
#######################################################
#                                                     #
#                        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   37 (   37),  selected   37 , name T0301TS464_2_2
# Molecule2: number of CA atoms  391 ( 2894),  selected   37 , name T0301.pdb
# PARAMETERS: T0301TS464_2_2.T0301.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:    22       312 - 361         4.84    12.05
  LCS_AVERAGE:      4.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       316 - 360         1.91    11.94
  LONGEST_CONTINUOUS_SEGMENT:    17       345 - 361         1.92    11.93
  LCS_AVERAGE:      2.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       346 - 353         0.96    12.60
  LCS_AVERAGE:      1.64

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:  391
LCS_GDT     I     146     I     146      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   20   21   24   26   27 
LCS_GDT     A     147     A     147      7    7   14     5    6    7    7    7    8   10   12   12   13   13   14   15   16   20   22   22   24   26   27 
LCS_GDT     H     148     H     148      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   16   20   20   21   24   26   27 
LCS_GDT     V     149     V     149      7    7   14     5    6    7    7    7    8   10   12   12   13   13   14   15   16   20   20   21   24   26   27 
LCS_GDT     P     150     P     150      7    7   14     5    6    7    7    7    8   10   12   12   13   13   14   15   16   20   20   21   24   26   27 
LCS_GDT     V     151     V     151      7    7   14     3    6    7    7    7    8   10   12   12   13   13   14   15   16   20   20   21   22   23   26 
LCS_GDT     S     152     S     152      7    7   14     3    4    7    7    7    8   10   12   12   13   13   14   15   16   20   20   21   22   23   26 
LCS_GDT     G     153     G     153      6    7   14     4    5    6    6    6    8   10   12   12   13   13   14   15   16   20   20   21   22   23   26 
LCS_GDT     G     154     G     154      6    7   14     4    5    6    6    6    8   10   12   12   13   13   14   15   16   18   18   21   22   23   26 
LCS_GDT     Q     155     Q     155      6    7   14     4    5    6    6    6    8   10   12   12   13   13   14   15   16   20   20   21   22   23   26 
LCS_GDT     V     156     V     156      6    7   14     4    5    6    6    6    7   10   12   12   13   13   14   15   16   20   20   21   22   26   27 
LCS_GDT     Q     157     Q     157      6    7   14     3    5    6    6    6    6    9   12   12   13   13   14   15   16   20   22   22   24   26   27 
LCS_GDT     E     158     E     158      6    7   14     3    4    6    6    6    6    8   10   10   13   13   14   15   16   20   22   22   23   26   27 
LCS_GDT     T     159     T     159      3    5   14     3    3    4    4    5    6    8    8   10   10   11   12   12   12   13   14   21   23   23   24 
LCS_GDT     G     160     G     160      3    5   14     3    3    3    4    5    6    8    8    9    9   11   12   12   12   12   14   14   17   17   23 
LCS_GDT     L     312     L     312      4    5   22     3    4    4    4    5    5    5    6    7    7    7    7    7   13   13   13   14   16   16   22 
LCS_GDT     H     313     H     313      4    5   22     3    4    4    4    5    5    5    7    7    9   10   13   14   19   20   21   21   23   23   24 
LCS_GDT     H     314     H     314      4    5   22     3    4    4    4    5    5    5    5    7    9   13   17   19   19   20   21   21   23   26   26 
LCS_GDT     A     315     A     315      4    5   22     3    4    4    4    5    5    7   11   15   17   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     M     316     M     316      3   17   22     0    3    3    6   12   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     S     345     S     345      7   17   22     5    5    8   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     A     346     A     346      8   17   22     3    6   10   13   14   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     V     347     V     347      8   17   22     3    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     R     348     R     348      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     F     349     F     349      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     G     350     G     350      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     H     351     H     351      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     P     352     P     352      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     S     353     S     353      8   17   22     4    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   23   26   27 
LCS_GDT     G     354     G     354      7   17   22     5    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     T     355     T     355      7   17   22     3    6    6   11   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     L     356     L     356      7   17   22     5    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     R     357     R     357      7   17   22     3    4    5   11   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     V     358     V     358      7   17   22     5    6   10   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     G     359     G     359      7   17   22     3    6    6   11   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     A     360     A     360      7   17   22     5    6    9   13   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_GDT     E     361     E     361      7   17   22     3    6    6   10   16   18   18   18   18   18   18   19   19   19   20   22   22   24   26   27 
LCS_AVERAGE  LCS_A:   3.13  (   1.64    2.95    4.80 )

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      5      6     10     13     16     18     18     18     18     18     18     19     19     19     20     22     22     24     26     27 
GDT PERCENT_CA   1.28   1.53   2.56   3.32   4.09   4.60   4.60   4.60   4.60   4.60   4.60   4.86   4.86   4.86   5.12   5.63   5.63   6.14   6.65   6.91
GDT RMS_LOCAL    0.30   0.43   1.13   1.36   1.86   2.01   2.01   2.01   2.01   2.01   2.01   2.71   2.71   2.71   3.39   4.81   4.81   6.26   6.50   6.63
GDT RMS_ALL_CA  23.71  23.14  12.05  12.19  11.91  11.84  11.84  11.84  11.84  11.84  11.84  11.73  11.73  11.73  11.78  10.81  10.81   9.76   9.74   9.73

