
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0349AL242_5
# Molecule2: number of CA atoms   75 ( 1131),  selected   32 , name T0349.pdb
# PARAMETERS: T0349AL242_5.T0349.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:    13        30 - 42          4.77    19.11
  LONGEST_CONTINUOUS_SEGMENT:    13        35 - 47          4.88    20.60
  LONGEST_CONTINUOUS_SEGMENT:    13        42 - 54          4.17    15.29
  LCS_AVERAGE:     17.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        46 - 53          1.51    16.16
  LCS_AVERAGE:      8.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        24 - 27          0.91    17.37
  LONGEST_CONTINUOUS_SEGMENT:     4        38 - 41          0.44    24.60
  LONGEST_CONTINUOUS_SEGMENT:     4        42 - 45          0.67    22.20
  LONGEST_CONTINUOUS_SEGMENT:     4        46 - 49          0.22    16.58
  LONGEST_CONTINUOUS_SEGMENT:     4        48 - 51          0.63    15.54
  LONGEST_CONTINUOUS_SEGMENT:     4        50 - 53          0.77    16.47
  LCS_AVERAGE:      4.83

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:   75
LCS_GDT     A      23     A      23      3    6   12     3    3    6    7    8   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     D      24     D      24      4    6   12     3    3    4    6    8   11   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     I      25     I      25      4    6   12     3    4    6    7    8   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     G      26     G      26      4    6   12     3    3    5    6    8   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     H      27     H      27      4    6   12     3    3    5    6    8   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     L      28     L      28      3    6   12     3    4    6    7    8   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     V      29     V      29      3    5   12     3    3    5    6    8    8   13   13   15   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     L      30     L      30      3    5   13     3    3    5    5    7    7    8   13   14   16   17   19   19   20   20   21   22   22   22   23 
LCS_GDT     D      31     D      31      3    5   13     3    3    5    5    7    7    8    8    9   11   12   14   18   20   20   21   22   22   22   23 
LCS_GDT     Q      32     Q      32      3    5   13     3    3    3    4    5    6    8    8    8   10   10   11   11   15   16   16   16   17   21   23 
LCS_GDT     N      33     N      33      3    5   13     3    3    3    4    5    6    7    8    8   10   10   11   11   13   16   16   16   17   19   19 
LCS_GDT     M      34     M      34      3    5   13     3    3    3    4    5    5    7    8    8    9    9   10   11   11   14   14   14   16   19   19 
LCS_GDT     S      35     S      35      3    5   13     3    3    3    4    4    5    8    8    8   10   10   12   13   14   15   16   16   17   19   19 
LCS_GDT     I      36     I      36      3    5   13     3    3    3    4    4    6    8    8    9   10   11   12   13   14   15   16   16   17   19   19 
LCS_GDT     L      37     L      37      3    6   13     3    3    4    4    5    7    8    8    9   10   11   11   12   13   15   16   16   17   19   19 
LCS_GDT     E      38     E      38      4    6   13     3    4    4    5    6    7    8    8    9   10   11   12   13   14   15   16   16   17   19   19 
LCS_GDT     G      39     G      39      4    6   13     3    4    4    5    6    7    8    8    9   10   11   12   13   14   15   16   16   17   19   19 
LCS_GDT     S      40     S      40      4    6   13     3    4    4    5    6    7    8    8    9   10   11   12   13   14   15   16   16   17   19   19 
LCS_GDT     L      41     L      41      4    6   13     3    4    4    5    6    7    8    8    9   10   11   11   13   14   15   16   16   17   19   19 
