    9     0    3    3    3    3    3    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     V     161     V     161      3    3    9     0    3    3    3    3    3    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     F     162     F     162      3    3    9     0    3    3    3    3    3    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     L     163     L     163      3    3    9     0    3    3    3    3    3    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     T     164     T     164      3    3    9     0    3    3    3    3    3    4    5    6    6    7    7    8    8    9    9   10   10   10   10 
LCS_GDT     D     165     D     165      3    3    8     0    3    3    3    3    3    4    4    5    6    7    7    7    8    8    9   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.52  (   0.90    1.01    2.66 )

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      3      3      3      4      4      4      5      6      6      7      7      8      8      9      9     10     10     10     10 
GDT PERCENT_CA   0.90   0.90   0.90   0.90   1.19   1.19   1.19   1.49   1.79   1.79   2.09   2.09   2.39   2.39   2.69   2.69   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.23   0.23   0.23   0.23   1.63   1.63   1.63   3.16   3.43   3.43   3.94   3.94   4.53   4.53   4.98   4.98   5.51   5.51   5.51   5.51
GDT RMS_ALL_CA  10.50  10.50  10.50  10.50   8.78   8.78   8.78   5.84   7.01   7.01   6.38   6.38   5.86   5.86   5.65   5.65   5.51   5.51   5.51   5.51

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          7.850
LGA    N     157      N     157          8.587
LGA    E     158      E     158          7.288
LGA    D     159      D     159          3.866
LGA    A     160      A     160          2.163
LGA    V     161      V     161          2.540
LGA    F     162      F     162          3.139
LGA    L     163      L     163          3.731
LGA    T     164      T     164          6.383
LGA    D     165      D     165          7.886

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      5    3.16     1.493     1.394     0.153

LGA_LOCAL      RMSD =  3.158  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.842  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  5.508  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.481223 * X  +   0.695073 * Y  +  -0.534132 * Z  +  35.466427
  Y_new =   0.848066 * X  +  -0.214959 * Y  +   0.484331 * Z  +  81.310371
  Z_new =   0.221829 * X  +  -0.686051 * Y  +  -0.692911 * Z  +  77.114456 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.361170    0.780423  [ DEG:  -135.2850     44.7149 ]
  Theta =  -0.223690   -2.917903  [ DEG:   -12.8165   -167.1835 ]
  Phi   =   1.054665   -2.086927  [ DEG:    60.4279   -119.5721 ]
 
