
#######################################################
#                                                     #
#                        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_2_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_2_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:    10       156 - 165         4.55     4.55
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       158 - 161         1.14     6.94
  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         0.55    10.17
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.12     9.06
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.97     8.10
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.49     8.97
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.42     7.82
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.52    11.16
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.71    10.29
  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    3   10     0    3    3    3    4    5    6    6    6    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      3    3   10     1    3    3    3    4    5    6    6    6    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      3    4   10     3    3    4    4    4    5    6    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      3    4   10     3    3    4    4    4    5    6    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      3    4   10     3    3    4    4    4    5    6    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      3    4   10     3    3    4    4    4    5    6    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      3    3   10     3    3    3    3    3    3    4    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    3   10     3    3    3    3    3    3    4    6    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    3   10     0    3    3    3    3    3    4    6    7    7    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    3   10     0    3    3    3    3    3    4    5    6    6    8    8   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.63  (   0.90    1.01    2.99 )

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      4      4      4      5      6      6      7      8      9      9     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.90   0.90   1.19   1.19   1.19   1.49   1.79   1.79   2.09   2.39   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.12   0.12   1.14   1.14   1.14   2.34   2.64   2.64   3.57   3.75   4.10   4.10   4.55   4.55   4.55   4.55   4.55   4.55   4.55   4.55
GDT RMS_ALL_CA   9.06   9.06   6.94   6.94   6.94   6.07   6.48   6.48   5.34   5.01   4.68   4.68   4.55   4.55   4.55   4.55   4.55   4.55   4.55   4.55

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          3.176
LGA    N     157      N     157          3.457
LGA    E     158      E     158          1.953
LGA    D     159      D     159          0.733
LGA    A     160      A     160          3.099
LGA    V     161      V     161          2.404
LGA    F     162      F     162          7.439
LGA    L     163      L     163          9.829
LGA    T     164      T     164          8.621
LGA    D     165      D     165         12.344

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      6    2.64     1.716     1.636     0.219

LGA_LOCAL      RMSD =  2.638  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.484  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  4.549  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.422129 * X  +  -0.249879 * Y  +   0.871417 * Z  +  50.634327
  Y_new =   0.898958 * X  +   0.239409 * Y  +  -0.366820 * Z  +  56.452583
  Z_new =  -0.116964 * X  +   0.938213 * Y  +   0.325693 * Z  + -46.389515 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.236670   -1.904922  [ DEG:    70.8560   -109.1440 ]
  Theta =   0.117232    3.024360  [ DEG:     6.7169    173.2831 ]
  Phi   =   1.131783   -2.009810  [ DEG:    64.8464   -115.1536 ]
 
