
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0342AL333_4-D1
# Molecule2: number of CA atoms  122 (  967),  selected   27 , name T0342_D1.pdb
# PARAMETERS: T0342AL333_4-D1.T0342_D1.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:    14       102 - 115         4.73    16.06
  LONGEST_CONTINUOUS_SEGMENT:    14       107 - 120         4.54    15.41
  LCS_AVERAGE:     11.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       104 - 113         1.98    16.84
  LCS_AVERAGE:      5.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       108 - 114         0.82    15.52
  LCS_AVERAGE:      3.58

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:  122
LCS_GDT     G      81     G      81      3    3   11     3    3    3    3    4    4    5    6    8    9    9    9   10   11   13   13   13   13   13   13 
LCS_GDT     V      82     V      82      3    3   11     3    3    3    3    3    3    4    6    8    9    9    9   10   11   13   13   13   13   13   13 
LCS_GDT     V      83     V      83      3    3   11     3    3    3    3    3    3    3    3    3    3    3    3    7    8   13   13   13   13   13   13 
LCS_GDT     Q      97     Q      97      3    6   13     2    3    3    5    5    6    6    8    8    9    9   10   12   13   15   15   17   18   19   19 
LCS_GDT     E      98     E      98      3    6   13     2    3    3    5    5    6    6    8    8    9    9   11   13   15   15   16   18   19   20   21 
LCS_GDT     G      99     G      99      3    6   13     1    3    3    4    4    6    6    8    8    9   10   11   13   15   16   18   19   20   20   21 
LCS_GDT     V     100     V     100      3    6   13     2    3    3    5    5    6    6    8    8    9    9   10   12   12   16   18   19   20   20   21 
LCS_GDT     K     101     K     101      3    6   13     3    3    3    5    5    7    7    8    8    9   10   10   12   13   16   18   19   20   20   21 
LCS_GDT     S     102     S     102      4    6   14     3    3    4    5    5    7    7    8    8   10   11   12   12   13   16   18   19   20   20   21 
LCS_GDT     G     103     G     103      4    6   14     3    3    4    4    5    7    7    8    9   10   11   12   12   13   15   17   19   20   20   21 
LCS_GDT     M     104     M     104      4   10   14     4    5    6    7    8    9   10   10   11   11   12   12   12   14   15   17   18   20   20   21 
LCS_GDT     Y     105     Y     105      4   10   14     4    5    6    7    8    9   10   10   11   11   12   12   12   14   16   18   19   20   20   21 
LCS_GDT     V     106     V     106      4   10   14     4    5    6    7    8    9   10   10   11   11   12   12   13   15   16   18   19   20   20   21 
LCS_GDT     V     107     V     107      4   10   14     4    5    6    7    8    9   10   10   11   11   12   12   13   15   16   18   19   20   20   21 
LCS_GDT     I     108     I     108      7   10   14     4    6    7    7    7    9   10   10   11   12   12   13   13   15   15   18   19   20   20   21 
LCS_GDT     E     109     E     109      7   10   14     4    6    7    7    8    9   10   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     V     110     V     110      7   10   14     4    6    7    7    8    9   10   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     K     111     K     111      7   10   14     4    6    7    7    8    9   10   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     V     112     V     112      7   10   14     3    6    7    7    8    9   10   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     A     113     A     113      7   10   14     4    6    7    7    8    9   10   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     T     114     T     114      7    8   14     4    5    7    7    7    8    8   10   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     Q     115     Q     115      4    6   14     4    4    4    5    6    6    8    9   10   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     E     116     E     116      4    6   14     4    4    4    5    6    6    8    9   11   12   12   13   13   14   15   15   17   18   19   20 
