
#######################################################
#                                                     #
#                        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   18 (   18),  selected   18 , name T0372TS464_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   18 , name T0372_D1.pdb
# PARAMETERS: T0372TS464_4_2-D1.T0372_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:    13       102 - 114         1.98    14.15
  LCS_AVERAGE:      8.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       102 - 114         1.98    14.15
  LCS_AVERAGE:      8.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       102 - 108         0.87    12.57
  LCS_AVERAGE:      4.10

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:  126
LCS_GDT     K       5     K       5      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    6    6 
LCS_GDT     D       6     D       6      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    6    6 
LCS_GDT     I       7     I       7      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    6    6 
LCS_GDT     T       8     T       8      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    6    6 
LCS_GDT     L       9     L       9      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     102     A     102      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     103     D     103      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     104     L     104      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     105     E     105      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     106     A     106      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     107     I     107      7   13   13     4    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     108     L     108      7   13   13     4    5    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     109     P     109      4   13   13     4    4    4    4   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     110     E     110      4   13   13     4    4    4    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     R     111     R     111      4   13   13     3    4    4   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     112     F     112      4   13   13     3    6    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     113     I     113      4   13   13     3    5    6   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     114     F     114      4   13   13     3    5    6   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   7.07  (   4.10    8.55    8.55 )

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      6      7     10     11     12     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   3.17   4.76   5.56   7.94   8.73   9.52  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32
GDT RMS_LOCAL    0.15   0.48   0.71   1.38   1.48   1.77   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98   1.98
GDT RMS_ALL_CA  13.14  13.88  13.68  13.94  13.75  14.03  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15  14.15

#      Molecule1      Molecule2       DISTANCE
LGA    K       5      K       5         26.676
LGA    D       6      D       6         27.027
LGA    I       7      I       7         25.135
LGA    T       8      T       8         26.729
LGA    L       9      L       9         27.640
LGA    A     102      A     102          1.050
LGA    D     103      D     103          0.934
LGA    L     104      L     104          0.859
LGA    E     105      E     105          1.751
LGA    A     106      A     106          1.780
LGA    I     107      I     107          0.851
LGA    L     108      L     108          3.023
LGA    P     109      P     109          2.755
LGA    E     110      E     110          3.297
LGA    R     111      R     111          2.516
LGA    F     112      F     112          1.773
LGA    I     113      I     113          1.020
LGA    F     114      F     114          1.788

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  126    4.0     13    1.98     8.333     8.763     0.625

LGA_LOCAL      RMSD =  1.980  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.148  Number of atoms =   18 
Std_ALL_ATOMS  RMSD = 11.402  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.280263 * X  +  -0.334479 * Y  +  -0.899764 * Z  +  57.903385
  Y_new =   0.726166 * X  +  -0.539151 * Y  +   0.426614 * Z  +  -5.586888
  Z_new =  -0.627802 * X  +  -0.772942 * Y  +   0.091783 * Z  + 107.469902 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.452604    1.688988  [ DEG:   -83.2281     96.7719 ]
  Theta =   0.678726    2.462866  [ DEG:    38.8882    141.1118 ]
  Phi   =   1.202461   -1.939132  [ DEG:    68.8959   -111.1041 ]
 
# 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: T0372TS464_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  126   4.0   13   1.98   8.763    11.40
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  LYS     5      25.384  57.112 -11.061  1.00  0.00
ATOM      2  CA  ASP     6      25.409  53.676  -9.456  1.00  0.00
ATOM      3  CA  ILE     7      25.931  52.628  -5.867  1.00  0.00
ATOM      4  CA  THR     8      27.301  49.449  -4.307  1.00  0.00
ATOM      5  CA  LEU     9      26.817  48.973  -0.543  1.00  0.00
ATOM      6  CA  ALA   102      20.022  57.374   3.518  1.00  0.00
ATOM      7  CA  ASP   103      23.357  58.915   2.560  1.00  0.00
ATOM      8  CA  LEU   104      23.562  56.928  -0.700  1.00  0.00
ATOM      9  CA  GLU   105      20.114  58.263  -1.513  1.00  0.00
ATOM     10  CA  ALA   106      21.550  61.776  -1.817  1.00  0.00
ATOM     11  CA  ILE   107      23.449  60.990  -5.005  1.00  0.00
ATOM     12  CA  LEU   108      20.256  59.595  -6.549  1.00  0.00
ATOM     13  CA  PRO   109      21.804  56.516  -8.153  1.00  0.00
ATOM     14  CA  GLU   110      20.028  54.938 -11.115  1.00  0.00
ATOM     15  CA  ARG   111      20.855  51.601  -9.562  1.00  0.00
ATOM     16  CA  PHE   112      21.700  50.587  -6.025  1.00  0.00
ATOM     17  CA  ILE   113      23.151  47.180  -5.314  1.00  0.00
ATOM     18  CA  PHE   114      23.647  45.912  -1.772  1.00  0.00
TER
END
