
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_1-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: T0378TS247_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_1-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 T0378TS247_1-D1
PFRMAT TS
TARGET T0378
MODEL  1
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       0.767  24.746  40.360  1.00 0.00         0
ATOM      2  CA  PRO    83       1.352  23.649  41.111  1.00 0.00         0
ATOM      3  C   PRO    83       1.670  24.238  42.478  1.00 0.00         0
ATOM      4  O   PRO    83       2.479  25.161  42.566  1.00 0.00         0
ATOM      5  CB  PRO    83       2.589  23.263  40.298  1.00 0.00         0
ATOM      6  CG  PRO    83       2.280  23.713  38.909  1.00 0.00         0
ATOM      7  CD  PRO    83       1.502  24.992  39.050  1.00 0.00         0
ATOM      8  N   LEU    84       1.043  23.713  43.528  1.00 0.00         0
ATOM      9  CA  LEU    84       1.249  24.226  44.873  1.00 0.00         0
ATOM     10  C   LEU    84       2.450  23.545  45.511  1.00 0.00         0
ATOM     11  O   LEU    84       2.481  22.324  45.662  1.00 0.00         0
ATOM     12  CB  LEU    84       0.017  23.964  45.741  1.00 0.00         0
ATOM     13  CG  LEU    84       0.103  24.427  47.198  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.221  25.942  47.273  1.00 0.00         0
ATOM     15  CD2 LEU    84      -1.138  24.008  47.969  1.00 0.00         0
ATOM     16  N   MET    85       3.442  24.350  45.887  1.00 0.00         0
ATOM     17  CA  MET    85       4.611  23.838  46.584  1.00 0.00         0
ATOM     18  C   MET    85       4.308  23.594  48.060  1.00 0.00         0
ATOM     19  O   MET    85       3.649  24.390  48.734  1.00 0.00         0
ATOM     20  CB  MET    85       5.767  24.836  46.496  1.00 0.00         0
ATOM     21  CG  MET    85       6.259  25.093  45.080  1.00 0.00         0
ATOM     22  SD  MET    85       6.839  23.593  44.263  1.00 0.00         0
ATOM     23  CE  MET    85       8.307  23.232  45.222  1.00 0.00         0
ATOM     24  N   ALA    86       4.807  22.464  48.558  1.00 0.00         0
ATOM     25  CA  ALA    86       4.655  22.070  49.950  1.00 0.00         0
ATOM     26  C   ALA    86       6.020  21.780  50.565  1.00 0.00         0
ATOM     27  O   ALA    86       7.013  21.676  49.841  1.00 0.00         0
ATOM     28  CB  ALA    86       3.798  20.818  50.056  1.00 0.00         0
ATOM     29  N   VAL    87       6.083  21.648  51.899  1.00 0.00         0
ATOM     30  CA  VAL    87       7.325  21.490  52.670  1.00 0.00         0
ATOM     31  C   VAL    87       8.267  20.421  52.115  1.00 0.00         0
ATOM     32  O   VAL    87       9.470  20.649  51.960  1.00 0.00         0
ATOM     33  CB  VAL    87       7.037  21.087  54.128  1.00 0.00         0
ATOM     34  CG1 VAL    87       8.327  20.725  54.846  1.00 0.00         0
ATOM     35  CG2 VAL    87       6.377  22.236  54.876  1.00 0.00         0
ATOM     36  N   PHE    88       7.729  19.237  51.809  1.00 0.00         0
ATOM     37  CA  PHE    88       8.508  18.136  51.251  1.00 0.00         0
ATOM     38  C   PHE    88       9.083  18.386  49.858  1.00 0.00         0
ATOM     39  O   PHE    88       9.973  17.663  49.407  1.00 0.00         0
ATOM     40  CB  PHE    88       7.646  16.877  51.129  1.00 0.00         0
ATOM     41  CG  PHE    88       7.344  16.221  52.446  1.00 0.00         0
ATOM     42  CD1 PHE    88       6.114  16.393  53.056  1.00 0.00         0
ATOM     43  CD2 PHE    88       8.290  15.429  53.075  1.00 0.00         0
ATOM     44  CE1 PHE    88       5.836  15.789  54.268  1.00 0.00         0
ATOM     45  CE2 PHE    88       8.012  14.824  54.286  1.00 0.00         0
ATOM     46  CZ  PHE    88       6.791  15.001  54.882  1.00 0.00         0
ATOM     47  N   ASP    89       8.593  19.412  49.151  1.00 0.00         0
ATOM     48  CA  ASP    89       9.150  19.800  47.858  1.00 0.00         0
ATOM     49  C   ASP    89      10.407  20.647  48.001  1.00 0.00         0
ATOM     50  O   ASP    89      11.106  20.867  47.011  1.00 0.00         0
ATOM     51  CB  ASP    89       8.132  20.618  47.061  1.00 0.00         0
ATOM     52  CG  ASP    89       6.979  19.777  46.551  1.00 0.00         0
ATOM     53  OD1 ASP    89       7.097  18.533  46.570  1.00 0.00         0
ATOM     54  OD2 ASP    89       5.957  20.361  46.132  1.00 0.00         0
TER
END
