
#######################################################
#                                                     #
#                        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   46 (   46),  selected   46 , name T0363TS393_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS393_5-D1.T0363_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:    42        15 - 56          4.92     5.66
  LCS_AVERAGE:     90.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        24 - 35          1.93    10.89
  LONGEST_CONTINUOUS_SEGMENT:    12        38 - 49          1.98    10.52
  LCS_AVERAGE:     23.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        38 - 47          0.99    10.56
  LCS_AVERAGE:     12.00

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:   46
LCS_GDT     N      11     N      11      5   11   38     0    4    7    8   13   15   18   22   24   27   29   33   34   36   38   41   43   45   46   46 
LCS_GDT     Q      12     Q      12      6   11   38     3    4    7    8   13   17   22   24   27   30   31   33   35   39   41   42   44   45   46   46 
LCS_GDT     I      13     I      13      6   11   38     3    4    8   10   14   17   22   24   27   30   34   36   38   39   41   42   44   45   46   46 
LCS_GDT     N      14     N      14      6   11   38     3    4    7    8   11   12   18   22   27   30   31   34   35   39   41   42   44   45   46   46 
LCS_GDT     I      15     I      15      6   11   42     3    4    7   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     E      16     E      16      6   11   42     3    4    7   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     I      17     I      17      6   11   42     3    4    7    7   13   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     A      18     A      18      4   11   42     3    9    9   10   13   15   19   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     Y      19     Y      19      4   11   42     1    4    4    8   13   13   17   18   24   26   31   32   32   34   37   42   44   45   46   46 
LCS_GDT     A      20     A      20      4   11   42     0    3    5    8   13   14   17   21   24   30   31   32   32   37   41   42   44   45   46   46 
LCS_GDT     F      21     F      21      4   11   42     3    3    5    8   11   12   22   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     P      22     P      22      4   10   42     3    4    5    8   13   16   22   24   27   30   31   33   37   39   41   42   44   45   46   46 
LCS_GDT     E      23     E      23      4   11   42     3    4    6   10   14   17   22   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     R      24     R      24      4   12   42     3    4    7    9   14   17   22   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     Y      25     Y      25      4   12   42     0    4    7    9   14   17   22   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     Y      26     Y      26      4   12   42     3    4    7    9   14   17   22   24   27   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     L      27     L      27      4   12   42     3    4    8   10   14   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     K      28     K      28      4   12   42     3    4    7    8   14   17   22   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     S      29     S      29      4   12   42     3    4    7    9   14   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     F      30     F      30      4   12   42     4    4    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     Q      31     Q      31      4   12   42     4    5    8   14   15   17   22   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     V      32     V      32      4   12   42     4    5    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     D      33     D      33      4   12   42     4    5    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     E      34     E      34      4   12   42     3    4    4   10   13   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     G      35     G      35      4   12   42     3    4    5    8   13   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     I      36     I      36      4    7   42     3    5    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     T      37     T      37      3    9   42     3    3    3    6   10   12   19   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     V      38     V      38     10   12   42     7    9    9   10   12   15   19   22   27   30   31   33   36   38   41   42   44   45   46   46 
LCS_GDT     Q      39     Q      39     10   12   42     7    9    9   10   12   16   22   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     T      40     T      40     10   12   42     7    9    9   10   14   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     A      41     A      41     10   12   42     7    9    9   10   12   16   21   24   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     I      42     I      42     10   12   42     7    9    9   10   12   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     T      43     T      43     10   12   42     7    9    9   10   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     Q      44     Q      44     10   12   42     7    9    9   10   12   16   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     S      45     S      45     10   12   42     4    9    9   10   12   16   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     G      46     G      46     10   12   42     3    3    7   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     I      47     I      47     10   12   42     3    4    9   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     L      48     L      48      4   12   42     3    3    6    7    9   12   16   17   28   31   33   35   38   39   41   42   44   45   46   46 
LCS_GDT     S      49     S      49      4   12   42     3    3    5    5    9   12   14   17   28   31   32   34   37   38   40   42   44   45   46   46 
LCS_GDT     Q      50     Q      50      4    6   42     3    3    9   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     F      51     F      51      4    6   42     3    4    4    4    5    6   16   20   24   30   32   34   38   39   41   42   44   45   46   46 
LCS_GDT     P      52     P      52      4    6   42     3    4    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     E      53     E      53      4    6   42     3    4    8   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     I      54     I      54      4    6   42     1    4    6   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     D      55     D      55      3    6   42     1    5    6   14   15   17   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_GDT     L      56     L      56      3    5   42     0    3    6    9   12   16   24   26   28   31   35   36   38   39   41   42   44   45   46   46 
LCS_AVERAGE  LCS_A:  41.86  (  12.00   23.02   90.55 )

