
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_4-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          3.44     3.44
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.54     3.84
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.70     4.73
  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     3    5    5    5    5    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    5    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    5    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    5    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    5    6    6    6    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      3    6    7     0    3    3    5    5    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    4    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      5      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   5.62   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    0.31   0.70   0.70   0.70   0.70   1.54   1.54   1.54   1.54   1.54   1.54   1.54   3.44   3.44   3.44   3.44   3.44   3.44   3.44   3.44
GDT RMS_ALL_CA   4.37   4.73   4.73   4.73   4.73   3.84   3.84   3.84   3.84   3.84   3.84   3.84   3.44   3.44   3.44   3.44   3.44   3.44   3.44   3.44

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.020
LGA    L      84      L      84          1.313
LGA    M      85      M      85          0.456
LGA    A      86      A      86          1.079
LGA    V      87      V      87          0.789
LGA    F      88      F      88          2.523
LGA    D      89      D      89          9.440

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.54     6.461     6.434     0.367

LGA_LOCAL      RMSD =  1.536  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.841  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.445  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.803402 * X  +  -0.154022 * Y  +  -0.575171 * Z  +  79.243782
  Y_new =   0.441433 * X  +  -0.802333 * Y  +  -0.401745 * Z  +  75.872826
  Z_new =  -0.399601 * X  +  -0.576662 * Y  +   0.712586 * Z  + 113.922729 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.680357    2.461235  [ DEG:   -38.9816    141.0184 ]
  Theta =   0.411082    2.730511  [ DEG:    23.5533    156.4467 ]
  Phi   =   2.639168   -0.502425  [ DEG:   151.2132    -28.7868 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_4-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   1.54   6.434     3.44
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT 1gz0_C
ATOM   1000  N   PRO    83       0.766  24.774  40.421  1.00  0.00
ATOM   1000  CA  PRO    83       1.322  23.792  41.330  1.00  0.00
ATOM   1000  C   PRO    83       1.320  24.441  42.675  1.00  0.00
ATOM   1000  O   PRO    83       1.155  25.660  42.747  1.00  0.00
ATOM   1000  CB  PRO    83       2.780  23.606  40.868  1.00  0.00
ATOM   1000  CG  PRO    83       3.146  24.897  40.066  1.00  0.00
ATOM   1000  CD  PRO    83       1.795  25.601  39.774  1.00  0.00
ATOM   1000  N   LEU    84       1.529  23.655  43.741  1.00  0.00
ATOM   1000  CA  LEU    84       1.520  24.242  45.044  1.00  0.00
ATOM   1000  C   LEU    84       2.544  23.488  45.802  1.00  0.00
ATOM   1000  O   LEU    84       2.285  22.391  46.291  1.00  0.00
ATOM   1000  CB  LEU    84       0.172  24.185  45.787  1.00  0.00
ATOM   1000  CG  LEU    84       0.108  25.039  47.079  1.00  0.00
ATOM   1000  CD1 LEU    84       0.772  24.382  48.309  1.00  0.00
ATOM   1000  CD2 LEU    84       0.604  26.489  46.886  1.00  0.00
ATOM   1000  N   MET    85       3.732  24.081  45.917  1.00  0.00
ATOM   1000  CA  MET    85       4.844  23.417  46.510  1.00  0.00
ATOM   1000  C   MET    85       4.599  23.389  47.983  1.00  0.00
ATOM   1000  O   MET    85       4.370  24.411  48.634  1.00  0.00
ATOM   1000  CB  MET    85       6.117  24.197  46.272  1.00  0.00
ATOM   1000  CG  MET    85       6.799  24.039  44.915  1.00  0.00
ATOM   1000  SD  MET    85       5.860  24.771  43.535  1.00  0.00
ATOM   1000  CE  MET    85       6.942  24.134  42.227  1.00  0.00
ATOM   1000  N   ALA    86       4.656  22.168  48.527  1.00  0.00
ATOM   1000  CA  ALA    86       4.405  21.913  49.912  1.00  0.00
ATOM   1000  C   ALA    86       5.778  21.844  50.498  1.00  0.00
ATOM   1000  O   ALA    86       6.751  21.888  49.749  1.00  0.00
ATOM   1000  CB  ALA    86       3.702  20.564  50.152  1.00  0.00
ATOM   1000  N   VAL    87       5.887  21.723  51.849  1.00  0.00
ATOM   1000  CA  VAL    87       7.132  21.591  52.574  1.00  0.00
ATOM   1000  C   VAL    87       8.117  20.687  51.914  1.00  0.00
ATOM   1000  O   VAL    87       9.308  20.993  51.862  1.00  0.00
ATOM   1000  CB  VAL    87       6.972  21.162  54.046  1.00  0.00
ATOM   1000  CG1 VAL    87       6.067  19.940  54.240  1.00  0.00
ATOM   1000  CG2 VAL    87       8.331  20.908  54.755  1.00  0.00
ATOM   1000  N   PHE    88       7.633  19.555  51.390  1.00  0.00
ATOM   1000  CA  PHE    88       8.477  18.454  51.067  1.00  0.00
ATOM   1000  C   PHE    88       9.044  18.700  49.688  1.00  0.00
ATOM   1000  O   PHE    88      10.083  18.152  49.332  1.00  0.00
ATOM   1000  CB  PHE    88       7.693  17.122  51.114  1.00  0.00
ATOM   1000  CG  PHE    88       8.525  15.919  50.783  1.00  0.00
ATOM   1000  CD1 PHE    88       9.891  15.848  50.973  1.00  0.00
ATOM   1000  CD2 PHE    88       7.904  14.809  50.259  1.00  0.00
ATOM   1000  CE1 PHE    88      10.623  14.845  50.401  1.00  0.00
ATOM   1000  CE2 PHE    88       8.627  13.689  49.926  1.00  0.00
ATOM   1000  CZ  PHE    88      10.002  13.706  49.947  1.00  0.00
ATOM   1000  N   ASP    89       8.423  19.572  48.876  1.00  0.00
ATOM   1000  CA  ASP    89       8.867  19.702  47.505  1.00  0.00
ATOM   1000  C   ASP    89      10.062  20.577  47.496  1.00  0.00
ATOM   1000  O   ASP    89      10.793  20.623  46.506  1.00  0.00
ATOM   1000  CB  ASP    89       7.879  20.400  46.558  1.00  0.00
ATOM   1000  CG  ASP    89       6.745  19.449  46.209  1.00  0.00
ATOM   1000  OD1 ASP    89       6.853  18.219  46.464  1.00  0.00
ATOM   1000  OD2 ASP    89       5.720  19.964  45.691  1.00  0.00
TER
END
