
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0378AL242_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected    5 , name T0378_D1.pdb
# PARAMETERS: T0378AL242_3-D1.T0378_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        85 - 89          2.99     2.99
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        85 - 88          1.06     3.76
  LCS_AVERAGE:      4.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.07     4.77
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.56     3.45
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.70     6.61
  LCS_AVERAGE:      3.37

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:   89
LCS_GDT     M      85     M      85      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A      86     A      86      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V      87     V      87      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      88     F      88      3    4    5     0    3    4    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D      89     D      89      3    3    5     0    3    3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   4.42  (   3.37    4.27    5.62 )

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      4      4      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   3.37   3.37   4.49   4.49   4.49   4.49   4.49   4.49   4.49   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62
GDT RMS_LOCAL    0.07   0.07   1.06   1.06   1.06   1.06   1.06   1.06   1.06   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_ALL_CA   4.77   4.77   3.76   3.76   3.76   3.76   3.76   3.76   3.76   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99

#      Molecule1      Molecule2       DISTANCE
LGA    M      85      M      85          1.102
LGA    A      86      A      86          0.751
LGA    V      87      V      87          0.788
LGA    F      88      F      88          1.433
LGA    D      89      D      89          8.145

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   89    4.0      4    1.06     4.494     4.621     0.346

LGA_LOCAL      RMSD =  1.055  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.763  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.992  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.773736 * X  +  -0.148556 * Y  +   0.615844 * Z  + -13.721332
  Y_new =  -0.323488 * X  +  -0.928475 * Y  +   0.182455 * Z  + 110.704231
  Z_new =   0.544691 * X  +  -0.340390 * Y  +  -0.766450 * Z  +  91.427307 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.723645    0.417947  [ DEG:  -156.0534     23.9466 ]
  Theta =  -0.576020   -2.565572  [ DEG:   -33.0035   -146.9965 ]
  Phi   =  -0.396000    2.745593  [ DEG:   -22.6891    157.3109 ]
 
# 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: T0378AL242_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL242_3-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   89   4.0    4   1.06   4.621     2.99
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL242_3-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   MET    85       4.020  23.063  45.548  1.00  0.00              
ATOM      2  CA  MET    85       5.101  22.520  46.358  1.00  0.00              
ATOM      3  C   MET    85       4.805  22.626  47.837  1.00  0.00              
ATOM      4  O   MET    85       4.360  23.670  48.307  1.00  0.00              
ATOM      5  N   ALA    86       5.048  21.542  48.566  1.00  0.00              
ATOM      6  CA  ALA    86       4.842  21.540  50.008  1.00  0.00              
ATOM      7  C   ALA    86       6.231  21.549  50.634  1.00  0.00              
ATOM      8  O   ALA    86       7.215  21.194  49.982  1.00  0.00              
ATOM      9  N   VAL    87       6.302  21.957  51.894  1.00  0.00              
ATOM     10  CA  VAL    87       7.555  22.032  52.630  1.00  0.00              
ATOM     11  C   VAL    87       8.420  20.811  52.417  1.00  0.00              
ATOM     12  O   VAL    87       9.640  20.909  52.303  1.00  0.00              
ATOM     13  N   PHE    88       7.767  19.659  52.349  1.00  0.00              
ATOM     14  CA  PHE    88       8.450  18.386  52.174  1.00  0.00              
ATOM     15  C   PHE    88       9.251  18.286  50.885  1.00  0.00              
ATOM     16  O   PHE    88      10.369  17.774  50.898  1.00  0.00              
ATOM     17  N   ASP    89       8.700  18.764  49.774  1.00  0.00              
ATOM     18  CA  ASP    89       9.429  18.655  48.514  1.00  0.00              
ATOM     19  C   ASP    89      10.370  19.816  48.198  1.00  0.00              
ATOM     20  O   ASP    89      10.803  19.981  47.057  1.00  0.00              
END
