
#######################################################
#                                                     #
#                        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    5 (   25),  selected    5 , name T0320TS239_4_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    5 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_4_1-D1.T0320_D1.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:     5         1 - 6           1.43     1.43
  LCS_AVERAGE:      2.34

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         1 - 6           1.43     1.43
  LCS_AVERAGE:      2.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4         2 - 6           0.87     1.95
  LCS_AVERAGE:      1.50

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:  214
LCS_GDT     M       1     M       1      0    5    5     0    0    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     Q       2     Q       2      4    5    5     2    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S       4     S       4      4    5    5     3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K       5     K       5      4    5    5     3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A       6     A       6      4    5    5     3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.06  (   1.50    2.34    2.34 )

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      3      3      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.40   1.40   1.87   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34   2.34
GDT RMS_LOCAL    0.02   0.02   0.87   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43
GDT RMS_ALL_CA   2.33   2.33   1.95   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          1.824
LGA    Q       2      Q       2          1.580
LGA    S       4      S       4          1.914
LGA    K       5      K       5          0.654
LGA    A       6      A       6          0.495

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  214    4.0      5    1.43     2.103     2.228     0.328

LGA_LOCAL      RMSD =  1.425  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.425  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.425  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.282365 * X  +  -0.667070 * Y  +   0.689411 * Z  +  23.197166
  Y_new =   0.957710 * X  +   0.237468 * Y  +  -0.162481 * Z  +  -1.563160
  Z_new =  -0.055327 * X  +   0.706135 * Y  +   0.705912 * Z  + -51.334850 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.785556   -2.356037  [ DEG:    45.0090   -134.9910 ]
  Theta =   0.055355    3.086237  [ DEG:     3.1716    176.8284 ]
  Phi   =   1.284087   -1.857506  [ DEG:    73.5727   -106.4273 ]
 
# 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: T0320TS239_4_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_4_1-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  214   4.0    5   1.43   2.228     1.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_4_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       6.125  43.453  23.169  1.00  9.99
ATOM      2  CA  MET     1       6.239  42.076  22.638  1.00  9.99
ATOM      3  C   MET     1       6.972  41.232  23.684  1.00  9.99
ATOM      4  O   MET     1       6.609  40.036  23.753  1.00  9.99
ATOM      5  CB  MET     1       6.948  42.034  21.304  1.00  9.99
ATOM      6  N   GLN     2       7.819  41.809  24.499  1.00  9.99
ATOM      7  CA  GLN     2       8.461  41.042  25.565  1.00  9.99
ATOM      8  C   GLN     2       7.445  40.434  26.494  1.00  9.99
ATOM      9  O   GLN     2       7.486  39.233  26.883  1.00  9.99
ATOM     10  CB  GLN     2       9.538  41.889  26.257  1.00  9.99
ATOM     11  N   SER     4       6.515  41.245  26.974  1.00  9.99
ATOM     12  CA  SER     4       5.456  40.809  27.860  1.00  9.99
ATOM     13  C   SER     4       4.577  39.781  27.211  1.00  9.99
ATOM     14  O   SER     4       4.161  38.771  27.821  1.00  9.99
ATOM     15  CB  SER     4       4.573  42.005  28.284  1.00  9.99
ATOM     16  N   LYS     5       4.276  39.896  25.939  1.00  9.99
ATOM     17  CA  LYS     5       3.473  38.985  25.190  1.00  9.99
ATOM     18  C   LYS     5       4.206  37.630  25.149  1.00  9.99
ATOM     19  O   LYS     5       3.615  36.569  25.367  1.00  9.99
ATOM     20  CB  LYS     5       3.146  39.440  23.799  1.00  9.99
ATOM     21  N   ALA     6       5.477  37.602  24.762  1.00  9.99
ATOM     22  CA  ALA     6       6.223  36.351  24.640  1.00  9.99
ATOM     23  C   ALA     6       6.364  35.692  26.001  1.00  9.99
ATOM     24  O   ALA     6       6.143  34.464  26.104  1.00  9.99
ATOM     25  CB  ALA     6       7.612  36.638  24.070  1.00  9.99
TER
END
