
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0350AL509_1
# Molecule2: number of CA atoms  109 ( 1798),  selected   25 , name T0350.pdb
# PARAMETERS: T0350AL509_1.T0350.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:    17        14 - 35          4.89    13.24
  LONGEST_CONTINUOUS_SEGMENT:    17        15 - 36          4.99    12.33
  LCS_AVERAGE:     13.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        30 - 37          1.90    15.33
  LCS_AVERAGE:      4.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          0.96    23.19
  LCS_AVERAGE:      3.78

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:  109
LCS_GDT     V      12     V      12      0    0   10     4    5    5    6    6    6    6    6    7    7   10   10   10   10   10   11   13   15   15   17 
LCS_GDT     W      13     W      13      0    0   11     4    5    5    5    5    5    5    7    8    9   10   10   10   10   13   14   14   16   17   17 
LCS_GDT     D      14     D      14      6    6   17     4    5    5    6    6    6    6    7    8    9   12   14   14   16   17   18   18   18   19   20 
LCS_GDT     R      15     R      15      6    6   17     4    5    5    6    6    6    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     Y      16     Y      16      6    6   17     4    5    5    6    7    7    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     D      17     D      17      6    6   17     4    5    5    6    7    7    7    7    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     T      18     T      18      6    6   17     3    5    5    6    6    6    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     Q      19     Q      19      6    6   17     4    5    5    6    6    6    6    7    8   10   12   14   15   16   17   18   18   18   19   20 
LCS_GDT     I      20     I      20      3    4   17     4    5    5    5    6    6    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     H      21     H      21      3    4   17     3    3    4    5    6    6    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     N      22     N      22      3    4   17     3    3    3    5    6    6    6    7    9   11   12   14   14   16   17   18   18   18   19   19 
LCS_GDT     Q      23     Q      23      3    4   17     3    3    3    4    4    6    7    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     K      24     K      24      3    3   17     3    3    3    3    3    5    6    6    7   11   12   14   15   16   17   18   18   18   19   20 
LCS_GDT     V      30     V      30      3    8   17     0    3    5    6    7    8    8    8    8    9   10   12   14   16   17   18   18   18   19   20 
LCS_GDT     P      31     P      31      4    8   17     3    3    5    6    7    8    8    8    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     V      32     V      32      4    8   17     3    3    5    6    7    8    8    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     H      33     H      33      5    8   17     3    4    5    6    7    8    8    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     Q      34     Q      34      5    8   17     4    4    5    6    7    8    8    9    9   11   13   14   15   16   17   18   18   18   19   20 
LCS_GDT     V      35     V      35      5    8   17     4    4    5    6    7    8    8    8    9   11   13   14   15   15   17   18   18   18   19   20 
LCS_GDT     S      36     S      36      5    8   17     3    4    5    6    7    8    8    8    8   11   13   14   15   15   17   18   18   18   19   20 
LCS_GDT     Y      37     Y      37      5    8    9     3    4    5    6    7    8    8    8    8    9   10   11   13   15   16   17   18   18   19   20 
LCS_GDT     T      38     T      38      4    4    7     1    3    4    4    4    4    5    5    7    7    9    9    9   11   13   16   17   17   18   20 
