
#######################################################
#                                                     #
#                        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   52 (   52),  selected   47 , name T0342TS464_4_2
# Molecule2: number of CA atoms  169 ( 1343),  selected   47 , name T0342.pdb
# PARAMETERS: T0342TS464_4_2.T0342.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:    32       138 - 169         4.92     8.47
  LCS_AVERAGE:     17.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       135 - 154         1.86    11.25
  LCS_AVERAGE:      8.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       136 - 153         0.80    11.24
  LCS_AVERAGE:      5.95

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:  169
LCS_GDT     E      78     E      78      3    3    9     0    3    3    3    3    3    4    4    6   14   17   18   20   22   23   24   26   30   32   32 
LCS_GDT     V      79     V      79      3    3   11     1    3    3    3    3    5    5    6   10   14   17   18   20   30   32   34   35   36   38   39 
LCS_GDT     W      80     W      80      3    3   29     0    3    3    4    4    5    5    8   10   24   26   28   30   31   33   34   36   37   38   39 
LCS_GDT     G      81     G      81      3    3   29     0    3    5    8   15   15   20   21   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     V      82     V      82      3    3   29    10   18   18   19   19   19   20   21   23   25   26   27   30   31   33   34   36   37   38   39 
LCS_GDT     V      83     V      83      3    3   29     3    3    3    3    8   14   17   19   20   23   23   26   28   30   32   34   36   37   38   39 
LCS_GDT     W      84     W      84      3    4   29     3    3    3    3    6   12   17   19   19   22   23   26   28   31   32   34   36   37   38   39 
LCS_GDT     K      85     K      85      3    4   29     1    3    3    7   11   16   17   19   20   22   23   24   25   26   27   29   31   32   35   37 
LCS_GDT     M      86     M      86      3    4   29     1    3    3    3    5    7    9    9   13   17   19   20   21   22   23   24   24   25   25   26 
LCS_GDT     P     135     P     135      3   20   31     3    3    3    3    4    5    6    9   23   25   26   27   28   30   31   33   34   35   35   36 
LCS_GDT     S     136     S     136     18   20   31    14   18   18   19   19   19   20   21   23   25   26   27   29   31   32   33   34   36   38   39 
LCS_GDT     P     137     P     137     18   20   31    14   18   18   19   19   19   20   21   23   25   26   27   29   31   32   33   34   36   38   39 
LCS_GDT     Q     138     Q     138     18   20   32    14   18   18   19   19   19   20   21   23   25   26   27   29   31   33   34   36   37   38   39 
LCS_GDT     Y     139     Y     139     18   20   32    14   18   18   19   19   19   20   21   23   25   26   27   29   31   33   34   36   37   38   39 
LCS_GDT     K     140     K     140     18   20   32    14   18   18   19   19   19   20   21   23   25   26   27   29   31   33   34   36   37   38   39 
LCS_GDT     K     141     K     141     18   20   32    14   18   18   19   19   19   20   21   23   25   26   28   30   31   33   34   36   37   38   39 
LCS_GDT     I     142     I     142     18   20   32     8   18   18   19   19   19   20   21   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     I     143     I     143     18   20   32    10   18   18   19   19   19   20   21   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     C     144     C     144     18   20   32    14   18   18   19   19   19   20   21   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     M     145     M     145     18   20   32    14   18   18   19   19   19   20   21   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     G     146     G     146     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     A     147     A     147     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     K     148     K     148     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     E     149     E     149     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     N     150     N     150     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     G     151     G     151     18   20   32    11   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     L     152     L     152     18   20   32    14   18   18   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     P     153     P     153     18   20   32     4    7   13   19   19   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     L     154     L     154      7   20   32     4    6    9   14   15   16   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     E     155     E     155      9   17   32     9    9   10   14   15   16   18   22   23   24   26   29   30   31   33   34   36   37   38   39 
LCS_GDT     Y     156     Y     156      9   17   32     9    9   10   14   18   19   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     Q     157     Q     157      9   17   32     9    9   10   14   15   16   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     E     158     E     158      9   17   32     9    9   10   14   15   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     K     159     K     159      9   17   32     9    9   10   14   15   18   20   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     L     160     L     160      9   17   32     9    9   10   14   15   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     K     161     K     161      9   17   32     9    9   10   14   15   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     A     162     A     162      9   17   32     9    9   10   14   15   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     I     163     I     163      9   17   32     9    9    9   14   14   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     E     164     E     164      3   17   32     3    3    4    4   15   16   18   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     P     165     P     165      3   17   32     3    3    6   11   14   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     N     166     N     166      3    5   32     3    3    6    9   13   16   19   22   23   26   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     D     167     D     167      4    5   32     3    4    6    9   13   16   19   22   23   26   27   29   30   31   33   34   36   37   37   39 
LCS_GDT     Y     168     Y     168      4    5   32     3    4    4    4    5    8    8   12   19   22   27   29   30   31   33   34   36   37   38   39 
LCS_GDT     T     169     T     169      4    5   32     3    4    4    4    5    6    7    8   18   22   25   29   30   31   32   34   36   37   37   39 
LCS_GDT     G     170     G     170      4    5   31     3    4    4    4    5    6    7    7    7    8    9   10   11   12   12   21   23   31   34   34 
LCS_GDT     K     171     K     171      3    5   30     3    3    3    4    4    6    7    7    7    8    8    9   11   12   12   18   27   30   31   34 
LCS_GDT     V     172     V     172      3    5   28     3    3    3    4    4    6    7    7    7    7    8    8   11   11   12   14   16   28   31   34 
LCS_AVERAGE  LCS_A:  10.72  (   5.95    8.21   17.99 )

