
#######################################################
#                                                     #
#                        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   36 (  177),  selected   19 , name T0368TS239_5_2
# Molecule2: number of CA atoms  157 ( 1171),  selected   19 , name T0368.pdb
# PARAMETERS: T0368TS239_5_2.T0368.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:    19       139 - 157         1.55     1.55
  LCS_AVERAGE:     12.10

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       139 - 157         1.55     1.55
  LCS_AVERAGE:     12.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       140 - 156         0.96     1.68
  LONGEST_CONTINUOUS_SEGMENT:    17       141 - 157         0.88     1.81
  LCS_AVERAGE:     10.36

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:  157
LCS_GDT     P     139     P     139      3   19   19     3    3    4    6    9   13   17   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     G     140     G     140     17   19   19     4   11   15   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     141     K     141     17   19   19     4   11   15   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E     142     E     142     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     R     143     R     143     17   19   19     7   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     M     144     M     144     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     M     145     M     145     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E     146     E     146     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V     147     V     147     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     148     A     148     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I     149     I     149     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     D     150     D     150     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     R     151     R     151     17   19   19     7   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I     152     I     152     17   19   19     8   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     153     A     153     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q     154     Q     154     17   19   19     9   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     155     L     155     17   19   19     7   14   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     G     156     G     156     17   19   19     5    9   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     157     A     157     17   19   19     3    9   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  11.52  (  10.36   12.10   12.10 )

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      9     14     16     17     18     18     18     19     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   5.73   8.92  10.19  10.83  11.46  11.46  11.46  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10
GDT RMS_LOCAL    0.26   0.53   0.76   0.88   1.06   1.06   1.06   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55
GDT RMS_ALL_CA   1.81   1.79   1.88   1.81   1.66   1.66   1.66   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55

#      Molecule1      Molecule2       DISTANCE
LGA    P     139      P     139          3.935
LGA    G     140      G     140          0.926
LGA    K     141      K     141          1.814
LGA    E     142      E     142          1.476
LGA    R     143      R     143          0.795
LGA    M     144      M     144          0.882
LGA    M     145      M     145          0.947
LGA    E     146      E     146          0.816
LGA    V     147      V     147          0.517
LGA    A     148      A     148          0.726
LGA    I     149      I     149          0.241
LGA    D     150      D     150          0.480
LGA    R     151      R     151          0.565
LGA    I     152      I     152          1.205
LGA    A     153      A     153          1.444
LGA    Q     154      Q     154          0.839
LGA    L     155      L     155          1.900
LGA    G     156      G     156          3.409
LGA    A     157      A     157          3.395

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36  157    4.0     19    1.55    10.987    11.501     1.152

LGA_LOCAL      RMSD =  1.549  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.735  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  1.549  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.578761 * X  +  -0.813946 * Y  +   0.050279 * Z  + 145.097336
  Y_new =   0.091682 * X  +   0.003680 * Y  +  -0.995781 * Z  +  23.173145
  Z_new =   0.810327 * X  +   0.580929 * Y  +   0.076755 * Z  +  44.661942 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.439433   -1.702159  [ DEG:    82.4735    -97.5265 ]
  Theta =  -0.944710   -2.196882  [ DEG:   -54.1279   -125.8721 ]
  Phi   =   0.157106   -2.984487  [ DEG:     9.0015   -170.9985 ]
 
