
#######################################################
#                                                     #
#                        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   44 (   44),  selected   44 , name T0356TS464_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected   44 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_2-D3.T0356_D3.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:    19       366 - 384         4.94    14.77
  LCS_AVERAGE:     11.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       396 - 402         1.14    21.85
  LCS_AVERAGE:      3.79

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       396 - 400         0.56    22.03
  LONGEST_CONTINUOUS_SEGMENT:     5       398 - 402         0.78    22.29
  LCS_AVERAGE:      3.03

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:  120
LCS_GDT     E     359     E     359      3    4   14     3    3    3    3    5    6    6    8    9   10   11   13   16   17   19   20   22   25   26   26 
LCS_GDT     G     360     G     360      4    4   14     3    3    4    5    6    6    7    8    9   11   14   15   17   19   21   23   24   25   26   26 
LCS_GDT     C     361     C     361      4    4   14     3    3    4    4    6    7    8    9   10   13   15   17   17   19   21   23   24   25   26   26 
LCS_GDT     S     362     S     362      4    5   14     3    3    5    7    8    9    9   10   12   14   16   17   17   19   22   23   24   25   26   26 
LCS_GDT     Y     363     Y     363      4    5   14     3    4    5    6    8    9    9   10   12   14   16   17   17   19   22   23   24   25   26   26 
LCS_GDT     R     364     R     364      4    5   14     3    4    6    7    8    9    9   10   12   14   16   17   17   19   22   23   24   25   26   26 
LCS_GDT     L     365     L     365      4    5   14     3    4    6    7    8    9    9   10   12   14   16   17   17   19   22   23   24   25   26   26 
LCS_GDT     A     366     A     366      3    5   19     3    4    6    7    8    9    9   10   12   14   16   17   17   19   22   23   24   25   26   26 
LCS_GDT     V     367     V     367      3    3   19     3    4    4    5    6    6    7    8   11   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     V     368     V     368      3    3   19     0    3    3    4    4    6    6    8   11   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     T     369     T     369      3    4   19     0    4    4    4    5    5    7    8   11   13   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     I     370     I     370      3    4   19     3    3    4    4    5    6    8    9   10   13   15   17   18   19   22   23   24   25   26   26 
LCS_GDT     K     371     K     371      3    4   19     3    3    4    4    5    5    8    9   10   12   15   16   18   19   19   20   22   25   25   26 
LCS_GDT     K     372     K     372      3    4   19     3    3    4    4    5    6    8    9   10   13   15   17   18   19   22   23   24   25   26   26 
LCS_GDT     Q     373     Q     373      3    4   19     3    3    3    4    4    5    8    9   10   12   15   17   18   19   22   23   24   25   26   26 
LCS_GDT     Y     374     Y     374      4    4   19     3    4    4    4    4    5    7    7   10   12   13   17   18   19   22   23   24   25   26   26 
LCS_GDT     A     375     A     375      4    4   19     3    4    4    5    5    6    8    9   10   13   15   17   18   19   22   23   24   25   26   26 
LCS_GDT     G     376     G     376      4    4   19     3    4    4    4    5    5    6    9   10   12   13   15   18   19   22   22   24   25   26   26 
LCS_GDT     H     377     H     377      4    4   19     3    4    4    5    5    6    8    9   11   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     A     378     A     378      4    4   19     3    3    6    7    8    9    9    9   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     K     379     K     379      4    4   19     3    3    4    5    8    9    9    9   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     R     380     R     380      4    4   19     3    4    6    7    8    9    9    9   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     V     381     V     381      4    4   19     3    4    6    7    8    9    9    9   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     M     382     M     382      3    5   19     1    3    4    5    7    8    9   10   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     M     383     M     383      3    5   19     0    3    4    5    7    8    9   10   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     G     384     G     384      3    5   19     0    3    4    5    7    8    8    9   12   14   16   17   18   19   22   23   24   25   26   26 
LCS_GDT     K     396     K     396      5    7   11     4    5    7    7    7    8    8    8    8   10   10   11   12   13   13   15   15   18   20   21 
LCS_GDT     F     397     F     397      5    7   11     4    5    7    7    7    8    8    8    8   10   10   11   12   13   16   19   19   20   21   21 
LCS_GDT     V     398     V     398      5    7   11     4    5    7    7    7    8    8    8    8   10   13   14   16   17   19   20   21   23   24   25 
LCS_GDT     I     399     I     399      5    7   11     4    5    7    7    7    8    8    8   10   11   13   14   16   17   19   20   21   23   24   25 
LCS_GDT     V     400     V     400      5    7   11     3    5    7    7    7    8    9   10   11   11   13   14   16   17   19   20   22   25   26   26 
LCS_GDT     C     401     C     401      5    7   11     3    4    7    7    7    8    8    8    8   10   13   13   15   17   18   19   22   23   24   25 
LCS_GDT     D     402     D     402      5    7   11     3    4    7    7    7    8    8    8    8   10   10   12   13   15   18   19   19   20   22   25 
LCS_GDT     I     435     I     435      3    4    7     3    3    3    3    4    4    5    7   10   10   12   14   16   17   19   20   21   23   24   25 
LCS_GDT     D     436     D     436      3    4    6     3    3    3    3    4    4    5    8    8   10   12   14   16   17   19   19   21   23   24   25 
LCS_GDT     Y     437     Y     437      3    4    6     3    3    3    3    4    4    5    8    8   10   12   14   16   17   19   20   21   23   24   25 
LCS_GDT     L     438     L     438      3    4    6     0    3    3    3    4    4    5   10   11   11   12   14   16   17   19   20   21   23   24   25 
LCS_GDT     D     439     D     439      3    3    6     0    3    3    3    4    8    9   10   11   11   11   14   16   17   19   20   21   23   24   25 
LCS_GDT     S     445     S     445      3    4    6     3    3    3    4    4    4    5    6    6    6    6    8    8    9   10   10   13   13   15   17 
LCS_GDT     G     446     G     446      3    4    6     3    3    3    4    4    4    5    6    6    6    6    8    8    9   11   13   19   21   24   26 
LCS_GDT     L     447     L     447      3    4    6     3    3    3    4    4    4    5    6    6    6    6    8   10   12   13   13   14   15   17   18 
LCS_GDT     G     448     G     448      3    4    6     0    3    3    4    4    4    5    6    6    8    8    8   10   11   13   13   16   18   19   19 
LCS_GDT     S     449     S     449      3    3    6     0    3    3    3    3    4    5    6    6    8    8   10   10   14   16   17   19   20   21   26 
LCS_GDT     K     450     K     450      3    3    6     0    3    3    3    3    5    6    6    7    9   10   13   13   15   16   18   19   22   24   26 
LCS_AVERAGE  LCS_A:   6.08  (   3.03    3.79   11.42 )