LCS_GDT     G      42     G      42      4    6   13     3    4    4    5    6    7    8    8    9   10   11   12   13   14   16   21   22   22   22   23 
LCS_GDT     V      43     V      43      4    5   13     3    4    4    4    4    5    6    8   11   11   12   12   13   14   20   21   22   22   22   23 
LCS_GDT     I      44     I      44      4    5   13     3    4    4    5    9    9   10   11   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     P      45     P      45      4    5   13     0    4    4    4    4    6   10   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     R      46     R      46      4    8   13     4    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     R      47     R      47      4    8   13     4    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     V      48     V      48      4    8   13     4    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     L      49     L      49      4    8   13     4    4    5    6    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     V      50     V      50      4    8   13     3    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     H      51     H      51      4    8   13     3    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     E      52     E      52      4    8   13     3    4    6    7    9    9   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     D      53     D      53      4    8   13     3    4    6    7    9   12   13   14   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_GDT     D      54     D      54      3    3   13     3    3    3    3    3    4    8   13   17   17   18   19   19   20   20   21   22   22   22   23 
LCS_AVERAGE  LCS_A:   9.99  (   4.83    8.08   17.04 )

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      4      6      7      9     12     13     14     17     17     18     19     19     20     20     21     22     22     22     23 
GDT PERCENT_CA   5.33   5.33   8.00   9.33  12.00  16.00  17.33  18.67  22.67  22.67  24.00  25.33  25.33  26.67  26.67  28.00  29.33  29.33  29.33  30.67
GDT RMS_LOCAL    0.22   0.22   1.07   1.27   1.74   2.24   2.37   2.56   3.24   3.24   3.43   3.70   3.70   4.21   4.18   4.62   5.00   5.00   5.00   5.79
GDT RMS_ALL_CA  16.58  16.58  14.45  14.47  15.96  14.71  14.69  14.63  14.29  14.29  14.18  13.90  13.90  13.60  13.84  13.55  13.39  13.39  13.39  13.04

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      A      23          2.845
LGA    D      24      D      24          3.921
LGA    I      25      I      25          2.001
LGA    G      26      G      26          2.731
LGA    H      27      H      27          2.877
LGA    L      28      L      28          1.205
LGA    V      29      V      29          4.425
LGA    L      30      L      30          7.076
LGA    D      31      D      31         10.188
LGA    Q      32      Q      32         16.334
LGA    N      33      N      33         21.747
LGA    M      34      M      34         27.293
LGA    S      35      S      35         27.134
LGA    I      36      I      36         28.259
LGA    L      37      L      37         29.329
LGA    E      38      E      38         29.598
LGA    G      39      G      39         23.171
LGA    S      40      S      40         19.338
LGA    L      41      L      41         17.084
LGA    G      42      G      42         12.618
LGA    V      43      V      43         11.984
LGA    I      44      I      44          8.186
LGA    P      45      P      45          6.392
LGA    R      46      R      46          1.087
LGA    R      47      R      47          2.835
LGA    V      48      V      48          1.137
LGA    L      49      L      49          3.403
LGA    V      50      V      50          0.584
LGA    H      51      H      51          3.162
LGA    E      52      E      52          3.394
