
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0378AL333_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   11 , name T0378_D1.pdb
# PARAMETERS: T0378AL333_3-D1.T0378_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:     9         1 - 87          4.89     6.54
  LONGEST_CONTINUOUS_SEGMENT:     9         2 - 88          4.68     5.89
  LONGEST_CONTINUOUS_SEGMENT:     9         6 - 89          4.75     6.51
  LCS_AVERAGE:     10.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         6 - 11          1.12     7.93
  LCS_AVERAGE:      4.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.70     7.93
  LONGEST_CONTINUOUS_SEGMENT:     5         7 - 11          0.78     7.84
  LCS_AVERAGE:      4.29

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:   89
LCS_GDT     M       1     M       1      0    0    9     0    0    0    0    2    4    4    6    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     L       2     L       2      3    3    9     0    0    3    3    4    4    5    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     Q       6     Q       6      5    6    9     3    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     I       7     I       7      5    6    9     3    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     K       8     K       8      5    6    9     3    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     F       9     F       9      5    6    9     3    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     L      10     L      10      5    6    9     3    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     R      11     R      11      5    6    9     2    5    5    6    6    6    6    7    7    8    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     V      87     V      87      3    3    9     0    3    3    3    3    3    3    4    4    5    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     F      88     F      88      3    3    9     0    3    3    3    3    3    3    4    4    5    8    8    9   10   11   11   11   11   11   11 
LCS_GDT     D      89     D      89      3    3    9     0    3    3    3    3    3    3    3    3    5    8    8    9   10   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   6.44  (   4.29    4.90   10.11 )

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      3      5      5      6      6      6      6      7      7      8      8      8      9     10     11     11     11     11     11     11 
GDT PERCENT_CA   3.37   5.62   5.62   6.74   6.74   6.74   6.74   7.87   7.87   8.99   8.99   8.99  10.11  11.24  12.36  12.36  12.36  12.36  12.36  12.36
GDT RMS_LOCAL    0.07   0.70   0.70   1.12   1.12   1.12   1.12   2.59   2.59   3.08   3.08   3.08   4.64   5.03   5.39   5.39   5.39   5.39   5.39   5.39
GDT RMS_ALL_CA   7.28   7.93   7.93   7.93   7.93   7.93   7.93   7.35   7.35   7.80   7.80   7.80   5.98   5.66   5.39   5.39   5.39   5.39   5.39   5.39

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.523
LGA    L       2      L       2          3.949
LGA    Q       6      Q       6          3.366
LGA    I       7      I       7          1.943
LGA    K       8      K       8          2.771
LGA    F       9      F       9          3.519
LGA    L      10      L      10          2.670
LGA    R      11      R      11          1.609
LGA    V      87      V      87         13.395
LGA    F      88      F      88         15.623
LGA    D      89      D      89         13.429

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   89    4.0      7    2.59     8.146     7.080     0.260

LGA_LOCAL      RMSD =  2.589  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.890  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  5.393  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.871718 * X  +   0.382569 * Y  +   0.306183 * Z  +  34.524685
  Y_new =   0.418874 * X  +   0.257548 * Y  +   0.870754 * Z  +  12.458057
  Z_new =   0.254267 * X  +   0.887305 * Y  +  -0.384758 * Z  +  47.591133 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.979950   -1.161643  [ DEG:   113.4428    -66.5572 ]
  Theta =  -0.257090   -2.884503  [ DEG:   -14.7301   -165.2699 ]
  Phi   =   2.693654   -0.447939  [ DEG:   154.3350    -25.6650 ]
 
# 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: T0378AL333_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL333_3-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   89   4.0    7   2.59   7.080     5.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL333_3-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   MET     1       1.598  34.178  51.030  1.00  0.00              
ATOM      2  CA  MET     1       2.518  35.317  51.329  1.00  0.00              
ATOM      3  C   MET     1       3.749  34.894  52.124  1.00  0.00              
ATOM      4  O   MET     1       4.869  35.289  51.797  1.00  0.00              
ATOM      5  N   LEU     2       3.546  34.105  53.176  1.00  0.00              
ATOM      6  CA  LEU     2       4.676  33.666  53.981  1.00  0.00              
ATOM      7  C   LEU     2       5.317  32.446  53.320  1.00  0.00              
ATOM      8  O   LEU     2       6.463  32.101  53.596  1.00  0.00              
ATOM      9  N   GLN     6       4.579  31.794  52.435  1.00  0.00              
ATOM     10  CA  GLN     6       5.119  30.638  51.734  1.00  0.00              
ATOM     11  C   GLN     6       6.147  31.203  50.744  1.00  0.00              
ATOM     12  O   GLN     6       7.202  30.616  50.483  1.00  0.00              
ATOM     13  N   ILE     7       5.813  32.375  50.221  1.00  0.00              
ATOM     14  CA  ILE     7       6.630  33.103  49.264  1.00  0.00              
ATOM     15  C   ILE     7       7.839  33.752  49.939  1.00  0.00              
ATOM     16  O   ILE     7       8.931  33.824  49.371  1.00  0.00              
ATOM     17  N   LYS     8       7.645  34.207  51.169  1.00  0.00              
ATOM     18  CA  LYS     8       8.710  34.888  51.879  1.00  0.00              
ATOM     19  C   LYS     8       9.288  34.044  53.027  1.00  0.00              
ATOM     20  O   LYS     8      10.487  33.768  53.060  1.00  0.00              
ATOM     21  N   PHE     9       8.434  33.603  53.940  1.00  0.00              
ATOM     22  CA  PHE     9       8.883  32.813  55.082  1.00  0.00              
ATOM     23  C   PHE     9       9.641  31.567  54.656  1.00  0.00              
ATOM     24  O   PHE     9      10.486  31.077  55.395  1.00  0.00              
ATOM     25  N   LEU    10       9.363  31.061  53.464  1.00  0.00              
ATOM     26  CA  LEU    10      10.039  29.852  53.021  1.00  0.00              
ATOM     27  C   LEU    10      11.161  30.085  52.017  1.00  0.00              
ATOM     28  O   LEU    10      12.325  30.215  52.391  1.00  0.00              
ATOM     29  N   ARG    11      10.796  30.118  50.741  1.00  0.00              
ATOM     30  CA  ARG    11      11.745  30.307  49.663  1.00  0.00              
ATOM     31  C   ARG    11      12.734  31.414  50.004  1.00  0.00              
ATOM     32  O   ARG    11      13.941  31.190  50.047  1.00  0.00              
ATOM     33  N   VAL    87      12.199  32.604  50.262  1.00  0.00              
ATOM     34  CA  VAL    87      12.988  33.781  50.589  1.00  0.00              
ATOM     35  C   VAL    87      14.007  33.557  51.714  1.00  0.00              
ATOM     36  O   VAL    87      15.194  33.815  51.534  1.00  0.00              
ATOM     37  N   PHE    88      13.535  33.071  52.858  1.00  0.00              
ATOM     38  CA  PHE    88      14.374  32.820  54.036  1.00  0.00              
ATOM     39  C   PHE    88      15.407  31.706  53.851  1.00  0.00              
ATOM     40  O   PHE    88      16.564  31.876  54.244  1.00  0.00              
ATOM     41  N   ASP    89      15.018  30.573  53.266  1.00  0.00              
ATOM     42  CA  ASP    89      15.988  29.496  53.078  1.00  0.00              
ATOM     43  C   ASP    89      17.088  29.877  52.079  1.00  0.00              
ATOM     44  O   ASP    89      18.248  29.529  52.269  1.00  0.00              
END