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     14     18     18     19     19     19     20     22     23     26     27     29     30     31     33     34     36     37     38     39 
GDT PERCENT_CA   8.28  10.65  10.65  11.24  11.24  11.24  11.83  13.02  13.61  15.38  15.98  17.16  17.75  18.34  19.53  20.12  21.30  21.89  22.49  23.08
GDT RMS_LOCAL    0.31   0.44   0.44   0.79   0.79   0.79   1.34   2.70   2.37   3.61   3.73   3.95   4.18   4.15   4.76   4.88   5.30   5.41   5.66   5.77
GDT RMS_ALL_CA  11.33  11.20  11.20  11.18  11.18  11.18  10.94   9.67  10.33   8.66   8.61   8.66   8.60   9.56   8.61   8.72   8.26   8.25   8.49   8.29

#      Molecule1      Molecule2       DISTANCE
LGA    E      78      E      78         18.379
LGA    V      79      V      79         12.644
LGA    W      80      W      80         10.011
LGA    G      81      G      81          6.754
LGA    V      82      V      82          7.059
LGA    V      83      V      83          8.818
LGA    W      84      W      84          7.511
LGA    K      85      K      85         12.569
LGA    M      86      M      86         17.573
LGA    P     135      P     135         21.351
LGA    S     136      S     136         19.004
LGA    P     137      P     137         17.626
LGA    Q     138      Q     138         15.953
LGA    Y     139      Y     139         14.940
LGA    K     140      K     140         13.445
LGA    K     141      K     141         11.541
LGA    I     142      I     142          9.508
LGA    I     143      I     143          8.289
LGA    C     144      C     144          7.584
LGA    M     145      M     145          5.639
LGA    G     146      G     146          3.665
LGA    A     147      A     147          3.070
LGA    K     148      K     148          3.655
LGA    E     149      E     149          1.804
LGA    N     150      N     150          2.340
LGA    G     151      G     151          2.753
LGA    L     152      L     152          0.766
LGA    P     153      P     153          0.358
LGA    L     154      L     154          1.073
LGA    E     155      E     155          3.853
LGA    Y     156      Y     156          2.373
LGA    Q     157      Q     157          3.231
LGA    E     158      E     158          2.965
LGA    K     159      K     159          1.389
LGA    L     160      L     160          2.034
LGA    K     161      K     161          3.182
LGA    A     162      A     162          1.507
LGA    I     163      I     163          2.632
LGA    E     164      E     164          3.647
LGA    P     165      P     165          1.924
LGA    N     166      N     166          3.969
LGA    D     167      D     167          3.626
LGA    Y     168      Y     168          9.069
LGA    T     169      T     169          7.450
LGA    G     170      G     170         13.599
LGA    K     171      K     171         12.611
LGA    V     172      V     172         12.742

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   52  169    4.0     22    2.70    13.757    12.210     0.785

LGA_LOCAL      RMSD =  2.702  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.533  Number of atoms =   47 
Std_ALL_ATOMS  RMSD =  8.085  (standard rmsd on all 47 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.662025 * X  +   0.339884 * Y  +   0.667984 * Z  + -61.766483
  Y_new =   0.569184 * X  +   0.807838 * Y  +   0.153062 * Z  + -37.892193
  Z_new =  -0.487599 * X  +   0.481536 * Y  +  -0.728265 * Z  + -18.966156 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.557377   -0.584215  [ DEG:   146.5269    -33.4731 ]
  Theta =   0.509338    2.632255  [ DEG:    29.1829    150.8171 ]
  Phi   =   2.431458   -0.710134  [ DEG:   139.3123    -40.6877 ]
 
