
#######################################################
#                                                     #
#                        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   35 (   35),  selected   35 , name T0384TS464_2_2
# Molecule2: number of CA atoms  303 ( 2393),  selected   35 , name T0384.pdb
# PARAMETERS: T0384TS464_2_2.T0384.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:    23       277 - 299         4.95    11.34
  LONGEST_CONTINUOUS_SEGMENT:    23       278 - 300         4.91    11.89
  LONGEST_CONTINUOUS_SEGMENT:    23       279 - 301         4.48    12.68
  LCS_AVERAGE:      7.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       291 - 301         1.71    13.87
  LCS_AVERAGE:      2.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       292 - 301         0.32    12.75
  LCS_AVERAGE:      1.91

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:  303
LCS_GDT     Q     267     Q     267      3    3   14     0    3    3    3    4    4    5    5    6    7    9   11   16   17   19   19   25   25   25   31 
LCS_GDT     L     268     L     268      3    3   15     3    3    3    3    4    4    5    5    7    9    9   11   16   17   19   24   25   25   25   31 
LCS_GDT     P     269     P     269      3    3   15     3    3    3    3    4    4    5    5    7    9   10   11   16   19   21   24   25   28   29   31 
LCS_GDT     I     270     I     270      3    3   20     3    3    3    3    4    4    5    8    9   12   15   18   21   25   26   28   30   31   31   31 
LCS_GDT     Q     271     Q     271      3    3   20     3    4    4    4    4    5    8   10   13   14   15   18   21   25   26   28   30   31   31   31 
LCS_GDT     Q     272     Q     272      3    3   20     3    4    4    4    6    7    8   10   11   14   15   18   21   24   26   28   30   31   31   31 
LCS_GDT     A     273     A     273      4    4   20     3    4    4    5    6    7    8   10   13   14   15   19   21   25   26   28   30   31   31   31 
LCS_GDT     P     274     P     274      4    4   20     3    3    4    4    5    7    7    9   13   14   16   19   22   25   26   28   30   31   31   31 
LCS_GDT     H     275     H     275      4    4   20     3    3    4    4    5    7    8   10   13   14   16   19   22   25   26   28   30   31   31   31 
LCS_GDT     T     276     T     276      4    5   21     3    3    4    5    6    7    7    9    9   13   16   19   22   25   26   28   30   31   31   31 
LCS_GDT     M     277     M     277      4    5   23     3    6    6    7    7    7    8   10   13   14   17   20   22   25   26   28   30   31   31   31 
LCS_GDT     T     278     T     278      4    6   23     3    4    4    5    6    8    9   11   13   14   16   19   22   25   26   28   30   31   31   31 
LCS_GDT     E     279     E     279      5    6   23     4    5    6    7    8    9   10   11   14   16   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     E     280     E     280      5    6   23     4    5    6    7    8   10   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     V     281     V     281      5    6   23     4    5    6    7    8    9   10   11   13   15   18   20   22   23   23   24   24   25   28   29 
LCS_GDT     A     282     A     282      5    6   23     4    5    6    7    8    9   10   11   13   16   17   20   22   25   26   28   29   31   31   31 
LCS_GDT     A     283     A     283      5    6   23     4    5    6    7   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     F     284     F     284      5    7   23     5    6   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     A     285     A     285      5    7   23     5    6    6    7    8    9   10   11   13   16   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     H     286     H     286      5    7   23     5    6    6    7    8   11   12   15   16   17   17   20   22   25   26   28   30   31   31   31 
LCS_GDT     M     287     M     287      5    7   23     5    6    6    7    8    9   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     I     288     I     288      5    7   23     5    6    6    7    8   11   13   14   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     Q     289     Q     289      3    7   23     3    5    6    7    8   10   13   14   14   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     Q     290     Q     290      4    7   23     3    4    5    6    8   11   13   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     P     291     P     291      4   11   23     3    4    5    6    8   12   13   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     D     292     D     292     10   11   23     7   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     L     293     L     293     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     N     294     N     294     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     L     295     L     295     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     Y     296     Y     296     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     Q     297     Q     297     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     T     298     T     298     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     W     299     W     299     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     L     300     L     300     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_GDT     Y     301     Y     301     10   11   23     9   10   11   11   12   12   14   16   17   18   18   20   22   25   26   28   30   31   31   31 
LCS_AVERAGE  LCS_A:   3.80  (   1.91    2.32    7.17 )

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      9     10     11     11     12     12     14     16     17     18     18     20     22     25     26     28     30     31     31     31 
GDT PERCENT_CA   2.97   3.30   3.63   3.63   3.96   3.96   4.62   5.28   5.61   5.94   5.94   6.60   7.26   8.25   8.58   9.24   9.90  10.23  10.23  10.23
GDT RMS_LOCAL    0.25   0.32   0.74   0.74   1.19   1.19   1.71   2.67   3.00   3.24   3.24   3.78   4.39   5.29   5.39   5.67   6.01   6.15   6.15   6.15
GDT RMS_ALL_CA  12.80  12.75  13.53  13.53  13.39  13.39  13.16  12.90  13.41  13.60  13.60  13.94  12.69   9.54   9.30   8.61   7.66   7.72   7.72   7.72