# 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_2_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_2_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    6   2.64   1.636     4.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1g6o_A
ATOM   1209  N   THR   156      28.459  25.140  15.434  1.00  0.00
ATOM   1210  CA  THR   156      29.266  25.460  14.291  1.00  0.00
ATOM   1211  C   THR   156      28.419  25.623  13.071  1.00  0.00
ATOM   1212  O   THR   156      28.815  25.307  11.950  1.00  0.00
ATOM   1213  CB  THR   156      30.298  24.355  14.001  1.00  0.00
ATOM   1214  OG1 THR   156      29.621  23.110  13.784  1.00  0.00
ATOM   1215  CG2 THR   156      31.254  24.197  15.173  1.00  0.00
ATOM   1216  N   ASN   157      27.195  26.142  13.276  1.00  0.00
ATOM   1217  CA  ASN   157      26.351  26.509  12.176  1.00  0.00
ATOM   1218  C   ASN   157      26.121  27.983  12.344  1.00  0.00
ATOM   1219  O   ASN   157      25.951  28.460  13.463  1.00  0.00
ATOM   1220  CB  ASN   157      25.035  25.731  12.229  1.00  0.00
ATOM   1221  CG  ASN   157      25.235  24.235  12.084  1.00  0.00
ATOM   1222  OD1 ASN   157      25.645  23.754  11.027  1.00  0.00
ATOM   1223  ND2 ASN   157      24.947  23.495  13.148  1.00  0.00
ATOM   1224  N   GLU   158      26.133  28.761  11.241  1.00  0.00
ATOM   1225  CA  GLU   158      26.076  30.190  11.400  1.00  0.00
ATOM   1226  C   GLU   158      24.715  30.671  11.760  1.00  0.00
ATOM   1227  O   GLU   158      23.729  30.423  11.066  1.00  0.00
ATOM   1228  CB  GLU   158      26.479  30.891  10.101  1.00  0.00
ATOM   1229  CG  GLU   158      27.910  30.618   9.667  1.00  0.00
ATOM   1230  CD  GLU   158      28.059  29.293   8.948  1.00  0.00
ATOM   1231  OE1 GLU   158      27.026  28.642   8.681  1.00  0.00
ATOM   1232  OE2 GLU   158      29.208  28.904   8.651  1.00  0.00
ATOM   1233  N   ASP   159      24.642  31.351  12.917  1.00  0.00
ATOM   1234  CA  ASP   159      23.443  31.998  13.339  1.00  0.00
ATOM   1235  C   ASP   159      23.240  33.293  12.606  1.00  0.00
ATOM   1236  O   ASP   159      22.109  33.621  12.253  1.00  0.00
ATOM   1237  CB  ASP   159      23.499  32.304  14.837  1.00  0.00
ATOM   1238  CG  ASP   159      23.369  31.057  15.691  1.00  0.00
ATOM   1239  OD1 ASP   159      22.967  30.006  15.150  1.00  0.00
ATOM   1240  OD2 ASP   159      23.669  31.133  16.902  1.00  0.00
ATOM   1241  N   ALA   160      24.317  34.064  12.331  1.00  0.00
ATOM   1242  CA  ALA   160      24.099  35.322  11.666  1.00  0.00
ATOM   1243  C   ALA   160      25.264  35.666  10.783  1.00  0.00
ATOM   1244  O   ALA   160      26.389  35.211  10.984  1.00  0.00
ATOM   1245  CB  ALA   160      23.926  36.437  12.685  1.00  0.00
ATOM   1246  N   VAL   161      25.002  36.485   9.743  1.00  0.00
ATOM   1247  CA  VAL   161      26.037  36.948   8.864  1.00  0.00
ATOM   1248  C   VAL   161      26.008  38.433   8.966  1.00  0.00
ATOM   1249  O   VAL   161      25.038  39.062   8.544  1.00  0.00
ATOM   1250  CB  VAL   161      25.786  36.501   7.411  1.00  0.00
ATOM   1251  CG1 VAL   161      26.880  37.025   6.496  1.00  0.00
ATOM   1252  CG2 VAL   161      25.767  34.982   7.317  1.00  0.00
ATOM   1253  N   PHE   162      27.070  39.053   9.509  1.00  0.00
ATOM   1254  CA  PHE   162      27.002  40.477   9.608  1.00  0.00
ATOM   1255  C   PHE   162      27.743  41.053   8.452  1.00  0.00
ATOM   1256  O   PHE   162      28.938  40.821   8.280  1.00  0.00
ATOM   1257  CB  PHE   162      27.634  40.955  10.916  1.00  0.00
ATOM   1258  CG  PHE   162      26.869  40.547  12.144  1.00  0.00
ATOM   1259  CD1 PHE   162      27.165  39.365  12.800  1.00  0.00
ATOM   1260  CD2 PHE   162      25.854  41.345  12.640  1.00  0.00
ATOM   1261  CE1 PHE   162      26.461  38.989  13.929  1.00  0.00
ATOM   1262  CE2 PHE   162      25.150  40.970  13.769  1.00  0.00
ATOM   1263  CZ  PHE   162      25.450  39.799  14.413  1.00  0.00
ATOM   1264  N   LEU   163      27.023  41.833   7.625  1.00  0.00
ATOM   1265  CA  LEU   163      27.613  42.486   6.497  1.00  0.00
ATOM   1266  C   LEU   163      27.865  43.888   6.922  1.00  0.00
ATOM   1267  O   LEU   163      27.033  44.507   7.581  1.00  0.00
ATOM   1268  CB  LEU   163      26.665  42.446   5.297  1.00  0.00
ATOM   1269  CG  LEU   163      26.282  41.057   4.782  1.00  0.00
ATOM   1270  CD1 LEU   163      25.276  41.163   3.647  1.00  0.00
ATOM   1271  CD2 LEU   163      27.508  40.320   4.263  1.00  0.00
ATOM   1272  N   THR   164      29.045  44.424   6.570  1.00  0.00
ATOM   1273  CA  THR   164      29.316  45.790   6.898  1.00  0.00
ATOM   1274  C   THR   164      29.564  46.489   5.609  1.00  0.00
ATOM   1275  O   THR   164      30.101  45.906   4.670  1.00  0.00
ATOM   1276  CB  THR   164      30.548  45.918   7.813  1.00  0.00
ATOM   1277  OG1 THR   164      30.341  45.150   9.006  1.00  0.00
ATOM   1278  CG2 THR   164      30.778  47.372   8.197  1.00  0.00
ATOM   1279  N   ASP   165      29.143  47.763   5.526  1.00  0.00
ATOM   1280  CA  ASP   165      29.362  48.498   4.322  1.00  0.00
ATOM   1281  C   ASP   165      30.873  48.638   4.198  1.00  0.00
ATOM   1282  O   ASP   165      31.386  48.588   3.048  1.00  0.00
ATOM   1283  CB  ASP   165      28.691  49.870   4.401  1.00  0.00
ATOM   1284  CG  ASP   165      28.642  50.575   3.060  1.00  0.00
ATOM   1285  OD1 ASP   165      28.941  49.924   2.037  1.00  0.00
ATOM   1286  OD2 ASP   165      28.305  51.778   3.032  1.00  0.00
TER
END