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      9      9     14     15     17     24     26     28     31     35     36     38     39     41     42     44     45     46     46 
GDT PERCENT_CA  15.22  19.57  19.57  30.43  32.61  36.96  52.17  56.52  60.87  67.39  76.09  78.26  82.61  84.78  89.13  91.30  95.65  97.83 100.00 100.00
GDT RMS_LOCAL    0.32   0.50   0.50   1.55   1.65   2.04   2.81   2.92   3.07   3.37   4.13   4.20   4.35   4.49   4.75   4.85   5.09   5.23   5.38   5.38
GDT RMS_ALL_CA   9.85  10.12  10.12   7.11   7.17   7.50   6.53   6.53   6.55   6.80   5.56   5.50   5.53   5.47   5.41   5.53   5.49   5.41   5.38   5.38

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         12.545
LGA    Q      12      Q      12         10.235
LGA    I      13      I      13          5.778
LGA    N      14      N      14          7.405
LGA    I      15      I      15          2.275
LGA    E      16      E      16          0.886
LGA    I      17      I      17          3.717
LGA    A      18      A      18          8.319
LGA    Y      19      Y      19         13.252
LGA    A      20      A      20         13.066
LGA    F      21      F      21         10.249
LGA    P      22      P      22         13.956
LGA    E      23      E      23         11.071
LGA    R      24      R      24         11.619
LGA    Y      25      Y      25         10.657
LGA    Y      26      Y      26          8.177
LGA    L      27      L      27          3.732
LGA    K      28      K      28          3.909
LGA    S      29      S      29          3.088
LGA    F      30      F      30          2.511
LGA    Q      31      Q      31          3.795
LGA    V      32      V      32          2.967
LGA    D      33      D      33          3.210
LGA    E      34      E      34          3.467
LGA    G      35      G      35          3.609
LGA    I      36      I      36          1.921
LGA    T      37      T      37          4.518
LGA    V      38      V      38          7.485
LGA    Q      39      Q      39          4.658
LGA    T      40      T      40          3.569
LGA    A      41      A      41          5.188
LGA    I      42      I      42          3.379
LGA    T      43      T      43          1.498
LGA    Q      44      Q      44          3.430
LGA    S      45      S      45          3.735
LGA    G      46      G      46          2.854
LGA    I      47      I      47          2.282
LGA    L      48      L      48          5.830
LGA    S      49      S      49          6.246
LGA    Q      50      Q      50          3.031
LGA    F      51      F      51          5.278
LGA    P      52      P      52          2.249
LGA    E      53      E      53          1.728
LGA    I      54      I      54          2.588
LGA    D      55      D      55          0.981
LGA    L      56      L      56          2.377

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     26    2.92    49.457    43.778     0.861

LGA_LOCAL      RMSD =  2.921  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.515  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.384  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.859528 * X  +   0.394671 * Y  +  -0.324726 * Z  +  23.069910
  Y_new =   0.475903 * X  +  -0.386379 * Y  +   0.790081 * Z  +  12.449879
  Z_new =   0.186354 * X  +  -0.833634 * Y  +  -0.519929 * Z  +   5.304309 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.128452    1.013140  [ DEG:  -121.9513     58.0487 ]
  Theta =  -0.187450   -2.954143  [ DEG:   -10.7401   -169.2599 ]
  Phi   =   0.505664   -2.635929  [ DEG:    28.9724   -151.0276 ]
 
