
#######################################################
#                                                     #
#                        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 T0321TS464_2_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   21 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_2_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:    12         5 - 88          4.97     8.67
  LCS_AVERAGE:     12.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        88 - 95          0.34    16.00
  LCS_AVERAGE:      6.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        88 - 95          0.34    16.00
  LCS_AVERAGE:      6.99

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     E       3     E       3      5    5   11     5    5    5    5    5    5    5    6    6    7    7    8   10   10   12   14   15   18   18   20 
LCS_GDT     I       4     I       4      5    5   11     5    5    5    5    5    5    5    6    6    7    7    8   10   10   12   14   17   18   18   20 
LCS_GDT     Y       5     Y       5      5    5   12     5    5    5    5    5    5    5    6    8    8   10   11   13   14   15   16   17   18   18   20 
LCS_GDT     D       6     D       6      5    5   12     5    5    5    5    5    5    5    6    8    8   10   11   13   14   15   16   17   18   18   20 
LCS_GDT     A       7     A       7      5    5   12     5    5    5    5    5    5    5    6    8    8   10   10   12   14   15   16   17   18   18   20 
LCS_GDT     V      18     V      18      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     D      19     D      19      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     E      20     E      20      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     L      21     L      21      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     V      22     V      22      7    7   12     3    5    7    7    7    7    7    7    7    8   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     C      23     C      23      7    7   12     4    6    7    7    7    7    7    7    8    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     G      24     G      24      7    7   12     5    6    7    7    7    7    7    7    7    8   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     N      87     N      87      3    3   12     3    3    3    3    4    5    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     N      88     N      88      8    8   12     7    8    8    8    8    8    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     P      89     P      89      8    8   11     7    8    8    8    8    8    8    8    9    9    9   10   13   15   16   16   16   16   17   20 
LCS_GDT     Q      90     Q      90      8    8   11     7    8    8    8    8    8    8    8    9    9    9   10   13   15   16   16   16   16   17   20 
LCS_GDT     V      91     V      91      8    8   11     7    8    8    8    8    8    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     A      92     A      92      8    8   11     7    8    8    8    8    8    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     R      93     R      93      8    8   11     7    8    8    8    8    8    8    8    9    9    9   12   13   15   16   16   16   16   17   20 
LCS_GDT     E      94     E      94      8    8   11     7    8    8    8    8    8    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_GDT     H      95     H      95      8    8   11     3    8    8    8    8    8    8    8    9    9   10   12   13   15   16   16   17   18   18   20 
LCS_AVERAGE  LCS_A:   8.68  (   6.99    6.99   12.05 )

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      7      8      8      8      8      8      8      8      9      9     10     12     13     15     16     16     17     18     18     20 
GDT PERCENT_CA   7.29   8.33   8.33   8.33   8.33   8.33   8.33   8.33   9.38   9.38  10.42  12.50  13.54  15.62  16.67  16.67  17.71  18.75  18.75  20.83
GDT RMS_LOCAL    0.19   0.34   0.34   0.34   0.34   0.34   0.34   0.34   2.09   2.09   4.02   4.74   4.89   5.36   5.56   5.56   6.10   6.34   6.34   7.07
GDT RMS_ALL_CA  16.04  16.00  16.00  16.00  16.00  16.00  16.00  16.00  15.80  15.80   9.43   8.94   9.16  10.43  10.30  10.30   7.50   7.53   7.53   7.35

#      Molecule1      Molecule2       DISTANCE
LGA    E       3      E       3         32.079
LGA    I       4      I       4         27.161
LGA    Y       5      Y       5         27.836
LGA    D       6      D       6         28.934
LGA    A       7      A       7         22.701
LGA    V      18      V      18         15.818
LGA    D      19      D      19         15.523
LGA    E      20      E      20         11.573
LGA    L      21      L      21          9.272
LGA    V      22      V      22         12.397
LGA    C      23      C      23         14.269
LGA    G      24      G      24         18.771
LGA    N      87      N      87          7.657
LGA    N      88      N      88          0.097
LGA    P      89      P      89          0.213
LGA    Q      90      Q      90          0.284
LGA    V      91      V      91          0.370
LGA    A      92      A      92          0.322
LGA    R      93      R      93          0.249
LGA    E      94      E      94          0.366
LGA    H      95      H      95          0.609

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   96    4.0      8    0.34    10.417     9.264     1.806

LGA_LOCAL      RMSD =  0.343  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.998  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  7.284  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.911519 * X  +   0.410222 * Y  +  -0.029182 * Z  + -62.038467
  Y_new =  -0.380856 * X  +   0.868781 * Y  +   0.316493 * Z  +  32.460152
  Z_new =   0.155185 * X  +  -0.277375 * Y  +   0.948146 * Z  +  23.663877 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.284603    2.856989  [ DEG:   -16.3066    163.6934 ]
  Theta =  -0.155815   -2.985778  [ DEG:    -8.9275   -171.0725 ]
  Phi   =  -0.395778    2.745814  [ DEG:   -22.6764    157.3236 ]
 
# 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_2_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_2_2-D1.T0321_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   96   4.0    8   0.34   9.264     7.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3     -16.223  50.806  85.118  1.00  0.00
ATOM      2  CA  ILE     4     -13.152  51.343  82.922  1.00  0.00
ATOM      3  CA  TYR     5     -10.536  50.774  85.642  1.00  0.00
ATOM      4  CA  ASP     6     -12.642  48.063  87.318  1.00  0.00
ATOM      5  CA  ALA     7     -13.384  46.335  84.052  1.00  0.00
ATOM      6  CA  VAL    18      -0.278  53.087  69.621  1.00  0.00
ATOM      7  CA  ASP    19      -3.082  50.521  69.937  1.00  0.00
ATOM      8  CA  GLU    20      -6.065  52.554  71.098  1.00  0.00
ATOM      9  CA  LEU    21      -7.083  56.076  71.887  1.00  0.00
ATOM     10  CA  VAL    22      -9.145  57.401  74.694  1.00  0.00
ATOM     11  CA  CYS    23     -10.683  60.734  73.727  1.00  0.00
ATOM     12  CA  GLY    24     -12.732  62.229  76.543  1.00  0.00
ATOM     13  CA  ASN    87     -12.632  51.831  76.813  1.00  0.00
ATOM     14  CA  ASN    88      -9.242  50.480  75.664  1.00  0.00
ATOM     15  CA  PRO    89      -8.260  50.120  79.333  1.00  0.00
ATOM     16  CA  GLN    90     -11.318  48.037  80.249  1.00  0.00
ATOM     17  CA  VAL    91     -10.780  45.966  77.113  1.00  0.00
ATOM     18  CA  ALA    92      -7.108  45.313  77.998  1.00  0.00
ATOM     19  CA  ARG    93      -7.746  44.525  81.663  1.00  0.00
ATOM     20  CA  GLU    94     -10.563  42.085  80.892  1.00  0.00
ATOM     21  CA  HIS    95      -8.866  40.413  77.906  1.00  0.00
TER
END
