
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0320AL333_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   13 , name T0320_D2.pdb
# PARAMETERS: T0320AL333_2-D2.T0320_D2.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       232 - 244         4.36     4.36
  LCS_AVERAGE:     17.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       232 - 237         1.97     4.87
  LONGEST_CONTINUOUS_SEGMENT:     6       233 - 238         1.42     6.44
  LONGEST_CONTINUOUS_SEGMENT:     6       237 - 242         1.34     7.80
  LCS_AVERAGE:      7.59

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       233 - 237         0.42     5.82
  LONGEST_CONTINUOUS_SEGMENT:     5       237 - 241         0.51     7.70
  LCS_AVERAGE:      6.01

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:   73
LCS_GDT     P     232     P     232      3    6   13     3    3    4    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     N     233     N     233      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     P     234     P     234      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     H     235     H     235      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     L     236     L     236      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     R     237     R     237      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     K     238     K     238      5    6   13     4    5    5    5    6    6    7    9   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     D     239     D     239      5    6   13     4    5    5    5    6    6    7    8   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     S     240     S     240      5    6   13     4    5    5    5    6    6    8    9   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     N     241     N     241      5    6   13     4    5    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     N     242     N     242      3    6   13     3    4    5    6    7    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     P     243     P     243      3    3   13     3    3    4    6    6    8    9   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_GDT     A     244     A     244      3    3   13     3    3    4    4    4    4    7   10   10   11   11   11   11   12   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:  10.47  (   6.01    7.59   17.81 )

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      6      7      8      9     10     10     11     11     11     11     12     13     13     13     13     13     13 
GDT PERCENT_CA   5.48   6.85   6.85   8.22   9.59  10.96  12.33  13.70  13.70  15.07  15.07  15.07  15.07  16.44  17.81  17.81  17.81  17.81  17.81  17.81
GDT RMS_LOCAL    0.12   0.42   0.42   1.16   1.64   1.95   2.24   2.74   2.74   3.07   3.07   3.07   3.07   3.78   4.36   4.36   4.36   4.36   4.36   4.36
GDT RMS_ALL_CA   5.58   5.82   5.82   5.00   4.75   4.72   4.64   4.72   4.72   4.58   4.58   4.58   4.58   4.45   4.36   4.36   4.36   4.36   4.36   4.36

#      Molecule1      Molecule2       DISTANCE
LGA    P     232      P     232          3.718
LGA    N     233      N     233          3.182
LGA    P     234      P     234          2.948
LGA    H     235      H     235          2.335
LGA    L     236      L     236          1.976
LGA    R     237      R     237          2.515
LGA    K     238      K     238          4.704
LGA    D     239      D     239          9.630
LGA    S     240      S     240          8.755
LGA    N     241      N     241          3.516
LGA    N     242      N     242          2.212
LGA    P     243      P     243          1.887
LGA    A     244      A     244          3.513

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   73    4.0     10    2.74    11.644    10.765     0.352

LGA_LOCAL      RMSD =  2.738  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.583  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  4.357  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.630684 * X  +   0.220919 * Y  +   0.743930 * Z  + -31.197313
  Y_new =  -0.776020 * X  +   0.186291 * Y  +   0.602568 * Z  + -23.859358
  Z_new =  -0.005469 * X  +  -0.957335 * Y  +   0.288928 * Z  + 134.529160 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.277685    1.863908  [ DEG:   -73.2059    106.7941 ]
  Theta =   0.005469    3.136124  [ DEG:     0.3133    179.6867 ]
  Phi   =  -0.888350    2.253243  [ DEG:   -50.8987    129.1013 ]
 
