
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_1_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         4.34     4.34
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       156 - 159         1.77     8.14
  LONGEST_CONTINUOUS_SEGMENT:     4       157 - 160         1.86     6.99
  LONGEST_CONTINUOUS_SEGMENT:     4       161 - 164         1.65     8.05
  LCS_AVERAGE:      1.16

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         0.10     5.96
  LONGEST_CONTINUOUS_SEGMENT:     3       157 - 159         0.59    13.17
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.34     7.87
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.80     7.53
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.61     7.36
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.54    11.06
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.32    11.15
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.71    11.45
  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   10     3    3    3    4    4    5    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      3    4   10     3    3    3    4    4    5    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      3    4   10     3    3    3    4    4    5    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      3    4   10     3    3    3    3    4    5    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      3    4   10     3    3    3    4    4    5    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      3    4   10     0    3    3    4    4    4    6    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      3    4   10     3    3    3    4    4    4    5    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    4   10     3    3    3    4    4    4    4    6    8    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    4   10     3    3    3    4    4    4    4    6    7    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    3   10     0    3    3    3    3    3    4    6    6    7    7   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.68  (   0.90    1.16    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      3      4      4      5      6      6      8      9      9     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.90   0.90   0.90   1.19   1.19   1.49   1.79   1.79   2.39   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.10   0.10   0.10   1.34   1.34   2.01   2.62   2.62   3.71   3.99   3.99   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34
GDT RMS_ALL_CA   5.96   5.96   5.96   7.26   7.26   6.96   6.09   6.09   4.64   4.44   4.44   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          2.121
LGA    N     157      N     157          2.300
LGA    E     158      E     158          2.780
LGA    D     159      D     159          2.821
LGA    A     160      A     160          1.922
LGA    V     161      V     161          3.463
LGA    F     162      F     162          8.021
LGA    L     163      L     163          9.860
LGA    T     164      T     164          6.912
LGA    D     165      D     165         10.987

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      6    2.62     1.716     1.689     0.221

LGA_LOCAL      RMSD =  2.619  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.093  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  4.339  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.483917 * X  +  -0.565352 * Y  +   0.667983 * Z  + -20.309540
  Y_new =  -0.633509 * X  +  -0.752913 * Y  +  -0.178290 * Z  +  75.454231
  Z_new =   0.603730 * X  +  -0.336896 * Y  +  -0.722503 * Z  +  61.129276 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.705275    0.436318  [ DEG:  -155.0008     24.9992 ]
  Theta =  -0.648172   -2.493421  [ DEG:   -37.1375   -142.8625 ]
  Phi   =  -0.918479    2.223114  [ DEG:   -52.6250    127.3750 ]
 
