
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0363AL333_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   35 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_1-D1.T0363_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:    32        14 - 56          4.85     5.32
  LCS_AVERAGE:     66.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        24 - 45          1.99     5.81
  LCS_AVERAGE:     36.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          0.76     6.12
  LCS_AVERAGE:     16.21

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:   46
LCS_GDT     N      11     N      11      5    8    9     3    4    6    7    7    8    8    8   12   16   19   24   28   28   31   32   34   35   35   35 
LCS_GDT     Q      12     Q      12      5    8    9     4    5    6    7    7    8    8    8   12   16   19   25   28   28   31   32   34   35   35   35 
LCS_GDT     I      13     I      13      5    8   31     4    5    6    7    7    8    8    8    8   16   19   22   23   23   30   32   34   35   35   35 
LCS_GDT     N      14     N      14      5    8   32     4    5    6    7    7    8    8    8   12   16   19   22   23   27   31   32   34   35   35   35 
LCS_GDT     I      15     I      15      5    8   32     4    5    6    7    7    8    9    9   13   16   19   22   23   23   28   32   34   35   35   35 
LCS_GDT     E      16     E      16      5    8   32     4    5    6    7    9   10   11   13   13   16   19   22   24   28   31   32   34   35   35   35 
LCS_GDT     I      17     I      17      5    8   32     3    4    5    7    7    8    8   10   12   14   19   22   23   28   31   32   34   35   35   35 
LCS_GDT     A      18     A      18      4    8   32     3    4    5    5    6    8    8   13   16   23   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     E      23     E      23      4    7   32     3    3    4    4    6    7    7    7   12   13   14   24   26   27   28   31   34   35   35   35 
LCS_GDT     R      24     R      24      4   22   32     3    3    5    6   16   19   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     Y      25     Y      25      8   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     Y      26     Y      26      8   22   32     4    7   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     L      27     L      27      8   22   32     4    7   11   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     K      28     K      28      8   22   32     4    7    9   15   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     S      29     S      29      8   22   32     3    7    9   15   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     F      30     F      30      8   22   32     3    7   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     Q      31     Q      31      8   22   32     3    8   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     V      32     V      32      8   22   32     3    7   13   15   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     D      33     D      33      8   22   32     3    7   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     E      34     E      34     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     G      35     G      35     11   22   32     3   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     I      36     I      36     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     T      37     T      37     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     V      38     V      38     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     Q      39     Q      39     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     T      40     T      40     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     A      41     A      41     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     I      42     I      42     11   22   32     6   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     T      43     T      43     11   22   32     4   10   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     Q      44     Q      44     11   22   32     3   11   13   16   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     S      45     S      45      9   22   32     3    5    8    9   12   16   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     G      46     G      46      6   17   32     3    4    7    9   10   15   17   20   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     I      47     I      47      6   12   32     3    4    6    8   10   11   13   14   20   25   25   26   28   28   31   32   34   35   35   35 
LCS_GDT     D      55     D      55      0    0   32     0    0    0    0    0    2    8   10   15   17   19   24   26   27   28   31   34   35   35   35 
LCS_GDT     L      56     L      56      0    0   32     0    0    0    6   21   21   22   23   24   25   25   26   28   28   31   32   34   35   35   35 
