
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS168_5-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          1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36         5 - 40          1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        20 - 40          0.90     2.50
  LCS_AVERAGE:     51.77

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     15   36   36     8   12   19   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     15   36   36     8   13   15   25   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     15   36   36     8   13   15   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     15   36   36     8   13   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     15   36   36     8   13   18   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     15   36   36     8   13   15   23   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     15   36   36     8   13   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     15   36   36     8   13   19   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      13     L      13     15   36   36     7   13   15   15   28   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      14     A      14     15   36   36     7   13   15   15   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     15   36   36     7   14   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     15   36   36     7   13   15   15   26   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     15   36   36     7   13   15   15   16   18   27   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     15   36   36     7   13   18   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     20   36   36     7   13   15   15   29   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     21   36   36     9   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     21   36   36     3   10   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     21   36   36     3    3   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     21   36   36     7   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     21   36   36     6   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     21   36   36     8   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     21   36   36     4   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     21   36   36     8   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     21   36   36     8   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     21   36   36    10   18   20   26   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     21   36   36     8   18   20   25   31   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     21   36   36     8   16   20   23   27   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.92  (  51.77  100.00  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     18     20     26     31     33     35     36     36     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  27.78  50.00  55.56  72.22  86.11  91.67  97.22 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.41   0.64   0.78   1.30   1.55   1.68   1.84   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94
GDT RMS_ALL_CA   2.45   2.49   2.53   2.02   1.97   1.97   1.95   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.988
LGA    K       6      K       6          3.044
LGA    I       7      I       7          2.071
LGA    A       8      A       8          1.986
LGA    R       9      R       9          3.165
LGA    I      10      I      10          2.791
LGA    N      11      N      11          1.959
LGA    E      12      E      12          2.861
LGA    L      13      L      13          3.890
LGA    A      14      A      14          2.391
LGA    A      15      A      15          2.341
LGA    K      16      K      16          3.973
LGA    A      17      A      17          3.994
LGA    K      18      K      18          1.474
LGA    A      19      A      19          3.790
LGA    G      20      G      20          2.249
LGA    V      21      V      21          1.889
LGA    I      22      I      22          2.468
LGA    T      23      T      23          0.503
LGA    E      24      E      24          1.192
LGA    E      25      E      25          1.113
LGA    E      26      E      26          1.128
LGA    K      27      K      27          0.950
LGA    A      28      A      28          0.722
LGA    E      29      E      29          0.837
LGA    Q      30      Q      30          1.093
LGA    Q      31      Q      31          1.214
LGA    K      32      K      32          1.362
LGA    L      33      L      33          0.959
LGA    R      34      R      34          0.978
LGA    Q      35      Q      35          0.266
LGA    E      36      E      36          0.856
LGA    Y      37      Y      37          1.407
LGA    L      38      L      38          0.736
LGA    K      39      K      39          1.189
LGA    G      40      G      40          2.124

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     36    1.94    80.556    89.206     1.764

LGA_LOCAL      RMSD =  1.941  Number of atoms =   36  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.157  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  1.941  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.620427 * X  +   0.426288 * Y  +   0.658293 * Z  +   4.970446
  Y_new =   0.688597 * X  +   0.697847 * Y  +   0.197086 * Z  +   2.177154
  Z_new =  -0.375373 * X  +   0.575576 * Y  +  -0.726504 * Z  +  -6.740037 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.471593   -0.670000  [ DEG:   141.6118    -38.3882 ]
  Theta =   0.384799    2.756794  [ DEG:    22.0473    157.9527 ]
  Phi   =   2.304164   -0.837429  [ DEG:   132.0189    -47.9811 ]
 
# 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_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_5-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   36   1.94  89.206     1.94
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_5-D1
PFRMAT TS
TARGET T0335
MODEL 5
PARENT N/A
ATOM      5  CA  ALA     5       1.158 -10.546  -7.603  1.00 25.00           C
ATOM      6  CA  LYS     6       2.163  -6.853  -7.728  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.465  -5.865  -8.459  1.00 25.00           C
ATOM      8  CA  ALA     8      -2.664  -7.989  -5.507  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.074  -6.326  -3.228  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.228  -2.868  -4.398  1.00 25.00           C
ATOM     11  CA  ASN    11      -4.871  -3.819  -3.697  1.00 25.00           C
ATOM     12  CA  GLU    12      -3.906  -5.035  -0.196  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.051  -1.749   0.461  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.115   0.239  -0.694  1.00 25.00           C
ATOM     15  CA  ALA    15      -7.359  -1.826   1.624  1.00 25.00           C
ATOM     16  CA  LYS    16      -4.970  -1.183   4.548  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.010   2.571   3.789  1.00 25.00           C
ATOM     18  CA  LYS    18      -8.838   2.537   3.703  1.00 25.00           C
ATOM     19  CA  ALA    19      -8.923   0.707   7.066  1.00 25.00           C
ATOM     20  CA  GLY    20      -9.537   0.430  10.842  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.992   3.174  11.051  1.00 25.00           C
ATOM     22  CA  ILE    22      -3.994   2.005   8.944  1.00 25.00           C
ATOM     23  CA  THR    23      -2.057   4.328  11.249  1.00 25.00           C
ATOM     24  CA  GLU    24       1.329   6.061  11.215  1.00 25.00           C
ATOM     25  CA  GLU    25       3.963   3.346  10.614  1.00 25.00           C
ATOM     26  CA  GLU    26       1.411   1.273   8.649  1.00 25.00           C
ATOM     27  CA  LYS    27       0.514   4.338   6.535  1.00 25.00           C
ATOM     28  CA  ALA    28       4.225   4.976   5.838  1.00 25.00           C
ATOM     29  CA  GLU    29       4.683   1.319   4.797  1.00 25.00           C
ATOM     30  CA  GLN    30       1.661   1.580   2.459  1.00 25.00           C
ATOM     31  CA  GLN    31       3.102   4.776   0.914  1.00 25.00           C
ATOM     32  CA  LYS    32       6.472   3.034   0.392  1.00 25.00           C
ATOM     33  CA  LEU    33       4.710   0.073  -1.280  1.00 25.00           C
ATOM     34  CA  ARG    34       2.801   2.473  -3.573  1.00 25.00           C
ATOM     35  CA  GLN    35       6.074   4.229  -4.502  1.00 25.00           C
ATOM     36  CA  GLU    36       7.695   0.849  -5.282  1.00 25.00           C
ATOM     37  CA  TYR    37       4.708  -0.104  -7.480  1.00 25.00           C
ATOM     38  CA  LEU    38       4.972   3.237  -9.333  1.00 25.00           C
ATOM     39  CA  LYS    39       8.717   2.659  -9.889  1.00 25.00           C
ATOM     40  CA  GLY    40       8.001  -0.852 -11.240  1.00 25.00           C
TER
END
