
#######################################################
#                                                     #
#                        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_3_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_3_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         4.69     4.69
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       162 - 165         1.78     8.04
  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         0.20     6.44
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.25     8.72
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.88     7.54
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.81     8.16
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.96    11.52
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.74     9.15
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.44    13.09
  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     3    3    3    3    4    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      3    3   10     3    3    3    3    4    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      3    3   10     3    3    3    3    4    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      3    3   10     3    3    3    3    4    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      3    3   10     3    3    3    3    4    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      3    3   10     0    3    3    3    3    4    6    6    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      3    4   10     0    3    3    4    4    4    4    5    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    4   10     3    3    3    4    4    4    4    5    7    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    4   10     3    3    3    4    4    4    4    5    5    8    8    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    4   10     3    3    3    4    4    4    4    5    5    8    8    9   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      3      4      4      4      6      6      7      8      8      9     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.90   0.90   0.90   1.19   1.19   1.19   1.79   1.79   2.09   2.39   2.39   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.20   0.20   0.20   1.78   1.77   1.77   2.85   2.85   3.73   3.82   3.82   4.43   4.69   4.69   4.69   4.69   4.69   4.69   4.69   4.69
GDT RMS_ALL_CA   6.44   6.44   6.44   8.04   7.78   7.78   6.78   6.78   4.99   5.18   5.18   4.94   4.69   4.69   4.69   4.69   4.69   4.69   4.69   4.69

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          2.870
LGA    N     157      N     157          2.418
LGA    E     158      E     158          3.105
LGA    D     159      D     159          2.781
LGA    A     160      A     160          2.294
LGA    V     161      V     161          3.474
LGA    F     162      F     162          8.383
LGA    L     163      L     163          8.552
LGA    T     164      T     164          9.068
LGA    D     165      D     165         13.625

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      6    2.85     1.716     1.584     0.203

LGA_LOCAL      RMSD =  2.851  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.783  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  4.690  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.321580 * X  +  -0.104794 * Y  +   0.941066 * Z  + -49.022755
  Y_new =   0.860349 * X  +  -0.382738 * Y  +  -0.336618 * Z  + -10.366282
  Z_new =   0.395458 * X  +   0.917894 * Y  +  -0.032922 * Z  + -110.070122 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.606647   -1.534945  [ DEG:    92.0541    -87.9459 ]
  Theta =  -0.406566   -2.735027  [ DEG:   -23.2945   -156.7055 ]
  Phi   =   1.213097   -1.928496  [ DEG:    69.5053   -110.4947 ]
 