# 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: T0368TS239_5_2                                
REMARK     2: T0368.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0368TS239_5_2.T0368.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   36  157   4.0   19   1.55  11.501     1.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0368TS239_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0368
PARENT 1hz4_A
ATOM    621  N   PRO   139      87.068  48.463  67.109  1.00  9.99
ATOM    622  CA  PRO   139      85.929  49.087  66.437  1.00  9.99
ATOM    623  C   PRO   139      86.138  49.507  64.971  1.00  9.99
ATOM    624  O   PRO   139      87.174  50.060  64.605  1.00  9.99
ATOM    625  CB  PRO   139      85.449  50.259  67.291  1.00  9.99
ATOM    626  N   GLY   140      85.130  49.267  64.118  1.00  9.99
ATOM    627  CA  GLY   140      85.171  49.585  62.684  1.00  9.99
ATOM    628  C   GLY   140      85.668  50.955  62.239  1.00  9.99
ATOM    629  O   GLY   140      86.367  51.078  61.234  1.00  9.99
ATOM    630  N   LYS   141      85.304  51.995  62.978  1.00  9.99
ATOM    631  CA  LYS   141      85.702  53.339  62.619  1.00  9.99
ATOM    632  C   LYS   141      87.215  53.522  62.657  1.00  9.99
ATOM    633  O   LYS   141      87.765  54.465  62.081  1.00  9.99
ATOM    634  CB  LYS   141      85.038  54.318  63.567  1.00  9.99
ATOM    635  N   GLU   142      87.880  52.620  63.355  1.00  9.99
ATOM    636  CA  GLU   142      89.329  52.664  63.463  1.00  9.99
ATOM    637  C   GLU   142      89.909  52.511  62.045  1.00  9.99
ATOM    638  O   GLU   142      90.948  53.106  61.728  1.00  9.99
ATOM    639  CB  GLU   142      89.771  51.518  64.377  1.00  9.99
ATOM    640  N   ARG   143      89.246  51.739  61.182  1.00  9.99
ATOM    641  CA  ARG   143      89.746  51.580  59.813  1.00  9.99
ATOM    642  C   ARG   143      89.718  52.897  59.049  1.00  9.99
ATOM    643  O   ARG   143      90.637  53.203  58.294  1.00  9.99
ATOM    644  CB  ARG   143      88.922  50.537  59.049  1.00  9.99
ATOM    645  N   MET   144      88.667  53.690  59.235  1.00  9.99
ATOM    646  CA  MET   144      88.577  54.957  58.519  1.00  9.99
ATOM    647  C   MET   144      89.760  55.843  58.946  1.00  9.99
ATOM    648  O   MET   144      90.423  56.475  58.117  1.00  9.99
ATOM    649  CB  MET   144      87.230  55.619  58.844  1.00  9.99
ATOM    650  N   MET   145      90.040  55.874  60.244  1.00  9.99
ATOM    651  CA  MET   145      91.144  56.680  60.746  1.00  9.99
ATOM    652  C   MET   145      92.488  56.221  60.184  1.00  9.99
ATOM    653  O   MET   145      93.278  57.051  59.713  1.00  9.99
ATOM    654  CB  MET   145      91.185  56.636  62.277  1.00  9.99
ATOM    655  N   GLU   146      92.775  54.918  60.219  1.00  9.99
ATOM    656  CA  GLU   146      94.065  54.490  59.688  1.00  9.99
ATOM    657  C   GLU   146      94.129  54.681  58.176  1.00  9.99
ATOM    658  O   GLU   146      95.213  54.859  57.620  1.00  9.99
ATOM    659  CB  GLU   146      94.435  53.022  60.079  1.00  9.99
ATOM    660  N   VAL   147      92.979  54.695  57.515  1.00  9.99
ATOM    661  CA  VAL   147      92.969  54.910  56.075  1.00  9.99
ATOM    662  C   VAL   147      93.343  56.364  55.766  1.00  9.99
ATOM    663  O   VAL   147      94.161  56.621  54.881  1.00  9.99
ATOM    664  CB  VAL   147      91.597  54.588  55.492  1.00  9.99
ATOM    665  N   ALA   148      92.762  57.327  56.486  1.00  9.99
ATOM    666  CA  ALA   148      93.127  58.715  56.202  1.00  9.99
ATOM    667  C   ALA   148      94.540  59.016  56.708  1.00  9.99
ATOM    668  O   ALA   148      95.221  59.891  56.165  1.00  9.99
ATOM    669  CB  ALA   148      92.082  59.746  56.730  1.00  9.99
ATOM    670  N   ILE   149      95.003  58.288  57.720  1.00  9.99
ATOM    671  CA  ILE   149      96.377  58.465  58.181  1.00  9.99
ATOM    672  C   ILE   149      97.275  57.950  57.049  1.00  9.99
ATOM    673  O   ILE   149      98.296  58.565  56.726  1.00  9.99
ATOM    674  CB  ILE   149      96.608  57.683  59.494  1.00  9.99
ATOM    675  N   ASP   150      96.888  56.838  56.426  1.00  9.99
