
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS393_4-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        11 - 52          4.72     6.63
  LONGEST_CONTINUOUS_SEGMENT:    42        12 - 53          4.90     6.47
  LCS_AVERAGE:     88.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        11 - 20          1.81    14.22
  LONGEST_CONTINUOUS_SEGMENT:    10        24 - 33          1.67    12.71
  LONGEST_CONTINUOUS_SEGMENT:    10        37 - 46          1.59    13.39
  LONGEST_CONTINUOUS_SEGMENT:    10        45 - 54          1.83    15.33
  LCS_AVERAGE:     20.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        38 - 45          0.39    15.29
  LONGEST_CONTINUOUS_SEGMENT:     8        46 - 53          0.88    16.58
  LCS_AVERAGE:     12.38

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   10   42     2    4    6    8    9   10   12   18   22   23   26   31   35   38   39   41   42   42   42   43 
LCS_GDT     Q      12     Q      12      5   10   42     2    4    6    8    9   12   14   18   22   27   31   36   37   38   40   41   42   42   42   43 
LCS_GDT     I      13     I      13      5   10   42     3    3    5    8   13   18   22   26   29   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     N      14     N      14      5   10   42     3    4    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     I      15     I      15      5   10   42     3    4    6   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     E      16     E      16      5   10   42     4    4    8   10   13   16   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     I      17     I      17      5   10   42     4    4    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     A      18     A      18      5   10   42     4    4    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Y      19     Y      19      5   10   42     4    4    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     A      20     A      20      5   10   42     3    4    5    5    8   13   15   19   23   27   32   36   37   38   40   41   42   42   42   43 
LCS_GDT     F      21     F      21      4    8   42     3    4    7   10   13   16   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     P      22     P      22      4    8   42     3    4    6    8   10   13   16   19   24   27   32   36   37   38   40   41   42   42   42   43 
LCS_GDT     E      23     E      23      4    8   42     3    4    5   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     R      24     R      24      4   10   42     3    4    6    9   10   14   19   25   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Y      25     Y      25      4   10   42     3    4    7    8   11   16   22   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Y      26     Y      26      4   10   42     4    4    5    9   10   14   18   25   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     L      27     L      27      4   10   42     4    6    7   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     K      28     K      28      5   10   42     4    6    7    9   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     S      29     S      29      5   10   42     4    4    6    9   11   17   22   25   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     F      30     F      30      5   10   42     3    4    6    9   12   17   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Q      31     Q      31      5   10   42     3    4    6    9   10   14   22   24   30   32   34   35   37   38   40   41   42   42   42   43 
LCS_GDT     V      32     V      32      5   10   42     4    6    7   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     D      33     D      33      4   10   42     4    6    7   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     E      34     E      34      4    7   42     3    4    4    5   10   15   22   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     G      35     G      35      4    7   42     3    4    6    7   10   15   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     I      36     I      36      4    5   42     3    4    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     T      37     T      37      3   10   42     3    3    4    6    9   12   17   23   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     V      38     V      38      8   10   42     7    8    8    8    9   12   20   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Q      39     Q      39      8   10   42     7    8    8    8    9   13   17   23   30   31   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     T      40     T      40      8   10   42     7    8    8    8   11   16   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     A      41     A      41      8   10   42     7    8    8    8   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     I      42     I      42      8   10   42     7    8    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     T      43     T      43      8   10   42     7    8    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Q      44     Q      44      8   10   42     7    8    8    8   12   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     S      45     S      45      8   10   42     6    8    8    8    9   10   17   20   28   32   34   35   37   38   40   41   42   42   42   43 
LCS_GDT     G      46     G      46      8   10   42     4    7    8   10   10   14   18   25   30   32   34   35   37   38   39   41   42   42   42   43 
LCS_GDT     I      47     I      47      8   10   42     4    7    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     L      48     L      48      8   10   42     4    7    8   10   10   16   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     S      49     S      49      8   10   42     4    7    8   10   13   18   23   26   30   32   34   36   37   38   40   41   42   42   42   43 
LCS_GDT     Q      50     Q      50      8   10   42     4    7    8   10   10   11   11   16   21   24   29   34   36   38   40   41   42   42   42   43 
LCS_GDT     F      51     F      51      8   10   42     4    7    8   10   10   11   11   16   22   25   29   33   37   38   40   41   42   42   42   43 
LCS_GDT     P      52     P      52      8   10   42     3    7    8   10   10   14   18   20   24   27   32   36   37   38   40   41   42   42   42   43 
LCS_GDT     E      53     E      53      8   10   42     3    6    8   10   10   11   12   14   20   24   27   32   35   38   39   39   40   42   42   43 
LCS_GDT     I      54     I      54      4   10   24     3    4    8   10   10   11   14   18   20   24   26   28   31   32   34   39   40   40   41   41 
LCS_GDT     D      55     D      55      4    5   24     3    4    4    4    7   10   14   18   19   22   23   28   30   32   34   39   39   40   41   41 
LCS_GDT     L      56     L      56      4    5   24     3    4    4    5    7   10   14   18   19   22   22   24   30   31   31   33   35   38   40   41 
LCS_AVERAGE  LCS_A:  40.53  (  12.38   20.46   88.75 )