LCS_AVERAGE  LCS_A:  39.71  (  16.21   36.27   66.65 )

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      6     11     13     16     21     21     22     23     24     25     25     26     28     28     31     32     34     35     35     35 
GDT PERCENT_CA  13.04  23.91  28.26  34.78  45.65  45.65  47.83  50.00  52.17  54.35  54.35  56.52  60.87  60.87  67.39  69.57  73.91  76.09  76.09  76.09
GDT RMS_LOCAL    0.32   0.70   0.84   1.19   1.58   1.58   1.84   2.04   2.34   2.65   2.65   2.99   3.74   3.74   4.55   4.77   5.10   5.25   5.25   5.25
GDT RMS_ALL_CA   5.90   6.05   6.07   5.97   6.06   6.06   5.95   5.86   5.78   5.72   5.72   5.60   5.41   5.41   5.28   5.28   5.28   5.25   5.25   5.25

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          9.365
LGA    Q      12      Q      12          9.714
LGA    I      13      I      13         11.367
LGA    N      14      N      14         11.032
LGA    I      15      I      15         11.763
LGA    E      16      E      16         10.817
LGA    I      17      I      17         10.710
LGA    A      18      A      18          7.881
LGA    E      23      E      23          7.394
LGA    R      24      R      24          3.640
LGA    Y      25      Y      25          1.303
LGA    Y      26      Y      26          2.086
LGA    L      27      L      27          2.534
LGA    K      28      K      28          2.903
LGA    S      29      S      29          2.616
LGA    F      30      F      30          1.876
LGA    Q      31      Q      31          1.841
LGA    V      32      V      32          3.047
LGA    D      33      D      33          2.179
LGA    E      34      E      34          1.643
LGA    G      35      G      35          1.971
LGA    I      36      I      36          1.348
LGA    T      37      T      37          0.323
LGA    V      38      V      38          0.601
LGA    Q      39      Q      39          0.353
LGA    T      40      T      40          0.586
LGA    A      41      A      41          0.733
LGA    I      42      I      42          0.909
LGA    T      43      T      43          1.151
LGA    Q      44      Q      44          1.173
LGA    S      45      S      45          3.875
LGA    G      46      G      46          5.450
LGA    I      47      I      47          6.765
LGA    D      55      D      55          7.590
LGA    L      56      L      56          3.438

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   46    4.0     23    2.04    44.565    43.841     1.076

LGA_LOCAL      RMSD =  2.037  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.745  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  5.254  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.614495 * X  +   0.018366 * Y  +  -0.788707 * Z  +  22.497835
  Y_new =   0.776024 * X  +   0.194098 * Y  +  -0.600094 * Z  +   5.390275
  Z_new =   0.142065 * X  +  -0.980810 * Y  +  -0.133524 * Z  +   3.823166 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.706101    1.435491  [ DEG:   -97.7524     82.2476 ]
  Theta =  -0.142547   -2.999046  [ DEG:    -8.1673   -171.8327 ]
  Phi   =   2.240548   -0.901045  [ DEG:   128.3739    -51.6261 ]
 
# 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: T0363AL333_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   46   4.0   23   2.04  43.841     5.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_1-D1
REMARK Aligment from pdb entry: 1rws_A
ATOM      1  N   ASN    11      22.364   3.534   6.507  1.00  0.00              
ATOM      2  CA  ASN    11      22.634   5.000   6.519  1.00  0.00              
ATOM      3  C   ASN    11      23.809   5.318   5.604  1.00  0.00              
ATOM      4  O   ASN    11      24.920   4.855   5.779  1.00  0.00              
ATOM      5  N   GLN    12      23.528   6.103   4.613  1.00  0.00              
ATOM      6  CA  GLN    12      24.563   6.488   3.619  1.00  0.00              
ATOM      7  C   GLN    12      24.821   7.989   3.736  1.00  0.00              
ATOM      8  O   GLN    12      24.048   8.728   4.311  1.00  0.00              
ATOM      9  N   ILE    13      25.963   8.411   3.285  1.00  0.00              
ATOM     10  CA  ILE    13      26.365   9.836   3.460  1.00  0.00              
ATOM     11  C   ILE    13      26.450  10.551   2.112  1.00  0.00              
ATOM     12  O   ILE    13      26.497   9.947   1.058  1.00  0.00              
ATOM     13  N   ASN    14      26.492  11.859   2.169  1.00  0.00              
ATOM     14  CA  ASN    14      26.599  12.722   0.955  1.00  0.00              
ATOM     15  C   ASN    14      27.598  13.802   1.304  1.00  0.00              
ATOM     16  O   ASN    14      27.730  14.199   2.438  1.00  0.00              
ATOM     17  N   ILE    15      28.398  14.162   0.352  1.00  0.00              
ATOM     18  CA  ILE    15      29.517  15.112   0.617  1.00  0.00              
ATOM     19  C   ILE    15      29.534  16.238  -0.424  1.00  0.00              
