
#######################################################
#                                                     #
#                        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 T0378TS050_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS050_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          3.32     3.32
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        83 - 88          1.50     3.70
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        83 - 87          0.77     4.59
  LONGEST_CONTINUOUS_SEGMENT:     5        84 - 88          0.93     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    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    0.22   0.22   0.77   0.77   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   3.32   3.32   3.32   3.32   3.32   3.32   3.32
GDT RMS_ALL_CA   4.08   4.08   4.59   4.59   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.32   3.32   3.32   3.32   3.32   3.32   3.32

#      Molecule1      Molecule2       DISTANCE
LGA    P      83      P      83          2.155
LGA    L      84      L      84          1.174
LGA    M      85      M      85          0.556
LGA    A      86      A      86          1.089
LGA    V      87      V      87          0.754
LGA    F      88      F      88          2.332
LGA    D      89      D      89          9.068

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      6    1.50     6.180     6.385     0.375

LGA_LOCAL      RMSD =  1.501  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.699  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.319  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.908753 * X  +   0.108592 * Y  +   0.402958 * Z  +   0.767139
  Y_new =   0.263004 * X  +   0.600668 * Y  +  -0.755001 * Z  +  24.745754
  Z_new =  -0.324032 * X  +   0.792089 * Y  +   0.517299 * Z  +  40.359562 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.992258   -2.149335  [ DEG:    56.8522   -123.1478 ]
  Theta =   0.329988    2.811605  [ DEG:    18.9069    161.0931 ]
  Phi   =   0.281715   -2.859878  [ DEG:    16.1411   -163.8589 ]
 
# 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: T0378TS050_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS050_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   1.50   6.385     3.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS050_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 1zjr_A
ATOM      1  N   PRO    83       0.767  24.746  40.360  1.00 15.00
ATOM      2  CA  PRO    83       1.352  23.649  41.111  1.00 15.00
ATOM      3  C   PRO    83       1.670  24.238  42.478  1.00 15.00
ATOM      4  O   PRO    83       2.479  25.161  42.566  1.00 15.00
ATOM      5  CB  PRO    83       2.589  23.263  40.298  1.00 15.00
ATOM      6  CG  PRO    83       2.280  23.713  38.909  1.00 15.00
ATOM      7  CD  PRO    83       1.502  24.992  39.050  1.00 15.00
ATOM      8  N   LEU    84       1.043  23.713  43.528  1.00 15.00
ATOM      9  CA  LEU    84       1.249  24.226  44.873  1.00 15.00
ATOM     10  C   LEU    84       2.450  23.545  45.511  1.00 15.00
ATOM     11  O   LEU    84       2.481  22.324  45.662  1.00 15.00
ATOM     12  CB  LEU    84       0.017  23.964  45.741  1.00 15.00
ATOM     13  CG  LEU    84       0.103  24.427  47.198  1.00 15.00
ATOM     14  CD1 LEU    84       0.221  25.942  47.273  1.00 15.00
ATOM     15  CD2 LEU    84      -1.138  24.008  47.969  1.00 15.00
ATOM     16  N   MET    85       3.442  24.350  45.887  1.00 15.00
ATOM     17  CA  MET    85       4.611  23.838  46.584  1.00 15.00
ATOM     18  C   MET    85       4.308  23.594  48.060  1.00 15.00
ATOM     19  O   MET    85       3.649  24.390  48.734  1.00 15.00
ATOM     20  CB  MET    85       5.767  24.836  46.496  1.00 15.00
ATOM     21  CG  MET    85       6.259  25.093  45.080  1.00 15.00
ATOM     22  SD  MET    85       6.839  23.593  44.263  1.00 15.00
ATOM     23  CE  MET    85       8.307  23.232  45.222  1.00 15.00
ATOM     24  N   ALA    86       4.807  22.464  48.558  1.00 15.00
ATOM     25  CA  ALA    86       4.655  22.070  49.950  1.00 15.00
ATOM     26  C   ALA    86       6.020  21.780  50.565  1.00 15.00
ATOM     27  O   ALA    86       7.013  21.676  49.841  1.00 15.00
ATOM     28  CB  ALA    86       3.798  20.818  50.056  1.00 15.00
ATOM     29  N   VAL    87       6.083  21.648  51.899  1.00 15.00
ATOM     30  CA  VAL    87       7.325  21.490  52.670  1.00 15.00
ATOM     31  C   VAL    87       8.267  20.421  52.115  1.00 15.00
ATOM     32  O   VAL    87       9.470  20.649  51.960  1.00 15.00
ATOM     33  CB  VAL    87       7.037  21.087  54.128  1.00 15.00
ATOM     34  CG1 VAL    87       8.327  20.725  54.846  1.00 15.00
ATOM     35  CG2 VAL    87       6.377  22.236  54.876  1.00 15.00
ATOM     36  N   PHE    88       7.729  19.237  51.809  1.00 15.00
ATOM     37  CA  PHE    88       8.508  18.136  51.251  1.00 15.00
ATOM     38  C   PHE    88       9.083  18.386  49.858  1.00 15.00
ATOM     39  O   PHE    88       9.973  17.663  49.407  1.00 15.00
ATOM     40  CB  PHE    88       7.646  16.877  51.129  1.00 15.00
ATOM     41  CG  PHE    88       7.344  16.221  52.446  1.00 15.00
ATOM     42  CD1 PHE    88       6.114  16.393  53.056  1.00 15.00
ATOM     43  CD2 PHE    88       8.290  15.429  53.075  1.00 15.00
ATOM     44  CE1 PHE    88       5.836  15.789  54.268  1.00 15.00
ATOM     45  CE2 PHE    88       8.012  14.824  54.286  1.00 15.00
ATOM     46  CZ  PHE    88       6.791  15.001  54.882  1.00 15.00
ATOM     47  N   ASP    89       8.593  19.412  49.151  1.00 15.00
ATOM     48  CA  ASP    89       9.150  19.800  47.858  1.00 15.00
ATOM     49  C   ASP    89      10.407  20.647  48.001  1.00 15.00
ATOM     50  O   ASP    89      11.106  20.867  47.011  1.00 15.00
ATOM     51  CB  ASP    89       8.132  20.618  47.061  1.00 15.00
ATOM     52  CG  ASP    89       6.979  19.777  46.551  1.00 15.00
ATOM     53  OD1 ASP    89       7.097  18.533  46.570  1.00 15.00
ATOM     54  OD2 ASP    89       5.957  20.361  46.132  1.00 15.00
TER
END
