
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0350AL509_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   16 , name T0350_D1.pdb
# PARAMETERS: T0350AL509_1-D1.T0350_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:    10        12 - 21          4.67    20.92
  LONGEST_CONTINUOUS_SEGMENT:    10        14 - 37          4.51    11.18
  LCS_AVERAGE:      9.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          0.96    21.41
  LCS_AVERAGE:      4.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          0.96    21.41
  LCS_AVERAGE:      3.98

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:   91
LCS_GDT     V      12     V      12      0    0   10     4    5    5    5    5    5    7    9    9    9   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     W      13     W      13      0    0   10     4    5    5    5    6    6    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     D      14     D      14      6    6   10     4    5    5    6    6    6    6    7    7   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     R      15     R      15      6    6   10     4    5    5    6    6    6    6    7    7    8    8    8    9   10   14   14   14   14   15   15 
LCS_GDT     Y      16     Y      16      6    6   10     4    5    5    6    6    6    6    7    7    8    8   11   12   13   14   14   14   14   15   15 
LCS_GDT     D      17     D      17      6    6   10     4    5    5    6    6    6    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     T      18     T      18      6    6   10     4    5    5    6    6    6    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     Q      19     Q      19      6    6   10     4    5    5    6    6    6    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     I      20     I      20      3    4   10     4    5    5    5    6    6    6    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     H      21     H      21      3    4   10     3    3    3    4    4    4    5    5    6    8    8    8    9   10   10   10   10   12   14   15 
LCS_GDT     S      36     S      36      0    0   10     0    0    1    1    2    3    4    5    6    8    8    8   10   11   11   12   14   14   15   15 
LCS_GDT     Y      37     Y      37      0    0   10     0    0    1    1    2    3    3    4    5    5    7   10   11   13   14   14   14   14   15   15 
LCS_GDT     T      38     T      38      4    4    5     1    3    4    5    6    6    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     N      39     N      39      4    4    5     0    3    4    5    6    6    6    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     A      41     A      41      4    4    5     0    3    4    4    4    4    4    5    5   10   11   11   12   13   14   14   14   14   15   15 
LCS_GDT     E      42     E      42      4    4    5     0    3    4    4    4    5    7    9    9   10   11   11   12   13   14   14   14   14   15   15 
LCS_AVERAGE  LCS_A:   5.91  (   3.98    4.12    9.62 )

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      6      6      7      9      9     10     11     11     12     13     14     14     14     14     15     15 
GDT PERCENT_CA   4.40   5.49   5.49   6.59   6.59   6.59   7.69   9.89   9.89  10.99  12.09  12.09  13.19  14.29  15.38  15.38  15.38  15.38  16.48  16.48
GDT RMS_LOCAL    0.31   0.46   0.46   0.96   0.96   0.96   2.53   2.93   2.93   3.64   3.84   3.84   4.20   4.69   4.98   4.98   4.98   4.98   5.63   5.63
GDT RMS_ALL_CA  23.07  22.99  22.99  21.41  21.41  21.41   6.55   6.67   6.67   7.14   6.86   6.86   6.82   6.46   6.47   6.47   6.47   6.47   6.33   6.33

#      Molecule1      Molecule2       DISTANCE
LGA    V      12      V      12          3.560
LGA    W      13      W      13          1.177
LGA    D      14      D      14          7.989
LGA    R      15      R      15          9.580
LGA    Y      16      Y      16          7.962
LGA    D      17      D      17          3.655
LGA    T      18      T      18          1.774
LGA    Q      19      Q      19          1.534
LGA    I      20      I      20          3.926
LGA    H      21      H      21         10.909
LGA    S      36      S      36         13.134
LGA    Y      37      Y      37          7.828
LGA    T      38      T      38          2.284
LGA    N      39      N      39          4.000
LGA    A      41      A      41          6.450
LGA    E      42      E      42          3.151

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   91    4.0      9    2.93     9.341     7.792     0.297

LGA_LOCAL      RMSD =  2.934  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.580  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  6.272  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.190058 * X  +   0.720204 * Y  +   0.667222 * Z  + -74.556488
  Y_new =  -0.977012 * X  +   0.205596 * Y  +   0.056380 * Z  +  49.513126
  Z_new =  -0.096573 * X  +  -0.662599 * Y  +   0.742722 * Z  + -25.430773 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.728445    2.413147  [ DEG:   -41.7368    138.2632 ]
  Theta =   0.096724    3.044869  [ DEG:     5.5419    174.4581 ]
  Phi   =  -1.378666    1.762926  [ DEG:   -78.9918    101.0082 ]
 