# 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_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_1_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   2.62   1.689     4.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1h3o_B
ATOM   1209  N   THR   156      29.919  26.277  14.787  1.00  0.00
ATOM   1210  CA  THR   156      28.528  26.394  15.115  1.00  0.00
ATOM   1211  C   THR   156      27.811  26.340  13.816  1.00  0.00
ATOM   1212  O   THR   156      26.784  25.680  13.675  1.00  0.00
ATOM   1213  CB  THR   156      28.229  27.717  15.844  1.00  0.00
ATOM   1214  OG1 THR   156      28.958  27.762  17.077  1.00  0.00
ATOM   1215  CG2 THR   156      26.742  27.835  16.145  1.00  0.00
ATOM   1216  N   ASN   157      28.367  27.052  12.823  1.00  0.00
ATOM   1217  CA  ASN   157      27.821  27.043  11.506  1.00  0.00
ATOM   1218  C   ASN   157      26.397  27.482  11.591  1.00  0.00
ATOM   1219  O   ASN   157      25.583  27.127  10.740  1.00  0.00
ATOM   1220  CB  ASN   157      27.891  25.637  10.907  1.00  0.00
ATOM   1221  CG  ASN   157      27.814  25.644   9.392  1.00  0.00
ATOM   1222  OD1 ASN   157      28.228  26.606   8.745  1.00  0.00
ATOM   1223  ND2 ASN   157      27.283  24.568   8.823  1.00  0.00
ATOM   1224  N   GLU   158      26.059  28.286  12.618  1.00  0.00
ATOM   1225  CA  GLU   158      24.715  28.768  12.710  1.00  0.00
ATOM   1226  C   GLU   158      24.650  30.010  11.891  1.00  0.00
ATOM   1227  O   GLU   158      25.673  30.634  11.614  1.00  0.00
ATOM   1228  CB  GLU   158      24.353  29.070  14.165  1.00  0.00
ATOM   1229  CG  GLU   158      25.099  30.255  14.758  1.00  0.00
ATOM   1230  CD  GLU   158      24.659  30.572  16.173  1.00  0.00
ATOM   1231  OE1 GLU   158      23.485  30.957  16.360  1.00  0.00
ATOM   1232  OE2 GLU   158      25.488  30.435  17.098  1.00  0.00
ATOM   1233  N   ASP   159      23.434  30.392  11.463  1.00  0.00
ATOM   1234  CA  ASP   159      23.318  31.562  10.644  1.00  0.00
ATOM   1235  C   ASP   159      23.873  32.700  11.433  1.00  0.00
ATOM   1236  O   ASP   159      23.504  32.916  12.585  1.00  0.00
ATOM   1237  CB  ASP   159      21.853  31.827  10.291  1.00  0.00
ATOM   1238  CG  ASP   159      21.311  30.841   9.275  1.00  0.00
ATOM   1239  OD1 ASP   159      22.116  30.077   8.701  1.00  0.00
ATOM   1240  OD2 ASP   159      20.083  30.832   9.053  1.00  0.00
ATOM   1241  N   ALA   160      24.807  33.451  10.820  1.00  0.00
ATOM   1242  CA  ALA   160      25.412  34.557  11.495  1.00  0.00
ATOM   1243  C   ALA   160      25.395  35.701  10.542  1.00  0.00
ATOM   1244  O   ALA   160      25.270  35.515   9.333  1.00  0.00
ATOM   1245  CB  ALA   160      26.841  34.218  11.891  1.00  0.00
ATOM   1246  N   VAL   161      25.491  36.928  11.082  1.00  0.00
ATOM   1247  CA  VAL   161      25.479  38.102  10.266  1.00  0.00
ATOM   1248  C   VAL   161      26.837  38.284   9.682  1.00  0.00
ATOM   1249  O   VAL   161      27.845  37.933  10.295  1.00  0.00
ATOM   1250  CB  VAL   161      25.113  39.354  11.085  1.00  0.00
ATOM   1251  CG1 VAL   161      25.263  40.608  10.236  1.00  0.00
ATOM   1252  CG2 VAL   161      23.675  39.272  11.571  1.00  0.00
ATOM   1253  N   PHE   162      26.885  38.815   8.446  1.00  0.00
ATOM   1254  CA  PHE   162      28.132  39.119   7.811  1.00  0.00
ATOM   1255  C   PHE   162      28.398  40.540   8.179  1.00  0.00
ATOM   1256  O   PHE   162      27.504  41.220   8.683  1.00  0.00
ATOM   1257  CB  PHE   162      28.020  38.943   6.296  1.00  0.00
ATOM   1258  CG  PHE   162      27.865  37.513   5.862  1.00  0.00
ATOM   1259  CD1 PHE   162      26.612  36.981   5.613  1.00  0.00
ATOM   1260  CD2 PHE   162      28.974  36.699   5.703  1.00  0.00
ATOM   1261  CE1 PHE   162      26.470  35.666   5.214  1.00  0.00
ATOM   1262  CE2 PHE   162      28.831  35.384   5.303  1.00  0.00
ATOM   1263  CZ  PHE   162      27.586  34.866   5.059  1.00  0.00
ATOM   1264  N   LEU   163      29.639  41.024   7.970  1.00  0.00
ATOM   1265  CA  LEU   163      29.933  42.373   8.348  1.00  0.00
ATOM   1266  C   LEU   163      28.989  43.257   7.610  1.00  0.00
ATOM   1267  O   LEU   163      28.753  43.087   6.415  1.00  0.00
ATOM   1268  CB  LEU   163      31.376  42.728   7.985  1.00  0.00
ATOM   1269  CG  LEU   163      31.860  44.117   8.410  1.00  0.00
ATOM   1270  CD1 LEU   163      31.905  44.231   9.925  1.00  0.00
ATOM   1271  CD2 LEU   163      33.256  44.388   7.870  1.00  0.00
ATOM   1272  N   THR   164      28.415  44.230   8.340  1.00  0.00
ATOM   1273  CA  THR   164      27.459  45.129   7.773  1.00  0.00
ATOM   1274  C   THR   164      28.170  46.414   7.516  1.00  0.00
ATOM   1275  O   THR   164      29.188  46.707   8.142  1.00  0.00
ATOM   1276  CB  THR   164      26.276  45.370   8.730  1.00  0.00
ATOM   1277  OG1 THR   164      26.745  46.008   9.924  1.00  0.00
ATOM   1278  CG2 THR   164      25.616  44.052   9.103  1.00  0.00
ATOM   1279  N   ASP   165      27.651  47.206   6.561  1.00  0.00
ATOM   1280  CA  ASP   165      28.266  48.458   6.242  1.00  0.00
ATOM   1281  C   ASP   165      28.154  49.340   7.480  1.00  0.00
ATOM   1282  O   ASP   165      29.221  49.741   8.018  1.00  0.00
ATOM   1283  CB  ASP   165      27.556  49.117   5.058  1.00  0.00
ATOM   1284  CG  ASP   165      28.307  50.322   4.526  1.00  0.00
ATOM   1285  OD1 ASP   165      29.437  50.573   4.996  1.00  0.00
ATOM   1286  OD2 ASP   165      27.766  51.015   3.639  1.00  0.00
TER
END
