
#######################################################
#                                                     #
#                        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 (   41),  selected    6 , name T0382TS009_1_2
# Molecule2: number of CA atoms  121 (  929),  selected    6 , name T0382.pdb
# PARAMETERS: T0382TS009_1_2.T0382.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:     6        94 - 99          3.33     3.33
  LCS_AVERAGE:      4.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        94 - 97          0.91     5.14
  LCS_AVERAGE:      3.03

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        94 - 97          0.91     5.14
  LCS_AVERAGE:      2.20

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:  121
LCS_GDT     E      94     E      94      4    4    6     3    3    4    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A      95     A      95      4    4    6     3    3    4    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I      96     I      96      4    4    6     3    3    4    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     V      97     V      97      4    4    6     0    3    4    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S      98     S      98      0    3    6     0    0    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S      99     S      99      0    3    6     0    0    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.40  (   2.20    3.03    4.96 )

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      3      3      4      4      4      4      4      5      5      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.48   2.48   3.31   3.31   3.31   3.31   3.31   4.13   4.13   4.96   4.96   4.96   4.96   4.96   4.96   4.96   4.96   4.96   4.96   4.96
GDT RMS_LOCAL    0.08   0.08   0.91   0.91   0.91   0.91   0.91   2.38   2.38   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33
GDT RMS_ALL_CA   5.03   5.03   5.14   5.14   5.14   5.14   5.14   3.93   3.93   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33

#      Molecule1      Molecule2       DISTANCE
LGA    E      94      E      94          2.012
LGA    A      95      A      95          2.027
LGA    I      96      I      96          1.090
LGA    V      97      V      97          2.257
LGA    S      98      S      98          3.716
LGA    S      99      S      99          8.015

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  121    4.0      5    2.38     3.719     3.654     0.202

LGA_LOCAL      RMSD =  2.377  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.926  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.330  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.921149 * X  +   0.024945 * Y  +   0.388410 * Z  + -17.436182
  Y_new =  -0.366791 * X  +   0.278166 * Y  +  -0.887743 * Z  +  64.935768
  Z_new =  -0.130187 * X  +  -0.960209 * Y  +  -0.247082 * Z  + -24.556099 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.822654    1.318939  [ DEG:  -104.4304     75.5696 ]
  Theta =   0.130557    3.011035  [ DEG:     7.4804    172.5196 ]
  Phi   =  -2.762648    0.378944  [ DEG:  -158.2881     21.7119 ]
 
# 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: T0382TS009_1_2                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_1_2.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  121   4.0    5   2.38   3.654     3.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_1_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                            
ATOM    731  N   GLU    94     -21.100  54.424   7.455  1.00  0.00              
ATOM    732  CA  GLU    94     -21.596  54.902   8.740  1.00  0.00              
ATOM    733  C   GLU    94     -22.518  53.877   9.391  1.00  0.00              
ATOM    734  O   GLU    94     -22.614  53.802  10.616  1.00  0.00              
ATOM    735  CB  GLU    94     -20.431  55.230   9.676  1.00  0.00              
ATOM    736  CG  GLU    94     -20.080  56.709   9.734  1.00  0.00              
ATOM    737  CD  GLU    94     -19.050  57.020  10.802  1.00  0.00              
ATOM    738  OE1 GLU    94     -17.846  57.061  10.471  1.00  0.00              
ATOM    739  OE2 GLU    94     -19.446  57.224  11.968  1.00  0.00              
ATOM    740  N   ALA    95     -23.197  53.088   8.563  1.00  0.00              
ATOM    741  CA  ALA    95     -24.112  52.066   9.057  1.00  0.00              
ATOM    742  C   ALA    95     -23.755  51.645  10.478  1.00  0.00              
ATOM    743  O   ALA    95     -24.594  51.684  11.377  1.00  0.00              
ATOM    744  CB  ALA    95     -25.546  52.570   9.004  1.00  0.00              
ATOM    745  N   ILE    96     -22.502  51.244  10.674  1.00  0.00              
ATOM    746  CA  ILE    96     -22.021  50.806  12.015  1.00  0.00              
ATOM    747  C   ILE    96     -22.302  51.866  13.075  1.00  0.00              
ATOM    748  O   ILE    96     -22.298  53.062  12.788  1.00  0.00              
ATOM    749  CB  ILE    96     -22.674  49.478  12.444  1.00  0.00              
ATOM    750  CG2 ILE    96     -21.979  48.302  11.775  1.00  0.00              
ATOM    751  CG1 ILE    96     -24.167  49.486  12.108  1.00  0.00              
ATOM    752  CD1 ILE    96     -24.710  48.131  11.710  1.00  0.00              
ATOM    753  N   VAL    97     -22.546  51.417  14.303  1.00  0.00              
ATOM    754  CA  VAL    97     -22.835  52.346  15.433  1.00  0.00              
ATOM    755  C   VAL    97     -23.057  51.580  16.732  1.00  0.00              
ATOM    756  O   VAL    97     -23.473  50.422  16.720  1.00  0.00              
ATOM    757  CB  VAL    97     -21.695  53.362  15.634  1.00  0.00              
ATOM    758  CG1 VAL    97     -21.754  54.447  14.570  1.00  0.00              
ATOM    759  CG2 VAL    97     -20.346  52.660  15.616  1.00  0.00              
ATOM    760  N   SER    98     -22.776  52.235  17.854  1.00  0.00              
ATOM    761  CA  SER    98     -22.943  51.618  19.165  1.00  0.00              
ATOM    762  C   SER    98     -22.459  52.542  20.276  1.00  0.00              
ATOM    763  O   SER    98     -22.194  53.722  20.045  1.00  0.00              
ATOM    764  CB  SER    98     -24.409  51.241  19.395  1.00  0.00              
ATOM    765  OG  SER    98     -24.518  49.953  19.979  1.00  0.00              
ATOM    766  N   SER    99     -22.345  51.998  21.484  1.00  0.00              
ATOM    767  CA  SER    99     -21.892  52.773  22.633  1.00  0.00              
ATOM    768  C   SER    99     -21.970  51.953  23.916  1.00  0.00              
ATOM    769  O   SER    99     -22.223  52.491  24.994  1.00  0.00              
ATOM    770  CB  SER    99     -20.462  53.271  22.414  1.00  0.00              
ATOM    771  OG  SER    99     -20.328  54.625  22.808  1.00  0.00              
TER
END
