
#######################################################
#                                                     #
#                        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    8 (   32),  selected    8 , name T0304AL586_1-D1
# Molecule2: number of CA atoms  101 (  799),  selected    8 , name T0304_D1.pdb
# PARAMETERS: T0304AL586_1-D1.T0304_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:     8       110 - 117         3.09     3.09
  LCS_AVERAGE:      7.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       110 - 115         1.33     4.44
  LCS_AVERAGE:      5.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       110 - 114         0.70     4.83
  LCS_AVERAGE:      4.21

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:  101
LCS_GDT     V     110     V     110      5    6    8     3    5    5    5    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     Y     111     Y     111      5    6    8     3    5    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     112     L     112      5    6    8     3    5    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     113     A     113      5    6    8     3    5    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     114     V     114      5    6    8     3    5    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     Y     115     Y     115      3    6    8     3    3    4    5    6    6    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     P     116     P     116      3    5    8     3    3    3    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     T     117     T     117      3    5    8     3    3    3    5    5    5    5    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   5.94  (   4.21    5.69    7.92 )

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      5      6      6      6      7      7      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.97   4.95   4.95   4.95   5.94   5.94   5.94   6.93   6.93   7.92   7.92   7.92   7.92   7.92   7.92   7.92   7.92   7.92   7.92   7.92
GDT RMS_LOCAL    0.19   0.70   0.70   0.70   1.33   1.33   1.33   2.78   2.42   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09
GDT RMS_ALL_CA   4.42   4.83   4.83   4.83   4.44   4.44   4.44   3.48   3.74   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09   3.09

#      Molecule1      Molecule2       DISTANCE
LGA    V     110      V     110          6.552
LGA    Y     111      Y     111          3.060
LGA    L     112      L     112          3.080
LGA    A     113      A     113          2.376
LGA    V     114      V     114          1.060
LGA    Y     115      Y     115          1.870
LGA    P     116      P     116          3.451
LGA    T     117      T     117          3.624

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  101    4.0      7    2.78     6.188     6.235     0.243

LGA_LOCAL      RMSD =  2.782  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.484  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.088  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.870265 * X  +   0.397747 * Y  +   0.290579 * Z  +  49.952602
  Y_new =  -0.380472 * X  +   0.168106 * Y  +   0.909385 * Z  +  26.198345
  Z_new =   0.312857 * X  +  -0.901963 * Y  +   0.297629 * Z  +  44.643757 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.252068    1.889525  [ DEG:   -71.7382    108.2618 ]
  Theta =  -0.318199   -2.823393  [ DEG:   -18.2315   -161.7685 ]
  Phi   =  -0.412151    2.729442  [ DEG:   -23.6145    156.3855 ]
 
# 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: T0304AL586_1-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304AL586_1-D1.T0304_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  101   4.0    7   2.78   6.235     3.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL586_1-D1
REMARK Aligment from pdb entry: 1fmb
ATOM      1  N   VAL   110      43.970  33.079  45.885  1.00  0.00              
ATOM      2  CA  VAL   110      43.101  32.262  44.991  1.00  0.00              
ATOM      3  C   VAL   110      43.974  31.149  44.407  1.00  0.00              
ATOM      4  O   VAL   110      45.192  31.210  44.399  1.00  0.00              
ATOM      5  N   TYR   111      43.262  30.146  43.960  1.00  0.00              
ATOM      6  CA  TYR   111      43.842  28.921  43.432  1.00  0.00              
ATOM      7  C   TYR   111      43.505  28.736  41.974  1.00  0.00              
ATOM      8  O   TYR   111      42.358  28.846  41.613  1.00  0.00              
ATOM      9  N   LEU   112      44.512  28.420  41.156  1.00  0.00              
ATOM     10  CA  LEU   112      44.298  28.162  39.738  1.00  0.00              
ATOM     11  C   LEU   112      44.568  26.671  39.581  1.00  0.00              
ATOM     12  O   LEU   112      45.677  26.218  39.876  1.00  0.00              
ATOM     13  N   ALA   113      43.596  25.954  39.120  1.00  0.00              
ATOM     14  CA  ALA   113      43.585  24.509  38.929  1.00  0.00              
ATOM     15  C   ALA   113      44.067  24.080  37.540  1.00  0.00              
ATOM     16  O   ALA   113      44.054  22.882  37.208  1.00  0.00              
ATOM     17  N   VAL   114      44.439  25.107  36.749  1.00  0.00              
ATOM     18  CA  VAL   114      45.031  24.873  35.428  1.00  0.00              
ATOM     19  C   VAL   114      44.194  24.292  34.335  1.00  0.00              
ATOM     20  O   VAL   114      44.686  24.011  33.236  1.00  0.00              
ATOM     21  N   TYR   115      42.853  24.289  34.506  1.00  0.00              
ATOM     22  CA  TYR   115      41.917  23.959  33.438  1.00  0.00              
ATOM     23  C   TYR   115      41.985  25.064  32.361  1.00  0.00              
ATOM     24  O   TYR   115      41.748  24.768  31.190  1.00  0.00              
ATOM     25  N   PRO   116      42.299  26.271  32.794  1.00  0.00              
ATOM     26  CA  PRO   116      42.443  27.384  31.831  1.00  0.00              
ATOM     27  C   PRO   116      43.785  28.044  32.056  1.00  0.00              
ATOM     28  O   PRO   116      44.515  27.752  33.049  1.00  0.00              
ATOM     29  N   THR   117      44.265  28.896  31.104  1.00  0.00              
ATOM     30  CA  THR   117      45.596  29.479  31.420  1.00  0.00              
ATOM     31  C   THR   117      45.395  30.352  32.670  1.00  0.00              
ATOM     32  O   THR   117      44.354  31.049  32.724  1.00  0.00              
END
