
#######################################################
#                                                     #
#                        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 T0363TS599_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS599_2-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:    46        11 - 56          2.96     2.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28        11 - 38          1.99     4.18
  LCS_AVERAGE:     58.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        11 - 26          0.93     5.56
  LONGEST_CONTINUOUS_SEGMENT:    16        32 - 47          0.98     4.42
  LCS_AVERAGE:     32.56

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     16   28   46     6   11   17   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      12     Q      12     16   28   46     6   11   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      13     I      13     16   28   46     5   11   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     N      14     N      14     16   28   46     6   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      15     I      15     16   28   46     6   11   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      16     E      16     16   28   46     5   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      17     I      17     16   28   46     5   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      18     A      18     16   28   46     4   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      19     Y      19     16   28   46     3   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      20     A      20     16   28   46     3   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      21     F      21     16   28   46     5   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      22     P      22     16   28   46     3    9   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      23     E      23     16   28   46     3    8   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     R      24     R      24     16   28   46     3   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      25     Y      25     16   28   46     3   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      26     Y      26     16   28   46     3   11   17   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      27     L      27     12   28   46     4    9   16   22   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     K      28     K      28      7   28   46     6   11   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      29     S      29      7   28   46     4    9   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      30     F      30      8   28   46     4    8   16   23   26   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      31     Q      31      8   28   46     4    8   15   23   27   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      32     V      32     16   28   46     3    8   16   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      33     D      33     16   28   46     6   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      34     E      34     16   28   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      35     G      35     16   28   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      36     I      36     16   28   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      37     T      37     16   28   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      38     V      38     16   28   46     8   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      39     Q      39     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      40     T      40     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      41     A      41     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      42     I      42     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      43     T      43     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      44     Q      44     16   26   46     9   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      45     S      45     16   26   46     8   12   18   23   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      46     G      46     16   26   46     5   12   17   21   31   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      47     I      47     16   26   46     7   11   16   21   26   37   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      48     L      48     15   26   46     7   11   15   19   25   32   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      49     S      49     15   26   46     7   11   15   19   25   32   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      50     Q      50     15   26   46     7   11   15   21   25   29   40   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      51     F      51     15   26   46     7   11   15   19   25   29   38   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      52     P      52     15   26   46     7   11   15   18   22   28   37   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      53     E      53     15   26   46     7   11   15   18   22   27   31   39   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      54     I      54     15   26   46     4   11   15   18   22   27   35   43   44   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      55     D      55     15   23   46     4    4   13   18   20   24   31   37   43   46   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      56     L      56     15   23   46     3    3    3   18   20   24   31   35   43   46   46   46   46   46   46   46   46   46   46   46 
LCS_AVERAGE  LCS_A:  63.82  (  32.56   58.88  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      9     12     18     23     31     37     40     43     44     46     46     46     46     46     46     46     46     46     46     46 
GDT PERCENT_CA  19.57  26.09  39.13  50.00  67.39  80.43  86.96  93.48  95.65 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.42   0.96   1.26   1.86   2.12   2.43   2.71   2.80   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96
GDT RMS_ALL_CA   3.82   3.77   4.35   4.60   3.99   3.68   3.24   3.02   2.98   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96   2.96

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          3.800
LGA    Q      12      Q      12          3.222
LGA    I      13      I      13          3.410
LGA    N      14      N      14          2.664
LGA    I      15      I      15          2.612
LGA    E      16      E      16          1.713
LGA    I      17      I      17          2.005
LGA    A      18      A      18          2.456
LGA    Y      19      Y      19          3.463
LGA    A      20      A      20          2.934
LGA    F      21      F      21          3.674
LGA    P      22      P      22          3.688
LGA    E      23      E      23          2.709
LGA    R      24      R      24          3.329
LGA    Y      25      Y      25          3.016
LGA    Y      26      Y      26          3.380
LGA    L      27      L      27          1.820
LGA    K      28      K      28          1.749
LGA    S      29      S      29          1.810
LGA    F      30      F      30          3.044
LGA    Q      31      Q      31          3.004
LGA    V      32      V      32          2.656
LGA    D      33      D      33          1.017
LGA    E      34      E      34          1.281
LGA    G      35      G      35          2.047
LGA    I      36      I      36          2.400
LGA    T      37      T      37          3.425
LGA    V      38      V      38          3.262
LGA    Q      39      Q      39          3.333
LGA    T      40      T      40          3.022
LGA    A      41      A      41          2.219
LGA    I      42      I      42          2.250
LGA    T      43      T      43          2.776
LGA    Q      44      Q      44          2.351
LGA    S      45      S      45          1.210
LGA    G      46      G      46          0.137
LGA    I      47      I      47          1.809
LGA    L      48      L      48          2.303
LGA    S      49      S      49          2.186
LGA    Q      50      Q      50          2.685
LGA    F      51      F      51          3.362
LGA    P      52      P      52          3.813
LGA    E      53      E      53          4.844
LGA    I      54      I      54          3.940
LGA    D      55      D      55          5.363
LGA    L      56      L      56          4.963

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     43    2.71    67.391    71.195     1.532

