
#######################################################
#                                                     #
#                        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    6 (   24),  selected    6 , name T0316AL333_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected    6 , name T0316_D2.pdb
# PARAMETERS: T0316AL333_2-D2.T0316_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:     5       220 - 224         3.25     6.00
  LONGEST_CONTINUOUS_SEGMENT:     5       221 - 283         4.90     5.49
  LCS_AVERAGE:      8.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       220 - 222         0.70     9.78
  LONGEST_CONTINUOUS_SEGMENT:     3       221 - 223         0.53     6.74
  LONGEST_CONTINUOUS_SEGMENT:     3       222 - 224         0.90     7.92
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       220 - 222         0.70     9.78
  LONGEST_CONTINUOUS_SEGMENT:     3       222 - 224         0.90     7.92
  LCS_AVERAGE:      4.17

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:   60
LCS_GDT     G     220     G     220      3    3    5     0    3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6 
LCS_GDT     R     221     R     221      3    3    5     0    3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6 
LCS_GDT     M     222     M     222      3    3    5     1    3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6 
LCS_GDT     M     223     M     223      3    3    5     0    3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6 
LCS_GDT     T     224     T     224      3    3    5     0    3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6 
LCS_GDT     L     283     L     283      0    0    5     0    0    0    0    0    0    0    0    0    0    0    0    3    3    3    5    5    6    6    6 
LCS_AVERAGE  LCS_A:   5.56  (   4.17    4.17    8.33 )

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      1      3      3      3      3      3      4      4      5      5      5      5      5      5      5      5      5      6      6      6 
GDT PERCENT_CA   1.67   5.00   5.00   5.00   5.00   5.00   6.67   6.67   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33  10.00  10.00  10.00
GDT RMS_LOCAL   31.63   0.53   0.53   0.53   0.53   0.53   2.34   2.34   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   5.17   5.17   5.17
GDT RMS_ALL_CA   6.74   6.74   6.74   6.74   6.74   6.74   5.89   5.89   6.00   6.00   6.00   6.00   6.00   6.00   6.00   6.00   6.00   5.17   5.17   5.17

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220          7.874
LGA    R     221      R     221          2.650
LGA    M     222      M     222          0.756
LGA    M     223      M     223          2.220
LGA    T     224      T     224          3.070
LGA    L     283      L     283         11.142

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   60    4.0      4    2.34     6.250     5.961     0.164

LGA_LOCAL      RMSD =  2.342  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.889  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  5.166  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.713499 * X  +   0.643989 * Y  +  -0.276038 * Z  + -32.281746
  Y_new =  -0.435690 * X  +   0.716332 * Y  +   0.545016 * Z  + -13.223570
  Z_new =   0.548720 * X  +  -0.268601 * Y  +   0.791682 * Z  + -17.934984 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.327093    2.814500  [ DEG:   -18.7410    161.2590 ]
  Theta =  -0.580832   -2.560760  [ DEG:   -33.2792   -146.7208 ]
  Phi   =  -0.548205    2.593387  [ DEG:   -31.4099    148.5901 ]
 
# 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: T0316AL333_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_2-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   60   4.0    4   2.34   5.961     5.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_2-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    781  N   GLY   220      42.973  18.388 -27.287  1.00  0.00              
ATOM    782  CA  GLY   220      41.544  18.614 -27.452  1.00  0.00              
ATOM    783  C   GLY   220      40.774  18.365 -26.149  1.00  0.00              
ATOM    784  O   GLY   220      39.601  17.987 -26.165  1.00  0.00              
ATOM    785  N   ARG   221      41.430  18.591 -25.020  1.00  0.00              
ATOM    786  CA  ARG   221      40.777  18.373 -23.744  1.00  0.00              
ATOM    787  C   ARG   221      39.469  19.138 -23.633  1.00  0.00              
ATOM    788  O   ARG   221      38.445  18.580 -23.239  1.00  0.00              
ATOM    789  N   MET   222      39.505  20.421 -23.968  1.00  0.00              
ATOM    790  CA  MET   222      38.308  21.243 -23.871  1.00  0.00              
ATOM    791  C   MET   222      37.163  20.724 -24.738  1.00  0.00              
ATOM    792  O   MET   222      35.993  20.945 -24.427  1.00  0.00              
ATOM    793  N   MET   223      37.498  20.033 -25.820  1.00  0.00              
ATOM    794  CA  MET   223      36.488  19.502 -26.716  1.00  0.00              
ATOM    795  C   MET   223      35.843  18.273 -26.080  1.00  0.00              
ATOM    796  O   MET   223      34.633  18.066 -26.173  1.00  0.00              
ATOM    797  N   THR   224      36.659  17.466 -25.417  1.00  0.00              
ATOM    798  CA  THR   224      36.174  16.262 -24.755  1.00  0.00              
ATOM    799  C   THR   224      35.210  16.616 -23.625  1.00  0.00              
ATOM    800  O   THR   224      34.239  15.899 -23.371  1.00  0.00              
ATOM    801  N   LEU   283      35.488  17.731 -22.957  1.00  0.00              
ATOM    802  CA  LEU   283      34.688  18.192 -21.835  1.00  0.00              
ATOM    803  C   LEU   283      33.293  18.644 -22.235  1.00  0.00              
ATOM    804  O   LEU   283      32.330  18.411 -21.506  1.00  0.00              
END