# 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-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0350AL509_1-D1.T0350_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   91   4.0    9   2.93   7.792     6.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL509_1-D1
REMARK Aligment from pdb entry: 1g8x_A
ATOM      1  N   VAL    12       6.406  -6.516 -10.260  1.00  0.00              
ATOM      2  CA  VAL    12       5.959  -7.729 -10.928  1.00  0.00              
ATOM      3  C   VAL    12       6.718  -7.984 -12.223  1.00  0.00              
ATOM      4  O   VAL    12       6.794  -9.116 -12.685  1.00  0.00              
ATOM      5  N   TRP    13       7.295  -6.948 -12.812  1.00  0.00              
ATOM      6  CA  TRP    13       7.989  -7.158 -14.070  1.00  0.00              
ATOM      7  C   TRP    13       9.476  -7.437 -14.019  1.00  0.00              
ATOM      8  O   TRP    13      10.040  -7.877 -15.015  1.00  0.00              
ATOM      9  N   ASP    14      10.216 -12.466 -18.419  1.00  0.00              
ATOM     10  CA  ASP    14      10.468 -12.451 -19.861  1.00  0.00              
ATOM     11  C   ASP    14       9.233 -12.037 -20.661  1.00  0.00              
ATOM     12  O   ASP    14       8.105 -12.297 -20.254  1.00  0.00              
ATOM     13  N   ARG    15       9.462 -11.408 -21.809  1.00  0.00              
ATOM     14  CA  ARG    15       8.383 -10.922 -22.662  1.00  0.00              
ATOM     15  C   ARG    15       7.147 -11.804 -22.724  1.00  0.00              
ATOM     16  O   ARG    15       6.021 -11.310 -22.583  1.00  0.00              
ATOM     17  N   TYR    16       7.340 -13.103 -22.914  1.00  0.00              
ATOM     18  CA  TYR    16       6.201 -14.009 -23.010  1.00  0.00              
ATOM     19  C   TYR    16       5.783 -14.664 -21.686  1.00  0.00              
ATOM     20  O   TYR    16       4.958 -15.570 -21.673  1.00  0.00              
ATOM     21  N   ASP    17       6.359 -14.208 -20.578  1.00  0.00              
ATOM     22  CA  ASP    17       6.018 -14.735 -19.253  1.00  0.00              
ATOM     23  C   ASP    17       5.052 -13.787 -18.542  1.00  0.00              
ATOM     24  O   ASP    17       4.470 -14.133 -17.507  1.00  0.00              
ATOM     25  N   THR    18       4.900 -12.584 -19.086  1.00  0.00              
ATOM     26  CA  THR    18       3.989 -11.617 -18.512  1.00  0.00              
ATOM     27  C   THR    18       3.167 -10.958 -19.590  1.00  0.00              
ATOM     28  O   THR    18       3.476 -11.071 -20.766  1.00  0.00              
ATOM     29  N   GLN    19       2.115 -10.270 -19.165  1.00  0.00              
ATOM     30  CA  GLN    19       1.209  -9.553 -20.049  1.00  0.00              
ATOM     31  C   GLN    19       1.958  -8.416 -20.743  1.00  0.00              
ATOM     32  O   GLN    19       2.963  -7.935 -20.235  1.00  0.00              
ATOM     33  N   ILE    20       1.489  -7.984 -21.925  1.00  0.00              
ATOM     34  CA  ILE    20       2.153  -6.887 -22.648  1.00  0.00              
ATOM     35  C   ILE    20       2.159  -5.643 -21.762  1.00  0.00              
ATOM     36  O   ILE    20       1.189  -5.391 -21.053  1.00  0.00              
ATOM     37  N   HIS    21       3.236  -4.864 -21.804  1.00  0.00              
ATOM     38  CA  HIS    21       3.328  -3.669 -20.967  1.00  0.00              
ATOM     39  C   HIS    21       4.576  -2.857 -21.279  1.00  0.00              
ATOM     40  O   HIS    21       5.609  -3.429 -21.626  1.00  0.00              
ATOM     77  N   SER    36      12.797   2.720 -29.442  1.00  0.00              
ATOM     78  CA  SER    36      12.262   3.652 -30.436  1.00  0.00              
ATOM     79  C   SER    36      10.746   3.730 -30.317  1.00  0.00              
ATOM     80  O   SER    36      10.041   2.805 -30.717  1.00  0.00              
ATOM     81  N   TYR    37      10.259   4.845 -29.767  1.00  0.00              
ATOM     82  CA  TYR    37       8.824   5.085 -29.542  1.00  0.00              
ATOM     83  C   TYR    37       8.214   6.113 -30.498  1.00  0.00              
ATOM     84  O   TYR    37       8.397   7.306 -30.312  1.00  0.00              
ATOM     85  N   THR    38       0.756  12.686 -33.196  1.00  0.00              
ATOM     86  CA  THR    38       0.730  13.651 -32.118  1.00  0.00              
ATOM     87  C   THR    38      -0.451  13.362 -31.193  1.00  0.00              
ATOM     88  O   THR    38      -1.600  13.403 -31.615  1.00  0.00              
ATOM     89  N   ASN    39      -0.182  13.084 -29.928  1.00  0.00              
ATOM     90  CA  ASN    39      -1.269  12.804 -29.011  1.00  0.00              
ATOM     91  C   ASN    39      -1.518  11.314 -28.861  1.00  0.00              
ATOM     92  O   ASN    39      -2.455  10.880 -28.197  1.00  0.00              
ATOM     93  N   ALA    41      -0.669  10.513 -29.474  1.00  0.00              
ATOM     94  CA  ALA    41      -0.832   9.075 -29.386  1.00  0.00              
ATOM     95  C   ALA    41      -0.374   8.487 -28.043  1.00  0.00              
ATOM     96  O   ALA    41      -0.796   7.391 -27.680  1.00  0.00              
ATOM     97  N   GLU    42       0.505   9.203 -27.333  1.00  0.00              
ATOM     98  CA  GLU    42       0.993   8.746 -26.038  1.00  0.00              
ATOM     99  C   GLU    42       2.484   8.448 -25.956  1.00  0.00              
ATOM    100  O   GLU    42       2.933   7.771 -25.026  1.00  0.00              
END
