
#######################################################
#                                                     #
#                        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    5 (   37),  selected    5 , name T0320TS268_5_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected    5 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_5_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:     5       228 - 232         0.87     0.87
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         0.87     0.87
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         0.87     0.87
  LCS_AVERAGE:      6.85

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     N     228     N     228      5    5    5     3    3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     N     229     N     229      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     230     S     230      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     231     L     231      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     P     232     P     232      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   6.85  (   6.85    6.85    6.85 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   5.48   5.48   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85
GDT RMS_LOCAL    0.24   0.24   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87
GDT RMS_ALL_CA   1.48   1.48   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          1.453
LGA    N     229      N     229          0.379
LGA    S     230      S     230          0.574
LGA    L     231      L     231          0.820
LGA    P     232      P     232          0.719

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   73    4.0      5    0.87     6.507     6.741     0.516

LGA_LOCAL      RMSD =  0.869  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.869  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.869  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.908982 * X  +  -0.188773 * Y  +   0.371640 * Z  +  -9.037166
  Y_new =  -0.378382 * X  +  -0.747705 * Y  +   0.545678 * Z  +  50.086006
  Z_new =   0.174868 * X  +  -0.636633 * Y  +  -0.751079 * Z  +  69.889297 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.438479    0.703114  [ DEG:  -139.7146     40.2854 ]
  Theta =  -0.175771   -2.965821  [ DEG:   -10.0710   -169.9290 ]
  Phi   =  -0.394453    2.747140  [ DEG:   -22.6005    157.3995 ]
 
# 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: T0320TS268_5_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_5_2-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   73   4.0    5   0.87   6.741     0.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_5_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1kqp_A
ATOM   1861  N   ASN   228      29.328  20.401   4.565  1.00  0.00
ATOM   1862  CA  ASN   228      29.084  20.937   5.873  1.00  0.00
ATOM   1863  C   ASN   228      28.925  19.759   6.779  1.00  0.00
ATOM   1864  O   ASN   228      28.931  18.617   6.322  1.00  0.00
ATOM   1865  CB  ASN   228      27.818  21.794   5.873  1.00  0.00
ATOM   1866  CG  ASN   228      26.565  20.982   5.608  1.00  0.00
ATOM   1867  OD1 ASN   228      26.621  19.759   5.484  1.00  0.00
ATOM   1868  ND2 ASN   228      25.428  21.663   5.521  1.00  0.00
ATOM   1869  N   ASN   229      28.807  19.994   8.100  1.00  0.00
ATOM   1870  CA  ASN   229      28.649  18.882   8.988  1.00  0.00
ATOM   1871  C   ASN   229      27.375  18.187   8.637  1.00  0.00
ATOM   1872  O   ASN   229      27.352  16.965   8.492  1.00  0.00
ATOM   1873  CB  ASN   229      28.590  19.361  10.440  1.00  0.00
ATOM   1874  CG  ASN   229      29.941  19.817  10.958  1.00  0.00
ATOM   1875  OD1 ASN   229      30.981  19.469  10.399  1.00  0.00
ATOM   1876  ND2 ASN   229      29.928  20.602  12.029  1.00  0.00
ATOM   1877  N   SER   230      26.273  18.940   8.468  1.00  0.00
ATOM   1878  CA  SER   230      25.061  18.264   8.116  1.00  0.00
ATOM   1879  C   SER   230      24.359  19.070   7.066  1.00  0.00
ATOM   1880  O   SER   230      24.205  20.283   7.195  1.00  0.00
ATOM   1881  CB  SER   230      24.154  18.117   9.339  1.00  0.00
ATOM   1882  OG  SER   230      22.945  17.460   9.003  1.00  0.00
ATOM   1883  N   LEU   231      23.926  18.404   5.977  1.00  0.00
ATOM   1884  CA  LEU   231      23.224  19.096   4.937  1.00  0.00
ATOM   1885  C   LEU   231      22.084  18.207   4.541  1.00  0.00
ATOM   1886  O   LEU   231      22.235  16.988   4.493  1.00  0.00
ATOM   1887  CB  LEU   231      24.149  19.351   3.744  1.00  0.00
ATOM   1888  CG  LEU   231      23.512  20.012   2.521  1.00  0.00
ATOM   1889  CD1 LEU   231      23.126  21.451   2.827  1.00  0.00
ATOM   1890  CD2 LEU   231      24.479  20.018   1.347  1.00  0.00
ATOM   1891  N   PRO   232      20.936  18.762   4.277  1.00  0.00
ATOM   1892  CA  PRO   232      19.859  17.900   3.876  1.00  0.00
ATOM   1893  C   PRO   232      20.052  17.473   2.461  1.00  0.00
ATOM   1894  O   PRO   232      19.045  17.405   1.706  1.00  0.00
ATOM   1895  CB  PRO   232      18.609  18.765   4.047  1.00  0.00
ATOM   1896  CG  PRO   232      19.062  20.147   3.711  1.00  0.00
ATOM   1897  CD  PRO   232      20.451  20.277   4.269  1.00  0.00
TER
END
