
#######################################################
#                                                     #
#                        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   13 (   13),  selected   13 , name T0320TS464_4_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   13 , name T0320_D2.pdb
# PARAMETERS: T0320TS464_4_1-D2.T0320_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:    13       292 - 304         4.61     4.61
  LCS_AVERAGE:     17.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       295 - 302         1.35     6.94
  LCS_AVERAGE:      9.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       295 - 299         0.28     6.60
  LCS_AVERAGE:      5.69

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:   73
LCS_GDT     Y     292     Y     292      3    4   13     2    3    5    5    5    6    7    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     L     293     L     293      3    4   13     3    3    5    5    5    5    7    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     V     294     V     294      3    4   13     3    3    3    4    5    6    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     D     295     D     295      5    8   13     5    5    6    8    8    8    8    9    9   10   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     D     296     D     296      5    8   13     5    5    6    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     T     297     T     297      5    8   13     5    5    6    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     L     298     L     298      5    8   13     5    5    6    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     E     299     E     299      5    8   13     5    5    6    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     R     300     R     300      4    8   13     4    4    5    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     A     301     A     301      4    8   13     4    4    6    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     G     302     G     302      4    8   13     3    4    5    8    8    8    8    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     R     303     R     303      4    5   13     3    4    4    4    4    5    5    9   11   11   11   12   12   12   12   12   12   13   13   13 
LCS_GDT     I     304     I     304      4    5   13     0    4    4    4    4    5    5    5    5    6    9    9    9    9    9    9   11   13   13   13 
LCS_AVERAGE  LCS_A:  10.85  (   5.69    9.06   17.81 )

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      5      6      8      8      8      8      9     11     11     11     12     12     12     12     12     12     13     13     13 
GDT PERCENT_CA   6.85   6.85   8.22  10.96  10.96  10.96  10.96  12.33  15.07  15.07  15.07  16.44  16.44  16.44  16.44  16.44  16.44  17.81  17.81  17.81
GDT RMS_LOCAL    0.28   0.28   0.95   1.35   1.35   1.35   1.35   2.32   3.68   3.68   3.68   3.92   3.92   3.92   3.92   3.92   3.92   4.61   4.61   4.61
GDT RMS_ALL_CA   6.60   6.60   7.19   6.94   6.94   6.94   6.94   6.27   4.73   4.73   4.73   4.75   4.75   4.75   4.75   4.75   4.75   4.61   4.61   4.61

#      Molecule1      Molecule2       DISTANCE
LGA    Y     292      Y     292          9.660
LGA    L     293      L     293          8.321
LGA    V     294      V     294          3.937
LGA    D     295      D     295          3.412
LGA    D     296      D     296          1.250
LGA    T     297      T     297          2.125
LGA    L     298      L     298          2.341
LGA    E     299      E     299          1.485
LGA    R     300      R     300          3.111
LGA    A     301      A     301          2.049
LGA    G     302      G     302          2.685
LGA    R     303      R     303          6.115
LGA    I     304      I     304         12.138

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   73    4.0      9    2.32    11.644    11.452     0.371

LGA_LOCAL      RMSD =  2.325  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.611  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  4.607  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.596555 * X  +   0.736853 * Y  +   0.318073 * Z  + -85.874420
  Y_new =   0.771875 * X  +   0.635317 * Y  +  -0.024113 * Z  + -108.610786
  Z_new =  -0.219845 * X  +   0.231127 * Y  +  -0.947760 * Z  +   5.498618 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.902394   -0.239198  [ DEG:   166.2950    -13.7051 ]
  Theta =   0.221655    2.919937  [ DEG:    12.6999    167.3001 ]
  Phi   =   2.228771   -0.912821  [ DEG:   127.6992    -52.3008 ]
 
# 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: T0320TS464_4_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_1-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   73   4.0    9   2.32  11.452     4.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM     81  CA  TYR   292       8.017   9.928  15.185  1.00  0.00
ATOM     82  CA  LEU   293      10.383   6.939  14.910  1.00  0.00
ATOM     83  CA  VAL   294      11.451   7.738  11.344  1.00  0.00
ATOM     84  CA  ASP   295      12.133  11.381  12.371  1.00  0.00
ATOM     85  CA  ASP   296      14.609  10.045  14.947  1.00  0.00
ATOM     86  CA  THR   297      16.381   7.844  12.412  1.00  0.00
ATOM     87  CA  LEU   298      16.720  10.729   9.951  1.00  0.00
ATOM     88  CA  GLU   299      18.242  12.874  12.729  1.00  0.00
ATOM     89  CA  ARG   300      20.571  10.050  13.779  1.00  0.00
ATOM     90  CA  ALA   301      22.024   9.965  10.261  1.00  0.00
ATOM     91  CA  GLY   302      22.248  13.703   9.678  1.00  0.00
ATOM     92  CA  ARG   303      19.412  13.807   7.132  1.00  0.00
ATOM     93  CA  ILE   304      16.666  15.665   9.078  1.00  0.00
TER
END
