
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0319AL381_3
# Molecule2: number of CA atoms  135 ( 1055),  selected   13 , name T0319.pdb
# PARAMETERS: T0319AL381_3.T0319.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       106 - 118         1.87     1.87
  LCS_AVERAGE:      9.63

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       106 - 118         1.87     1.87
  LCS_AVERAGE:      9.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       109 - 118         0.56     3.24
  LCS_AVERAGE:      6.32

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:  135
LCS_GDT     A     106     A     106      3   13   13     0    3    3    5    6   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     107     E     107      4   13   13     0    3    4   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     G     108     G     108      4   13   13     3    3    5   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     109     E     109     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     M     110     M     110     10   13   13     4   10   10   10   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     111     K     111     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     C     112     C     112     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     R     113     R     113     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     N     114     N     114     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     C     115     C     115     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     G     116     G     116     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     H     117     H     117     10   13   13     4   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     118     I     118     10   13   13     7   10   10   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   8.53  (   6.32    9.63    9.63 )

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      7     10     10     10     11     12     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   5.19   7.41   7.41   7.41   8.15   8.89   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63   9.63
GDT RMS_LOCAL    0.36   0.56   0.56   0.56   1.42   1.59   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87
GDT RMS_ALL_CA   3.04   3.24   3.24   3.24   1.91   1.98   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87

#      Molecule1      Molecule2       DISTANCE
LGA    A     106      A     106          3.443
LGA    E     107      E     107          2.059
LGA    G     108      G     108          1.700
LGA    E     109      E     109          2.744
LGA    M     110      M     110          3.215
LGA    K     111      K     111          1.259
LGA    C     112      C     112          0.443
LGA    R     113      R     113          0.861
LGA    N     114      N     114          1.287
LGA    C     115      C     115          0.988
LGA    G     116      G     116          1.090
LGA    H     117      H     117          1.234
LGA    I     118      I     118          0.968

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  135    4.0     13    1.87     8.519     8.990     0.659

LGA_LOCAL      RMSD =  1.874  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.874  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  1.874  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.330901 * X  +   0.432150 * Y  +   0.838899 * Z  +  12.438096
  Y_new =   0.880808 * X  +   0.460465 * Y  +   0.110228 * Z  +   8.197124
  Z_new =  -0.338648 * X  +   0.775383 * Y  +  -0.533009 * Z  +  19.394911 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.173026   -0.968567  [ DEG:   124.5052    -55.4948 ]
  Theta =   0.345480    2.796113  [ DEG:    19.7945    160.2054 ]
  Phi   =   1.930162   -1.211431  [ DEG:   110.5901    -69.4099 ]
 
# 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: T0319AL381_3                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_3.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  135   4.0   13   1.87   8.990     1.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_3
REMARK Aligment from pdb entry: 1dl6A
ATOM      1  N   ALA   106      19.354  10.951  11.692  1.00  0.00              
ATOM      2  CA  ALA   106      19.261  12.086  12.599  1.00  0.00              
ATOM      3  C   ALA   106      18.527  13.240  11.932  1.00  0.00              
ATOM      4  O   ALA   106      18.933  13.729  10.878  1.00  0.00              
ATOM      5  N   GLU   107      17.445  13.665  12.560  1.00  0.00              
ATOM      6  CA  GLU   107      16.628  14.764  12.051  1.00  0.00              
ATOM      7  C   GLU   107      15.774  14.315  10.871  1.00  0.00              
ATOM      8  O   GLU   107      15.422  15.118  10.006  1.00  0.00              
ATOM      9  N   GLY   108      15.441  13.028  10.841  1.00  0.00              
ATOM     10  CA  GLY   108      14.628  12.496   9.762  1.00  0.00              
ATOM     11  C   GLY   108      13.310  11.921  10.249  1.00  0.00              
ATOM     12  O   GLY   108      12.393  11.704   9.458  1.00  0.00              
ATOM     13  N   GLU   109      13.212  11.673  11.554  1.00  0.00              
ATOM     14  CA  GLU   109      11.996  11.121  12.140  1.00  0.00              
ATOM     15  C   GLU   109      11.766   9.688  11.670  1.00  0.00              
ATOM     16  O   GLU   109      12.615   9.101  10.998  1.00  0.00              
ATOM     17  N   MET   110      10.612   9.132  12.026  1.00  0.00              
ATOM     18  CA  MET   110      10.267   7.769  11.639  1.00  0.00              
ATOM     19  C   MET   110       9.029   7.759  10.749  1.00  0.00              
ATOM     20  O   MET   110       7.953   8.188  11.165  1.00  0.00              
ATOM     21  N   LYS   111       9.187   7.279   9.518  1.00  0.00              
ATOM     22  CA  LYS   111       8.093   7.230   8.573  1.00  0.00              
ATOM     23  C   LYS   111       7.660   5.796   8.284  1.00  0.00              
ATOM     24  O   LYS   111       8.440   4.859   8.439  1.00  0.00              
ATOM     25  N   CYS   112       6.409   5.633   7.856  1.00  0.00              
ATOM     26  CA  CYS   112       5.877   4.311   7.539  1.00  0.00              
ATOM     27  C   CYS   112       5.890   4.075   6.029  1.00  0.00              
ATOM     28  O   CYS   112       5.535   4.962   5.255  1.00  0.00              
ATOM     29  N   ARG   113       6.310   2.875   5.584  1.00  0.00              
ATOM     30  CA  ARG   113       6.373   2.543   4.157  1.00  0.00              
ATOM     31  C   ARG   113       5.001   2.257   3.546  1.00  0.00              
ATOM     32  O   ARG   113       4.898   1.930   2.363  1.00  0.00              
ATOM     33  N   ASN   114       3.949   2.379   4.352  1.00  0.00              
ATOM     34  CA  ASN   114       2.593   2.130   3.878  1.00  0.00              
ATOM     35  C   ASN   114       1.755   3.408   3.916  1.00  0.00              
ATOM     36  O   ASN   114       1.538   4.043   2.883  1.00  0.00              
ATOM     37  N   CYS   115       1.288   3.791   5.105  1.00  0.00              
ATOM     38  CA  CYS   115       0.484   5.005   5.241  1.00  0.00              
ATOM     39  C   CYS   115       1.327   6.249   4.980  1.00  0.00              
ATOM     40  O   CYS   115       0.792   7.345   4.807  1.00  0.00              
ATOM     41  N   GLY   116       2.647   6.078   4.954  1.00  0.00              
ATOM     42  CA  GLY   116       3.530   7.203   4.716  1.00  0.00              
ATOM     43  C   GLY   116       3.387   8.273   5.776  1.00  0.00              
ATOM     44  O   GLY   116       3.148   9.440   5.463  1.00  0.00              
ATOM     45  N   HIS   117       3.532   7.878   7.038  1.00  0.00              
ATOM     46  CA  HIS   117       3.416   8.819   8.143  1.00  0.00              
ATOM     47  C   HIS   117       4.794   9.286   8.595  1.00  0.00              
ATOM     48  O   HIS   117       5.809   8.852   8.052  1.00  0.00              
ATOM     49  N   ILE   118       4.818  10.171   9.585  1.00  0.00              
ATOM     50  CA  ILE   118       6.070  10.701  10.110  1.00  0.00              
ATOM     51  C   ILE   118       5.966  10.972  11.608  1.00  0.00              
ATOM     52  O   ILE   118       5.547  12.051  12.025  1.00  0.00              
END
