
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0301AL333_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   17 , name T0301_D2.pdb
# PARAMETERS: T0301AL333_2-D2.T0301_D2.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:     7       356 - 376         4.62    21.13
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       356 - 374         1.27    20.25
  LCS_AVERAGE:      1.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       356 - 359         0.33    20.29
  LONGEST_CONTINUOUS_SEGMENT:     4       374 - 377         0.96    19.25
  LCS_AVERAGE:      1.63

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:  191
LCS_GDT     A     257     A     257      3    3    6     0    3    3    3    3    3    4    4    5    5    6    6    6    6    6    7    7    7    8    8 
LCS_GDT     L     258     L     258      3    3    6     1    3    3    3    3    4    4    4    5    5    6    6    6    6    6    7    7    7    8    8 
LCS_GDT     R     259     R     259      3    4    6     1    3    3    4    4    4    5    5    5    5    6    6    6    6    6    7    7    7    8    8 
LCS_GDT     M     260     M     260      3    4    6     0    3    3    4    4    4    5    5    5    5    6    6    6    6    6    7    7    7    8    8 
LCS_GDT     G     261     G     261      3    4    6     0    3    3    4    4    4    5    5    5    5    5    5    5    5    6    7    7    7    8    8 
LCS_GDT     L     262     L     262      3    4    6     0    3    3    4    4    4    5    5    5    5    5    5    5    5    6    6    6    7    8    8 
LCS_GDT     I     263     I     263      3    4    6     0    3    3    4    4    4    5    5    5    5    5    5    5    5    6    6    6    7    7    7 
LCS_GDT     P     331     P     331      0    0    0     1    2    4    4    4    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     G     332     G     332      0    0    0     1    1    3    4    4    4    5    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     L     356     L     356      4    5    7     4    4    4    5    5    5    5    5    6    6    6    6    6    6    7    7    7    7    7    9 
LCS_GDT     R     357     R     357      4    5    7     4    4    4    5    5    5    5    5    6    6    6    6    6    6    7    7    8    8    9    9 
LCS_GDT     V     358     V     358      4    5    7     4    4    4    5    5    5    5    5    6    6    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     G     359     G     359      4    5    7     4    4    4    5    5    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     A     374     A     374      4    5    7     3    3    4    5    5    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     I     375     I     375      4    4    7     3    3    4    4    4    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     M     376     M     376      4    4    7     3    3    4    4    4    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_GDT     S     377     S     377      4    4    6     0    3    4    4    4    5    6    7    7    7    7    7    7    8    8    8    8    8    9    9 
LCS_AVERAGE  LCS_A:   2.19  (   1.63    1.94    2.99 )

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      4      4      5      5      5      6      7      7      7      7      7      7      8      8      8      8      8      9      9 
GDT PERCENT_CA   2.09   2.09   2.09   2.62   2.62   2.62   3.14   3.66   3.66   3.66   3.66   3.66   3.66   4.19   4.19   4.19   4.19   4.19   4.71   4.71
GDT RMS_LOCAL    0.33   0.33   0.33   1.27   1.27   1.27   2.44   2.91   2.91   2.91   2.91   2.91   2.91   4.11   4.11   4.11   4.11   4.11   5.65   5.65
GDT RMS_ALL_CA  20.29  20.29  20.29  20.25  20.25  20.25  17.31  17.10  17.10  17.10  17.10  17.10  17.10  19.57  19.57  19.57  19.57  19.57  20.19  20.19

#      Molecule1      Molecule2       DISTANCE
LGA    A     257      A     257         27.206
LGA    L     258      L     258         27.979
LGA    R     259      R     259         26.352
LGA    M     260      M     260         20.447
LGA    G     261      G     261         22.312
LGA    L     262      L     262         19.905
LGA    I     263      I     263         24.821
LGA    P     331      P     331          3.045
LGA    G     332      G     332          3.566
LGA    L     356      L     356         20.762
LGA    R     357      R     357         15.533
LGA    V     358      V     358          9.642
LGA    G     359      G     359          3.738
LGA    A     374      A     374          3.599
LGA    I     375      I     375          1.824
LGA    M     376      M     376          2.286
LGA    S     377      S     377          1.369

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  191    4.0      7    2.91     3.141     2.807     0.232

LGA_LOCAL      RMSD =  2.911  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.099  Number of atoms =   17 
Std_ALL_ATOMS  RMSD = 13.560  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.098076 * X  +  -0.982879 * Y  +   0.155979 * Z  + 108.935547
  Y_new =  -0.967331 * X  +  -0.130972 * Y  +  -0.217064 * Z  +  35.866131
  Z_new =   0.233777 * X  +  -0.129595 * Y  +  -0.963615 * Z  +  39.828030 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.007907    0.133686  [ DEG:  -172.3404      7.6596 ]
  Theta =  -0.235961   -2.905632  [ DEG:   -13.5195   -166.4805 ]
  Phi   =  -1.469754    1.671839  [ DEG:   -84.2107     95.7893 ]
 
