
#######################################################
#                                                     #
#                        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 T0318TS022_5_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_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:    10       156 - 165         4.80     4.80
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       157 - 160         1.70     9.77
  LONGEST_CONTINUOUS_SEGMENT:     4       158 - 161         1.83     7.62
  LCS_AVERAGE:      1.04

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         0.90    16.03
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.79    10.72
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.51     9.55
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.62     8.77
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.60     7.98
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.54     9.65
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.65    12.00
  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    3    3    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      3    4   10     0    3    3    3    4    4    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      3    4   10     0    3    3    3    4    4    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      3    4   10     1    3    3    3    4    4    5    5    6    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      3    4   10     1    3    3    3    4    4    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      3    4   10     0    3    3    3    4    4    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      3    3   10     0    3    3    3    3    4    5    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    3   10     0    3    3    3    3    4    4    5    7    8    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    3   10     0    3    3    3    3    4    4    5    6    7    8    9    9   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    3   10     0    3    3    3    3    4    4    5    5    7    7    9    9   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.64  (   0.90    1.04    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      1      3      3      3      4      4      5      5      7      8      8      9      9     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.30   0.90   0.90   0.90   1.19   1.19   1.49   1.49   2.09   2.39   2.39   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL   31.62   0.51   0.51   0.51   1.70   1.70   2.54   2.54   3.61   3.95   3.95   4.32   4.32   4.80   4.80   4.80   4.80   4.80   4.80   4.80
GDT RMS_ALL_CA   6.11   9.55   9.55   9.55   9.77   9.77   6.56   6.56   5.42   5.34   5.34   5.00   5.00   4.80   4.80   4.80   4.80   4.80   4.80   4.80

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          8.110
LGA    N     157      N     157          2.634
LGA    E     158      E     158          2.521
LGA    D     159      D     159          0.574
LGA    A     160      A     160          3.434
LGA    V     161      V     161          2.597
LGA    F     162      F     162          7.099
LGA    L     163      L     163          9.150
LGA    T     164      T     164          7.914
LGA    D     165      D     165         11.662

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      5    2.54     1.567     1.529     0.190

LGA_LOCAL      RMSD =  2.536  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.563  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  4.804  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.830460 * X  +   0.197143 * Y  +   0.521028 * Z  + -15.878428
  Y_new =  -0.457222 * X  +  -0.293106 * Y  +   0.839665 * Z  +  64.702927
  Z_new =   0.318251 * X  +  -0.935534 * Y  +  -0.153274 * Z  +  32.093323 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.733190    1.408403  [ DEG:   -99.3045     80.6955 ]
  Theta =  -0.323883   -2.817709  [ DEG:   -18.5572   -161.4428 ]
  Phi   =  -0.503277    2.638316  [ DEG:   -28.8356    151.1644 ]
 