LGA    D      53      D      53          2.784
LGA    D      54      D      54          5.718

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   75    4.0     14    2.56    15.333    14.688     0.525

LGA_LOCAL      RMSD =  2.564  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.439  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 11.286  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.479156 * X  +   0.179704 * Y  +   0.859137 * Z  +  -0.724721
  Y_new =  -0.247971 * X  +   0.966658 * Y  +  -0.063896 * Z  +   7.331098
  Z_new =  -0.841974 * X  +  -0.182424 * Y  +   0.507741 * Z  +  -1.589193 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.344923    2.796669  [ DEG:   -19.7627    160.2374 ]
  Theta =   1.000932    2.140661  [ DEG:    57.3492    122.6508 ]
  Phi   =  -0.477561    2.664031  [ DEG:   -27.3623    152.6377 ]
 
# 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: T0349AL242_5                                  
REMARK     2: T0349.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_5.T0349.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   75   4.0   14   2.56  14.688    11.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_5
REMARK Aligment from pdb entry: 1ews_A
ATOM      1  N   ALA    23      -6.015  14.066   7.126  1.00  0.00              
ATOM      2  CA  ALA    23      -4.678  13.478   6.839  1.00  0.00              
ATOM      3  C   ALA    23      -3.983  14.371   5.784  1.00  0.00              
ATOM      4  O   ALA    23      -4.572  14.626   4.749  1.00  0.00              
ATOM      5  N   ASP    24      -2.773  14.827   6.042  1.00  0.00              
ATOM      6  CA  ASP    24      -1.988  15.622   5.048  1.00  0.00              
ATOM      7  C   ASP    24      -1.707  14.757   3.809  1.00  0.00              
ATOM      8  O   ASP    24      -1.746  15.232   2.691  1.00  0.00              
ATOM      9  N   ILE    25      -1.432  13.505   4.075  1.00  0.00              
ATOM     10  CA  ILE    25      -1.136  12.516   2.993  1.00  0.00              
ATOM     11  C   ILE    25      -2.472  11.872   2.560  1.00  0.00              
ATOM     12  O   ILE    25      -3.524  12.351   2.940  1.00  0.00              
ATOM     13  N   GLY    26      -2.410  10.814   1.786  1.00  0.00              
ATOM     14  CA  GLY    26      -3.665  10.132   1.322  1.00  0.00              
ATOM     15  C   GLY    26      -3.386   8.752   0.707  1.00  0.00              
ATOM     16  O   GLY    26      -2.467   8.599  -0.075  1.00  0.00              
ATOM     17  N   HIS    27      -4.195   7.790   1.079  1.00  0.00              
ATOM     18  CA  HIS    27      -4.035   6.400   0.552  1.00  0.00              
ATOM     19  C   HIS    27      -4.829   6.194  -0.749  1.00  0.00              
ATOM     20  O   HIS    27      -6.036   6.340  -0.770  1.00  0.00              
ATOM     21  N   LEU    28      -4.111   5.860  -1.793  1.00  0.00              
ATOM     22  CA  LEU    28      -4.721   5.619  -3.142  1.00  0.00              
ATOM     23  C   LEU    28      -3.907   4.540  -3.880  1.00  0.00              
ATOM     24  O   LEU    28      -2.751   4.329  -3.573  1.00  0.00              
ATOM     25  N   VAL    29      -4.536   3.889  -4.831  1.00  0.00              
ATOM     26  CA  VAL    29      -3.834   2.822  -5.623  1.00  0.00              
ATOM     27  C   VAL    29      -2.741   3.509  -6.457  1.00  0.00              
ATOM     28  O   VAL    29      -1.672   2.974  -6.672  1.00  0.00              
ATOM     29  N   LEU    30      -3.087   4.692  -6.897  1.00  0.00              
ATOM     30  CA  LEU    30      -2.183   5.545  -7.727  1.00  0.00              
ATOM     31  C   LEU    30      -2.318   6.980  -7.205  1.00  0.00              
ATOM     32  O   LEU    30      -3.306   7.317  -6.580  1.00  0.00              
ATOM     33  N   ASP    31      -1.333   7.792  -7.479  1.00  0.00              