LCS_GDT     G     117     G     117      4    6   14     4    4    4    5    6    6    8    9    9   10   11   13   13   13   15   15   17   18   19   19 
LCS_GDT     K     118     K     118      3    4   14     3    3    3    3    5    6    8    9   11   12   12   13   13   15   15   18   19   20   20   21 
LCS_GDT     E     119     E     119      3    4   14     3    3    3    4    4    5    8    8   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_GDT     I     120     I     120      3    3   14     0    3    3    4    4    5    6    8   11   12   12   13   13   15   16   18   19   20   20   21 
LCS_AVERAGE  LCS_A:   6.78  (   3.58    5.71   11.05 )

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      4      6      7      7      8      9     10     10     11     12     12     13     13     15     16     18     19     20     20     21 
GDT PERCENT_CA   3.28   4.92   5.74   5.74   6.56   7.38   8.20   8.20   9.02   9.84   9.84  10.66  10.66  12.30  13.11  14.75  15.57  16.39  16.39  17.21
GDT RMS_LOCAL    0.27   0.60   0.82   0.82   1.40   1.74   1.98   1.98   2.53   3.51   3.51   3.86   3.86   5.27   6.11   6.30   6.53   6.69   6.69   6.96
GDT RMS_ALL_CA  18.04  15.71  15.52  15.52  17.03  17.13  16.84  16.84  16.40  17.46  17.46  18.00  18.00  13.35  14.21  14.07  14.27  14.34  14.34  14.00

#      Molecule1      Molecule2       DISTANCE
LGA    G      81      G      81         40.002
LGA    V      82      V      82         38.682
LGA    V      83      V      83         35.699
LGA    Q      97      Q      97         25.136
LGA    E      98      E      98         18.915
LGA    G      99      G      99         17.730
LGA    V     100      V     100         17.527
LGA    K     101      K     101         17.564
LGA    S     102      S     102         12.011
LGA    G     103      G     103          8.896
LGA    M     104      M     104          1.753
LGA    Y     105      Y     105          1.023
LGA    V     106      V     106          1.317
LGA    V     107      V     107          0.827
LGA    I     108      I     108          3.378
LGA    E     109      E     109          1.996
LGA    V     110      V     110          1.777
LGA    K     111      K     111          0.637
LGA    V     112      V     112          2.122
LGA    A     113      A     113          3.041
LGA    T     114      T     114          6.281
LGA    Q     115      Q     115          9.103
LGA    E     116      E     116         15.467
LGA    G     117      G     117         15.546
LGA    K     118      K     118         12.396
LGA    E     119      E     119         13.565
LGA    I     120      I     120         12.855

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  122    4.0     10    1.98     8.402     7.675     0.481

LGA_LOCAL      RMSD =  1.981  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.843  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 12.624  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.926917 * X  +  -0.157631 * Y  +  -0.340553 * Z  +  -7.512359
  Y_new =  -0.330802 * X  +   0.085260 * Y  +  -0.939841 * Z  + 132.537323
  Z_new =   0.177184 * X  +   0.983810 * Y  +   0.026885 * Z  + -52.030045 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.543476   -1.598117  [ DEG:    88.4347    -91.5653 ]
  Theta =  -0.178124   -2.963468  [ DEG:   -10.2058   -169.7942 ]
  Phi   =  -0.342794    2.798798  [ DEG:   -19.6407    160.3593 ]
 
# 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: T0342AL333_4-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0342AL333_4-D1.T0342_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  122   4.0   10   1.98   7.675    12.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0342AL333_4-D1
REMARK Aligment from pdb entry: 1xgs_A
ATOM      1  N   GLY    81     -15.822 118.032  11.562  1.00  0.00              
ATOM      2  CA  GLY    81     -15.979 117.747  10.153  1.00  0.00              
ATOM      3  C   GLY    81     -14.697 117.285   9.493  1.00  0.00              
ATOM      4  O   GLY    81     -14.491 117.492   8.306  1.00  0.00              
ATOM      5  N   VAL    82     -13.823 116.645  10.252  1.00  0.00              