# 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: T0363TS393_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_5-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   46   46   4.0   26   2.92  43.778     5.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_5-D1
PFRMAT TS
TARGET T0363
MODEL 5
PARENT N/A
ATOM     11  CA  ASN    11       9.589   9.570  15.001  1.00 25.00           C
ATOM     12  CA  GLN    12      12.873  10.076  13.145  1.00 25.00           C
ATOM     13  CA  ILE    13      16.267  10.714  11.601  1.00 25.00           C
ATOM     14  CA  ASN    14      19.845  11.973  12.037  1.00 25.00           C
ATOM     15  CA  ILE    15      21.008  11.980   8.430  1.00 25.00           C
ATOM     16  CA  GLU    16      21.556  14.042   5.260  1.00 25.00           C
ATOM     17  CA  ILE    17      22.519  14.728   1.596  1.00 25.00           C
ATOM     18  CA  ALA    18      23.927  12.010  -0.722  1.00 25.00           C
ATOM     19  CA  TYR    19      25.131   9.941  -3.690  1.00 25.00           C
ATOM     20  CA  ALA    20      27.816  12.367  -4.979  1.00 25.00           C
ATOM     21  CA  PHE    21      28.204  15.614  -6.922  1.00 25.00           C
ATOM     22  CA  PRO    22      29.565  15.432 -10.478  1.00 25.00           C
ATOM     23  CA  GLU    23      28.562  17.745 -13.287  1.00 25.00           C
ATOM     24  CA  ARG    24      26.477  14.938 -14.677  1.00 25.00           C
ATOM     25  CA  TYR    25      24.576  15.316 -11.420  1.00 25.00           C
ATOM     26  CA  TYR    26      23.335  14.703  -7.913  1.00 25.00           C
ATOM     27  CA  LEU    27      23.409  15.690  -4.199  1.00 25.00           C
ATOM     28  CA  LYS    28      20.057  14.495  -2.762  1.00 25.00           C
ATOM     29  CA  SER    29      18.722  11.339  -1.110  1.00 25.00           C
ATOM     30  CA  PHE    30      20.259  10.228   2.219  1.00 25.00           C
ATOM     31  CA  GLN    31      18.803   8.619   5.352  1.00 25.00           C
ATOM     32  CA  VAL    32      20.512   6.732   8.141  1.00 25.00           C
ATOM     33  CA  ASP    33      20.959   4.924  11.514  1.00 25.00           C
ATOM     34  CA  GLU    34      23.033   2.792  13.875  1.00 25.00           C
ATOM     35  CA  GLY    35      26.113   4.140  15.661  1.00 25.00           C
ATOM     36  CA  ILE    36      25.381   7.648  14.243  1.00 25.00           C
ATOM     37  CA  THR    37      24.227   8.959  10.855  1.00 25.00           C
ATOM     38  CA  VAL    38      26.090   6.357   8.832  1.00 25.00           C
ATOM     39  CA  GLN    39      29.087   8.064  10.497  1.00 25.00           C
ATOM     40  CA  THR    40      31.341   5.134   9.501  1.00 25.00           C
ATOM     41  CA  ALA    41      30.077   5.356   5.893  1.00 25.00           C
ATOM     42  CA  ILE    42      30.776   9.121   5.853  1.00 25.00           C
ATOM     43  CA  THR    43      34.313   8.503   7.186  1.00 25.00           C
ATOM     44  CA  GLN    44      34.901   5.864   4.473  1.00 25.00           C
ATOM     45  CA  SER    45      33.675   8.311   1.794  1.00 25.00           C
ATOM     46  CA  GLY    46      34.058  11.905   2.928  1.00 25.00           C
ATOM     47  CA  ILE    47      32.725  15.454   2.843  1.00 25.00           C
ATOM     48  CA  LEU    48      33.231  18.763   1.083  1.00 25.00           C
ATOM     49  CA  SER    49      36.125  18.466  -1.409  1.00 25.00           C
ATOM     50  CA  GLN    50      37.262  15.212   0.262  1.00 25.00           C
ATOM     51  CA  PHE    51      37.671  15.256   4.054  1.00 25.00           C
ATOM     52  CA  PRO    52      40.986  16.985   3.526  1.00 25.00           C
ATOM     53  CA  GLU    53      39.015  20.267   3.958  1.00 25.00           C
ATOM     54  CA  ILE    54      37.525  21.741   7.117  1.00 25.00           C
ATOM     55  CA  ASP    55      38.799  18.556   8.848  1.00 25.00           C
ATOM     56  CA  LEU    56      35.143  17.418   9.193  1.00 25.00           C
TER
END