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     10     13     18     23     26     30     32     34     36     37     38     40     41     42     42     42     43 
GDT PERCENT_CA  15.22  17.39  17.39  21.74  28.26  39.13  50.00  56.52  65.22  69.57  73.91  78.26  80.43  82.61  86.96  89.13  91.30  91.30  91.30  93.48
GDT RMS_LOCAL    0.32   0.39   0.39   1.34   1.89   2.40   2.75   2.92   3.31   3.42   3.53   4.00   3.91   4.05   4.46   4.56   4.72   4.72   4.72   5.02
GDT RMS_ALL_CA  14.80  15.29  15.29   7.23   7.32   7.04   6.97   6.98   7.71   7.56   7.41   6.52   7.36   7.33   6.61   6.72   6.63   6.63   6.63   6.42

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         11.521
LGA    Q      12      Q      12          8.864
LGA    I      13      I      13          3.687
LGA    N      14      N      14          0.738
LGA    I      15      I      15          2.322
LGA    E      16      E      16          3.293
LGA    I      17      I      17          2.672
LGA    A      18      A      18          2.674
LGA    Y      19      Y      19          2.898
LGA    A      20      A      20          7.003
LGA    F      21      F      21          3.776
LGA    P      22      P      22          6.903
LGA    E      23      E      23          3.708
LGA    R      24      R      24          4.057
LGA    Y      25      Y      25          3.394
LGA    Y      26      Y      26          5.017
LGA    L      27      L      27          2.308
LGA    K      28      K      28          2.624
LGA    S      29      S      29          4.498
LGA    F      30      F      30          3.217
LGA    Q      31      Q      31          4.830
LGA    V      32      V      32          2.035
LGA    D      33      D      33          2.124
LGA    E      34      E      34          3.980
LGA    G      35      G      35          3.007
LGA    I      36      I      36          3.011
LGA    T      37      T      37          6.026
LGA    V      38      V      38          4.899
LGA    Q      39      Q      39          5.599
LGA    T      40      T      40          3.723
LGA    A      41      A      41          1.543
LGA    I      42      I      42          2.919
LGA    T      43      T      43          3.391
LGA    Q      44      Q      44          2.711
LGA    S      45      S      45          6.863
LGA    G      46      G      46          6.636
LGA    I      47      I      47          1.571
LGA    L      48      L      48          3.131
LGA    S      49      S      49          3.229
LGA    Q      50      Q      50          8.359
LGA    F      51      F      51          9.591
LGA    P      52      P      52          9.001
LGA    E      53      E      53         14.587
LGA    I      54      I      54         16.307
LGA    D      55      D      55         19.002
LGA    L      56      L      56         19.936

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     26    2.92    46.196    41.777     0.860

LGA_LOCAL      RMSD =  2.922  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.040  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  6.150  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.042188 * X  +  -0.835954 * Y  +   0.547176 * Z  +  22.041271
  Y_new =   0.983814 * X  +  -0.060704 * Y  +  -0.168594 * Z  +  12.083388
  Z_new =   0.174153 * X  +   0.545432 * Y  +   0.819862 * Z  +   4.164114 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.587037   -2.554555  [ DEG:    33.6348   -146.3652 ]
  Theta =  -0.175046   -2.966547  [ DEG:   -10.0294   -169.9706 ]
  Phi   =   1.527941   -1.613652  [ DEG:    87.5446    -92.4554 ]
 