ATOM      6  CA  VAL    82     -12.591 116.159   9.666  1.00  0.00              
ATOM      7  C   VAL    82     -12.116 114.887  10.370  1.00  0.00              
ATOM      8  O   VAL    82     -12.277 114.762  11.573  1.00  0.00              
ATOM      9  N   VAL    83     -11.596 113.928   9.615  1.00  0.00              
ATOM     10  CA  VAL    83     -11.090 112.686  10.199  1.00  0.00              
ATOM     11  C   VAL    83      -9.560 112.632  10.164  1.00  0.00              
ATOM     12  O   VAL    83      -8.908 113.193   9.273  1.00  0.00              
ATOM     13  N   GLN    97      -8.994 111.997  11.179  1.00  0.00              
ATOM     14  CA  GLN    97      -7.562 111.848  11.282  1.00  0.00              
ATOM     15  C   GLN    97      -7.294 110.360  11.375  1.00  0.00              
ATOM     16  O   GLN    97      -8.172 109.588  11.772  1.00  0.00              
ATOM     17  N   GLU    98      -6.096 109.972  10.967  1.00  0.00              
ATOM     18  CA  GLU    98      -5.658 108.595  11.017  1.00  0.00              
ATOM     19  C   GLU    98      -5.136 108.269  12.412  1.00  0.00              
ATOM     20  O   GLU    98      -4.398 109.050  13.006  1.00  0.00              
ATOM     21  N   GLY    99      -5.562 107.128  12.945  1.00  0.00              
ATOM     22  CA  GLY    99      -5.148 106.673  14.267  1.00  0.00              
ATOM     23  C   GLY    99      -4.871 105.164  14.183  1.00  0.00              
ATOM     24  O   GLY    99      -5.343 104.488  13.276  1.00  0.00              
ATOM     25  N   VAL   100      -3.988 104.650  15.043  1.00  0.00              
ATOM     26  CA  VAL   100      -3.694 103.210  15.016  1.00  0.00              
ATOM     27  C   VAL   100      -4.922 102.476  15.582  1.00  0.00              
ATOM     28  O   VAL   100      -5.671 103.047  16.391  1.00  0.00              
ATOM     29  N   LYS   101      -5.097 101.179  15.258  1.00  0.00              
ATOM     30  CA  LYS   101      -4.285 100.293  14.421  1.00  0.00              
ATOM     31  C   LYS   101      -4.577 100.357  12.934  1.00  0.00              
ATOM     32  O   LYS   101      -5.543 100.972  12.509  1.00  0.00              
ATOM     33  N   SER   102      -3.722  99.709  12.159  1.00  0.00              
ATOM     34  CA  SER   102      -3.899  99.600  10.720  1.00  0.00              
ATOM     35  C   SER   102      -4.462  98.191  10.607  1.00  0.00              
ATOM     36  O   SER   102      -3.788  97.235  10.974  1.00  0.00              
ATOM     37  N   GLY   103      -5.722  98.060  10.211  1.00  0.00              
ATOM     38  CA  GLY   103      -6.343  96.744  10.108  1.00  0.00              
ATOM     39  C   GLY   103      -6.679  96.340   8.690  1.00  0.00              
ATOM     40  O   GLY   103      -7.237  95.271   8.479  1.00  0.00              
ATOM     41  N   MET   104      -6.391  97.230   7.742  1.00  0.00              
ATOM     42  CA  MET   104      -6.673  97.049   6.322  1.00  0.00              
ATOM     43  C   MET   104      -5.459  97.482   5.518  1.00  0.00              
ATOM     44  O   MET   104      -4.847  98.494   5.822  1.00  0.00              
ATOM     45  N   TYR   105      -5.145  96.735   4.464  1.00  0.00              
ATOM     46  CA  TYR   105      -4.004  97.033   3.607  1.00  0.00              
ATOM     47  C   TYR   105      -4.424  96.832   2.176  1.00  0.00              
ATOM     48  O   TYR   105      -5.478  96.271   1.887  1.00  0.00              
ATOM     49  N   VAL   106      -3.553  97.228   1.268  1.00  0.00              
ATOM     50  CA  VAL   106      -3.851  97.064  -0.124  1.00  0.00              
ATOM     51  C   VAL   106      -2.578  96.961  -0.911  1.00  0.00              
ATOM     52  O   VAL   106      -1.631  97.711  -0.684  1.00  0.00              
ATOM     53  N   VAL   107      -2.558  95.991  -1.807  1.00  0.00              
ATOM     54  CA  VAL   107      -1.423  95.756  -2.683  1.00  0.00              
ATOM     55  C   VAL   107      -1.372  96.908  -3.684  1.00  0.00              
ATOM     56  O   VAL   107      -2.360  97.186  -4.372  1.00  0.00              
ATOM     57  N   ILE   108       2.001  97.796  -5.621  1.00  0.00              
