
#######################################################
#                                                     #
#                        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    7 (   34),  selected    7 , name T0316TS102_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected    7 , name T0316_D2.pdb
# PARAMETERS: T0316TS102_5-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:     7       269 - 275         1.46     1.46
  LCS_AVERAGE:     11.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       269 - 275         1.46     1.46
  LCS_AVERAGE:     11.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       270 - 275         0.47     2.75
  LCS_AVERAGE:      9.29

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     K     269     K     269      3    7    7     3    3    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     N     270     N     270      6    7    7     4    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     I     271     I     271      6    7    7     3    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     272     L     272      6    7    7     4    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     Y     273     Y     273      6    7    7     4    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     V     274     V     274      6    7    7     4    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G     275     G     275      6    7    7     4    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  10.87  (   9.29   11.67   11.67 )

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      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   6.67  10.00  10.00  10.00  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67  11.67
GDT RMS_LOCAL    0.19   0.47   0.47   0.47   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46
GDT RMS_ALL_CA   3.17   2.75   2.75   2.75   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46

#      Molecule1      Molecule2       DISTANCE
LGA    K     269      K     269          1.350
LGA    N     270      N     270          0.671
LGA    I     271      I     271          1.582
LGA    L     272      L     272          1.579
LGA    Y     273      Y     273          2.309
LGA    V     274      V     274          1.452
LGA    G     275      G     275          0.512

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   60    4.0      7    1.46    10.833    11.294     0.448

LGA_LOCAL      RMSD =  1.462  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.462  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.462  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.209003 * X  +  -0.723974 * Y  +  -0.657403 * Z  +  98.537811
  Y_new =   0.516793 * X  +   0.652480 * Y  +  -0.554252 * Z  +  15.840797
  Z_new =   0.830206 * X  +  -0.223901 * Y  +   0.510515 * Z  + -71.787064 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.413315    2.728277  [ DEG:   -23.6812    156.3188 ]
  Theta =  -0.979478   -2.162115  [ DEG:   -56.1200   -123.8801 ]
  Phi   =   1.186482   -1.955110  [ DEG:    67.9804   -112.0196 ]
 
# 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: T0316TS102_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_5-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   60   4.0    7   1.46  11.294     1.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_5-D2
PFRMAT TS
TARGET T0316
MODEL 5
PARENT 1jcm_P
ATOM    615  N   LYS   269      44.008  12.523 -17.602  1.00  1.00
ATOM    616  CA  LYS   269      43.994  13.613 -18.566  1.00  1.00
ATOM    617  C   LYS   269      44.232  14.969 -17.918  1.00  1.00
ATOM    618  O   LYS   269      44.016  15.138 -16.715  1.00  1.00
ATOM    619  CB  LYS   269      42.667  13.626 -19.314  1.00  1.00
ATOM    620  N   ASN   270      44.684  15.926 -18.731  1.00  1.00
ATOM    621  CA  ASN   270      44.954  17.284 -18.278  1.00  1.00
ATOM    622  C   ASN   270      43.657  18.082 -18.205  1.00  1.00
ATOM    623  O   ASN   270      43.547  19.050 -17.452  1.00  1.00
ATOM    624  CB  ASN   270      45.919  17.992 -19.237  1.00  1.00
ATOM    625  N   ILE   271      42.673  17.664 -18.991  1.00  1.00
ATOM    626  CA  ILE   271      41.419  18.372 -19.008  1.00  1.00
ATOM    627  C   ILE   271      40.286  17.559 -19.587  1.00  1.00
ATOM    628  O   ILE   271      40.474  16.417 -20.024  1.00  1.00
ATOM    629  CB  ILE   271      41.596  19.624 -19.887  1.00  1.00
ATOM    630  N   LEU   272      39.108  18.173 -19.593  1.00  1.00
ATOM    631  CA  LEU   272      37.884  17.555 -20.077  1.00  1.00
ATOM    632  C   LEU   272      37.095  18.481 -20.975  1.00  1.00
ATOM    633  O   LEU   272      37.129  19.701 -20.823  1.00  1.00
ATOM    634  CB  LEU   272      36.979  17.196 -18.902  1.00  1.00
ATOM    635  N   TYR   273      36.381  17.874 -21.910  1.00  1.00
ATOM    636  CA  TYR   273      35.515  18.611 -22.809  1.00  1.00
ATOM    637  C   TYR   273      34.156  18.009 -22.488  1.00  1.00
ATOM    638  O   TYR   273      33.889  16.851 -22.778  1.00  1.00
ATOM    639  CB  TYR   273      35.904  18.376 -24.273  1.00  1.00
ATOM    640  N   VAL   274      33.306  18.813 -21.870  1.00  1.00
ATOM    641  CA  VAL   274      31.987  18.389 -21.429  1.00  1.00
ATOM    642  C   VAL   274      30.869  19.147 -22.132  1.00  1.00
ATOM    643  O   VAL   274      30.850  20.377 -22.127  1.00  1.00
ATOM    644  CB  VAL   274      31.888  18.613 -19.899  1.00  1.00
ATOM    645  N   GLY   275      29.940  18.401 -22.727  1.00  1.00
ATOM    646  CA  GLY   275      28.817  19.007 -23.422  1.00  1.00
ATOM    647  C   GLY   275      27.472  18.769 -22.748  1.00  1.00
ATOM    648  O   GLY   275      26.986  19.626 -22.005  1.00  1.00
TER
END
