
#######################################################
#                                                     #
#                        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   36 (   36),  selected   36 , name T0335TS168_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS168_2-D1.T0335_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:    36         5 - 40          2.19     2.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        15 - 40          1.94     2.39
  LCS_AVERAGE:     66.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        21 - 40          0.96     2.97
  LCS_AVERAGE:     50.62

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:   36
LCS_GDT     A       5     A       5     16   18   36     8   12   16   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     16   18   36     8   13   15   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     16   18   36     8   13   15   21   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     16   18   36     8   13   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     16   18   36     8   13   15   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     16   18   36     8   13   15   15   27   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     16   18   36     8   13   15   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     16   18   36     8   13   15   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      13     L      13     16   18   36     7   13   15   15   19   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      14     A      14     16   18   36     7   13   15   15   16   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     16   26   36     7   13   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     16   26   36     5   13   15   15   19   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     16   26   36     5   13   15   15   16   16   17   25   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     16   26   36     5   13   15   18   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     16   26   36     5   11   15   20   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     16   26   36     3    3    3   19   24   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     20   26   36     3    6   17   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     20   26   36     3   11   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     20   26   36     3    8   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     20   26   36     6   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     20   26   36     8   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     20   26   36     4   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     20   26   36    10   16   18   22   28   33   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     20   26   36     8   13   18   21   25   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  72.22  (  50.62   66.05  100.00 )

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     10     16     18     22     28     33     34     35     36     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  27.78  44.44  50.00  61.11  77.78  91.67  94.44  97.22 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.62   0.71   1.20   1.57   1.94   1.99   2.07   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19
GDT RMS_ALL_CA   3.14   2.84   2.89   2.52   2.35   2.21   2.21   2.20   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.812
LGA    K       6      K       6          2.369
LGA    I       7      I       7          2.117
LGA    A       8      A       8          1.289
LGA    R       9      R       9          2.418
LGA    I      10      I      10          2.812
LGA    N      11      N      11          1.764
LGA    E      12      E      12          1.991
LGA    L      13      L      13          3.914
LGA    A      14      A      14          3.154
LGA    A      15      A      15          1.280
LGA    K      16      K      16          3.490
LGA    A      17      A      17          4.938
LGA    K      18      K      18          2.507
LGA    A      19      A      19          2.266
LGA    G      20      G      20          3.190
LGA    V      21      V      21          2.474
LGA    I      22      I      22          1.425
LGA    T      23      T      23          1.879
LGA    E      24      E      24          1.421
LGA    E      25      E      25          0.877
LGA    E      26      E      26          1.129
LGA    K      27      K      27          1.247
LGA    A      28      A      28          0.828
LGA    E      29      E      29          0.899
LGA    Q      30      Q      30          1.536
LGA    Q      31      Q      31          1.523
LGA    K      32      K      32          1.650
LGA    L      33      L      33          1.409
LGA    R      34      R      34          1.363
LGA    Q      35      Q      35          0.839
LGA    E      36      E      36          1.655
LGA    Y      37      Y      37          2.126
LGA    L      38      L      38          1.403
LGA    K      39      K      39          2.023
LGA    G      40      G      40          3.082

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     35    2.07    75.694    78.233     1.612

LGA_LOCAL      RMSD =  2.071  Number of atoms =   35  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.202  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  2.194  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.137176 * X  +  -0.627433 * Y  +   0.766493 * Z  +   4.731117
  Y_new =  -0.969246 * X  +  -0.244631 * Y  +  -0.026788 * Z  +   1.695653
  Z_new =   0.204316 * X  +  -0.739245 * Y  +  -0.641694 * Z  +  -6.800361 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.285671    0.855922  [ DEG:  -130.9593     49.0407 ]
  Theta =  -0.205765   -2.935828  [ DEG:   -11.7895   -168.2105 ]
  Phi   =  -1.430202    1.711391  [ DEG:   -81.9445     98.0555 ]
 
# 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: T0335TS168_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_2-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   36   36   4.0   35   2.07  78.233     2.19
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_2-D1
PFRMAT TS
TARGET T0335
MODEL 2
PARENT N/A
ATOM      5  CA  ALA     5       0.485 -10.714  -6.622  1.00 25.00           C
ATOM      6  CA  LYS     6       1.312  -7.032  -7.276  1.00 25.00           C
ATOM      7  CA  ILE     7      -2.365  -6.324  -8.082  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.436  -8.066  -4.844  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.908  -5.984  -2.859  1.00 25.00           C
ATOM     10  CA  ILE    10      -2.236  -2.779  -4.483  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.824  -3.789  -3.600  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.770  -4.457   0.021  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.070  -1.029   0.185  1.00 25.00           C
ATOM     14  CA  ALA    14      -6.234   0.633  -1.189  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.357  -1.186   1.428  1.00 25.00           C
ATOM     16  CA  LYS    16      -5.976  -0.031   4.196  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.201   3.573   2.921  1.00 25.00           C
ATOM     18  CA  LYS    18     -10.025   3.352   2.899  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.993   2.010   6.486  1.00 25.00           C
ATOM     20  CA  GLY    20      -9.559   4.217   9.538  1.00 25.00           C
ATOM     21  CA  VAL    21      -7.132   2.403  11.821  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.274   3.294   9.530  1.00 25.00           C
ATOM     23  CA  THR    23      -2.813   6.266  11.377  1.00 25.00           C
ATOM     24  CA  GLU    24       1.041   6.135  11.449  1.00 25.00           C
ATOM     25  CA  GLU    25       3.546   3.289  10.908  1.00 25.00           C
ATOM     26  CA  GLU    26       0.905   1.300   8.975  1.00 25.00           C
ATOM     27  CA  LYS    27       0.154   4.362   6.800  1.00 25.00           C
ATOM     28  CA  ALA    28       3.893   4.813   6.102  1.00 25.00           C
ATOM     29  CA  GLU    29       4.183   1.119   5.133  1.00 25.00           C
ATOM     30  CA  GLN    30       1.182   1.476   2.781  1.00 25.00           C
ATOM     31  CA  GLN    31       2.772   4.570   1.181  1.00 25.00           C
ATOM     32  CA  LYS    32       6.058   2.663   0.702  1.00 25.00           C
ATOM     33  CA  LEU    33       4.164  -0.245  -0.918  1.00 25.00           C
ATOM     34  CA  ARG    34       2.373   2.196  -3.263  1.00 25.00           C
ATOM     35  CA  GLN    35       5.727   3.782  -4.216  1.00 25.00           C
ATOM     36  CA  GLU    36       7.191   0.315  -4.926  1.00 25.00           C
ATOM     37  CA  TYR    37       4.166  -0.542  -7.113  1.00 25.00           C
ATOM     38  CA  LEU    38       4.591   2.747  -9.030  1.00 25.00           C
ATOM     39  CA  LYS    39       8.306   1.985  -9.563  1.00 25.00           C
ATOM     40  CA  GLY    40       7.428  -1.514 -10.849  1.00 25.00           C
TER
END
