
#######################################################
#                                                     #
#                        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   12 (   12),  selected   12 , name T0330TS464_3_2-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected   12 , name T0330_D1.pdb
# PARAMETERS: T0330TS464_3_2-D1.T0330_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:    10         2 - 14          3.78     7.25
  LONGEST_CONTINUOUS_SEGMENT:    10         3 - 15          4.75     6.83
  LCS_AVERAGE:      6.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7         2 - 8           1.75     8.46
  LCS_AVERAGE:      3.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         3 - 8           0.64     7.83
  LCS_AVERAGE:      2.94

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:  153
LCS_GDT     S       2     S       2      3    7   10     3    3    3    5    5    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     R       3     R       3      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     T       4     T       4      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     L       5     L       5      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     V       6     V       6      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     L       7     L       7      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9    9   10   11   11   11   11   11   11 
LCS_GDT     F       8     F       8      6    7   10     4    6    6    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     G      12     G      12      3    4   10     3    3    3    3    4    5    5    6    7    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     T      13     T      13      3    4   10     3    3    3    6    6    7    8    8    8    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     L      14     L      14      3    4   10     3    3    3    3    4    5    5    6    7    8    9    9   10   10   11   11   11   11   11   11 
LCS_GDT     L      15     L      15      3    4   10     3    3    3    3    4    4    4    5    5    5    7    9   10   10   11   11   11   11   11   11 
LCS_GDT     K      16     K      16      3    4    6     0    3    3    3    4    4    4    5    5    5    5    5    6    6    6    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   4.34  (   2.94    3.76    6.32 )

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      6      7      8      8      8      8      9      9     10     10     11     11     11     11     11     11 
GDT PERCENT_CA   2.61   3.92   3.92   3.92   3.92   4.58   5.23   5.23   5.23   5.23   5.88   5.88   6.54   6.54   7.19   7.19   7.19   7.19   7.19   7.19
GDT RMS_LOCAL    0.29   0.64   0.64   0.64   0.64   1.41   2.08   2.08   2.08   2.08   2.88   2.88   4.82   4.82   5.03   5.03   5.03   5.03   5.03   5.03
GDT RMS_ALL_CA   7.71   7.83   7.83   7.83   7.83   7.70   7.63   7.63   7.63   7.63   7.76   7.76   6.51   6.51   6.75   6.75   6.75   6.75   6.75   6.75

#      Molecule1      Molecule2       DISTANCE
LGA    S       2      S       2          3.274
LGA    R       3      R       3          3.130
LGA    T       4      T       4          1.345
LGA    L       5      L       5          0.189
LGA    V       6      V       6          0.898
LGA    L       7      L       7          0.905
LGA    F       8      F       8          0.952
LGA    G      12      G      12          7.415
LGA    T      13      T      13          3.091
LGA    L      14      L      14          8.344
LGA    L      15      L      15         13.385
LGA    K      16      K      16         18.968

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  153    4.0      8    2.08     5.065     4.695     0.368

LGA_LOCAL      RMSD =  2.075  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.627  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  6.339  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.600433 * X  +   0.139597 * Y  +  -0.787396 * Z  +  74.273468
  Y_new =  -0.796937 * X  +  -0.023054 * Y  +   0.603622 * Z  +  80.429863
  Z_new =   0.066111 * X  +   0.989940 * Y  +   0.125092 * Z  + -33.298840 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.445099   -1.696494  [ DEG:    82.7981    -97.2019 ]
  Theta =  -0.066160   -3.075433  [ DEG:    -3.7907   -176.2093 ]
  Phi   =  -2.216487    0.925106  [ DEG:  -126.9953     53.0047 ]
 
# 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: T0330TS464_3_2-D1                             
REMARK     2: T0330_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2-D1.T0330_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  153   4.0    8   2.08   4.695     6.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM      1  CA  SER     2      20.618  57.406  35.920  1.00  0.00
ATOM      2  CA  ARG     3      23.920  55.678  35.142  1.00  0.00
ATOM      3  CA  THR     4      23.922  54.113  31.668  1.00  0.00
ATOM      4  CA  LEU     5      22.730  54.288  28.071  1.00  0.00
ATOM      5  CA  VAL     6      22.600  50.869  26.411  1.00  0.00
ATOM      6  CA  LEU     7      21.894  49.666  22.895  1.00  0.00
ATOM      7  CA  PHE     8      20.528  46.159  22.354  1.00  0.00
ATOM      8  CA  GLY    12      17.780  41.296  22.151  1.00  0.00
ATOM      9  CA  THR    13      21.527  41.201  22.779  1.00  0.00
ATOM     10  CA  LEU    14      23.425  43.967  24.585  1.00  0.00
ATOM     11  CA  LEU    15      25.910  45.531  22.149  1.00  0.00
ATOM     12  CA  LYS    16      26.988  48.862  23.616  1.00  0.00
TER
END
