
#######################################################
#                                                     #
#                        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 T0378TS247_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_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          3.34     3.34
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.47     3.73
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.70     4.61
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.94     3.62
  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     3    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    4    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    0.13   0.70   0.70   0.70   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   3.34   3.34   3.34   3.34   3.34   3.34   3.34
GDT RMS_ALL_CA   4.11   4.61   4.61   4.61   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.34   3.34   3.34   3.34   3.34   3.34   3.34

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.083
LGA    L      84      L      84          1.182
LGA    M      85      M      85          0.476
LGA    A      86      A      86          1.005
LGA    V      87      V      87          0.704
LGA    F      88      F      88          2.362
LGA    D      89      D      89          9.187

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.47     6.461     6.473     0.381

LGA_LOCAL      RMSD =  1.475  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.731  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.337  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.893524 * X  +   0.049659 * Y  +   0.446261 * Z  +   0.768984
  Y_new =   0.334357 * X  +   0.589780 * Y  +  -0.735095 * Z  +  24.832407
  Z_new =  -0.299700 * X  +   0.806036 * Y  +   0.510379 * Z  +  40.355675 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.006325   -2.135268  [ DEG:    57.6581   -122.3419 ]
  Theta =   0.304378    2.837215  [ DEG:    17.4396    162.5604 ]
  Phi   =   0.358069   -2.783523  [ DEG:    20.5159   -159.4841 ]
 
# 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: T0378TS247_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_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   1.47   6.473     3.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_2-D1
PFRMAT TS
TARGET T0378
MODEL  2
PARENT 1zjr_A 1gz0_A 1gz0_B 1gz0_C 1gz0_D 1gz0_F 1gz0_H 1v2x_A 1x7p_A 1ipa_A
ATOM      1  N   PRO    83       0.769  24.832  40.356  1.00 0.00         0
ATOM      2  CA  PRO    83       1.417  23.764  41.097  1.00 0.00         0
ATOM      3  C   PRO    83       1.668  24.339  42.484  1.00 0.00         0
ATOM      4  O   PRO    83       2.401  25.322  42.606  1.00 0.00         0
ATOM      5  CB  PRO    83       2.695  23.485  40.303  1.00 0.00         0
ATOM      6  CG  PRO    83       2.380  23.941  38.917  1.00 0.00         0
ATOM      7  CD  PRO    83       1.510  25.158  39.067  1.00 0.00         0
ATOM      8  N   LEU    84       1.072  23.744  43.515  1.00 0.00         0
ATOM      9  CA  LEU    84       1.242  24.237  44.872  1.00 0.00         0
ATOM     10  C   LEU    84       2.400  23.500  45.526  1.00 0.00         0
ATOM     11  O   LEU    84       2.406  22.271  45.614  1.00 0.00         0
ATOM     12  CB  LEU    84      -0.030  24.003  45.690  1.00 0.00         0
ATOM     13  CG  LEU    84       0.014  24.449  47.154  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.174  25.959  47.252  1.00 0.00         0
ATOM     15  CD2 LEU    84      -1.268  24.058  47.874  1.00 0.00         0
ATOM     16  N   MET    85       3.387  24.266  45.984  1.00 0.00         0
ATOM     17  CA  MET    85       4.550  23.688  46.634  1.00 0.00         0
ATOM     18  C   MET    85       4.279  23.436  48.111  1.00 0.00         0
ATOM     19  O   MET    85       3.710  24.269  48.822  1.00 0.00         0
ATOM     20  CB  MET    85       5.750  24.630  46.522  1.00 0.00         0
ATOM     21  CG  MET    85       6.207  24.886  45.095  1.00 0.00         0
ATOM     22  SD  MET    85       6.686  23.375  44.236  1.00 0.00         0
ATOM     23  CE  MET    85       8.166  22.926  45.140  1.00 0.00         0
ATOM     24  N   ALA    86       4.698  22.259  48.573  1.00 0.00         0
ATOM     25  CA  ALA    86       4.609  21.900  49.978  1.00 0.00         0
ATOM     26  C   ALA    86       6.007  21.717  50.554  1.00 0.00         0
ATOM     27  O   ALA    86       6.965  21.528  49.801  1.00 0.00         0
ATOM     28  CB  ALA    86       3.835  20.601  50.145  1.00 0.00         0
ATOM     29  N   VAL    87       6.122  21.773  51.891  1.00 0.00         0
ATOM     30  CA  VAL    87       7.369  21.586  52.640  1.00 0.00         0
ATOM     31  C   VAL    87       8.325  20.507  52.126  1.00 0.00         0
ATOM     32  O   VAL    87       9.545  20.696  52.075  1.00 0.00         0
ATOM     33  CB  VAL    87       7.094  21.194  54.104  1.00 0.00         0
ATOM     34  CG1 VAL    87       6.464  19.811  54.176  1.00 0.00         0
ATOM     35  CG2 VAL    87       8.389  21.175  54.902  1.00 0.00         0
ATOM     36  N   PHE    88       7.759  19.360  51.740  1.00 0.00         0
ATOM     37  CA  PHE    88       8.513  18.233  51.217  1.00 0.00         0
ATOM     38  C   PHE    88       9.218  18.555  49.901  1.00 0.00         0
ATOM     39  O   PHE    88      10.351  18.131  49.665  1.00 0.00         0
ATOM     40  CB  PHE    88       7.587  17.043  50.956  1.00 0.00         0
ATOM     41  CG  PHE    88       8.292  15.837  50.406  1.00 0.00         0
ATOM     42  CD1 PHE    88       9.011  14.997  51.239  1.00 0.00         0
ATOM     43  CD2 PHE    88       8.235  15.540  49.054  1.00 0.00         0
ATOM     44  CE1 PHE    88       9.659  13.887  50.731  1.00 0.00         0
ATOM     45  CE2 PHE    88       8.882  14.430  48.548  1.00 0.00         0
ATOM     46  CZ  PHE    88       9.592  13.605  49.381  1.00 0.00         0
ATOM     47  N   ASP    89       8.556  19.313  49.021  1.00 0.00         0
ATOM     48  CA  ASP    89       9.081  19.557  47.685  1.00 0.00         0
ATOM     49  C   ASP    89      10.045  20.733  47.627  1.00 0.00         0
ATOM     50  O   ASP    89      10.520  21.112  46.557  1.00 0.00         0
ATOM     51  CB  ASP    89       7.942  19.862  46.710  1.00 0.00         0
ATOM     52  CG  ASP    89       6.987  18.695  46.545  1.00 0.00         0
ATOM     53  OD1 ASP    89       7.466  17.562  46.331  1.00 0.00         0
ATOM     54  OD2 ASP    89       5.761  18.914  46.631  1.00 0.00         0
TER
END