ATOM     34  CA  ASP    31      -1.361   9.205  -7.013  1.00  0.00              
ATOM     35  C   ASP    31      -2.040  10.158  -8.000  1.00  0.00              
ATOM     36  O   ASP    31      -2.488   9.774  -9.063  1.00  0.00              
ATOM     37  N   GLN    32      -2.079  11.394  -7.571  1.00  0.00              
ATOM     38  CA  GLN    32      -2.689  12.500  -8.363  1.00  0.00              
ATOM     39  C   GLN    32      -1.568  13.090  -9.245  1.00  0.00              
ATOM     40  O   GLN    32      -0.407  12.890  -8.945  1.00  0.00              
ATOM     41  N   ASN    33      -1.917  13.793 -10.299  1.00  0.00              
ATOM     42  CA  ASN    33      -0.919  14.536 -11.128  1.00  0.00              
ATOM     43  C   ASN    33      -0.045  15.480 -10.278  1.00  0.00              
ATOM     44  O   ASN    33       1.069  15.784 -10.653  1.00  0.00              
ATOM     45  N   MET    34      -0.587  15.908  -9.162  1.00  0.00              
ATOM     46  CA  MET    34       0.148  16.832  -8.240  1.00  0.00              
ATOM     47  C   MET    34       0.680  16.122  -6.980  1.00  0.00              
ATOM     48  O   MET    34       1.404  16.723  -6.211  1.00  0.00              
ATOM     49  N   SER    35       0.309  14.876  -6.808  1.00  0.00              
ATOM     50  CA  SER    35       0.765  14.093  -5.614  1.00  0.00              
ATOM     51  C   SER    35       1.725  12.956  -6.030  1.00  0.00              
ATOM     52  O   SER    35       1.705  12.526  -7.166  1.00  0.00              
ATOM     53  N   ILE    36       2.537  12.509  -5.096  1.00  0.00              
ATOM     54  CA  ILE    36       3.524  11.406  -5.372  1.00  0.00              
ATOM     55  C   ILE    36       3.540  10.374  -4.226  1.00  0.00              
ATOM     56  O   ILE    36       3.284  10.712  -3.086  1.00  0.00              
ATOM     57  N   LEU    37       3.845   9.145  -4.575  1.00  0.00              
ATOM     58  CA  LEU    37       3.904   8.028  -3.581  1.00  0.00              
ATOM     59  C   LEU    37       4.835   8.339  -2.400  1.00  0.00              
ATOM     60  O   LEU    37       5.738   9.145  -2.509  1.00  0.00              
ATOM     61  N   GLU    38       4.570   7.673  -1.304  1.00  0.00              
ATOM     62  CA  GLU    38       5.384   7.863  -0.064  1.00  0.00              
ATOM     63  C   GLU    38       5.424   6.576   0.785  1.00  0.00              
ATOM     64  O   GLU    38       6.280   6.440   1.638  1.00  0.00              
ATOM     65  N   GLY    39       4.503   5.674   0.539  1.00  0.00              
ATOM     66  CA  GLY    39       4.469   4.395   1.318  1.00  0.00              
ATOM     67  C   GLY    39       3.514   3.364   0.701  1.00  0.00              
ATOM     68  O   GLY    39       3.222   3.416  -0.479  1.00  0.00              
ATOM     69  N   SER    40       3.059   2.456   1.534  1.00  0.00              
ATOM     70  CA  SER    40       2.118   1.379   1.087  1.00  0.00              
ATOM     71  C   SER    40       1.003   1.140   2.118  1.00  0.00              
ATOM     72  O   SER    40       1.244   0.610   3.184  1.00  0.00              
ATOM     73  N   LEU    41      -0.188   1.550   1.752  1.00  0.00              
ATOM     74  CA  LEU    41      -1.385   1.393   2.640  1.00  0.00              
ATOM     75  C   LEU    41      -2.206   0.153   2.261  1.00  0.00              
ATOM     76  O   LEU    41      -1.844  -0.587   1.366  1.00  0.00              
ATOM     77  N   GLY    42      -3.295  -0.024   2.966  1.00  0.00              
ATOM     78  CA  GLY    42      -4.202  -1.185   2.721  1.00  0.00              
ATOM     79  C   GLY    42      -3.854  -2.329   3.673  1.00  0.00              
ATOM     80  O   GLY    42      -3.234  -2.118   4.699  1.00  0.00              