ATOM     20  O   ILE    15      29.397  16.005  -1.607  1.00  0.00              
ATOM     21  N   GLU    16      29.746  17.458   0.009  1.00  0.00              
ATOM     22  CA  GLU    16      29.825  18.604  -0.944  1.00  0.00              
ATOM     23  C   GLU    16      30.892  19.588  -0.463  1.00  0.00              
ATOM     24  O   GLU    16      31.287  19.575   0.682  1.00  0.00              
ATOM     25  N   ILE    17      31.454  20.368  -1.350  1.00  0.00              
ATOM     26  CA  ILE    17      32.551  21.302  -0.978  1.00  0.00              
ATOM     27  C   ILE    17      31.982  22.630  -0.545  1.00  0.00              
ATOM     28  O   ILE    17      30.911  22.998  -0.982  1.00  0.00              
ATOM     29  N   ALA    18      32.450  23.056   0.598  1.00  0.00              
ATOM     30  CA  ALA    18      31.585  24.044   1.331  1.00  0.00              
ATOM     31  C   ALA    18      30.632  24.669   0.300  1.00  0.00              
ATOM     32  O   ALA    18      31.091  25.160  -0.713  1.00  0.00              
ATOM     33  N   GLU    23      29.340  24.779   0.555  1.00  0.00              
ATOM     34  CA  GLU    23      28.499  25.498  -0.445  1.00  0.00              
ATOM     35  C   GLU    23      28.989  25.179  -1.857  1.00  0.00              
ATOM     36  O   GLU    23      29.230  26.055  -2.664  1.00  0.00              
ATOM     37  N   ARG    24      29.101  23.920  -2.161  1.00  0.00              
ATOM     38  CA  ARG    24      29.535  23.497  -3.523  1.00  0.00              
ATOM     39  C   ARG    24      28.338  23.010  -4.338  1.00  0.00              
ATOM     40  O   ARG    24      28.408  22.914  -5.548  1.00  0.00              
ATOM     41  N   TYR    25      27.217  22.768  -3.712  1.00  0.00              
ATOM     42  CA  TYR    25      25.982  22.372  -4.428  1.00  0.00              
ATOM     43  C   TYR    25      25.893  20.863  -4.607  1.00  0.00              
ATOM     44  O   TYR    25      25.801  20.387  -5.721  1.00  0.00              
ATOM     45  N   TYR    26      26.008  20.096  -3.564  1.00  0.00              
ATOM     46  CA  TYR    26      26.024  18.623  -3.802  1.00  0.00              
ATOM     47  C   TYR    26      24.955  17.879  -3.009  1.00  0.00              
ATOM     48  O   TYR    26      25.148  17.391  -1.913  1.00  0.00              
ATOM     49  N   LEU    27      23.840  17.754  -3.663  1.00  0.00              
ATOM     50  CA  LEU    27      22.623  17.017  -3.194  1.00  0.00              
ATOM     51  C   LEU    27      22.616  15.580  -3.696  1.00  0.00              
ATOM     52  O   LEU    27      22.833  15.315  -4.862  1.00  0.00              
ATOM     53  N   LYS    28      22.289  14.651  -2.834  1.00  0.00              
ATOM     54  CA  LYS    28      22.174  13.234  -3.256  1.00  0.00              
ATOM     55  C   LYS    28      21.352  12.533  -2.170  1.00  0.00              
ATOM     56  O   LYS    28      21.894  12.274  -1.116  1.00  0.00              
ATOM     57  N   SER    29      20.054  12.423  -2.270  1.00  0.00              
ATOM     58  CA  SER    29      19.303  11.934  -1.064  1.00  0.00              
ATOM     59  C   SER    29      20.106  10.831  -0.369  1.00  0.00              
ATOM     60  O   SER    29      21.147  10.422  -0.844  1.00  0.00              
ATOM     61  N   PHE    30      19.728  10.445   0.834  1.00  0.00              
ATOM     62  CA  PHE    30      20.677   9.559   1.605  1.00  0.00              
ATOM     63  C   PHE    30      19.956   8.794   2.738  1.00  0.00              
ATOM     64  O   PHE    30      19.397   9.457   3.588  1.00  0.00              
ATOM     65  N   GLN    31      19.821   7.482   2.807  1.00  0.00              
ATOM     66  CA  GLN    31      18.999   6.847   3.894  1.00  0.00              
ATOM     67  C   GLN    31      19.513   7.311   5.267  1.00  0.00              
ATOM     68  O   GLN    31      19.815   8.469   5.477  1.00  0.00              
ATOM     69  N   VAL    32      19.611   6.405   6.201  1.00  0.00              
ATOM     70  CA  VAL    32      20.095   6.731   7.578  1.00  0.00              
ATOM     71  C   VAL    32      20.060   5.403   8.347  1.00  0.00              
ATOM     72  O   VAL    32      20.065   4.370   7.706  1.00  0.00              
ATOM     73  N   ASP    33      20.246   5.328   9.647  1.00  0.00              
ATOM     74  CA  ASP    33      20.491   3.945  10.169  1.00  0.00              
ATOM     75  C   ASP    33      20.260   3.750  11.688  1.00  0.00              
ATOM     76  O   ASP    33      19.140   3.915  12.131  1.00  0.00              
ATOM     77  N   GLU    34      21.216   3.341  12.517  1.00  0.00              
ATOM     78  CA  GLU    34      20.849   3.094  13.952  1.00  0.00              
ATOM     79  C   GLU    34      22.101   2.693  14.753  1.00  0.00              