#      Molecule1      Molecule2       DISTANCE
LGA    I     146      I     146         12.483
LGA    A     147      A     147         11.781
LGA    H     148      H     148         15.115
LGA    V     149      V     149         15.631
LGA    P     150      P     150         17.451
LGA    V     151      V     151         21.638
LGA    S     152      S     152         22.777
LGA    G     153      G     153         22.717
LGA    G     154      G     154         22.509
LGA    Q     155      Q     155         18.304
LGA    V     156      V     156         14.895
LGA    Q     157      Q     157         14.146
LGA    E     158      E     158         12.663
LGA    T     159      T     159         14.994
LGA    G     160      G     160         18.168
LGA    L     312      L     312         15.867
LGA    H     313      H     313         10.967
LGA    H     314      H     314         10.573
LGA    A     315      A     315          8.700
LGA    M     316      M     316          3.023
LGA    S     345      S     345          1.805
LGA    A     346      A     346          2.660
LGA    V     347      V     347          1.431
LGA    R     348      R     348          1.430
LGA    F     349      F     349          1.508
LGA    G     350      G     350          1.829
LGA    H     351      H     351          2.037
LGA    P     352      P     352          1.896
LGA    S     353      S     353          1.131
LGA    G     354      G     354          0.844
LGA    T     355      T     355          2.622
LGA    L     356      L     356          1.727
LGA    R     357      R     357          2.407
LGA    V     358      V     358          1.566
LGA    G     359      G     359          2.497
LGA    A     360      A     360          1.272
LGA    E     361      E     361          2.861

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   37  391    4.0     18    2.01     3.772     3.761     0.851

LGA_LOCAL      RMSD =  2.015  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.839  Number of atoms =   37 
Std_ALL_ATOMS  RMSD =  9.259  (standard rmsd on all 37 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.987868 * X  +  -0.041979 * Y  +   0.149516 * Z  + 105.399811
  Y_new =  -0.061489 * X  +   0.989820 * Y  +  -0.128355 * Z  +  -2.188268
  Z_new =  -0.142606 * X  +  -0.135991 * Y  +  -0.980393 * Z  +  62.730221 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.003762    0.137831  [ DEG:  -172.1029      7.8971 ]
  Theta =   0.143094    2.998499  [ DEG:     8.1987    171.8013 ]
  Phi   =  -3.079429    0.062164  [ DEG:  -176.4383      3.5617 ]
 
# 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: T0301TS464_2_2                                
REMARK     2: T0301.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_2_2.T0301.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   37  391   4.0   18   2.01   3.761     9.26
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  ILE   146      83.388  11.267  15.498  1.00  0.00
ATOM      2  CA  ALA   147      82.170  12.616  18.777  1.00  0.00
ATOM      3  CA  HIS   148      84.292  14.301  21.447  1.00  0.00
ATOM      4  CA  VAL   149      82.885  12.986  24.701  1.00  0.00
ATOM      5  CA  PRO   150      83.496  14.321  28.220  1.00  0.00
ATOM      6  CA  VAL   151      83.546  11.186  30.312  1.00  0.00
ATOM      7  CA  SER   152      83.022  13.170  33.523  1.00  0.00
ATOM      8  CA  GLY   153      79.948  15.124  32.471  1.00  0.00
ATOM      9  CA  GLY   154      78.599  12.353  30.197  1.00  0.00
ATOM     10  CA  GLN   155      77.944  14.693  27.254  1.00  0.00
ATOM     11  CA  VAL   156      79.246  15.134  23.696  1.00  0.00
ATOM     12  CA  GLN   157      81.227  18.409  23.480  1.00  0.00
ATOM     13  CA  GLU   158      81.782  18.576  19.729  1.00  0.00
ATOM     14  CA  THR   159      81.156  16.600  16.537  1.00  0.00
ATOM     15  CA  GLY   160      84.028  16.414  14.067  1.00  0.00
ATOM     16  CA  LEU   312      91.245   4.471  18.651  1.00  0.00
ATOM     17  CA  HIS   313      92.636   7.937  17.996  1.00  0.00
ATOM     18  CA  HIS   314      91.499  11.291  16.706  1.00  0.00
ATOM     19  CA  ALA   315      94.012  12.424  14.079  1.00  0.00
ATOM     20  CA  MET   316      94.953  15.366  16.332  1.00  0.00
ATOM     21  CA  SER   345      84.416  -1.246  14.872  1.00  0.00
ATOM     22  CA  ALA   346      83.212  -0.506  18.419  1.00  0.00
ATOM     23  CA  VAL   347      86.202   1.144  20.047  1.00  0.00
ATOM     24  CA  ARG   348      85.414   4.031  22.418  1.00  0.00
ATOM     25  CA  PHE   349      88.985   5.298  22.039  1.00  0.00
ATOM     26  CA  GLY   350      90.544   7.139  24.981  1.00  0.00
ATOM     27  CA  HIS   351      92.399  10.137  23.600  1.00  0.00
ATOM     28  CA  PRO   352      95.563  11.624  25.186  1.00  0.00
ATOM     29  CA  SER   353      93.491  14.500  26.569  1.00  0.00
ATOM     30  CA  GLY   354      90.984  12.293  28.359  1.00  0.00
ATOM     31  CA  THR   355      88.273  12.649  25.743  1.00  0.00
ATOM     32  CA  LEU   356      86.745   9.667  23.907  1.00  0.00
ATOM     33  CA  ARG   357      86.185   9.152  20.163  1.00  0.00
ATOM     34  CA  VAL   358      84.297   6.402  18.333  1.00  0.00
ATOM     35  CA  GLY   359      85.376   5.935  14.679  1.00  0.00
ATOM     36  CA  ALA   360      83.267   3.755  12.311  1.00  0.00
ATOM     37  CA  GLU   361      81.807   3.649   8.747  1.00  0.00
TER
END