LCS_GDT     N      39     N      39      4    4    5     0    3    4    4    4    4    5    5    7    7    9    9    9   11   12   13   14   15   17   19 
LCS_GDT     A      41     A      41      4    4    5     0    3    4    4    4    4    4    4    6    7    9    9   10   11   13   16   17   17   18   20 
LCS_GDT     E      42     E      42      4    4    5     0    3    4    4    4    4    4    4    7    7    8    8    9   11   12   13   14   15   17   19 
LCS_AVERAGE  LCS_A:   7.29  (   3.78    4.95   13.14 )

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      5      5      6      7      8      8      9      9     11     13     14     15     16     17     18     18     18     19     20 
GDT PERCENT_CA   3.67   4.59   4.59   5.50   6.42   7.34   7.34   8.26   8.26  10.09  11.93  12.84  13.76  14.68  15.60  16.51  16.51  16.51  17.43  18.35
GDT RMS_LOCAL    0.30   0.46   0.46   0.96   1.51   1.90   1.90   2.86   2.86   3.45   4.07   4.15   4.42   4.63   4.89   5.15   5.15   5.15   5.64   7.14
GDT RMS_ALL_CA  10.86  24.29  24.29  23.19  10.97  15.33  15.33  13.13  13.13  13.32  11.77  14.18  12.04  14.09  13.24  12.43  12.43  12.43  11.48   9.41

#      Molecule1      Molecule2       DISTANCE
LGA    V      12      V      12         17.735
LGA    W      13      W      13         14.834
LGA    D      14      D      14          7.346
LGA    R      15      R      15          3.719
LGA    Y      16      Y      16          2.783
LGA    D      17      D      17          5.852
LGA    T      18      T      18          1.305
LGA    Q      19      Q      19          6.317
LGA    I      20      I      20          3.679
LGA    H      21      H      21          2.518
LGA    N      22      N      22          6.773
LGA    Q      23      Q      23          1.344
LGA    K      24      K      24          5.698
LGA    V      30      V      30          7.498
LGA    P      31      P      31          4.959
LGA    V      32      V      32          3.892
LGA    H      33      H      33          2.277
LGA    Q      34      Q      34          3.608
LGA    V      35      V      35          6.926
LGA    S      36      S      36          8.899
LGA    Y      37      Y      37         14.238
LGA    T      38      T      38         26.412
LGA    N      39      N      39         27.728
LGA    A      41      A      41         27.596
LGA    E      42      E      42         28.773

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25  109    4.0      9    2.86     8.716     7.697     0.304

LGA_LOCAL      RMSD =  2.858  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.093  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  8.928  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.161675 * X  +  -0.153289 * Y  +  -0.974866 * Z  +  50.012379
  Y_new =   0.300823 * X  +   0.948501 * Y  +  -0.099254 * Z  + -68.478523
  Z_new =   0.939876 * X  +  -0.277216 * Y  +   0.199461 * Z  + -86.820686 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.947092    2.194501  [ DEG:   -54.2644    125.7356 ]
  Theta =  -1.222267   -1.919326  [ DEG:   -70.0307   -109.9693 ]
  Phi   =   1.077647   -2.063946  [ DEG:    61.7446   -118.2554 ]
 
# 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: T0350AL509_1                                  
REMARK     2: T0350.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0350AL509_1.T0350.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25  109   4.0    9   2.86   7.697     8.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL509_1
REMARK Aligment from pdb entry: 1g8x_A
ATOM      1  N   VAL    12      -5.085 -19.143 -20.077  1.00  0.00              
ATOM      2  CA  VAL    12      -4.036 -18.830 -19.119  1.00  0.00              
ATOM      3  C   VAL    12      -3.701 -17.345 -19.100  1.00  0.00              
ATOM      4  O   VAL    12      -3.186 -16.837 -18.112  1.00  0.00              