ATOM     81  N   VAL    43      -4.266  -3.512   3.297  1.00  0.00              
ATOM     82  CA  VAL    43      -3.998  -4.722   4.126  1.00  0.00              
ATOM     83  C   VAL    43      -2.663  -5.352   3.715  1.00  0.00              
ATOM     84  O   VAL    43      -1.712  -5.311   4.472  1.00  0.00              
ATOM     85  N   ILE    44      -2.624  -5.909   2.534  1.00  0.00              
ATOM     86  CA  ILE    44      -1.374  -6.553   2.019  1.00  0.00              
ATOM     87  C   ILE    44      -0.547  -5.502   1.250  1.00  0.00              
ATOM     88  O   ILE    44       0.078  -5.811   0.252  1.00  0.00              
ATOM     89  N   PRO    45      -0.576  -4.285   1.747  1.00  0.00              
ATOM     90  CA  PRO    45       0.170  -3.142   1.121  1.00  0.00              
ATOM     91  C   PRO    45      -0.240  -2.926  -0.351  1.00  0.00              
ATOM     92  O   PRO    45       0.479  -2.313  -1.120  1.00  0.00              
ATOM     93  N   ARG    46      -1.397  -3.441  -0.684  1.00  0.00              
ATOM     94  CA  ARG    46      -1.948  -3.326  -2.070  1.00  0.00              
ATOM     95  C   ARG    46      -2.112  -1.855  -2.486  1.00  0.00              
ATOM     96  O   ARG    46      -1.858  -1.500  -3.619  1.00  0.00              
ATOM     97  N   ARG    47      -2.533  -1.055  -1.541  1.00  0.00              
ATOM     98  CA  ARG    47      -2.737   0.403  -1.802  1.00  0.00              
ATOM     99  C   ARG    47      -1.416   1.131  -1.501  1.00  0.00              
ATOM    100  O   ARG    47      -0.511   0.553  -0.927  1.00  0.00              
ATOM    101  N   VAL    48      -1.351   2.378  -1.897  1.00  0.00              
ATOM    102  CA  VAL    48      -0.119   3.203  -1.671  1.00  0.00              
ATOM    103  C   VAL    48      -0.389   4.462  -0.856  1.00  0.00              
ATOM    104  O   VAL    48      -1.405   5.105  -1.032  1.00  0.00              
ATOM    105  N   LEU    49       0.542   4.777   0.010  1.00  0.00              
ATOM    106  CA  LEU    49       0.412   5.988   0.874  1.00  0.00              
ATOM    107  C   LEU    49       1.031   7.103   0.046  1.00  0.00              
ATOM    108  O   LEU    49       2.223   7.330   0.076  1.00  0.00              
ATOM    109  N   VAL    50       0.171   7.761  -0.678  1.00  0.00              
ATOM    110  CA  VAL    50       0.632   8.879  -1.543  1.00  0.00              
ATOM    111  C   VAL    50       0.483  10.227  -0.830  1.00  0.00              
ATOM    112  O   VAL    50      -0.607  10.603  -0.444  1.00  0.00              
ATOM    113  N   HIS    51       1.592  10.909  -0.679  1.00  0.00              
ATOM    114  CA  HIS    51       1.596  12.243   0.001  1.00  0.00              
ATOM    115  C   HIS    51       1.900  13.375  -0.991  1.00  0.00              
ATOM    116  O   HIS    51       2.560  13.170  -1.993  1.00  0.00              
ATOM    117  N   GLU    52       1.400  14.541  -0.660  1.00  0.00              
ATOM    118  CA  GLU    52       1.590  15.768  -1.505  1.00  0.00              
ATOM    119  C   GLU    52       3.052  16.055  -1.891  1.00  0.00              
ATOM    120  O   GLU    52       3.970  15.727  -1.164  1.00  0.00              
ATOM    121  N   ASP    53       3.201  16.666  -3.039  1.00  0.00              
ATOM    122  CA  ASP    53       4.554  17.025  -3.562  1.00  0.00              
ATOM    123  C   ASP    53       4.933  18.410  -3.013  1.00  0.00              
ATOM    124  O   ASP    53       4.722  19.421  -3.655  1.00  0.00              
ATOM    125  N   ASP    54       5.483  18.398  -1.823  1.00  0.00              
ATOM    126  CA  ASP    54       5.908  19.667  -1.146  1.00  0.00              
ATOM    127  C   ASP    54       7.404  19.617  -0.780  1.00  0.00              
ATOM    128  O   ASP    54       7.905  18.512  -0.628  1.00  0.00              
END