ATOM    676  CA  ASP   150      97.672  56.299  55.304  1.00  9.99
ATOM    677  C   ASP   150      97.713  57.293  54.143  1.00  9.99
ATOM    678  O   ASP   150      98.739  57.444  53.486  1.00  9.99
ATOM    679  CB  ASP   150      97.078  54.967  54.825  1.00  9.99
ATOM    680  N   ARG   151      96.600  57.962  53.881  1.00  9.99
ATOM    681  CA  ARG   151      96.552  58.931  52.788  1.00  9.99
ATOM    682  C   ARG   151      97.559  60.044  53.013  1.00  9.99
ATOM    683  O   ARG   151      98.265  60.472  52.093  1.00  9.99
ATOM    684  CB  ARG   151      95.147  59.524  52.673  1.00  9.99
ATOM    685  N   ILE   152      97.618  60.518  54.247  1.00  9.99
ATOM    686  CA  ILE   152      98.524  61.589  54.606  1.00  9.99
ATOM    687  C   ILE   152      99.977  61.102  54.508  1.00  9.99
ATOM    688  O   ILE   152     100.825  61.777  53.911  1.00  9.99
ATOM    689  CB  ILE   152      98.145  62.071  56.010  1.00  9.99
ATOM    690  N   ALA   153     100.263  59.919  55.042  1.00  9.99
ATOM    691  CA  ALA   153     101.615  59.365  54.974  1.00  9.99
ATOM    692  C   ALA   153     102.018  59.169  53.512  1.00  9.99
ATOM    693  O   ALA   153     103.175  59.371  53.134  1.00  9.99
ATOM    694  CB  ALA   153     101.682  58.029  55.721  1.00  9.99
ATOM    695  N   GLN   154     101.063  58.766  52.683  1.00  9.99
ATOM    696  CA  GLN   154     101.349  58.570  51.270  1.00  9.99
ATOM    697  C   GLN   154     101.736  59.912  50.637  1.00  9.99
ATOM    698  O   GLN   154     102.724  59.986  49.888  1.00  9.99
ATOM    699  CB  GLN   154     100.119  57.996  50.556  1.00  9.99
ATOM    700  N   LEU   155     100.979  60.969  50.928  1.00  9.99
ATOM    701  CA  LEU   155     101.324  62.276  50.345  1.00  9.99
ATOM    702  C   LEU   155     102.775  62.623  50.667  1.00  9.99
ATOM    703  O   LEU   155     103.517  63.111  49.806  1.00  9.99
ATOM    704  CB  LEU   155     100.394  63.373  50.881  1.00  9.99
ATOM    705  N   GLY   156     103.172  62.358  51.904  1.00  9.99
ATOM    706  CA  GLY   156     104.519  62.653  52.391  1.00  9.99
ATOM    707  C   GLY   156     105.581  61.647  51.965  1.00  9.99
ATOM    708  O   GLY   156     106.743  61.759  52.368  1.00  9.99
ATOM    709  N   ALA   157     105.174  60.656  51.175  1.00  9.99
ATOM    710  CA  ALA   157     106.066  59.625  50.670  1.00  9.99
ATOM    711  C   ALA   157     106.639  58.695  51.740  1.00  9.99
ATOM    712  O   ALA   157     107.733  58.158  51.591  1.00  9.99
ATOM    713  CB  ALA   157     107.196  60.263  49.846  1.00  9.99
ATOM    714  N   SER   158     105.891  58.508  52.823  1.00  9.99
ATOM    715  CA  SER   158     106.302  57.588  53.883  1.00  9.99
ATOM    716  C   SER   158     105.485  56.354  53.531  1.00  9.99
ATOM    717  O   SER   158     104.477  56.031  54.183  1.00  9.99
ATOM    718  CB  SER   158     105.921  58.156  55.240  1.00  9.99
ATOM    719  N   ASN   159     105.923  55.679  52.474  1.00  9.99
ATOM    720  CA  ASN   159     105.212  54.535  51.934  1.00  9.99
ATOM    721  C   ASN   159     105.133  53.301  52.812  1.00  9.99
ATOM    722  O   ASN   159     104.085  52.660  52.870  1.00  9.99
ATOM    723  CB  ASN   159     105.771  54.183  50.548  1.00  9.99
ATOM    724  N   GLN   160     106.219  52.944  53.488  1.00  9.99
ATOM    725  CA  GLN   160     106.147  51.771  54.352  1.00  9.99
ATOM    726  C   GLN   160     105.114  52.013  55.445  1.00  9.99
ATOM    727  O   GLN   160     104.310  51.132  55.754  1.00  9.99
ATOM    728  CB  GLN   160     107.502  51.458  54.989  1.00  9.99
ATOM    729  N   GLN   161     105.133  53.207  56.021  1.00  9.99
ATOM    730  CA  GLN   161     104.172  53.543  57.068  1.00  9.99
ATOM    731  C   GLN   161     102.751  53.576  56.503  1.00  9.99
ATOM    732  O   GLN   161     101.819  53.074  57.126  1.00  9.99
ATOM    733  CB  GLN   161     104.506  54.893  57.703  1.00  9.99
ATOM    734  N   LYS   162     102.582  54.155  55.322  1.00  9.99
ATOM    735  CA  LYS   162     101.249  54.216  54.726  1.00  9.99
ATOM    736  C   LYS   162     100.690  52.810  54.494  1.00  9.99
