
#######################################################
#                                                     #
#                        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_4_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_4_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:     8       156 - 163         4.58     6.05
  LONGEST_CONTINUOUS_SEGMENT:     8       157 - 164         4.69     5.76
  LONGEST_CONTINUOUS_SEGMENT:     8       158 - 165         4.70     5.92
  LCS_AVERAGE:      2.39

LCS - RMSD CUTOFF   2.00      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         0.70    13.40
  LONGEST_CONTINUOUS_SEGMENT:     3       157 - 159         0.52    10.97
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.83    11.16
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.61     7.91
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.97     8.79
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.59     9.91
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.73    11.05
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.79    12.52
  LCS_AVERAGE:      0.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       156 - 158         0.70    13.40
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.83    11.16
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.61     7.91
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.97     8.79
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.59     9.91
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.73    11.05
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.79    12.52
  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    3    8     0    3    3    3    3    3    4    5    6    6    6    7    8    8    9    9   10   10   10   10 
LCS_GDT     N     157     N     157      3    3    8     0    3    3    3    3    4    4    5    6    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     E     158     E     158      3    3    8     1    3    3    3    3    4    4    5    6    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     D     159     D     159      3    3    8     0    3    3    3    3    4    4    5    6    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     A     160     A     160      3    3    8     0    3    3    3    3    4    4    5    6    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     V     161     V     161      3    3    8     0    3    3    3    3    3    4    5    6    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     F     162     F     162      3    3    8     0    3    3    3    3    3    4    5    5    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     L     163     L     163      3    3    8     0    3    3    3    3    3    4    5    5    6    7    7    8    9    9    9   10   10   10   10 
LCS_GDT     T     164     T     164      3    3    8     0    3    3    3    3    3    4    4    5    6    7    7    8    9    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    6    7    8    9    9    9   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.39  (   0.90    0.90    2.39 )

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      1      3      3      3      3      4      4      5      6      6      7      7      8      9      9      9     10     10     10     10 
GDT PERCENT_CA   0.30   0.90   0.90   0.90   0.90   1.19   1.19   1.49   1.79   1.79   2.09   2.09   2.39   2.69   2.69   2.69   2.99   2.99   2.99   2.99
GDT RMS_LOCAL   31.63   0.52   0.52   0.52   0.52   2.43   2.43   3.04   3.42   3.42   4.13   3.97   4.58   5.07   5.07   5.07   5.55   5.55   5.55   5.55
GDT RMS_ALL_CA  10.97  10.97  10.97  10.97  10.97   7.59   7.59   6.26   6.95   6.95   6.13   6.66   6.05   5.69   5.69   5.69   5.55   5.55   5.55   5.55

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          6.000
LGA    N     157      N     157          3.379
LGA    E     158      E     158          2.361
LGA    D     159      D     159          3.511
LGA    A     160      A     160          1.965
LGA    V     161      V     161          3.589
LGA    F     162      F     162          6.610
LGA    L     163      L     163          8.383
LGA    T     164      T     164          9.451
LGA    D     165      D     165         10.326

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      5    3.04     1.493     1.352     0.159

LGA_LOCAL      RMSD =  3.035  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.261  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  5.554  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.847667 * X  +   0.404286 * Y  +   0.343530 * Z  + -54.429096
  Y_new =   0.309584 * X  +  -0.148902 * Y  +   0.939141 * Z  +  36.264187
  Z_new =   0.430834 * X  +   0.902430 * Y  +   0.001058 * Z  +  -6.127551 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.569624   -1.571969  [ DEG:    89.9328    -90.0672 ]
  Theta =  -0.445417   -2.696176  [ DEG:   -25.5205   -154.4795 ]
  Phi   =   2.791425   -0.350168  [ DEG:   159.9368    -20.0632 ]
 