# 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_3_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_3_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   2.85   1.584     4.69
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1tf7_A
ATOM   1209  N   THR   156      30.180  25.308  14.518  1.00  0.00
ATOM   1210  CA  THR   156      28.847  25.523  15.024  1.00  0.00
ATOM   1211  C   THR   156      27.907  25.819  13.892  1.00  0.00
ATOM   1212  O   THR   156      26.799  25.290  13.841  1.00  0.00
ATOM   1213  CB  THR   156      28.800  26.708  16.008  1.00  0.00
ATOM   1214  OG1 THR   156      29.639  26.429  17.135  1.00  0.00
ATOM   1215  CG2 THR   156      27.378  26.938  16.496  1.00  0.00
ATOM   1216  N   ASN   157      28.345  26.665  12.938  1.00  0.00
ATOM   1217  CA  ASN   157      27.584  26.999  11.765  1.00  0.00
ATOM   1218  C   ASN   157      26.249  27.608  12.073  1.00  0.00
ATOM   1219  O   ASN   157      25.236  27.161  11.542  1.00  0.00
ATOM   1220  CB  ASN   157      27.317  25.748  10.925  1.00  0.00
ATOM   1221  CG  ASN   157      26.875  26.079   9.513  1.00  0.00
ATOM   1222  OD1 ASN   157      27.208  27.137   8.979  1.00  0.00
ATOM   1223  ND2 ASN   157      26.122  25.171   8.902  1.00  0.00
ATOM   1224  N   GLU   158      26.192  28.640  12.936  1.00  0.00
ATOM   1225  CA  GLU   158      24.929  29.293  13.162  1.00  0.00
ATOM   1226  C   GLU   158      24.737  30.284  12.045  1.00  0.00
ATOM   1227  O   GLU   158      25.707  30.709  11.418  1.00  0.00
ATOM   1228  CB  GLU   158      24.932  30.013  14.511  1.00  0.00
ATOM   1229  CG  GLU   158      25.036  29.083  15.710  1.00  0.00
ATOM   1230  CD  GLU   158      24.949  29.824  17.031  1.00  0.00
ATOM   1231  OE1 GLU   158      24.926  31.072  17.010  1.00  0.00
ATOM   1232  OE2 GLU   158      24.903  29.155  18.085  1.00  0.00
ATOM   1233  N   ASP   159      23.472  30.652  11.733  1.00  0.00
ATOM   1234  CA  ASP   159      23.246  31.639  10.705  1.00  0.00
ATOM   1235  C   ASP   159      23.698  32.937  11.282  1.00  0.00
ATOM   1236  O   ASP   159      23.114  33.433  12.244  1.00  0.00
ATOM   1237  CB  ASP   159      21.763  31.696  10.334  1.00  0.00
ATOM   1238  CG  ASP   159      21.486  32.650   9.187  1.00  0.00
ATOM   1239  OD1 ASP   159      22.434  33.323   8.732  1.00  0.00
ATOM   1240  OD2 ASP   159      20.320  32.725   8.747  1.00  0.00
ATOM   1241  N   ALA   160      24.747  33.543  10.709  1.00  0.00
ATOM   1242  CA  ALA   160      25.151  34.773  11.306  1.00  0.00
ATOM   1243  C   ALA   160      25.312  35.773  10.224  1.00  0.00
ATOM   1244  O   ALA   160      25.345  35.423   9.047  1.00  0.00
ATOM   1245  CB  ALA   160      26.470  34.596  12.044  1.00  0.00
ATOM   1246  N   VAL   161      25.390  37.054  10.625  1.00  0.00
ATOM   1247  CA  VAL   161      25.515  38.199   9.774  1.00  0.00
ATOM   1248  C   VAL   161      26.766  38.887  10.212  1.00  0.00
ATOM   1249  O   VAL   161      27.675  38.237  10.723  1.00  0.00
ATOM   1250  CB  VAL   161      24.304  39.140   9.911  1.00  0.00
ATOM   1251  CG1 VAL   161      23.033  38.445   9.451  1.00  0.00
ATOM   1252  CG2 VAL   161      24.122  39.565  11.361  1.00  0.00
ATOM   1253  N   PHE   162      26.887  40.208   9.968  1.00  0.00
ATOM   1254  CA  PHE   162      28.087  40.854  10.422  1.00  0.00
ATOM   1255  C   PHE   162      27.767  42.175  11.050  1.00  0.00
ATOM   1256  O   PHE   162      26.652  42.684  10.949  1.00  0.00
ATOM   1257  CB  PHE   162      29.041  41.096   9.250  1.00  0.00
ATOM   1258  CG  PHE   162      28.508  42.049   8.221  1.00  0.00
ATOM   1259  CD1 PHE   162      28.788  43.402   8.298  1.00  0.00
ATOM   1260  CD2 PHE   162      27.725  41.593   7.174  1.00  0.00
ATOM   1261  CE1 PHE   162      28.297  44.280   7.350  1.00  0.00
ATOM   1262  CE2 PHE   162      27.233  42.472   6.226  1.00  0.00
ATOM   1263  CZ  PHE   162      27.517  43.809   6.310  1.00  0.00
ATOM   1264  N   LEU   163      28.769  42.734  11.761  1.00  0.00
ATOM   1265  CA  LEU   163      28.679  43.991  12.453  1.00  0.00
ATOM   1266  C   LEU   163      29.304  45.032  11.590  1.00  0.00
ATOM   1267  O   LEU   163      29.767  44.748  10.486  1.00  0.00
ATOM   1268  CB  LEU   163      29.414  43.918  13.793  1.00  0.00
ATOM   1269  CG  LEU   163      28.934  42.845  14.771  1.00  0.00
ATOM   1270  CD1 LEU   163      29.787  42.846  16.032  1.00  0.00
ATOM   1271  CD2 LEU   163      27.489  43.090  15.175  1.00  0.00
ATOM   1272  N   THR   164      29.293  46.292  12.070  1.00  0.00
ATOM   1273  CA  THR   164      29.904  47.338  11.313  1.00  0.00
ATOM   1274  C   THR   164      31.378  47.139  11.407  1.00  0.00
ATOM   1275  O   THR   164      31.912  46.792  12.459  1.00  0.00
ATOM   1276  CB  THR   164      29.531  48.726  11.864  1.00  0.00
ATOM   1277  OG1 THR   164      28.109  48.898  11.813  1.00  0.00
ATOM   1278  CG2 THR   164      30.188  49.823  11.040  1.00  0.00
ATOM   1279  N   ASP   165      32.076  47.338  10.273  1.00  0.00
ATOM   1280  CA  ASP   165      33.494  47.141  10.249  1.00  0.00
ATOM   1281  C   ASP   165      34.179  48.493  10.362  1.00  0.00
ATOM   1282  O   ASP   165      33.494  49.479  10.748  1.00  0.00
ATOM   1283  CB  ASP   165      33.919  46.466   8.943  1.00  0.00
ATOM   1284  CG  ASP   165      33.517  45.006   8.884  1.00  0.00
ATOM   1285  OD1 ASP   165      33.096  44.463   9.928  1.00  0.00
ATOM   1286  OD2 ASP   165      33.622  44.404   7.796  1.00  0.00
TER
END