ATOM      5  N   TRP    13      -4.000 -16.632 -20.177  1.00  0.00              
ATOM      6  CA  TRP    13      -3.653 -15.224 -20.199  1.00  0.00              
ATOM      7  C   TRP    13      -4.703 -14.229 -19.752  1.00  0.00              
ATOM      8  O   TRP    13      -4.372 -13.075 -19.505  1.00  0.00              
ATOM      9  N   ASP    14      -1.206  -9.987 -15.881  1.00  0.00              
ATOM     10  CA  ASP    14      -0.474  -8.765 -16.216  1.00  0.00              
ATOM     11  C   ASP    14       0.837  -9.055 -16.946  1.00  0.00              
ATOM     12  O   ASP    14       1.465 -10.086 -16.723  1.00  0.00              
ATOM     13  N   ARG    15       1.249  -8.127 -17.803  1.00  0.00              
ATOM     14  CA  ARG    15       2.462  -8.281 -18.598  1.00  0.00              
ATOM     15  C   ARG    15       3.619  -8.977 -17.901  1.00  0.00              
ATOM     16  O   ARG    15       4.231  -9.891 -18.470  1.00  0.00              
ATOM     17  N   TYR    16       3.918  -8.572 -16.673  1.00  0.00              
ATOM     18  CA  TYR    16       5.032  -9.175 -15.950  1.00  0.00              
ATOM     19  C   TYR    16       4.653 -10.357 -15.047  1.00  0.00              
ATOM     20  O   TYR    16       5.468 -10.828 -14.263  1.00  0.00              
ATOM     21  N   ASP    17       3.414 -10.827 -15.155  1.00  0.00              
ATOM     22  CA  ASP    17       2.946 -11.970 -14.366  1.00  0.00              
ATOM     23  C   ASP    17       2.966 -13.240 -15.216  1.00  0.00              
ATOM     24  O   ASP    17       2.815 -14.354 -14.699  1.00  0.00              
ATOM     25  N   THR    18       3.130 -13.070 -16.525  1.00  0.00              
ATOM     26  CA  THR    18       3.193 -14.206 -17.420  1.00  0.00              
ATOM     27  C   THR    18       4.319 -14.040 -18.407  1.00  0.00              
ATOM     28  O   THR    18       4.871 -12.959 -18.547  1.00  0.00              
ATOM     29  N   GLN    19       4.648 -15.132 -19.086  1.00  0.00              
ATOM     30  CA  GLN    19       5.697 -15.171 -20.092  1.00  0.00              
ATOM     31  C   GLN    19       5.316 -14.277 -21.271  1.00  0.00              
ATOM     32  O   GLN    19       4.140 -14.022 -21.500  1.00  0.00              
ATOM     33  N   ILE    20       6.308 -13.774 -22.025  1.00  0.00              
ATOM     34  CA  ILE    20       6.016 -12.913 -23.183  1.00  0.00              
ATOM     35  C   ILE    20       5.142 -13.687 -24.168  1.00  0.00              
ATOM     36  O   ILE    20       5.336 -14.886 -24.349  1.00  0.00              
ATOM     37  N   HIS    21       4.191 -13.011 -24.808  1.00  0.00              
ATOM     38  CA  HIS    21       3.299 -13.686 -25.748  1.00  0.00              
ATOM     39  C   HIS    21       2.388 -12.701 -26.466  1.00  0.00              
ATOM     40  O   HIS    21       1.995 -11.692 -25.882  1.00  0.00              
ATOM     41  N   ASN    22       2.017 -12.981 -27.714  1.00  0.00              
ATOM     42  CA  ASN    22       1.143 -12.036 -28.380  1.00  0.00              
ATOM     43  C   ASN    22      -0.155 -11.954 -27.564  1.00  0.00              
ATOM     44  O   ASN    22      -0.791 -10.897 -27.515  1.00  0.00              
ATOM     45  N   GLN    23      -0.535 -13.052 -26.901  1.00  0.00              
ATOM     46  CA  GLN    23      -1.754 -13.050 -26.085  1.00  0.00              
ATOM     47  C   GLN    23      -1.676 -12.086 -24.873  1.00  0.00              
ATOM     48  O   GLN    23      -2.667 -11.468 -24.486  1.00  0.00              
ATOM     49  N   LYS    24      -0.496 -11.951 -24.279  1.00  0.00              
ATOM     50  CA  LYS    24      -0.316 -11.075 -23.128  1.00  0.00              
ATOM     51  C   LYS    24      -0.497  -9.623 -23.528  1.00  0.00              
ATOM     52  O   LYS    24      -1.153  -8.856 -22.830  1.00  0.00              
