
#######################################################
#                                                     #
#                        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   21 (   21),  selected   21 , name T0365TS464_2_2-D1
# Molecule2: number of CA atoms  207 ( 1594),  selected   21 , name T0365_D1.pdb
# PARAMETERS: T0365TS464_2_2-D1.T0365_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:    21        14 - 163         4.70     4.70
  LCS_AVERAGE:     10.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        14 - 29          0.46     5.43
  LCS_AVERAGE:      6.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        14 - 29          0.46     5.43
  LCS_AVERAGE:      6.46

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:  207
LCS_GDT     P      14     P      14     16   16   21     3   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     I      15     I      15     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     K      16     K      16     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     P      17     P      17     16   16   21     4   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     L      18     L      18     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     Q      19     Q      19     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     E      20     E      20     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     H      21     H      21     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     M      22     M      22     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     D      23     D      23     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     K      24     K      24     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     V      25     V      25     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     Y      26     Y      26     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     D      27     D      27     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     C      28     C      28     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     A      29     A      29     16   16   21    14   16   16   16   16   16   16   16   16   16   16   17   18   20   20   21   21   21   21   21 
LCS_GDT     A     159     A     159      5    5   21     0    4    5    5    5    5    5    5    5    5    8   12   16   20   20   21   21   21   21   21 
LCS_GDT     K     160     K     160      5    5   21     4    4    5    5    5    5    5    5    5    5   10   13   18   20   20   21   21   21   21   21 
LCS_GDT     M     161     M     161      5    5   21     4    4    5    5    5    5    5    5    5    5    6   12   15   20   20   21   21   21   21   21 
LCS_GDT     I     162     I     162      5    5   21     4    4    5    5    5    5    5    5    5    5    5    5   10   13   16   21   21   21   21   21 
LCS_GDT     N     163     N     163      5    5   21     4    4    5    5    5    5    5    5    5    5   10   17   18   20   20   21   21   21   21   21 
LCS_AVERAGE  LCS_A:   7.69  (   6.46    6.46   10.14 )

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     14     16     16     16     16     16     16     16     16     16     16     17     18     20     20     21     21     21     21     21 
GDT PERCENT_CA   6.76   7.73   7.73   7.73   7.73   7.73   7.73   7.73   7.73   7.73   7.73   8.21   8.70   9.66   9.66  10.14  10.14  10.14  10.14  10.14
GDT RMS_LOCAL    0.38   0.46   0.46   0.46   0.46   0.46   0.46   0.46   0.46   0.46   0.46   2.37   3.29   4.31   4.31   4.70   4.70   4.70   4.70   4.70
GDT RMS_ALL_CA   5.42   5.43   5.43   5.43   5.43   5.43   5.43   5.43   5.43   5.43   5.43   5.14   4.94   4.74   4.74   4.70   4.70   4.70   4.70   4.70

#      Molecule1      Molecule2       DISTANCE
LGA    P      14      P      14          0.742
LGA    I      15      I      15          0.395
LGA    K      16      K      16          0.422
LGA    P      17      P      17          0.821
LGA    L      18      L      18          0.302
LGA    Q      19      Q      19          0.444
LGA    E      20      E      20          0.411
LGA    H      21      H      21          0.430
LGA    M      22      M      22          0.373
LGA    D      23      D      23          0.266
LGA    K      24      K      24          0.249
LGA    V      25      V      25          0.430
LGA    Y      26      Y      26          0.379
LGA    D      27      D      27          0.462
LGA    C      28      C      28          0.451
LGA    A      29      A      29          0.383
LGA    A     159      A     159         11.325
LGA    K     160      K     160         10.803
LGA    M     161      M     161         10.805
LGA    I     162      I     162         12.366
LGA    N     163      N     163         10.020

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  207    4.0     16    0.46     8.333     7.659     2.864

LGA_LOCAL      RMSD =  0.459  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.427  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  4.703  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.516024 * X  +  -0.691431 * Y  +  -0.505611 * Z  +  32.430119
  Y_new =   0.683069 * X  +  -0.024002 * Y  +   0.729960 * Z  +  -1.559313
  Z_new =  -0.516852 * X  +  -0.722044 * Y  +   0.459909 * Z  +  21.533295 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.003647    2.137946  [ DEG:   -57.5047    122.4953 ]
  Theta =   0.543170    2.598423  [ DEG:    31.1213    148.8787 ]
  Phi   =   0.923816   -2.217776  [ DEG:    52.9308   -127.0692 ]
 
# 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: T0365TS464_2_2-D1                             
REMARK     2: T0365_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0365TS464_2_2-D1.T0365_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  207   4.0   16   0.46   7.659     4.70
REMARK  ---------------------------------------------------------- 
MOLECULE T0365TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0365
PARENT N/A
ATOM     14  CA  PRO    14      34.819  17.779  22.300  1.00  0.00
ATOM     15  CA  ILE    15      33.508  20.183  24.975  1.00  0.00
ATOM     16  CA  LYS    16      31.097  17.393  25.954  1.00  0.00
ATOM     17  CA  PRO    17      34.047  15.386  27.328  1.00  0.00
ATOM     18  CA  LEU    18      34.806  18.252  29.701  1.00  0.00
ATOM     19  CA  GLN    19      31.088  18.449  30.554  1.00  0.00
ATOM     20  CA  GLU    20      30.864  14.900  31.927  1.00  0.00
ATOM     21  CA  HIS    21      33.975  15.285  34.097  1.00  0.00
ATOM     22  CA  MET    22      32.900  18.778  35.204  1.00  0.00
ATOM     23  CA  ASP    23      29.603  17.417  36.558  1.00  0.00
ATOM     24  CA  LYS    24      31.451  14.666  38.432  1.00  0.00
ATOM     25  CA  VAL    25      33.844  17.134  40.095  1.00  0.00
ATOM     26  CA  TYR    26      31.031  19.622  40.777  1.00  0.00
ATOM     27  CA  ASP    27      29.116  16.997  42.769  1.00  0.00
ATOM     28  CA  CYS    28      32.237  16.179  44.818  1.00  0.00
ATOM     29  CA  ALA    29      32.542  19.836  45.853  1.00  0.00
ATOM     30  CA  ALA   159      32.988  29.185  32.607  1.00  0.00
ATOM     31  CA  LYS   160      29.713  27.249  33.164  1.00  0.00
ATOM     32  CA  MET   161      28.980  25.182  36.285  1.00  0.00
ATOM     33  CA  ILE   162      31.882  26.586  38.330  1.00  0.00
ATOM     34  CA  ASN   163      31.046  30.151  37.229  1.00  0.00
TER
END