# 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: T0342TS464_4_2                                
REMARK     2: T0342.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0342TS464_4_2.T0342.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   52  169   4.0   22   2.70  12.210     8.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0342
PARENT N/A
ATOM      1  CA  ALA     2      22.345  80.472  19.995  1.00  0.00
ATOM      2  CA  ASN     3      21.456  76.936  21.089  1.00  0.00
ATOM      3  CA  SER     4      18.653  77.011  18.531  1.00  0.00
ATOM      4  CA  GLY     5      21.278  77.870  15.932  1.00  0.00
ATOM      5  CA  CYS     6      20.510  81.574  15.733  1.00  0.00
ATOM      6  CA  GLU    78       2.641  84.022  12.970  1.00  0.00
ATOM      7  CA  VAL    79       6.427  84.254  12.951  1.00  0.00
ATOM      8  CA  TRP    80       6.796  82.395   9.651  1.00  0.00
ATOM      9  CA  GLY    81       4.272  84.753   8.035  1.00  0.00
ATOM     10  CA  VAL    82       6.359  87.764   9.078  1.00  0.00
ATOM     11  CA  VAL    83       9.641  86.220   7.909  1.00  0.00
ATOM     12  CA  TRP    84       8.189  85.456   4.457  1.00  0.00
ATOM     13  CA  LYS    85       6.709  88.941   4.225  1.00  0.00
ATOM     14  CA  MET    86      10.130  90.501   4.845  1.00  0.00
ATOM     15  CA  PRO   135      10.430  79.834  30.809  1.00  0.00
ATOM     16  CA  SER   136      12.822  81.966  28.796  1.00  0.00
ATOM     17  CA  PRO   137      14.536  79.033  27.046  1.00  0.00
ATOM     18  CA  GLN   138      11.052  77.890  26.175  1.00  0.00
ATOM     19  CA  TYR   139      10.278  81.391  24.918  1.00  0.00
ATOM     20  CA  LYS   140      13.482  81.377  22.856  1.00  0.00
ATOM     21  CA  LYS   141      12.520  77.980  21.459  1.00  0.00
ATOM     22  CA  ILE   142       9.196  78.480  19.418  1.00  0.00
ATOM     23  CA  ILE   143      10.386  81.824  18.025  1.00  0.00
ATOM     24  CA  CYS   144      13.656  80.248  16.784  1.00  0.00
ATOM     25  CA  MET   145      11.099  77.770  15.485  1.00  0.00
ATOM     26  CA  GLY   146       9.208  80.569  13.705  1.00  0.00
ATOM     27  CA  ALA   147      12.430  81.982  12.237  1.00  0.00
ATOM     28  CA  LYS   148      13.131  78.570  10.729  1.00  0.00
ATOM     29  CA  GLU   149       9.585  77.856   9.576  1.00  0.00
ATOM     30  CA  ASN   150       9.413  81.055   7.538  1.00  0.00
ATOM     31  CA  GLY   151      13.108  81.259   6.680  1.00  0.00
ATOM     32  CA  LEU   152      13.921  84.503   8.454  1.00  0.00
ATOM     33  CA  PRO   153      17.431  85.262   9.745  1.00  0.00
ATOM     34  CA  LEU   154      17.977  83.922  13.270  1.00  0.00
ATOM     35  CA  GLU   155      16.539  86.437  15.710  1.00  0.00
ATOM     36  CA  TYR   156      14.036  88.292  13.500  1.00  0.00
ATOM     37  CA  GLN   157      10.992  87.322  15.632  1.00  0.00
ATOM     38  CA  GLU   158      12.960  88.258  18.751  1.00  0.00
ATOM     39  CA  LYS   159      13.640  91.778  17.465  1.00  0.00
ATOM     40  CA  LEU   160      10.050  92.251  16.292  1.00  0.00
ATOM     41  CA  LYS   161       8.500  90.806  19.489  1.00  0.00
ATOM     42  CA  ALA   162      10.784  92.970  21.670  1.00  0.00
ATOM     43  CA  ILE   163       9.703  96.171  19.902  1.00  0.00
ATOM     44  CA  GLU   164       6.028  95.743  19.171  1.00  0.00
ATOM     45  CA  PRO   165       4.729  93.404  21.832  1.00  0.00
ATOM     46  CA  ASN   166       3.661  96.047  24.318  1.00  0.00
ATOM     47  CA  ASP   167       1.762  93.752  26.774  1.00  0.00
ATOM     48  CA  TYR   168       4.272  90.877  26.685  1.00  0.00
ATOM     49  CA  THR   169       2.048  87.992  25.469  1.00  0.00
ATOM     50  CA  GLY   170       4.355  86.800  22.564  1.00  0.00
ATOM     51  CA  LYS   171       1.747  87.802  19.974  1.00  0.00
ATOM     52  CA  VAL   172       2.218  90.953  17.859  1.00  0.00
TER
END