# 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_4_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_4_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   3.04   1.352     5.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1l5g_A
ATOM   1209  N   THR   156      27.915  21.492  12.997  1.00  0.00
ATOM   1210  CA  THR   156      28.100  22.261  11.809  1.00  0.00
ATOM   1211  C   THR   156      27.833  23.660  12.232  1.00  0.00
ATOM   1212  O   THR   156      27.188  23.894  13.251  1.00  0.00
ATOM   1213  CB  THR   156      27.129  21.823  10.697  1.00  0.00
ATOM   1214  OG1 THR   156      25.779  22.049  11.120  1.00  0.00
ATOM   1215  CG2 THR   156      27.307  20.344  10.386  1.00  0.00
ATOM   1216  N   ASN   157      28.324  24.648  11.473  1.00  0.00
ATOM   1217  CA  ASN   157      28.187  25.966  12.002  1.00  0.00
ATOM   1218  C   ASN   157      27.007  26.651  11.414  1.00  0.00
ATOM   1219  O   ASN   157      26.701  26.519  10.230  1.00  0.00
ATOM   1220  CB  ASN   157      29.431  26.801  11.691  1.00  0.00
ATOM   1221  CG  ASN   157      30.659  26.317  12.434  1.00  0.00
ATOM   1222  OD1 ASN   157      30.553  25.719  13.506  1.00  0.00
ATOM   1223  ND2 ASN   157      31.833  26.574  11.868  1.00  0.00
ATOM   1224  N   GLU   158      26.287  27.383  12.283  1.00  0.00
ATOM   1225  CA  GLU   158      25.208  28.211  11.854  1.00  0.00
ATOM   1226  C   GLU   158      25.807  29.575  11.810  1.00  0.00
ATOM   1227  O   GLU   158      26.700  29.884  12.595  1.00  0.00
ATOM   1228  CB  GLU   158      24.046  28.132  12.845  1.00  0.00
ATOM   1229  CG  GLU   158      23.411  26.754  12.950  1.00  0.00
ATOM   1230  CD  GLU   158      22.235  26.725  13.905  1.00  0.00
ATOM   1231  OE1 GLU   158      21.952  27.768  14.530  1.00  0.00
ATOM   1232  OE2 GLU   158      21.596  25.658  14.028  1.00  0.00
ATOM   1233  N   ASP   159      25.371  30.414  10.854  1.00  0.00
ATOM   1234  CA  ASP   159      25.955  31.717  10.741  1.00  0.00
ATOM   1235  C   ASP   159      25.216  32.695  11.605  1.00  0.00
ATOM   1236  O   ASP   159      24.248  32.344  12.277  1.00  0.00
ATOM   1237  CB  ASP   159      25.896  32.207   9.292  1.00  0.00
ATOM   1238  CG  ASP   159      24.478  32.458   8.820  1.00  0.00
ATOM   1239  OD1 ASP   159      23.568  32.514   9.674  1.00  0.00
ATOM   1240  OD2 ASP   159      24.277  32.599   7.595  1.00  0.00
ATOM   1241  N   ALA   160      25.704  33.952  11.624  1.00  0.00
ATOM   1242  CA  ALA   160      25.070  35.031  12.326  1.00  0.00
ATOM   1243  C   ALA   160      25.063  36.163  11.352  1.00  0.00
ATOM   1244  O   ALA   160      26.007  36.313  10.579  1.00  0.00
ATOM   1245  CB  ALA   160      25.856  35.382  13.580  1.00  0.00
ATOM   1246  N   VAL   161      24.001  36.993  11.343  1.00  0.00
ATOM   1247  CA  VAL   161      24.028  38.016  10.340  1.00  0.00
ATOM   1248  C   VAL   161      23.430  39.270  10.888  1.00  0.00
ATOM   1249  O   VAL   161      22.537  39.239  11.733  1.00  0.00
ATOM   1250  CB  VAL   161      23.228  37.602   9.091  1.00  0.00
ATOM   1251  CG1 VAL   161      23.191  38.740   8.082  1.00  0.00
ATOM   1252  CG2 VAL   161      23.866  36.392   8.427  1.00  0.00
ATOM   1253  N   PHE   162      23.937  40.417  10.392  1.00  0.00
ATOM   1254  CA  PHE   162      23.489  41.719  10.798  1.00  0.00
ATOM   1255  C   PHE   162      22.954  42.397   9.579  1.00  0.00
ATOM   1256  O   PHE   162      23.594  42.409   8.529  1.00  0.00
ATOM   1257  CB  PHE   162      24.649  42.526  11.384  1.00  0.00
ATOM   1258  CG  PHE   162      25.213  41.944  12.649  1.00  0.00
ATOM   1259  CD1 PHE   162      26.274  41.056  12.607  1.00  0.00
ATOM   1260  CD2 PHE   162      24.683  42.286  13.881  1.00  0.00
ATOM   1261  CE1 PHE   162      26.792  40.521  13.771  1.00  0.00
ATOM   1262  CE2 PHE   162      25.202  41.751  15.045  1.00  0.00
ATOM   1263  CZ  PHE   162      26.253  40.873  14.994  1.00  0.00
ATOM   1264  N   LEU   163      21.742  42.975   9.686  1.00  0.00
ATOM   1265  CA  LEU   163      21.157  43.646   8.562  1.00  0.00
ATOM   1266  C   LEU   163      20.736  44.999   9.028  1.00  0.00
ATOM   1267  O   LEU   163      20.319  45.169  10.172  1.00  0.00
ATOM   1268  CB  LEU   163      19.947  42.867   8.043  1.00  0.00
ATOM   1269  CG  LEU   163      20.225  41.462   7.504  1.00  0.00
ATOM   1270  CD1 LEU   163      18.924  40.737   7.196  1.00  0.00
ATOM   1271  CD2 LEU   163      21.045  41.530   6.225  1.00  0.00
ATOM   1272  N   THR   164      20.850  46.010   8.146  1.00  0.00
ATOM   1273  CA  THR   164      20.457  47.336   8.518  1.00  0.00
ATOM   1274  C   THR   164      19.455  47.798   7.516  1.00  0.00
ATOM   1275  O   THR   164      19.451  47.354   6.368  1.00  0.00
ATOM   1276  CB  THR   164      21.658  48.299   8.528  1.00  0.00
ATOM   1277  OG1 THR   164      22.227  48.372   7.214  1.00  0.00
ATOM   1278  CG2 THR   164      22.723  47.811   9.499  1.00  0.00
ATOM   1279  N   ASP   165      18.555  48.702   7.937  1.00  0.00
ATOM   1280  CA  ASP   165      17.565  49.191   7.030  1.00  0.00
ATOM   1281  C   ASP   165      18.274  50.057   5.997  1.00  0.00
ATOM   1282  O   ASP   165      19.516  50.227   6.117  1.00  0.00
ATOM   1283  CB  ASP   165      16.518  50.020   7.774  1.00  0.00
ATOM   1284  CG  ASP   165      15.300  50.321   6.924  1.00  0.00
ATOM   1285  OD1 ASP   165      15.173  49.722   5.835  1.00  0.00
ATOM   1286  OD2 ASP   165      14.471  51.155   7.346  1.00  0.00
TER
END