LGA_LOCAL      RMSD =  2.706  Number of atoms =   43  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.963  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  2.963  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.655735 * X  +  -0.005095 * Y  +  -0.754974 * Z  +  24.577982
  Y_new =   0.194166 * X  +   0.965204 * Y  +  -0.175157 * Z  +  18.267710
  Z_new =   0.729597 * X  +  -0.261447 * Y  +  -0.631929 * Z  +   6.081492 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.749307    0.392286  [ DEG:  -157.5237     22.4763 ]
  Theta =  -0.817732   -2.323860  [ DEG:   -46.8526   -133.1474 ]
  Phi   =   2.853713   -0.287880  [ DEG:   163.5057    -16.4943 ]
 
# 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: T0363TS599_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_2-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   43   2.71  71.195     2.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_2-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM     11  CA  ASN    11      16.585   3.249  12.822  1.00  0.00              
ATOM     12  CA  GLN    12      16.949   5.160   9.516  1.00  0.00              
ATOM     13  CA  ILE    13      18.615   8.510   9.868  1.00  0.00              
ATOM     14  CA  ASN    14      18.993  10.692   6.748  1.00  0.00              
ATOM     15  CA  ILE    15      21.951  13.182   6.602  1.00  0.00              
ATOM     16  CA  GLU    16      21.789  15.871   3.865  1.00  0.00              
ATOM     17  CA  ILE    17      25.187  17.380   2.905  1.00  0.00              
ATOM     18  CA  ALA    18      25.083  20.435   0.611  1.00  0.00              
ATOM     19  CA  TYR    19      28.245  21.211  -1.359  1.00  0.00              
ATOM     20  CA  ALA    20      28.576  24.480  -3.027  1.00  0.00              
ATOM     21  CA  PHE    21      30.737  24.740  -6.095  1.00  0.00              
ATOM     22  CA  PRO    22      31.208  28.133  -7.631  1.00  0.00              
ATOM     23  CA  GLU    23      27.561  28.445  -8.710  1.00  0.00              
ATOM     24  CA  ARG    24      26.535  24.834  -8.801  1.00  0.00              
ATOM     25  CA  TYR    25      24.954  23.184  -5.840  1.00  0.00              
ATOM     26  CA  TYR    26      25.775  19.747  -5.160  1.00  0.00              
ATOM     27  CA  LEU    27      23.520  17.726  -2.974  1.00  0.00              
ATOM     28  CA  LYS    28      24.969  14.762  -1.129  1.00  0.00              
ATOM     29  CA  SER    29      22.639  12.400   0.720  1.00  0.00              
ATOM     30  CA  PHE    30      24.044  10.268   3.528  1.00  0.00              
ATOM     31  CA  GLN    31      22.079   7.475   5.002  1.00  0.00              
ATOM     32  CA  VAL    32      22.853   6.478   8.540  1.00  0.00              
ATOM     33  CA  ASP    33      21.728   3.193   9.978  1.00  0.00              
ATOM     34  CA  GLU    34      20.751   3.263  13.595  1.00  0.00              
ATOM     35  CA  GLY    35      23.675   2.815  15.805  1.00  0.00              
ATOM     36  CA  ILE    36      26.358   3.960  13.336  1.00  0.00              
ATOM     37  CA  THR    37      28.854   6.563  14.337  1.00  0.00              
ATOM     38  CA  VAL    38      29.178   9.781  12.414  1.00  0.00              
ATOM     39  CA  GLN    39      32.711   8.876  11.514  1.00  0.00              
ATOM     40  CA  THR    40      31.495   5.649   9.827  1.00  0.00              
ATOM     41  CA  ALA    41      28.824   7.420   7.861  1.00  0.00              
ATOM     42  CA  ILE    42      31.200  10.056   6.738  1.00  0.00              
ATOM     43  CA  THR    43      33.861   7.684   5.582  1.00  0.00              
ATOM     44  CA  GLN    44      31.466   5.608   3.603  1.00  0.00              
ATOM     45  CA  SER    45      30.054   8.592   1.783  1.00  0.00              
ATOM     46  CA  GLY    46      33.411  10.018   0.914  1.00  0.00              
ATOM     47  CA  ILE    47      32.803  13.158   2.881  1.00  0.00              
ATOM     48  CA  LEU    48      35.945  13.413   5.072  1.00  0.00              
ATOM     49  CA  SER    49      38.000  12.845   1.986  1.00  0.00              
ATOM     50  CA  GLN    50      36.226  15.646   0.059  1.00  0.00              
ATOM     51  CA  PHE    51      36.048  18.201   2.871  1.00  0.00              
ATOM     52  CA  PRO    52      39.097  17.863   5.087  1.00  0.00              
ATOM     53  CA  GLU    53      38.273  20.807   7.314  1.00  0.00              
ATOM     54  CA  ILE    54      34.903  19.396   8.341  1.00  0.00              
ATOM     55  CA  ASP    55      34.691  17.610  11.617  1.00  0.00              
ATOM     56  CA  LEU    56      32.955  14.240  11.405  1.00  0.00              
TER                                                                             
END
