
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_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:     7        83 - 89          3.31     3.31
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.49     3.69
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.76     4.58
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.92     3.61
  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    4    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    4    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    4    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    4    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    4    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    3    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      4      5      5      6      6      6      6      6      6      6      6      6      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.49   4.49   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    0.21   0.21   0.76   0.76   1.49   1.49   1.49   1.49   1.49   1.49   1.49   1.49   1.49   3.31   3.31   3.31   3.31   3.31   3.31   3.31
GDT RMS_ALL_CA   4.08   4.08   4.58   4.58   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.31   3.31   3.31   3.31   3.31   3.31   3.31

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.141
LGA    L      84      L      84          1.180
LGA    M      85      M      85          0.551
LGA    A      86      A      86          1.084
LGA    V      87      V      87          0.749
LGA    F      88      F      88          2.316
LGA    D      89      D      89          9.045

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.49     6.180     6.385     0.377

LGA_LOCAL      RMSD =  1.493  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.688  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.305  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.931386 * X  +   0.119590 * Y  +   0.343830 * Z  +   0.836359
  Y_new =   0.209730 * X  +   0.595715 * Y  +  -0.775330 * Z  +  24.781061
  Z_new =  -0.297546 * X  +   0.794243 * Y  +   0.529758 * Z  +  40.327702 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.982565   -2.159028  [ DEG:    56.2968   -123.7032 ]
  Theta =   0.302122    2.839471  [ DEG:    17.3103    162.6897 ]
  Phi   =   0.221487   -2.920106  [ DEG:    12.6902   -167.3098 ]
 
# 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_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_5-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   1.49   6.385     3.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
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       0.836  24.781  40.328  1.00 0.00         0
ATOM      2  CA  PRO    83       1.335  23.657  41.096  1.00 0.00         0
ATOM      3  C   PRO    83       1.634  24.263  42.458  1.00 0.00         0
ATOM      4  O   PRO    83       2.391  25.233  42.521  1.00 0.00         0
ATOM      5  CB  PRO    83       2.571  23.198  40.320  1.00 0.00         0
ATOM      6  CG  PRO    83       2.329  23.661  38.922  1.00 0.00         0
ATOM      7  CD  PRO    83       1.621  24.982  39.039  1.00 0.00         0
ATOM      8  N   LEU    84       1.057  23.714  43.523  1.00 0.00         0
ATOM      9  CA  LEU    84       1.261  24.246  44.860  1.00 0.00         0
ATOM     10  C   LEU    84       2.458  23.553  45.495  1.00 0.00         0
ATOM     11  O   LEU    84       2.490  22.328  45.616  1.00 0.00         0
ATOM     12  CB  LEU    84       0.024  24.005  45.727  1.00 0.00         0
ATOM     13  CG  LEU    84       0.107  24.490  47.176  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.234  26.005  47.230  1.00 0.00         0
ATOM     15  CD2 LEU    84      -1.141  24.090  47.949  1.00 0.00         0
ATOM     16  N   MET    85       3.444  24.351  45.898  1.00 0.00         0
ATOM     17  CA  MET    85       4.608  23.826  46.593  1.00 0.00         0
ATOM     18  C   MET    85       4.294  23.571  48.064  1.00 0.00         0
ATOM     19  O   MET    85       3.614  24.353  48.730  1.00 0.00         0
ATOM     20  CB  MET    85       5.770  24.818  46.517  1.00 0.00         0
ATOM     21  CG  MET    85       6.265  25.086  45.105  1.00 0.00         0
ATOM     22  SD  MET    85       6.839  23.593  44.273  1.00 0.00         0
ATOM     23  CE  MET    85       8.304  23.213  45.232  1.00 0.00         0
ATOM     24  N   ALA    86       4.807  22.450  48.568  1.00 0.00         0
ATOM     25  CA  ALA    86       4.644  22.052  49.956  1.00 0.00         0
ATOM     26  C   ALA    86       6.010  21.758  50.572  1.00 0.00         0
ATOM     27  O   ALA    86       6.998  21.642  49.843  1.00 0.00         0
ATOM     28  CB  ALA    86       3.781  20.803  50.052  1.00 0.00         0
ATOM     29  N   VAL    87       6.082  21.634  51.907  1.00 0.00         0
ATOM     30  CA  VAL    87       7.332  21.491  52.668  1.00 0.00         0
ATOM     31  C   VAL    87       8.276  20.421  52.119  1.00 0.00         0
ATOM     32  O   VAL    87       9.480  20.646  51.970  1.00 0.00         0
ATOM     33  CB  VAL    87       7.059  21.105  54.134  1.00 0.00         0
ATOM     34  CG1 VAL    87       8.359  20.757  54.844  1.00 0.00         0
ATOM     35  CG2 VAL    87       6.401  22.258  54.875  1.00 0.00         0
ATOM     36  N   PHE    88       7.737  19.240  51.810  1.00 0.00         0
ATOM     37  CA  PHE    88       8.520  18.137  51.265  1.00 0.00         0
ATOM     38  C   PHE    88       9.108  18.374  49.873  1.00 0.00         0
ATOM     39  O   PHE    88       9.982  17.629  49.429  1.00 0.00         0
ATOM     40  CB  PHE    88       7.661  16.877  51.146  1.00 0.00         0
ATOM     41  CG  PHE    88       7.331  16.242  52.466  1.00 0.00         0
ATOM     42  CD1 PHE    88       6.093  16.440  53.055  1.00 0.00         0
ATOM     43  CD2 PHE    88       8.255  15.446  53.119  1.00 0.00         0
ATOM     44  CE1 PHE    88       5.788  15.855  54.269  1.00 0.00         0
ATOM     45  CE2 PHE    88       7.950  14.863  54.334  1.00 0.00         0
ATOM     46  CZ  PHE    88       6.723  15.064  54.910  1.00 0.00         0
ATOM     47  N   ASP    89       8.649  19.407  49.156  1.00 0.00         0
ATOM     48  CA  ASP    89       9.216  19.780  47.862  1.00 0.00         0
ATOM     49  C   ASP    89      10.480  20.621  48.016  1.00 0.00         0
ATOM     50  O   ASP    89      11.200  20.824  47.039  1.00 0.00         0
ATOM     51  CB  ASP    89       8.208  20.598  47.052  1.00 0.00         0
ATOM     52  CG  ASP    89       7.052  19.760  46.543  1.00 0.00         0
ATOM     53  OD1 ASP    89       7.161  18.516  46.574  1.00 0.00         0
ATOM     54  OD2 ASP    89       6.037  20.348  46.114  1.00 0.00         0
TER
END
