
#######################################################
#                                                     #
#                        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    7 (   54),  selected    7 , name T0378TS302_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_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:     7        83 - 89          3.43     3.43
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.42     3.79
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.42     4.68
  LCS_AVERAGE:      4.98

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     P      83     P      83      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     L      84     L      84      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     M      85     M      85      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     A      86     A      86      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     V      87     V      87      5    6    7     4    5    5    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      3    6    7     1    3    4    5    6    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     D      89     D      89      3    3    7     0    3    3    3    3    3    4    4    4    4    6    6    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   6.37  (   4.98    6.26    7.87 )

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      4      5      5      5      6      6      6      6      6      6      6      6      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.49   5.62   5.62   5.62   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.28   0.42   0.42   0.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43
GDT RMS_ALL_CA   4.66   4.68   4.68   4.68   3.79   3.79   3.79   3.79   3.79   3.79   3.79   3.79   3.43   3.43   3.43   3.43   3.43   3.43   3.43   3.43

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          1.675
LGA    L      84      L      84          0.948
LGA    M      85      M      85          0.881
LGA    A      86      A      86          1.252
LGA    V      87      V      87          0.615
LGA    F      88      F      88          2.367
LGA    D      89      D      89          9.421

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.42     6.461     6.508     0.396

LGA_LOCAL      RMSD =  1.416  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.794  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.427  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.343710 * X  +  -0.194884 * Y  +  -0.918631 * Z  +  50.331650
  Y_new =   0.087014 * X  +  -0.967411 * Y  +   0.237789 * Z  +  99.665909
  Z_new =  -0.935036 * X  +  -0.161665 * Y  +  -0.315552 * Z  + 126.941818 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.668135    0.473458  [ DEG:  -152.8728     27.1271 ]
  Theta =   1.208360    1.933233  [ DEG:    69.2339    110.7661 ]
  Phi   =   0.247952   -2.893641  [ DEG:    14.2066   -165.7934 ]
 
# 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: T0378TS302_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_3-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   89   4.0    6   1.42   6.508     3.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1gz0_B
ATOM   1000  N   PRO    83       1.402  25.480  39.986  1.00  0.00
ATOM   1000  CA  PRO    83       1.421  24.295  40.817  1.00  0.00
ATOM   1000  C   PRO    83       1.384  24.829  42.212  1.00  0.00
ATOM   1000  O   PRO    83       0.962  25.970  42.380  1.00  0.00
ATOM   1000  CB  PRO    83       2.726  23.557  40.441  1.00  0.00
ATOM   1000  CG  PRO    83       3.645  24.612  39.750  1.00  0.00
ATOM   1000  CD  PRO    83       2.712  25.799  39.400  1.00  0.00
ATOM   1000  N   LEU    84       1.780  24.028  43.205  1.00  0.00
ATOM   1000  CA  LEU    84       1.379  24.169  44.568  1.00  0.00
ATOM   1000  C   LEU    84       2.374  23.236  45.143  1.00  0.00
ATOM   1000  O   LEU    84       2.901  22.398  44.417  1.00  0.00
ATOM   1000  CB  LEU    84      -0.027  23.655  44.954  1.00  0.00
ATOM   1000  CG  LEU    84      -1.178  24.698  44.959  1.00  0.00
ATOM   1000  CD1 LEU    84      -0.832  26.038  45.647  1.00  0.00
ATOM   1000  CD2 LEU    84      -1.822  24.906  43.573  1.00  0.00
ATOM   1000  N   MET    85       2.683  23.367  46.434  1.00  0.00
ATOM   1000  CA  MET    85       3.996  23.037  46.891  1.00  0.00
ATOM   1000  C   MET    85       3.763  22.911  48.345  1.00  0.00
ATOM   1000  O   MET    85       2.657  23.155  48.828  1.00  0.00
ATOM   1000  CB  MET    85       5.128  24.053  46.641  1.00  0.00
ATOM   1000  CG  MET    85       5.662  24.119  45.210  1.00  0.00
ATOM   1000  SD  MET    85       6.016  22.521  44.433  1.00  0.00
ATOM   1000  CE  MET    85       5.552  23.141  42.794  1.00  0.00
ATOM   1000  N   ALA    86       4.797  22.477  49.068  1.00  0.00
ATOM   1000  CA  ALA    86       4.649  21.883  50.350  1.00  0.00
ATOM   1000  C   ALA    86       6.062  21.900  50.789  1.00  0.00
ATOM   1000  O   ALA    86       6.928  22.288  50.012  1.00  0.00
ATOM   1000  CB  ALA    86       4.199  20.410  50.349  1.00  0.00
ATOM   1000  N   VAL    87       6.348  21.401  52.001  1.00  0.00
ATOM   1000  CA  VAL    87       7.621  21.694  52.608  1.00  0.00
ATOM   1000  C   VAL    87       8.517  20.555  52.149  1.00  0.00
ATOM   1000  O   VAL    87       9.734  20.578  52.321  1.00  0.00
ATOM   1000  CB  VAL    87       7.583  21.869  54.115  1.00  0.00
ATOM   1000  CG1 VAL    87       6.846  20.694  54.781  1.00  0.00
ATOM   1000  CG2 VAL    87       8.984  22.159  54.707  1.00  0.00
ATOM   1000  N   PHE    88       7.935  19.564  51.451  1.00  0.00
ATOM   1000  CA  PHE    88       8.633  18.332  51.204  1.00  0.00
ATOM   1000  C   PHE    88       8.833  18.348  49.721  1.00  0.00
ATOM   1000  O   PHE    88       9.474  17.459  49.171  1.00  0.00
ATOM   1000  CB  PHE    88       7.987  17.005  51.717  1.00  0.00
ATOM   1000  CG  PHE    88       8.054  16.931  53.232  1.00  0.00
ATOM   1000  CD1 PHE    88       9.041  17.617  53.922  1.00  0.00
ATOM   1000  CD2 PHE    88       7.366  15.971  53.960  1.00  0.00
ATOM   1000  CE1 PHE    88       9.018  17.763  55.283  1.00  0.00
ATOM   1000  CE2 PHE    88       7.615  15.874  55.319  1.00  0.00
ATOM   1000  CZ  PHE    88       8.215  16.908  55.985  1.00  0.00
ATOM   1000  N   ASP    89       8.421  19.445  49.058  1.00  0.00
ATOM   1000  CA  ASP    89       8.237  19.382  47.631  1.00  0.00
ATOM   1000  C   ASP    89       9.254  20.365  47.156  1.00  0.00
ATOM   1000  O   ASP    89       9.074  21.073  46.173  1.00  0.00
ATOM   1000  CB  ASP    89       6.870  19.827  47.071  1.00  0.00
ATOM   1000  CG  ASP    89       6.652  19.133  45.716  1.00  0.00
ATOM   1000  OD1 ASP    89       7.575  18.439  45.211  1.00  0.00
ATOM   1000  OD2 ASP    89       5.511  19.258  45.193  1.00  0.00
TER
END