ATOM     80  O   GLU    34      22.701   1.663  14.514  1.00  0.00              
ATOM     81  N   GLY    35      22.527   3.533  15.670  1.00  0.00              
ATOM     82  CA  GLY    35      23.773   3.232  16.446  1.00  0.00              
ATOM     83  C   GLY    35      24.924   4.131  15.962  1.00  0.00              
ATOM     84  O   GLY    35      25.865   4.419  16.677  1.00  0.00              
ATOM     85  N   ILE    36      24.842   4.536  14.731  1.00  0.00              
ATOM     86  CA  ILE    36      25.929   5.397  14.129  1.00  0.00              
ATOM     87  C   ILE    36      25.655   6.802  14.659  1.00  0.00              
ATOM     88  O   ILE    36      25.203   7.032  15.764  1.00  0.00              
ATOM     89  N   THR    37      26.415   7.600  14.036  1.00  0.00              
ATOM     90  CA  THR    37      26.815   8.956  14.477  1.00  0.00              
ATOM     91  C   THR    37      26.977   9.893  13.262  1.00  0.00              
ATOM     92  O   THR    37      27.419   9.445  12.223  1.00  0.00              
ATOM     93  N   VAL    38      26.950  11.203  13.441  1.00  0.00              
ATOM     94  CA  VAL    38      27.504  12.116  12.387  1.00  0.00              
ATOM     95  C   VAL    38      28.874  11.634  11.923  1.00  0.00              
ATOM     96  O   VAL    38      29.118  11.470  10.744  1.00  0.00              
ATOM     97  N   GLN    39      29.817  11.592  12.823  1.00  0.00              
ATOM     98  CA  GLN    39      31.223  11.341  12.433  1.00  0.00              
ATOM     99  C   GLN    39      31.255  10.264  11.351  1.00  0.00              
ATOM    100  O   GLN    39      31.630  10.509  10.222  1.00  0.00              
ATOM    101  N   THR    40      30.813   9.079  11.680  1.00  0.00              
ATOM    102  CA  THR    40      30.780   8.015  10.612  1.00  0.00              
ATOM    103  C   THR    40      30.265   8.573   9.282  1.00  0.00              
ATOM    104  O   THR    40      30.975   8.532   8.298  1.00  0.00              
ATOM    105  N   ALA    41      29.029   8.980   9.170  1.00  0.00              
ATOM    106  CA  ALA    41      28.555   9.384   7.812  1.00  0.00              
ATOM    107  C   ALA    41      29.666  10.201   7.143  1.00  0.00              
ATOM    108  O   ALA    41      29.980  10.043   5.980  1.00  0.00              
ATOM    109  N   ILE    42      30.298  11.010   7.924  1.00  0.00              
ATOM    110  CA  ILE    42      31.460  11.816   7.441  1.00  0.00              
ATOM    111  C   ILE    42      32.628  10.869   7.144  1.00  0.00              
ATOM    112  O   ILE    42      33.287  10.972   6.129  1.00  0.00              
ATOM    113  N   THR    43      32.753   9.842   7.935  1.00  0.00              
ATOM    114  CA  THR    43      33.722   8.747   7.626  1.00  0.00              
ATOM    115  C   THR    43      33.440   8.165   6.239  1.00  0.00              
ATOM    116  O   THR    43      34.351   7.767   5.539  1.00  0.00              
ATOM    117  N   GLN    44      32.204   8.126   5.810  1.00  0.00              
ATOM    118  CA  GLN    44      31.952   7.575   4.426  1.00  0.00              
ATOM    119  C   GLN    44      32.656   8.504   3.435  1.00  0.00              
ATOM    120  O   GLN    44      32.979   8.147   2.320  1.00  0.00              
ATOM    121  N   SER    45      33.017   9.640   3.934  1.00  0.00              
ATOM    122  CA  SER    45      33.849  10.548   3.106  1.00  0.00              
ATOM    123  C   SER    45      35.312  10.194   3.374  1.00  0.00              
ATOM    124  O   SER    45      36.208  10.744   2.766  1.00  0.00              
ATOM    125  N   GLY    46      35.571   9.404   4.385  1.00  0.00              
ATOM    126  CA  GLY    46      36.982   9.180   4.792  1.00  0.00              
ATOM    127  C   GLY    46      37.385  10.460   5.508  1.00  0.00              
ATOM    128  O   GLY    46      38.492  10.947   5.386  1.00  0.00              
ATOM    129  N   ILE    47      36.404  11.098   6.101  1.00  0.00              
ATOM    130  CA  ILE    47      36.586  12.465   6.678  1.00  0.00              
ATOM    131  C   ILE    47      35.606  12.600   7.859  1.00  0.00              
ATOM    132  O   ILE    47      34.509  13.083   7.670  1.00  0.00              
ATOM    133  N   ASP    55      36.057  12.471   9.077  1.00  0.00              
ATOM    134  CA  ASP    55      35.239  13.003  10.214  1.00  0.00              
ATOM    135  C   ASP    55      35.075  14.517  10.028  1.00  0.00              
ATOM    136  O   ASP    55      35.444  15.310  10.871  1.00  0.00              
ATOM    137  N   LEU    56      34.732  14.898   8.828  1.00  0.00              
ATOM    138  CA  LEU    56      34.790  16.363   8.493  1.00  0.00              
ATOM    139  C   LEU    56      36.170  16.908   8.867  1.00  0.00              
ATOM    140  O   LEU    56      36.288  17.436   9.955  1.00  0.00              
END