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      5      7      7      8      9      9     10     12     14     16     17     18     19     22     23     24     25     26     26 
GDT PERCENT_CA   3.33   4.17   5.83   5.83   6.67   7.50   7.50   8.33  10.00  11.67  13.33  14.17  15.00  15.83  18.33  19.17  20.00  20.83  21.67  21.67
GDT RMS_LOCAL    0.36   0.56   1.14   1.14   1.61   1.78   1.78   2.77   3.39   3.88   4.15   4.38   4.78   4.94   5.59   5.71   5.87   6.14   6.42   6.42
GDT RMS_ALL_CA  22.41  22.03  21.85  21.85  12.11  12.14  12.14  13.31  11.64  11.94  11.96  11.94  15.54  14.77  12.44  12.50  12.35  12.32  12.35  12.35

#      Molecule1      Molecule2       DISTANCE
LGA    E     359      E     359         14.495
LGA    G     360      G     360         11.769
LGA    C     361      C     361          9.185
LGA    S     362      S     362          3.035
LGA    Y     363      Y     363          2.483
LGA    R     364      R     364          1.752
LGA    L     365      L     365          1.694
LGA    A     366      A     366          2.219
LGA    V     367      V     367          9.270
LGA    V     368      V     368         12.602
LGA    T     369      T     369         13.004
LGA    I     370      I     370         16.594
LGA    K     371      K     371         23.572
LGA    K     372      K     372         22.252
LGA    Q     373      Q     373         22.352
LGA    Y     374      Y     374         22.823
LGA    A     375      A     375         23.167
LGA    G     376      G     376         18.463
LGA    H     377      H     377         18.626
LGA    A     378      A     378         12.619
LGA    K     379      K     379         11.264
LGA    R     380      R     380         11.113
LGA    V     381      V     381          9.551
LGA    M     382      M     382          3.291
LGA    M     383      M     383          2.676
LGA    G     384      G     384          4.451
LGA    K     396      K     396         16.728
LGA    F     397      F     397         13.589
LGA    V     398      V     398          9.553
LGA    I     399      I     399          8.050
LGA    V     400      V     400          3.493
LGA    C     401      C     401          7.979
LGA    D     402      D     402         10.241
LGA    I     435      I     435          5.853
LGA    D     436      D     436          7.564
LGA    Y     437      Y     437          6.183
LGA    L     438      L     438          3.722
LGA    D     439      D     439          3.700
LGA    S     445      S     445         18.246
LGA    G     446      G     446         18.354
LGA    L     447      L     447         19.912
LGA    G     448      G     448         18.609
LGA    S     449      S     449         20.700
LGA    K     450      K     450         18.849

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   44  120    4.0     10    2.77     9.375     8.060     0.348