# 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: T0318TS268_5_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_5_1-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  335   4.0    5   3.16   1.394     5.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1jv2_A
ATOM   1209  N   THR   156      31.151  20.455  14.891  1.00  0.00
ATOM   1210  CA  THR   156      29.755  20.205  14.699  1.00  0.00
ATOM   1211  C   THR   156      28.980  21.315  15.325  1.00  0.00
ATOM   1212  O   THR   156      28.005  21.794  14.748  1.00  0.00
ATOM   1213  CB  THR   156      29.326  18.874  15.343  1.00  0.00
ATOM   1214  OG1 THR   156      30.037  17.792  14.727  1.00  0.00
ATOM   1215  CG2 THR   156      27.833  18.650  15.158  1.00  0.00
ATOM   1216  N   ASN   157      29.380  21.775  16.521  1.00  0.00
ATOM   1217  CA  ASN   157      28.591  22.826  17.086  1.00  0.00
ATOM   1218  C   ASN   157      29.043  24.124  16.508  1.00  0.00
ATOM   1219  O   ASN   157      30.024  24.711  16.961  1.00  0.00
ATOM   1220  CB  ASN   157      28.757  22.863  18.607  1.00  0.00
ATOM   1221  CG  ASN   157      27.807  23.839  19.273  1.00  0.00
ATOM   1222  OD1 ASN   157      27.811  25.031  18.965  1.00  0.00
ATOM   1223  ND2 ASN   157      26.990  23.335  20.191  1.00  0.00
ATOM   1224  N   GLU   158      28.324  24.598  15.470  1.00  0.00
ATOM   1225  CA  GLU   158      28.647  25.858  14.871  1.00  0.00
ATOM   1226  C   GLU   158      27.420  26.352  14.174  1.00  0.00
ATOM   1227  O   GLU   158      26.636  25.567  13.646  1.00  0.00
ATOM   1228  CB  GLU   158      29.790  25.697  13.867  1.00  0.00
ATOM   1229  CG  GLU   158      30.251  27.001  13.238  1.00  0.00
ATOM   1230  CD  GLU   158      31.391  26.804  12.258  1.00  0.00
ATOM   1231  OE1 GLU   158      31.809  25.644  12.058  1.00  0.00
ATOM   1232  OE2 GLU   158      31.867  27.809  11.689  1.00  0.00
ATOM   1233  N   ASP   159      27.207  27.683  14.190  1.00  0.00
ATOM   1234  CA  ASP   159      26.101  28.277  13.494  1.00  0.00
ATOM   1235  C   ASP   159      26.385  29.743  13.411  1.00  0.00
ATOM   1236  O   ASP   159      26.926  30.317  14.353  1.00  0.00
ATOM   1237  CB  ASP   159      24.795  28.028  14.252  1.00  0.00
ATOM   1238  CG  ASP   159      23.568  28.322  13.411  1.00  0.00
ATOM   1239  OD1 ASP   159      23.382  29.493  13.019  1.00  0.00
ATOM   1240  OD2 ASP   159      22.792  27.380  13.143  1.00  0.00
ATOM   1241  N   ALA   160      26.063  30.394  12.275  1.00  0.00
ATOM   1242  CA  ALA   160      26.291  31.811  12.217  1.00  0.00
ATOM   1243  C   ALA   160      25.146  32.449  11.496  1.00  0.00
ATOM   1244  O   ALA   160      24.662  31.930  10.492  1.00  0.00
ATOM   1245  CB  ALA   160      27.586  32.110  11.476  1.00  0.00
ATOM   1246  N   VAL   161      24.669  33.604  12.006  1.00  0.00
ATOM   1247  CA  VAL   161      23.611  34.297  11.329  1.00  0.00
ATOM   1248  C   VAL   161      23.754  35.761  11.605  1.00  0.00
ATOM   1249  O   VAL   161      24.256  36.170  12.652  1.00  0.00
ATOM   1250  CB  VAL   161      22.226  33.827  11.814  1.00  0.00
ATOM   1251  CG1 VAL   161      22.034  34.167  13.283  1.00  0.00
ATOM   1252  CG2 VAL   161      21.124  34.504  11.015  1.00  0.00
ATOM   1253  N   PHE   162      23.319  36.587  10.630  1.00  0.00
ATOM   1254  CA  PHE   162      23.410  38.015  10.715  1.00  0.00
ATOM   1255  C   PHE   162      22.186  38.540  11.391  1.00  0.00
ATOM   1256  O   PHE   162      21.111  37.949  11.310  1.00  0.00
ATOM   1257  CB  PHE   162      23.517  38.629   9.318  1.00  0.00
ATOM   1258  CG  PHE   162      24.817  38.336   8.625  1.00  0.00
ATOM   1259  CD1 PHE   162      24.907  37.315   7.694  1.00  0.00
ATOM   1260  CD2 PHE   162      25.950  39.080   8.903  1.00  0.00
ATOM   1261  CE1 PHE   162      26.102  37.045   7.056  1.00  0.00
ATOM   1262  CE2 PHE   162      27.146  38.810   8.264  1.00  0.00
ATOM   1263  CZ  PHE   162      27.224  37.798   7.345  1.00  0.00
ATOM   1264  N   LEU   163      22.337  39.672  12.102  1.00  0.00
ATOM   1265  CA  LEU   163      21.204  40.316  12.697  1.00  0.00
ATOM   1266  C   LEU   163      21.309  41.752  12.298  1.00  0.00
ATOM   1267  O   LEU   163      22.377  42.351  12.400  1.00  0.00
ATOM   1268  CB  LEU   163      21.240  40.166  14.220  1.00  0.00
ATOM   1269  CG  LEU   163      20.121  40.862  14.996  1.00  0.00
ATOM   1270  CD1 LEU   163      18.776  40.215  14.698  1.00  0.00
ATOM   1271  CD2 LEU   163      20.370  40.774  16.494  1.00  0.00
ATOM   1272  N   THR   164      20.207  42.354  11.817  1.00  0.00
ATOM   1273  CA  THR   164      20.295  43.728  11.417  1.00  0.00
ATOM   1274  C   THR   164      19.026  44.391  11.839  1.00  0.00
ATOM   1275  O   THR   164      18.262  43.842  12.629  1.00  0.00
ATOM   1276  CB  THR   164      20.467  43.862   9.893  1.00  0.00
ATOM   1277  OG1 THR   164      20.766  45.224   9.560  1.00  0.00
ATOM   1278  CG2 THR   164      19.192  43.449   9.174  1.00  0.00
ATOM   1279  N   ASP   165      18.779  45.615  11.338  1.00  0.00
ATOM   1280  CA  ASP   165      17.576  46.300  11.700  1.00  0.00
ATOM   1281  C   ASP   165      16.386  45.426  11.316  1.00  0.00
ATOM   1282  O   ASP   165      15.251  45.769  11.746  1.00  0.00
ATOM   1283  CB  ASP   165      17.481  47.640  10.967  1.00  0.00
ATOM   1284  CG  ASP   165      18.478  48.659  11.484  1.00  0.00
ATOM   1285  OD1 ASP   165      19.028  48.445  12.584  1.00  0.00
ATOM   1286  OD2 ASP   165      18.708  49.671  10.789  1.00  0.00
TER
END
