
#######################################################
#                                                     #
#                        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_5_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   13 , name T0320_D2.pdb
# PARAMETERS: T0320TS464_5_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          3.938
LGA    D     295      D     295          3.413
LGA    D     296      D     296          1.249
LGA    T     297      T     297          2.125
LGA    L     298      L     298          2.341
LGA    E     299      E     299          1.486
LGA    R     300      R     300          3.112
LGA    A     301      A     301          2.049
LGA    G     302      G     302          2.685
LGA    R     303      R     303          6.116
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 =  -0.919658 * X  +   0.360510 * Y  +  -0.155761 * Z  +  -8.425946
  Y_new =   0.385953 * X  +   0.902993 * Y  +  -0.188793 * Z  + -36.281895
  Z_new =   0.072590 * X  +  -0.233742 * Y  +  -0.969585 * Z  +  32.148125 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.905032    0.236560  [ DEG:  -166.4461     13.5539 ]
  Theta =  -0.072653   -3.068939  [ DEG:    -4.1627   -175.8373 ]
  Phi   =   2.744245   -0.397348  [ DEG:   157.2336    -22.7664 ]
 
# 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_5_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_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_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM     59  CA  TYR   292       8.018   9.926  15.184  1.00  0.00
ATOM     60  CA  LEU   293      10.383   6.939  14.909  1.00  0.00
ATOM     61  CA  VAL   294      11.452   7.737  11.344  1.00  0.00
ATOM     62  CA  ASP   295      12.133  11.381  12.371  1.00  0.00
ATOM     63  CA  ASP   296      14.608  10.045  14.947  1.00  0.00
ATOM     64  CA  THR   297      16.381   7.844  12.412  1.00  0.00
ATOM     65  CA  LEU   298      16.720  10.730   9.952  1.00  0.00
ATOM     66  CA  GLU   299      18.243  12.874  12.729  1.00  0.00
ATOM     67  CA  ARG   300      20.571  10.049  13.780  1.00  0.00
ATOM     68  CA  ALA   301      22.024   9.965  10.259  1.00  0.00
ATOM     69  CA  GLY   302      22.247  13.703   9.678  1.00  0.00
ATOM     70  CA  ARG   303      19.412  13.807   7.132  1.00  0.00
ATOM     71  CA  ILE   304      16.666  15.666   9.079  1.00  0.00
TER
END