# 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_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_4-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  41.777     6.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_4-D1
PFRMAT TS
TARGET T0363
MODEL 4
PARENT N/A
ATOM     11  CA  ASN    11       7.851   7.300  12.511  1.00 25.00           C
ATOM     12  CA  GLN    12      11.077   8.061  10.678  1.00 25.00           C
ATOM     13  CA  ILE    13      14.489   8.626   9.095  1.00 25.00           C
ATOM     14  CA  ASN    14      17.126   8.608   6.403  1.00 25.00           C
ATOM     15  CA  ILE    15      17.898  12.270   5.830  1.00 25.00           C
ATOM     16  CA  GLU    16      21.477  11.142   5.420  1.00 25.00           C
ATOM     17  CA  ILE    17      24.539  13.452   5.261  1.00 25.00           C
ATOM     18  CA  ALA    18      24.969  16.834   3.452  1.00 25.00           C
ATOM     19  CA  TYR    19      28.150  18.501   2.083  1.00 25.00           C
ATOM     20  CA  ALA    20      28.815  17.622  -1.589  1.00 25.00           C
ATOM     21  CA  PHE    21      29.512  21.075  -2.968  1.00 25.00           C
ATOM     22  CA  PRO    22      28.716  21.699  -6.641  1.00 25.00           C
ATOM     23  CA  GLU    23      28.666  24.186  -9.551  1.00 25.00           C
ATOM     24  CA  ARG    24      27.530  27.149  -7.461  1.00 25.00           C
ATOM     25  CA  TYR    25      27.677  25.814  -3.864  1.00 25.00           C
ATOM     26  CA  TYR    26      24.902  23.236  -3.381  1.00 25.00           C
ATOM     27  CA  LEU    27      24.310  20.142  -1.255  1.00 25.00           C
ATOM     28  CA  LYS    28      23.790  16.464  -1.822  1.00 25.00           C
ATOM     29  CA  SER    29      25.018  13.258  -0.273  1.00 25.00           C
ATOM     30  CA  PHE    30      24.710   9.907   1.505  1.00 25.00           C
ATOM     31  CA  GLN    31      24.610   7.381   4.349  1.00 25.00           C
ATOM     32  CA  VAL    32      21.437   6.012   5.818  1.00 25.00           C
ATOM     33  CA  ASP    33      21.826   4.088   9.125  1.00 25.00           C
ATOM     34  CA  GLU    34      23.531   2.429  12.128  1.00 25.00           C
ATOM     35  CA  GLY    35      25.439   4.330  14.876  1.00 25.00           C
ATOM     36  CA  ILE    36      22.930   7.151  14.927  1.00 25.00           C
ATOM     37  CA  THR    37      21.487   8.699  11.699  1.00 25.00           C
ATOM     38  CA  VAL    38      24.295  10.434   9.747  1.00 25.00           C
ATOM     39  CA  GLN    39      26.725   8.400  11.896  1.00 25.00           C
ATOM     40  CA  THR    40      28.127   6.712   8.758  1.00 25.00           C
ATOM     41  CA  ALA    41      28.586  10.131   7.093  1.00 25.00           C
ATOM     42  CA  ILE    42      30.400  11.430  10.207  1.00 25.00           C
ATOM     43  CA  THR    43      32.687   8.357  10.185  1.00 25.00           C
ATOM     44  CA  GLN    44      33.455   8.924   6.477  1.00 25.00           C
ATOM     45  CA  SER    45      34.277  12.597   7.183  1.00 25.00           C
ATOM     46  CA  GLY    46      35.994  14.812   4.695  1.00 25.00           C
ATOM     47  CA  ILE    47      34.012  13.059   1.903  1.00 25.00           C
ATOM     48  CA  LEU    48      37.240  13.632  -0.023  1.00 25.00           C
ATOM     49  CA  SER    49      40.204  12.513   2.129  1.00 25.00           C
ATOM     50  CA  GLN    50      38.085   9.696   3.626  1.00 25.00           C
ATOM     51  CA  PHE    51      36.212   8.514   0.532  1.00 25.00           C
ATOM     52  CA  PRO    52      39.355   8.961  -1.457  1.00 25.00           C
ATOM     53  CA  GLU    53      39.534   8.872  -5.237  1.00 25.00           C
ATOM     54  CA  ILE    54      35.848   8.422  -6.180  1.00 25.00           C
ATOM     55  CA  ASP    55      35.868   5.536  -3.677  1.00 25.00           C
ATOM     56  CA  LEU    56      32.087   4.827  -3.351  1.00 25.00           C
TER
END
