
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_2-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          3.33     3.33
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.46     3.73
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.67     4.59
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.98     3.60
  LCS_AVERAGE:      5.30

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    6    6    6    6    6    6    6    6    6    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    6    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    6    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    6    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    6    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      5    6    7     0    3    5    5    6    6    6    6    6    6    6    6    6    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    6    6    6    6    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   6.47  (   5.30    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      6      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   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.16   0.67   0.67   0.67   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   3.33   3.33   3.33   3.33   3.33   3.33   3.33
GDT RMS_ALL_CA   4.12   4.59   4.59   4.59   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.33   3.33   3.33   3.33   3.33   3.33   3.33

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.038
LGA    L      84      L      84          1.206
LGA    M      85      M      85          0.421
LGA    A      86      A      86          0.897
LGA    V      87      V      87          0.655
LGA    F      88      F      88          2.411
LGA    D      89      D      89          9.209

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.46     6.461     6.473     0.384

LGA_LOCAL      RMSD =  1.462  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.735  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.326  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.819186 * X  +  -0.098566 * Y  +   0.564995 * Z  + -18.284153
  Y_new =  -0.382794 * X  +  -0.827551 * Y  +   0.410644 * Z  +  96.442886
  Z_new =   0.427086 * X  +  -0.552670 * Y  +  -0.715648 * Z  + 112.413506 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.483993    0.657599  [ DEG:  -142.3223     37.6777 ]
  Theta =  -0.441268   -2.700325  [ DEG:   -25.2828   -154.7172 ]
  Phi   =  -0.437136    2.704457  [ DEG:   -25.0460    154.9540 ]
 
# 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_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_2-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   1.46   6.473     3.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_2-D1
PFRMAT TS
TARGET T0378
MODEL  2
PARENT 1gz0_A
ATOM   1000  N   PRO    83       0.795  24.877  40.434  1.00  0.00
ATOM   1000  CA  PRO    83       1.502  23.865  41.195  1.00  0.00
ATOM   1000  C   PRO    83       1.678  24.427  42.574  1.00  0.00
ATOM   1000  O   PRO    83       2.275  25.494  42.719  1.00  0.00
ATOM   1000  CB  PRO    83       2.866  23.745  40.493  1.00  0.00
ATOM   1000  CG  PRO    83       3.094  25.097  39.738  1.00  0.00
ATOM   1000  CD  PRO    83       1.707  25.794  39.730  1.00  0.00
ATOM   1000  N   LEU    84       1.181  23.716  43.594  1.00  0.00
ATOM   1000  CA  LEU    84       1.263  24.219  44.931  1.00  0.00
ATOM   1000  C   LEU    84       2.377  23.448  45.569  1.00  0.00
ATOM   1000  O   LEU    84       2.337  22.219  45.596  1.00  0.00
ATOM   1000  CB  LEU    84      -0.031  24.001  45.729  1.00  0.00
ATOM   1000  CG  LEU    84       0.023  24.548  47.169  1.00  0.00
ATOM   1000  CD1 LEU    84       0.318  26.060  47.225  1.00  0.00
ATOM   1000  CD2 LEU    84      -1.259  24.205  47.942  1.00  0.00
ATOM   1000  N   MET    85       3.397  24.159  46.087  1.00  0.00
ATOM   1000  CA  MET    85       4.564  23.535  46.644  1.00  0.00
ATOM   1000  C   MET    85       4.321  23.289  48.097  1.00  0.00
ATOM   1000  O   MET    85       3.797  24.146  48.809  1.00  0.00
ATOM   1000  CB  MET    85       5.812  24.415  46.497  1.00  0.00
ATOM   1000  CG  MET    85       6.272  24.591  45.051  1.00  0.00
ATOM   1000  SD  MET    85       6.846  23.047  44.285  1.00  0.00
ATOM   1000  CE  MET    85       5.353  22.651  43.332  1.00  0.00
ATOM   1000  N   ALA    86       4.735  22.098  48.566  1.00  0.00
ATOM   1000  CA  ALA    86       4.550  21.711  49.938  1.00  0.00
ATOM   1000  C   ALA    86       5.940  21.685  50.480  1.00  0.00
ATOM   1000  O   ALA    86       6.883  21.612  49.694  1.00  0.00
ATOM   1000  CB  ALA    86       3.935  20.312  50.130  1.00  0.00
ATOM   1000  N   VAL    87       6.088  21.732  51.830  1.00  0.00
ATOM   1000  CA  VAL    87       7.343  21.699  52.554  1.00  0.00
ATOM   1000  C   VAL    87       8.287  20.676  51.993  1.00  0.00
ATOM   1000  O   VAL    87       9.489  20.913  51.904  1.00  0.00
ATOM   1000  CB  VAL    87       7.138  21.473  54.057  1.00  0.00
ATOM   1000  CG1 VAL    87       6.398  20.151  54.345  1.00  0.00
ATOM   1000  CG2 VAL    87       8.459  21.486  54.859  1.00  0.00
ATOM   1000  N   PHE    88       7.738  19.517  51.598  1.00  0.00
ATOM   1000  CA  PHE    88       8.479  18.381  51.176  1.00  0.00
ATOM   1000  C   PHE    88       9.229  18.674  49.899  1.00  0.00
ATOM   1000  O   PHE    88      10.370  18.240  49.768  1.00  0.00
ATOM   1000  CB  PHE    88       7.555  17.167  50.949  1.00  0.00
ATOM   1000  CG  PHE    88       6.998  16.663  52.257  1.00  0.00
ATOM   1000  CD1 PHE    88       5.722  16.988  52.678  1.00  0.00
ATOM   1000  CD2 PHE    88       7.724  15.778  53.027  1.00  0.00
ATOM   1000  CE1 PHE    88       5.216  16.483  53.854  1.00  0.00
ATOM   1000  CE2 PHE    88       7.216  15.260  54.199  1.00  0.00
ATOM   1000  CZ  PHE    88       5.954  15.609  54.615  1.00  0.00
ATOM   1000  N   ASP    89       8.653  19.442  48.947  1.00  0.00
ATOM   1000  CA  ASP    89       9.267  19.602  47.632  1.00  0.00
ATOM   1000  C   ASP    89      10.091  20.873  47.675  1.00  0.00
ATOM   1000  O   ASP    89      10.546  21.421  46.677  1.00  0.00
ATOM   1000  CB  ASP    89       8.239  19.678  46.474  1.00  0.00
ATOM   1000  CG  ASP    89       8.851  19.539  45.055  1.00  0.00
ATOM   1000  OD1 ASP    89       9.585  20.425  44.551  1.00  0.00
ATOM   1000  OD2 ASP    89       8.517  18.520  44.401  1.00  0.00
TER
END