ATOM     58  CA  ILE   108       3.006  97.729  -6.667  1.00  0.00              
ATOM     59  C   ILE   108       3.820  96.452  -6.634  1.00  0.00              
ATOM     60  O   ILE   108       4.118  95.923  -5.562  1.00  0.00              
ATOM     61  N   GLU   109       4.220  95.988  -7.817  1.00  0.00              
ATOM     62  CA  GLU   109       5.025  94.778  -7.930  1.00  0.00              
ATOM     63  C   GLU   109       6.505  95.119  -7.685  1.00  0.00              
ATOM     64  O   GLU   109       7.186  95.647  -8.568  1.00  0.00              
ATOM     65  N   VAL   110       6.974  94.848  -6.468  1.00  0.00              
ATOM     66  CA  VAL   110       8.356  95.116  -6.054  1.00  0.00              
ATOM     67  C   VAL   110       9.080  93.840  -5.596  1.00  0.00              
ATOM     68  O   VAL   110       8.455  92.913  -5.073  1.00  0.00              
ATOM     69  N   LYS   111      10.400  93.760  -5.818  1.00  0.00              
ATOM     70  CA  LYS   111      11.158  92.578  -5.397  1.00  0.00              
ATOM     71  C   LYS   111      11.278  92.576  -3.878  1.00  0.00              
ATOM     72  O   LYS   111      11.675  93.587  -3.276  1.00  0.00              
ATOM     73  N   VAL   112      10.863  91.477  -3.254  1.00  0.00              
ATOM     74  CA  VAL   112      10.931  91.362  -1.801  1.00  0.00              
ATOM     75  C   VAL   112      12.087  90.435  -1.548  1.00  0.00              
ATOM     76  O   VAL   112      12.157  89.361  -2.138  1.00  0.00              
ATOM     77  N   ALA   113      13.008  90.874  -0.698  1.00  0.00              
ATOM     78  CA  ALA   113      14.200  90.100  -0.377  1.00  0.00              
ATOM     79  C   ALA   113      13.900  88.916   0.556  1.00  0.00              
ATOM     80  O   ALA   113      14.492  87.856   0.419  1.00  0.00              
ATOM     81  N   THR   114      12.996  89.117   1.512  1.00  0.00              
ATOM     82  CA  THR   114      12.613  88.095   2.492  1.00  0.00              
ATOM     83  C   THR   114      11.633  87.048   1.913  1.00  0.00              
ATOM     84  O   THR   114      10.664  87.389   1.238  1.00  0.00              
ATOM     85  N   GLN   115      11.823  85.783   2.266  1.00  0.00              
ATOM     86  CA  GLN   115      10.975  84.699   1.750  1.00  0.00              
ATOM     87  C   GLN   115       9.535  84.591   2.242  1.00  0.00              
ATOM     88  O   GLN   115       8.647  84.314   1.440  1.00  0.00              
ATOM     89  N   GLU   116       9.290  84.730   3.543  1.00  0.00              
ATOM     90  CA  GLU   116       7.912  84.646   4.019  1.00  0.00              
ATOM     91  C   GLU   116       7.115  85.870   3.548  1.00  0.00              
ATOM     92  O   GLU   116       5.916  85.773   3.290  1.00  0.00              
ATOM     93  N   GLY   117       7.791  87.015   3.449  1.00  0.00              
ATOM     94  CA  GLY   117       7.170  88.244   2.969  1.00  0.00              
ATOM     95  C   GLY   117       6.834  88.025   1.495  1.00  0.00              
ATOM     96  O   GLY   117       5.736  88.332   1.038  1.00  0.00              
ATOM     97  N   LYS   118       7.768  87.442   0.760  1.00  0.00              
ATOM     98  CA  LYS   118       7.563  87.156  -0.650  1.00  0.00              
ATOM     99  C   LYS   118       6.413  86.154  -0.911  1.00  0.00              
ATOM    100  O   LYS   118       5.677  86.300  -1.891  1.00  0.00              
ATOM    101  N   GLU   119       6.283  85.126  -0.067  1.00  0.00              
ATOM    102  CA  GLU   119       5.203  84.145  -0.210  1.00  0.00              
ATOM    103  C   GLU   119       3.912  84.818   0.201  1.00  0.00              
ATOM    104  O   GLU   119       2.843  84.507  -0.315  1.00  0.00              
ATOM    105  N   ILE   120       4.010  85.702   1.187  1.00  0.00              
ATOM    106  CA  ILE   120       2.848  86.437   1.670  1.00  0.00              
ATOM    107  C   ILE   120       2.302  87.337   0.556  1.00  0.00              
ATOM    108  O   ILE   120       1.112  87.326   0.266  1.00  0.00              
END