LGA_LOCAL      RMSD =  2.772  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.600  Number of atoms =   44 
Std_ALL_ATOMS  RMSD = 11.290  (standard rmsd on all 44 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.800708 * X  +  -0.352517 * Y  +   0.484353 * Z  +  62.551861
  Y_new =   0.067736 * X  +  -0.750067 * Y  +  -0.657884 * Z  +  63.291245
  Z_new =   0.595213 * X  +   0.559581 * Y  +  -0.576707 * Z  +  38.890621 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.371265   -0.770328  [ DEG:   135.8634    -44.1365 ]
  Theta =  -0.637530   -2.504062  [ DEG:   -36.5278   -143.4722 ]
  Phi   =   0.084394   -3.057199  [ DEG:     4.8354   -175.1646 ]
 
# 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: T0356TS464_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   44  120   4.0   10   2.77   8.060    11.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D3
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM    107  CA  GLU   359      54.891  70.212  64.237  1.00  0.00
ATOM    108  CA  GLY   360      55.369  70.216  68.005  1.00  0.00
ATOM    109  CA  CYS   361      53.137  67.280  68.860  1.00  0.00
ATOM    110  CA  SER   362      53.715  65.157  71.976  1.00  0.00
ATOM    111  CA  TYR   363      56.160  62.306  71.329  1.00  0.00
ATOM    112  CA  ARG   364      54.237  59.454  69.745  1.00  0.00
ATOM    113  CA  LEU   365      51.321  61.406  68.285  1.00  0.00
ATOM    114  CA  ALA   366      52.020  60.929  64.578  1.00  0.00
ATOM    115  CA  VAL   367      52.692  57.249  65.258  1.00  0.00
ATOM    116  CA  VAL   368      49.317  56.850  66.978  1.00  0.00
ATOM    117  CA  THR   369      47.546  58.356  63.940  1.00  0.00
ATOM    118  CA  ILE   370      49.316  55.830  61.699  1.00  0.00
ATOM    119  CA  LYS   371      48.314  52.664  63.818  1.00  0.00
ATOM    120  CA  LYS   372      44.598  53.543  64.301  1.00  0.00
ATOM    121  CA  GLN   373      44.264  54.061  60.438  1.00  0.00
ATOM    122  CA  TYR   374      46.071  50.699  59.742  1.00  0.00
ATOM    123  CA  ALA   375      43.744  48.872  62.266  1.00  0.00
ATOM    124  CA  GLY   376      40.705  50.475  60.434  1.00  0.00
ATOM    125  CA  HIS   377      41.734  49.234  56.937  1.00  0.00
ATOM    126  CA  ALA   378      44.439  51.495  55.472  1.00  0.00
ATOM    127  CA  LYS   379      46.922  49.232  53.640  1.00  0.00
ATOM    128  CA  ARG   380      50.110  51.252  52.945  1.00  0.00
ATOM    129  CA  VAL   381      51.515  54.335  54.784  1.00  0.00
ATOM    130  CA  MET   382      52.263  57.759  53.222  1.00  0.00
ATOM    131  CA  MET   383      54.182  60.322  55.262  1.00  0.00
ATOM    132  CA  GLY   384      53.625  64.069  55.151  1.00  0.00
ATOM    133  CA  LYS   396      44.584  52.152  50.067  1.00  0.00
ATOM    134  CA  PHE   397      47.365  54.651  50.872  1.00  0.00
ATOM    135  CA  VAL   398      46.303  57.730  52.804  1.00  0.00
ATOM    136  CA  ILE   399      48.869  60.517  53.102  1.00  0.00
ATOM    137  CA  VAL   400      49.091  61.846  56.689  1.00  0.00
ATOM    138  CA  CYS   401      51.288  63.484  59.288  1.00  0.00
ATOM    139  CA  ASP   402      51.033  66.425  61.712  1.00  0.00
ATOM    140  CA  ILE   435      55.911  45.283  64.613  1.00  0.00
ATOM    141  CA  ASP   436      54.310  48.729  65.548  1.00  0.00
ATOM    142  CA  TYR   437      56.350  49.430  68.735  1.00  0.00
ATOM    143  CA  LEU   438      59.323  48.552  70.712  1.00  0.00
ATOM    144  CA  ASP   439      59.488  47.992  74.486  1.00  0.00
ATOM    145  CA  SER   445      59.526  61.233  65.668  1.00  0.00
ATOM    146  CA  GLY   446      60.762  63.797  63.163  1.00  0.00
ATOM    147  CA  LEU   447      57.171  64.787  62.321  1.00  0.00
ATOM    148  CA  GLY   448      56.234  65.007  66.009  1.00  0.00
ATOM    149  CA  SER   449      59.082  67.470  66.491  1.00  0.00
ATOM    150  CA  LYS   450      58.495  69.458  63.311  1.00  0.00
TER
END
