
#######################################################
#                                                     #
#                        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 T0378TS102_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected    5 , name T0378_D1.pdb
# PARAMETERS: T0378TS102_5-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        84 - 88          0.91     0.91
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.91     0.91
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.91     0.91
  LCS_AVERAGE:      5.62

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     L      84     L      84      5    5    5     3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     M      85     M      85      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A      86     A      86      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V      87     V      87      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      88     F      88      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.62  (   5.62    5.62    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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   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   5.62   5.62   5.62   5.62   5.62   5.62   5.62
GDT RMS_LOCAL    0.36   0.36   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91
GDT RMS_ALL_CA   1.42   1.42   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91

#      Molecule1      Molecule2       DISTANCE
LGA    L      84      L      84          1.151
LGA    M      85      M      85          0.896
LGA    A      86      A      86          0.922
LGA    V      87      V      87          0.582
LGA    F      88      F      88          0.899

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   89    4.0      5    0.91     5.337     5.529     0.496

LGA_LOCAL      RMSD =  0.908  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.908  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.908  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.392849 * X  +   0.301539 * Y  +   0.868760 * Z  + -45.356232
  Y_new =   0.247458 * X  +  -0.944529 * Y  +   0.215938 * Z  +  40.711086
  Z_new =   0.885683 * X  +   0.130151 * Y  +  -0.445675 * Z  +  54.090420 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.857463   -0.284130  [ DEG:   163.7206    -16.2794 ]
  Theta =  -1.087963   -2.053630  [ DEG:   -62.3357   -117.6643 ]
  Phi   =   0.562121   -2.579472  [ DEG:    32.2071   -147.7929 ]
 
# 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: T0378TS102_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS102_5-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    5   0.91   5.529     0.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS102_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 2ha8_A
ATOM      1  N   LEU    84       0.803  25.292  45.279  1.00  1.00
ATOM      2  CA  LEU    84       1.665  24.383  44.472  1.00  1.00
ATOM      3  C   LEU    84       3.023  24.184  45.126  1.00  1.00
ATOM      4  O   LEU    84       3.754  25.147  45.394  1.00  1.00
ATOM      5  CB  LEU    84       1.826  24.906  43.042  1.00  1.00
ATOM      6  N   MET    85       3.348  22.919  45.371  1.00  1.00
ATOM      7  CA  MET    85       4.574  22.547  46.062  1.00  1.00
ATOM      8  C   MET    85       4.297  22.128  47.494  1.00  1.00
ATOM      9  O   MET    85       3.669  22.869  48.255  1.00  1.00
ATOM     10  CB  MET    85       5.502  23.776  46.090  1.00  1.00
ATOM     11  N   ALA    86       4.764  20.940  47.851  1.00  1.00
ATOM     12  CA  ALA    86       4.626  20.435  49.205  1.00  1.00
ATOM     13  C   ALA    86       5.950  20.582  49.951  1.00  1.00
ATOM     14  O   ALA    86       6.960  20.027  49.527  1.00  1.00
ATOM     15  CB  ALA    86       4.208  18.969  49.172  1.00  1.00
ATOM     16  N   VAL    87       5.923  21.303  51.067  1.00  1.00
ATOM     17  CA  VAL    87       7.118  21.494  51.885  1.00  1.00
ATOM     18  C   VAL    87       7.498  20.234  52.650  1.00  1.00
ATOM     19  O   VAL    87       6.637  19.461  53.092  1.00  1.00
ATOM     20  CB  VAL    87       6.926  22.651  52.859  1.00  1.00
ATOM     21  N   PHE    88       8.798  20.028  52.807  1.00  1.00
ATOM     22  CA  PHE    88       9.303  18.960  53.652  1.00  1.00
ATOM     23  C   PHE    88       8.765  19.189  55.081  1.00  1.00
ATOM     24  O   PHE    88       8.688  20.328  55.543  1.00  1.00
ATOM     25  CB  PHE    88      10.855  18.942  53.626  1.00  1.00
TER
END