# 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: T0318TS022_5_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_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   2.54   1.529     4.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1urh_A
ATOM   1201  N   THR   156      29.875  24.374   6.215  1.00  0.00
ATOM   1202  CA  THR   156      28.814  24.589   7.163  1.00  0.00
ATOM   1203  C   THR   156      29.270  25.485   8.271  1.00  0.00
ATOM   1204  O   THR   156      30.441  25.485   8.646  1.00  0.00
ATOM   1205  CB  THR   156      28.342  23.265   7.791  1.00  0.00
ATOM   1206  OG1 THR   156      27.207  23.509   8.631  1.00  0.00
ATOM   1207  CG2 THR   156      29.450  22.647   8.628  1.00  0.00
ATOM   1208  N   ASN   157      28.322  26.288   8.804  1.00  0.00
ATOM   1209  CA  ASN   157      28.491  27.165   9.930  1.00  0.00
ATOM   1210  C   ASN   157      27.115  27.539  10.384  1.00  0.00
ATOM   1211  O   ASN   157      26.136  27.274   9.688  1.00  0.00
ATOM   1212  CB  ASN   157      29.280  28.411   9.524  1.00  0.00
ATOM   1213  CG  ASN   157      30.074  28.998  10.675  1.00  0.00
ATOM   1214  OD1 ASN   157      29.815  28.694  11.839  1.00  0.00
ATOM   1215  ND2 ASN   157      31.046  29.843  10.351  1.00  0.00
ATOM   1216  N   GLU   158      26.991  28.156  11.575  1.00  0.00
ATOM   1217  CA  GLU   158      25.674  28.452  12.059  1.00  0.00
ATOM   1218  C   GLU   158      25.642  29.833  12.636  1.00  0.00
ATOM   1219  O   GLU   158      26.681  30.443  12.883  1.00  0.00
ATOM   1220  CB  GLU   158      25.265  27.456  13.145  1.00  0.00
ATOM   1221  CG  GLU   158      26.119  27.521  14.400  1.00  0.00
ATOM   1222  CD  GLU   158      25.746  26.458  15.415  1.00  0.00
ATOM   1223  OE1 GLU   158      24.824  25.665  15.133  1.00  0.00
ATOM   1224  OE2 GLU   158      26.377  26.418  16.493  1.00  0.00
ATOM   1225  N   ASP   159      24.415  30.366  12.827  1.00  0.00
ATOM   1226  CA  ASP   159      24.192  31.663  13.403  1.00  0.00
ATOM   1227  C   ASP   159      24.282  32.695  12.325  1.00  0.00
ATOM   1228  O   ASP   159      24.958  32.503  11.316  1.00  0.00
ATOM   1229  CB  ASP   159      25.244  31.961  14.474  1.00  0.00
ATOM   1230  CG  ASP   159      25.049  31.130  15.728  1.00  0.00
ATOM   1231  OD1 ASP   159      23.977  30.506  15.867  1.00  0.00
ATOM   1232  OD2 ASP   159      25.970  31.104  16.572  1.00  0.00
ATOM   1233  N   ALA   160      23.565  33.821  12.513  1.00  0.00
ATOM   1234  CA  ALA   160      23.551  34.875  11.539  1.00  0.00
ATOM   1235  C   ALA   160      24.885  35.541  11.552  1.00  0.00
ATOM   1236  O   ALA   160      25.590  35.532  12.561  1.00  0.00
ATOM   1237  CB  ALA   160      22.470  35.892  11.874  1.00  0.00
ATOM   1238  N   VAL   161      25.275  36.124  10.401  1.00  0.00
ATOM   1239  CA  VAL   161      26.540  36.787  10.332  1.00  0.00
ATOM   1240  C   VAL   161      26.265  38.237  10.139  1.00  0.00
ATOM   1241  O   VAL   161      25.448  38.622   9.303  1.00  0.00
ATOM   1242  CB  VAL   161      27.391  36.261   9.162  1.00  0.00
ATOM   1243  CG1 VAL   161      28.710  37.016   9.080  1.00  0.00
ATOM   1244  CG2 VAL   161      27.695  34.782   9.347  1.00  0.00
ATOM   1245  N   PHE   162      26.936  39.090  10.931  1.00  0.00
ATOM   1246  CA  PHE   162      26.680  40.487  10.792  1.00  0.00
ATOM   1247  C   PHE   162      27.958  41.167  10.443  1.00  0.00
ATOM   1248  O   PHE   162      28.948  41.074  11.165  1.00  0.00
ATOM   1249  CB  PHE   162      26.136  41.065  12.100  1.00  0.00
ATOM   1250  CG  PHE   162      24.800  40.505  12.500  1.00  0.00
ATOM   1251  CD1 PHE   162      24.717  39.388  13.313  1.00  0.00
ATOM   1252  CD2 PHE   162      23.627  41.095  12.064  1.00  0.00
ATOM   1253  CE1 PHE   162      23.490  38.872  13.681  1.00  0.00
ATOM   1254  CE2 PHE   162      22.399  40.580  12.432  1.00  0.00
ATOM   1255  CZ  PHE   162      22.326  39.474  13.237  1.00  0.00
ATOM   1256  N   LEU   163      27.962  41.858   9.291  1.00  0.00
ATOM   1257  CA  LEU   163      29.095  42.647   8.924  1.00  0.00
ATOM   1258  C   LEU   163      28.559  44.031   8.815  1.00  0.00
ATOM   1259  O   LEU   163      27.473  44.237   8.278  1.00  0.00
ATOM   1260  CB  LEU   163      29.676  42.164   7.593  1.00  0.00
ATOM   1261  CG  LEU   163      30.168  40.715   7.555  1.00  0.00
ATOM   1262  CD1 LEU   163      30.596  40.331   6.146  1.00  0.00
ATOM   1263  CD2 LEU   163      31.360  40.528   8.482  1.00  0.00
ATOM   1264  N   THR   164      29.287  45.022   9.354  1.00  0.00
ATOM   1265  CA  THR   164      28.787  46.358   9.254  1.00  0.00
ATOM   1266  C   THR   164      29.220  46.869   7.927  1.00  0.00
ATOM   1267  O   THR   164      29.919  46.174   7.194  1.00  0.00
ATOM   1268  CB  THR   164      29.346  47.256  10.375  1.00  0.00
ATOM   1269  OG1 THR   164      30.769  47.359  10.243  1.00  0.00
ATOM   1270  CG2 THR   164      29.019  46.669  11.739  1.00  0.00
ATOM   1271  N   ASP   165      28.785  48.090   7.566  1.00  0.00
ATOM   1272  CA  ASP   165      29.172  48.650   6.307  1.00  0.00
ATOM   1273  C   ASP   165      30.695  48.630   6.261  1.00  0.00
ATOM   1274  O   ASP   165      31.255  47.973   5.344  1.00  0.00
ATOM   1275  CB  ASP   165      28.658  50.085   6.177  1.00  0.00
ATOM   1276  CG  ASP   165      28.830  50.641   4.777  1.00  0.00
ATOM   1277  OD1 ASP   165      29.237  49.875   3.879  1.00  0.00
ATOM   1278  OD2 ASP   165      28.559  51.844   4.578  1.00  0.00
TER
END