ATOM    737  O   LYS   162      99.521  52.542  54.769  1.00  9.99
ATOM    738  CB  LYS   162     101.300  54.994  53.415  1.00  9.99
ATOM    739  N   LYS   163     101.529  51.917  53.988  1.00  9.99
ATOM    740  CA  LYS   163     101.114  50.553  53.725  1.00  9.99
ATOM    741  C   LYS   163     100.727  49.859  55.021  1.00  9.99
ATOM    742  O   LYS   163      99.704  49.169  55.082  1.00  9.99
ATOM    743  CB  LYS   163     102.241  49.769  53.050  1.00  9.99
ATOM    744  N   PRO   164     101.541  50.030  56.060  1.00  9.99
ATOM    745  CA  PRO   164     101.235  49.397  57.339  1.00  9.99
ATOM    746  C   PRO   164      99.915  49.928  57.878  1.00  9.99
ATOM    747  O   PRO   164      99.133  49.181  58.466  1.00  9.99
ATOM    748  CB  PRO   164     102.355  49.656  58.342  1.00  9.99
ATOM    749  N   GLY   165      99.663  51.217  57.675  1.00  9.99
ATOM    750  CA  GLY   165      98.423  51.809  58.149  1.00  9.99
ATOM    751  C   GLY   165      97.249  51.184  57.395  1.00  9.99
ATOM    752  O   GLY   165      96.243  50.809  58.001  1.00  9.99
ATOM    753  N   TYR   166      97.372  51.055  56.077  1.00  9.99
ATOM    754  CA  TYR   166      96.301  50.449  55.295  1.00  9.99
ATOM    755  C   TYR   166      96.084  48.994  55.718  1.00  9.99
ATOM    756  O   TYR   166      94.946  48.542  55.820  1.00  9.99
ATOM    757  CB  TYR   166      96.624  50.515  53.806  1.00  9.99
ATOM    758  N   LYS   167      97.159  48.251  55.968  1.00  9.99
ATOM    759  CA  LYS   167      96.989  46.856  56.367  1.00  9.99
ATOM    760  C   LYS   167      96.332  46.746  57.742  1.00  9.99
ATOM    761  O   LYS   167      95.579  45.801  58.000  1.00  9.99
ATOM    762  CB  LYS   167      98.330  46.104  56.339  1.00  9.99
ATOM    763  N   ALA   168      96.587  47.704  58.627  1.00  9.99
ATOM    764  CA  ALA   168      95.947  47.654  59.937  1.00  9.99
ATOM    765  C   ALA   168      94.438  47.872  59.746  1.00  9.99
ATOM    766  O   ALA   168      93.633  47.311  60.486  1.00  9.99
ATOM    767  CB  ALA   168      96.546  48.690  60.900  1.00  9.99
ATOM    768  N   TRP   169      94.058  48.667  58.745  1.00  9.99
ATOM    769  CA  TRP   169      92.650  48.897  58.455  1.00  9.99
ATOM    770  C   TRP   169      91.988  47.610  57.982  1.00  9.99
ATOM    771  O   TRP   169      90.856  47.288  58.380  1.00  9.99
ATOM    772  CB  TRP   169      92.519  50.015  57.406  1.00  9.99
ATOM    773  N   TRP   170      92.683  46.882  57.110  1.00  9.99
ATOM    774  CA  TRP   170      92.190  45.613  56.607  1.00  9.99
ATOM    775  C   TRP   170      92.023  44.646  57.785  1.00  9.99
ATOM    776  O   TRP   170      91.029  43.924  57.862  1.00  9.99
ATOM    777  CB  TRP   170      93.173  45.050  55.542  1.00  9.99
ATOM    778  N   GLU   171      92.962  44.660  58.727  1.00  9.99
ATOM    779  CA  GLU   171      92.863  43.770  59.879  1.00  9.99
ATOM    780  C   GLU   171      91.664  44.146  60.753  1.00  9.99
ATOM    781  O   GLU   171      90.927  43.273  61.214  1.00  9.99
ATOM    782  CB  GLU   171      94.157  43.812  60.697  1.00  9.99
ATOM    783  N   PHE   172      91.460  45.442  60.976  1.00  9.99
ATOM    784  CA  PHE   172      90.319  45.899  61.777  1.00  9.99
ATOM    785  C   PHE   172      89.005  45.351  61.214  1.00  9.99
ATOM    786  O   PHE   172      88.098  44.996  61.969  1.00  9.99
ATOM    787  CB  PHE   172      90.237  47.451  61.801  1.00  9.99
ATOM    788  N   TRP   173      88.912  45.252  59.892  1.00  9.99
ATOM    789  CA  TRP   173      87.688  44.773  59.246  1.00  9.99
ATOM    790  C   TRP   173      87.723  43.294  58.861  1.00  9.99
ATOM    791  O   TRP   173      86.901  42.839  58.065  1.00  9.99
ATOM    792  CB  TRP   173      87.403  45.623  57.996  1.00  9.99
ATOM    793  N   SER   174      88.642  42.530  59.450  1.00  9.99
ATOM    794  CA  SER   174      88.783  41.122  59.089  1.00  9.99
ATOM    795  C   SER   174      87.547  40.253  59.276  1.00  9.99
ATOM    796  O   SER   174      87.386  39.259  58.564  1.00  9.99
ATOM    797  CB  SER   174      89.963  40.489  59.835  1.00  9.99
TER
END