# 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: T0320AL333_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320AL333_2-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   73   4.0   10   2.74  10.765     4.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL333_2-D2
REMARK Aligment from pdb entry: 1ojx_A
ATOM    733  N   PRO   232      21.665  14.367   4.731  1.00  0.00              
ATOM    734  CA  PRO   232      20.388  14.614   5.409  1.00  0.00              
ATOM    735  C   PRO   232      19.251  14.994   4.465  1.00  0.00              
ATOM    736  O   PRO   232      18.157  14.431   4.560  1.00  0.00              
ATOM    737  N   ASN   233      19.501  15.942   3.561  1.00  0.00              
ATOM    738  CA  ASN   233      18.443  16.458   2.697  1.00  0.00              
ATOM    739  C   ASN   233      18.008  15.411   1.660  1.00  0.00              
ATOM    740  O   ASN   233      16.821  15.234   1.430  1.00  0.00              
ATOM    741  N   PRO   234      18.971  14.715   1.056  1.00  0.00              
ATOM    742  CA  PRO   234      18.661  13.671   0.081  1.00  0.00              
ATOM    743  C   PRO   234      17.801  12.575   0.709  1.00  0.00              
ATOM    744  O   PRO   234      16.758  12.208   0.166  1.00  0.00              
ATOM    745  N   HIS   235      18.223  12.068   1.864  1.00  0.00              
ATOM    746  CA  HIS   235      17.474  11.011   2.530  1.00  0.00              
ATOM    747  C   HIS   235      16.087  11.477   3.021  1.00  0.00              
ATOM    748  O   HIS   235      15.120  10.725   2.938  1.00  0.00              
ATOM    749  N   LEU   236      16.004  12.710   3.523  1.00  0.00              
ATOM    750  CA  LEU   236      14.730  13.330   3.898  1.00  0.00              
ATOM    751  C   LEU   236      13.734  13.374   2.720  1.00  0.00              
ATOM    752  O   LEU   236      12.540  13.124   2.882  1.00  0.00              
ATOM    753  N   ARG   237      14.231  13.679   1.529  1.00  0.00              
ATOM    754  CA  ARG   237      13.372  13.737   0.344  1.00  0.00              
ATOM    755  C   ARG   237      12.885  12.340  -0.071  1.00  0.00              
ATOM    756  O   ARG   237      11.770  12.191  -0.576  1.00  0.00              
ATOM    757  N   LYS   238      13.708  11.317   0.155  1.00  0.00              
ATOM    758  CA  LYS   238      13.306   9.927  -0.115  1.00  0.00              
ATOM    759  C   LYS   238      12.236   9.444   0.884  1.00  0.00              
ATOM    760  O   LYS   238      11.296   8.714   0.521  1.00  0.00              
ATOM    761  N   ASP   239      12.359   9.871   2.136  1.00  0.00              
ATOM    762  CA  ASP   239      11.335   9.584   3.144  1.00  0.00              
ATOM    763  C   ASP   239       9.983  10.194   2.756  1.00  0.00              
ATOM    764  O   ASP   239       8.954   9.523   2.850  1.00  0.00              
ATOM    765  N   SER   240       9.992  11.456   2.327  1.00  0.00              
ATOM    766  CA  SER   240       8.777  12.142   1.868  1.00  0.00              
ATOM    767  C   SER   240       8.109  11.433   0.685  1.00  0.00              
ATOM    768  O   SER   240       6.888  11.340   0.624  1.00  0.00              
ATOM    769  N   ASN   241       8.905  10.960  -0.267  1.00  0.00              
ATOM    770  CA  ASN   241       8.353  10.238  -1.410  1.00  0.00              
ATOM    771  C   ASN   241       7.615   8.978  -0.960  1.00  0.00              
ATOM    772  O   ASN   241       6.540   8.668  -1.470  1.00  0.00              
ATOM    773  N   ASN   242       8.194   8.270   0.007  1.00  0.00              
ATOM    774  CA  ASN   242       7.611   7.032   0.514  1.00  0.00              
ATOM    775  C   ASN   242       6.325   7.295   1.286  1.00  0.00              
ATOM    776  O   ASN   242       5.317   6.646   1.032  1.00  0.00              
ATOM    777  N   PRO   243       6.369   8.249   2.220  1.00  0.00              
ATOM    778  CA  PRO   243       5.264   8.507   3.145  1.00  0.00              
ATOM    779  C   PRO   243       4.088   9.224   2.461  1.00  0.00              
ATOM    780  O   PRO   243       2.931   8.859   2.672  1.00  0.00              
ATOM    781  N   ALA   244       4.384  10.246   1.662  1.00  0.00              
ATOM    782  CA  ALA   244       3.354  11.024   0.964  1.00  0.00              
ATOM    783  C   ALA   244       3.024  10.407  -0.395  1.00  0.00              
ATOM    784  O   ALA   244       2.073  10.822  -1.045  1.00  0.00              
END