ATOM     53  N   VAL    30     -10.996   3.256 -19.914  1.00  0.00              
ATOM     54  CA  VAL    30     -12.064   3.766 -20.753  1.00  0.00              
ATOM     55  C   VAL    30     -11.466   4.604 -21.865  1.00  0.00              
ATOM     56  O   VAL    30     -11.986   5.668 -22.220  1.00  0.00              
ATOM     57  N   PRO    31     -10.367   4.089 -22.413  1.00  0.00              
ATOM     58  CA  PRO    31      -9.628   4.741 -23.488  1.00  0.00              
ATOM     59  C   PRO    31      -9.302   3.759 -24.623  1.00  0.00              
ATOM     60  O   PRO    31      -9.082   2.571 -24.380  1.00  0.00              
ATOM     61  N   VAL    32      -9.279   4.257 -25.861  1.00  0.00              
ATOM     62  CA  VAL    32      -8.980   3.419 -27.028  1.00  0.00              
ATOM     63  C   VAL    32      -7.563   2.879 -26.997  1.00  0.00              
ATOM     64  O   VAL    32      -6.648   3.538 -26.495  1.00  0.00              
ATOM     65  N   HIS    33      -7.376   1.698 -27.576  1.00  0.00              
ATOM     66  CA  HIS    33      -6.056   1.079 -27.623  1.00  0.00              
ATOM     67  C   HIS    33      -5.671   0.780 -29.068  1.00  0.00              
ATOM     68  O   HIS    33      -6.527   0.731 -29.956  1.00  0.00              
ATOM     69  N   GLN    34      -4.378   0.600 -29.313  1.00  0.00              
ATOM     70  CA  GLN    34      -3.931   0.236 -30.653  1.00  0.00              
ATOM     71  C   GLN    34      -2.739  -0.686 -30.585  1.00  0.00              
ATOM     72  O   GLN    34      -1.861  -0.543 -29.726  1.00  0.00              
ATOM     73  N   VAL    35      -2.738  -1.650 -31.493  1.00  0.00              
ATOM     74  CA  VAL    35      -1.655  -2.613 -31.616  1.00  0.00              
ATOM     75  C   VAL    35      -0.947  -2.390 -32.945  1.00  0.00              
ATOM     76  O   VAL    35      -1.468  -2.765 -33.999  1.00  0.00              
ATOM     77  N   SER    36       0.231  -1.774 -32.889  1.00  0.00              
ATOM     78  CA  SER    36       1.028  -1.505 -34.087  1.00  0.00              
ATOM     79  C   SER    36       2.040  -2.622 -34.303  1.00  0.00              
ATOM     80  O   SER    36       3.036  -2.708 -33.587  1.00  0.00              
ATOM     81  N   TYR    37       1.772  -3.469 -35.300  1.00  0.00              
ATOM     82  CA  TYR    37       2.617  -4.626 -35.638  1.00  0.00              
ATOM     83  C   TYR    37       3.422  -4.446 -36.928  1.00  0.00              
ATOM     84  O   TYR    37       2.878  -4.583 -38.013  1.00  0.00              
ATOM     85  N   THR    38       8.982  -8.187 -44.751  1.00  0.00              
ATOM     86  CA  THR    38       8.077  -9.093 -45.425  1.00  0.00              
ATOM     87  C   THR    38       8.420 -10.536 -45.055  1.00  0.00              
ATOM     88  O   THR    38       9.518 -11.006 -45.325  1.00  0.00              
ATOM     89  N   ASN    39       7.484 -11.250 -44.452  1.00  0.00              
ATOM     90  CA  ASN    39       7.761 -12.624 -44.083  1.00  0.00              
ATOM     91  C   ASN    39       8.211 -12.746 -42.638  1.00  0.00              
ATOM     92  O   ASN    39       8.578 -13.817 -42.164  1.00  0.00              
ATOM     93  N   ALA    41       8.178 -11.642 -41.918  1.00  0.00              
ATOM     94  CA  ALA    41       8.593 -11.666 -40.529  1.00  0.00              
ATOM     95  C   ALA    41       7.545 -12.277 -39.588  1.00  0.00              
ATOM     96  O   ALA    41       7.890 -12.713 -38.490  1.00  0.00              
ATOM     97  N   GLU    42       6.275 -12.279 -40.008  1.00  0.00              
ATOM     98  CA  GLU    42       5.204 -12.849 -39.201  1.00  0.00              
ATOM     99  C   GLU    42       4.136 -11.873 -38.726  1.00  0.00              
ATOM    100  O   GLU    42       3.380 -12.180 -37.799  1.00  0.00              
END