#      Molecule1      Molecule2       DISTANCE
LGA    Q     267      Q     267         30.070
LGA    L     268      L     268         29.660
LGA    P     269      P     269         25.532
LGA    I     270      I     270         22.234
LGA    Q     271      Q     271         24.473
LGA    Q     272      Q     272         22.442
LGA    A     273      A     273         18.964
LGA    P     274      P     274         21.363
LGA    H     275      H     275         20.879
LGA    T     276      T     276         19.615
LGA    M     277      M     277         15.650
LGA    T     278      T     278         15.854
LGA    E     279      E     279         11.001
LGA    E     280      E     280          3.995
LGA    V     281      V     281          7.851
LGA    A     282      A     282          8.820
LGA    A     283      A     283          3.238
LGA    F     284      F     284          2.322
LGA    A     285      A     285          6.715
LGA    H     286      H     286          6.423
LGA    M     287      M     287          3.993
LGA    I     288      I     288          5.204
LGA    Q     289      Q     289          5.706
LGA    Q     290      Q     290          3.771
LGA    P     291      P     291          2.608
LGA    D     292      D     292          3.989
LGA    L     293      L     293          1.991
LGA    N     294      N     294          2.335
LGA    L     295      L     295          3.012
LGA    Y     296      Y     296          1.339
LGA    Q     297      Q     297          1.219
LGA    T     298      T     298          2.956
LGA    W     299      W     299          1.917
LGA    L     300      L     300          2.203
LGA    Y     301      Y     301          3.790

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35  303    4.0     16    2.67     5.363     4.464     0.577

LGA_LOCAL      RMSD =  2.673  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.846  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  7.320  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.647421 * X  +  -0.760466 * Y  +  -0.050378 * Z  +  27.719742
  Y_new =   0.607884 * X  +   0.555129 * Y  +  -0.567723 * Z  +  63.559826
  Z_new =   0.459700 * X  +   0.336932 * Y  +   0.821677 * Z  +  63.129025 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.389143   -2.752449  [ DEG:    22.2963   -157.7037 ]
  Theta =  -0.477658   -2.663935  [ DEG:   -27.3678   -152.6322 ]
  Phi   =   0.753913   -2.387680  [ DEG:    43.1960   -136.8040 ]
 
# 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: T0384TS464_2_2                                
REMARK     2: T0384.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0384TS464_2_2.T0384.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35  303   4.0   16   2.67   4.464     7.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0384TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0384
PARENT N/A
ATOM      1  CA  GLN   267     -21.400  72.864  85.005  1.00  0.00
ATOM      2  CA  LEU   268     -20.249  74.118  88.400  1.00  0.00
ATOM      3  CA  PRO   269     -17.049  75.492  86.885  1.00  0.00
ATOM      4  CA  ILE   270     -18.899  76.962  83.914  1.00  0.00
ATOM      5  CA  GLN   271     -21.351  78.851  86.133  1.00  0.00
ATOM      6  CA  GLN   272     -18.611  80.178  88.415  1.00  0.00
ATOM      7  CA  ALA   273     -16.344  81.221  85.540  1.00  0.00
ATOM      8  CA  PRO   274     -19.196  82.937  83.702  1.00  0.00
ATOM      9  CA  HIS   275     -19.561  85.265  86.690  1.00  0.00
ATOM     10  CA  THR   276     -16.019  86.648  86.704  1.00  0.00
ATOM     11  CA  MET   277     -15.652  86.292  82.938  1.00  0.00
ATOM     12  CA  THR   278     -12.768  83.885  82.366  1.00  0.00
ATOM     13  CA  GLU   279     -12.767  80.605  80.445  1.00  0.00
ATOM     14  CA  GLU   280     -13.284  77.023  81.603  1.00  0.00
ATOM     15  CA  VAL   281     -10.013  75.772  80.093  1.00  0.00
ATOM     16  CA  ALA   282      -7.871  77.908  82.403  1.00  0.00
ATOM     17  CA  ALA   283      -9.703  76.315  85.317  1.00  0.00
ATOM     18  CA  PHE   284     -10.015  78.531  88.266  1.00  0.00
ATOM     19  CA  ALA   285      -6.407  79.555  87.968  1.00  0.00
ATOM     20  CA  HIS   286      -6.386  79.660  91.764  1.00  0.00
ATOM     21  CA  MET   287      -7.605  76.093  92.002  1.00  0.00
ATOM     22  CA  ILE   288      -5.182  74.453  89.545  1.00  0.00
ATOM     23  CA  GLN   289      -1.663  73.170  90.300  1.00  0.00
ATOM     24  CA  GLN   290       1.043  75.748  89.757  1.00  0.00
ATOM     25  CA  PRO   291       1.607  79.413  90.499  1.00  0.00
ATOM     26  CA  ASP   292      -1.752  81.102  90.329  1.00  0.00
ATOM     27  CA  LEU   293      -0.278  84.297  88.934  1.00  0.00
ATOM     28  CA  ASN   294       1.177  82.662  85.849  1.00  0.00
ATOM     29  CA  LEU   295      -1.736  80.263  85.360  1.00  0.00
ATOM     30  CA  TYR   296      -4.230  83.088  85.509  1.00  0.00
ATOM     31  CA  GLN   297      -2.349  84.936  82.798  1.00  0.00
ATOM     32  CA  THR   298      -2.239  81.738  80.783  1.00  0.00
ATOM     33  CA  TRP   299      -6.004  81.294  80.870  1.00  0.00
ATOM     34  CA  LEU   300      -6.738  84.890  79.934  1.00  0.00
ATOM     35  CA  TYR   301      -4.230  84.513  77.114  1.00  0.00
TER
END
