
#######################################################
#                                                     #
#                        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 (    7),  selected    7 , name T0321TS464_3_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected    7 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_3_2-D1.T0321_D1.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        84 - 90          3.31     3.31
  LCS_AVERAGE:      7.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        85 - 90          1.84     3.99
  LCS_AVERAGE:      5.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        86 - 90          0.76     5.31
  LCS_AVERAGE:      4.61

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:   96
LCS_GDT     A      84     A      84      3    4    7     3    3    3    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     Y      85     Y      85      3    6    7     3    3    4    4    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     Y      86     Y      86      5    6    7     3    4    5    5    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     N      87     N      87      5    6    7     3    4    5    5    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     N      88     N      88      5    6    7     3    4    5    5    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     P      89     P      89      5    6    7     3    4    5    5    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_GDT     Q      90     Q      90      5    6    7     3    4    5    5    5    6    6    6    6    6    6    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   5.95  (   4.61    5.95    7.29 )

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      4      5      5      5      6      6      6      6      6      6      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   3.12   4.17   5.21   5.21   5.21   6.25   6.25   6.25   6.25   6.25   6.25   7.29   7.29   7.29   7.29   7.29   7.29   7.29   7.29   7.29
GDT RMS_LOCAL    0.12   0.53   0.76   0.76   0.76   1.84   1.84   1.84   1.84   1.84   1.84   3.31   3.31   3.31   3.31   3.31   3.31   3.31   3.31   3.31
GDT RMS_ALL_CA   5.46   5.71   5.31   5.31   5.31   3.99   3.99   3.99   3.99   3.99   3.99   3.31   3.31   3.31   3.31   3.31   3.31   3.31   3.31   3.31

#      Molecule1      Molecule2       DISTANCE
LGA    A      84      A      84          9.547
LGA    Y      85      Y      85          2.696
LGA    Y      86      Y      86          2.650
LGA    N      87      N      87          0.667
LGA    N      88      N      88          2.097
LGA    P      89      P      89          0.972
LGA    Q      90      Q      90          0.555

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   96    4.0      6    1.84     5.729     5.956     0.309

LGA_LOCAL      RMSD =  1.843  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.992  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.310  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.103711 * X  +  -0.923486 * Y  +   0.369347 * Z  + -25.749340
  Y_new =  -0.946560 * X  +   0.205668 * Y  +   0.248445 * Z  +  97.147057
  Z_new =  -0.305398 * X  +  -0.323843 * Y  +  -0.895465 * Z  + 125.516571 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.794579    0.347013  [ DEG:  -160.1176     19.8824 ]
  Theta =   0.310357    2.831236  [ DEG:    17.7821    162.2179 ]
  Phi   =  -1.679927    1.461665  [ DEG:   -96.2528     83.7472 ]
 
# 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: T0321TS464_3_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_3_2-D1.T0321_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   96   4.0    6   1.84   5.956     3.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  ALA    84     -10.651  42.375  70.904  1.00  0.00
ATOM      2  CA  TYR    85     -10.816  46.024  69.903  1.00  0.00
ATOM      3  CA  TYR    86      -9.732  48.361  72.685  1.00  0.00
ATOM      4  CA  ASN    87      -6.156  49.406  73.359  1.00  0.00
ATOM      5  CA  ASN    88      -7.398  51.231  76.489  1.00  0.00
ATOM      6  CA  PRO    89      -8.076  49.300  79.681  1.00  0.00
ATOM      7  CA  GLN    90     -11.715  48.326  80.174  1.00  0.00
TER
END