# 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: T0301AL333_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL333_2-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  191   4.0    7   2.91   2.807    13.56
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL333_2-D2
REMARK Aligment from pdb entry: 1hnj_A
ATOM    405  N   ALA   257      82.190  16.598  17.362  1.00  0.00              
ATOM    406  CA  ALA   257      83.320  15.717  17.628  1.00  0.00              
ATOM    407  C   ALA   257      83.269  14.511  16.682  1.00  0.00              
ATOM    408  O   ALA   257      82.228  13.872  16.520  1.00  0.00              
ATOM    409  N   LEU   258      84.400  14.208  16.060  1.00  0.00              
ATOM    410  CA  LEU   258      84.483  13.067  15.155  1.00  0.00              
ATOM    411  C   LEU   258      85.379  11.989  15.755  1.00  0.00              
ATOM    412  O   LEU   258      86.550  12.255  16.039  1.00  0.00              
ATOM    413  N   ARG   259      84.809  10.807  15.974  1.00  0.00              
ATOM    414  CA  ARG   259      85.560   9.674  16.518  1.00  0.00              
ATOM    415  C   ARG   259      85.888   8.762  15.352  1.00  0.00              
ATOM    416  O   ARG   259      85.039   8.582  14.469  1.00  0.00              
ATOM    417  N   MET   260      87.102   8.237  15.274  1.00  0.00              
ATOM    418  CA  MET   260      87.414   7.283  14.191  1.00  0.00              
ATOM    419  C   MET   260      88.440   6.285  14.659  1.00  0.00              
ATOM    420  O   MET   260      89.161   6.525  15.647  1.00  0.00              
ATOM    421  N   GLY   261      88.492   5.139  13.974  1.00  0.00              
ATOM    422  CA  GLY   261      89.422   4.083  14.341  1.00  0.00              
ATOM    423  C   GLY   261      89.612   3.114  13.193  1.00  0.00              
ATOM    424  O   GLY   261      88.733   2.971  12.355  1.00  0.00              
ATOM    425  N   LEU   262      90.757   2.441  13.176  1.00  0.00              
ATOM    426  CA  LEU   262      91.124   1.489  12.114  1.00  0.00              
ATOM    427  C   LEU   262      91.827   0.348  12.845  1.00  0.00              
ATOM    428  O   LEU   262      92.656   0.575  13.725  1.00  0.00              
ATOM    429  N   ILE   263      91.521  -0.882  12.470  1.00  0.00              
ATOM    430  CA  ILE   263      92.120  -2.018  13.142  1.00  0.00              
ATOM    431  C   ILE   263      92.185  -3.278  12.316  1.00  0.00              
ATOM    432  O   ILE   263      91.814  -3.299  11.150  1.00  0.00              
ATOM    433  N   PRO   331      92.677  -4.321  12.965  1.00  0.00              
ATOM    434  CA  PRO   331      92.815  -5.637  12.366  1.00  0.00              
ATOM    435  C   PRO   331      91.518  -6.132  11.753  1.00  0.00              
ATOM    436  O   PRO   331      90.434  -5.926  12.292  1.00  0.00              
ATOM    437  N   GLY   332      91.643  -6.785  10.610  1.00  0.00              
ATOM    438  CA  GLY   332      90.481  -7.277   9.894  1.00  0.00              
ATOM    439  C   GLY   332      90.734  -7.273   8.385  1.00  0.00              
ATOM    440  O   GLY   332      90.725  -8.365   7.785  1.00  0.00              
ATOM    441  N   LEU   356      90.950  -6.102   7.759  1.00  0.00              
ATOM    442  CA  LEU   356      90.881  -4.799   8.390  1.00  0.00              
ATOM    443  C   LEU   356      89.439  -4.301   8.630  1.00  0.00              
ATOM    444  O   LEU   356      88.500  -4.624   7.897  1.00  0.00              
ATOM    445  N   ARG   357      89.311  -3.477   9.667  1.00  0.00              
ATOM    446  CA  ARG   357      88.036  -2.849  10.003  1.00  0.00              
ATOM    447  C   ARG   357      88.270  -1.378  10.294  1.00  0.00              
ATOM    448  O   ARG   357      89.366  -0.994  10.690  1.00  0.00              
ATOM    449  N   VAL   358      87.266  -0.543  10.060  1.00  0.00              
ATOM    450  CA  VAL   358      87.439   0.864  10.397  1.00  0.00              
ATOM    451  C   VAL   358      86.079   1.482  10.568  1.00  0.00              
ATOM    452  O   VAL   358      85.081   0.970  10.056  1.00  0.00              
ATOM    453  N   GLY   359      86.031   2.585  11.306  1.00  0.00              
ATOM    454  CA  GLY   359      84.735   3.172  11.542  1.00  0.00              
ATOM    455  C   GLY   359      84.816   4.572  12.077  1.00  0.00              
ATOM    456  O   GLY   359      85.844   5.047  12.498  1.00  0.00              
ATOM    457  N   ALA   374      83.676   5.223  12.108  1.00  0.00              
ATOM    458  CA  ALA   374      83.607   6.574  12.618  1.00  0.00              
ATOM    459  C   ALA   374      82.247   6.840  13.246  1.00  0.00              
ATOM    460  O   ALA   374      81.285   6.107  13.037  1.00  0.00              
ATOM    461  N   ILE   375      82.198   7.932  14.006  1.00  0.00              
ATOM    462  CA  ILE   375      80.972   8.444  14.600  1.00  0.00              
ATOM    463  C   ILE   375      81.074   9.976  14.671  1.00  0.00              
ATOM    464  O   ILE   375      82.108  10.525  15.082  1.00  0.00              
ATOM    465  N   MET   376      80.021  10.664  14.237  1.00  0.00              
ATOM    466  CA  MET   376      79.991  12.136  14.330  1.00  0.00              
ATOM    467  C   MET   376      79.032  12.453  15.478  1.00  0.00              
ATOM    468  O   MET   376      77.867  12.041  15.446  1.00  0.00              
ATOM    469  N   SER   377      79.504  13.179  16.484  1.00  0.00              
ATOM    470  CA  SER   377      78.695  13.434  17.667  1.00  0.00              
ATOM    471  C   SER   377      78.632  14.898  18.033  1.00  0.00              
ATOM    472  O   SER   377      79.666  15.577  18.043  1.00  0.00              
END
