
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS599_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:    38        11 - 48          4.74     6.38
  LONGEST_CONTINUOUS_SEGMENT:    38        12 - 49          4.91     5.98
  LONGEST_CONTINUOUS_SEGMENT:    38        13 - 50          4.94     5.78
  LCS_AVERAGE:     81.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        33 - 54          1.93     7.58
  LONGEST_CONTINUOUS_SEGMENT:    22        34 - 55          1.93     7.56
  LCS_AVERAGE:     46.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        40 - 53          0.91     8.78
  LONGEST_CONTINUOUS_SEGMENT:    14        41 - 54          0.99     8.98
  LCS_AVERAGE:     24.15

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     10   12   38     0    5   11   11   12   15   20   23   23   25   29   32   34   35   37   40   42   45   45   46 
LCS_GDT     Q      12     Q      12     10   21   38     3    9   11   11   12   12   20   23   23   23   25   27   34   35   35   37   38   41   45   46 
LCS_GDT     I      13     I      13     10   21   38     3    9   11   17   19   20   21   23   25   31   32   33   36   39   39   42   44   45   45   46 
LCS_GDT     N      14     N      14     10   21   38     3    9   11   11   19   20   21   23   25   29   29   33   36   39   39   42   44   45   45   46 
LCS_GDT     I      15     I      15     10   21   38     3    9   13   17   19   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     E      16     E      16     10   21   38     3    9   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     I      17     I      17     10   21   38     3    9   12   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     A      18     A      18     10   21   38     3    9   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     Y      19     Y      19     10   21   38     3    9   11   15   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     A      20     A      20     10   21   38     3    9   11   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     F      21     F      21     10   21   38     3    6   11   15   18   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     P      22     P      22      8   21   38     3    6   13   17   19   20   21   23   29   31   32   33   36   39   39   42   44   45   45   46 
LCS_GDT     E      23     E      23      8   21   38     3    6   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     R      24     R      24      8   21   38     3    7   13   17   19   20   21   23   29   31   32   33   36   39   39   41   44   45   45   46 
LCS_GDT     Y      25     Y      25      8   21   38     3    7   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     Y      26     Y      26      8   21   38     3    6   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     L      27     L      27      8   21   38     3    8   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     K      28     K      28      8   21   38     3    8   13   17   19   20   21   23   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     S      29     S      29      8   21   38     3    8   13   17   19   21   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     F      30     F      30      8   21   38     3    8   13   17   19   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     Q      31     Q      31      8   21   38     3    8   13   17   19   20   24   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     V      32     V      32      8   21   38     3    8   12   17   19   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     D      33     D      33      8   22   38     3    8   11   14   19   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     E      34     E      34     12   22   38     3    8   11   15   19   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     G      35     G      35     13   22   38     9   10   13   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     I      36     I      36     13   22   38     9   10   15   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     T      37     T      37     13   22   38     9   10   15   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     V      38     V      38     13   22   38     6   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     Q      39     Q      39     13   22   38     9   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     T      40     T      40     14   22   38     9   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     A      41     A      41     14   22   38     9   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     I      42     I      42     14   22   38     9   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     T      43     T      43     14   22   38     9   10   16   20   21   23   26   28   28   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     Q      44     Q      44     14   22   38     9   10   16   20   21   23   26   28   29   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     S      45     S      45     14   22   38     7   10   16   20   21   23   26   28   28   31   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     G      46     G      46     14   22   38     7   10   16   20   21   23   26   28   28   30   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     I      47     I      47     14   22   38     7   10   16   20   21   23   26   28   28   30   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     L      48     L      48     14   22   38     7   10   16   20   21   23   26   28   28   30   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     S      49     S      49     14   22   38     7   10   15   20   21   23   26   28   28   30   32   34   35   36   39   42   44   45   45   46 
LCS_GDT     Q      50     Q      50     14   22   38     7   10   16   20   21   23   26   28   28   30   31   34   35   36   39   42   44   45   45   46 
LCS_GDT     F      51     F      51     14   22   37     7   10   16   20   21   23   26   28   28   30   32   34   35   36   39   42   44   45   45   46 
LCS_GDT     P      52     P      52     14   22   35     7   10   16   20   21   23   26   28   28   30   32   34   35   36   39   42   44   45   45   46 
LCS_GDT     E      53     E      53     14   22   35     7   10   16   20   21   23   26   28   28   30   32   34   35   36   39   42   44   45   45   46 
LCS_GDT     I      54     I      54     14   22   35     3   10   13   18   21   22   26   28   28   30   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     D      55     D      55     12   22   35     3    9   12   15   17   21   22   24   28   30   32   34   36   39   39   42   44   45   45   46 
LCS_GDT     L      56     L      56      6   20   35     3    3    6   11   13   15   16   21   26   31   32   34   36   39   39   42   44   45   45   46 
LCS_AVERAGE  LCS_A:  50.76  (  24.15   46.27   81.85 )

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     10     16     20     21     23     26     28     29     31     32     34     36     39     39     42     44     45     45     46 
GDT PERCENT_CA  19.57  21.74  34.78  43.48  45.65  50.00  56.52  60.87  63.04  67.39  69.57  73.91  78.26  84.78  84.78  91.30  95.65  97.83  97.83 100.00
GDT RMS_LOCAL    0.34   0.40   1.04   1.43   1.51   1.96   2.25   2.48   3.46   3.65   3.47   3.59   4.32   4.65   4.65   5.05   5.27   5.46   5.46   5.62
GDT RMS_ALL_CA   6.60   6.63   8.56   8.04   7.89   7.98   7.81   7.86   7.29   6.80   6.61   6.66   6.01   5.88   5.88   5.75   5.69   5.63   5.63   5.62

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         12.874
LGA    Q      12      Q      12         12.359
LGA    I      13      I      13          7.218
LGA    N      14      N      14          5.761
LGA    I      15      I      15          3.012
LGA    E      16      E      16          3.690
LGA    I      17      I      17          7.159
LGA    A      18      A      18          9.905
LGA    Y      19      Y      19         12.954
LGA    A      20      A      20         15.289
LGA    F      21      F      21         15.474
LGA    P      22      P      22         18.618
LGA    E      23      E      23         16.935
LGA    R      24      R      24         16.032
LGA    Y      25      Y      25         13.643
LGA    Y      26      Y      26         13.065
LGA    L      27      L      27          8.893
LGA    K      28      K      28          6.422
LGA    S      29      S      29          3.614
LGA    F      30      F      30          2.551
LGA    Q      31      Q      31          3.955
LGA    V      32      V      32          2.544
LGA    D      33      D      33          2.164
LGA    E      34      E      34          1.837
LGA    G      35      G      35          1.700
LGA    I      36      I      36          0.895
LGA    T      37      T      37          1.473
LGA    V      38      V      38          2.795
LGA    Q      39      Q      39          2.080
LGA    T      40      T      40          1.249
LGA    A      41      A      41          2.098
LGA    I      42      I      42          2.120
LGA    T      43      T      43          1.361
LGA    Q      44      Q      44          1.606
LGA    S      45      S      45          2.471
LGA    G      46      G      46          2.044
LGA    I      47      I      47          1.386
LGA    L      48      L      48          1.394
LGA    S      49      S      49          3.420
LGA    Q      50      Q      50          3.449
LGA    F      51      F      51          1.231
LGA    P      52      P      52          3.087
LGA    E      53      E      53          3.049
LGA    I      54      I      54          3.825
LGA    D      55      D      55          7.319
LGA    L      56      L      56          9.202

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     28    2.48    54.348    53.405     1.085

LGA_LOCAL      RMSD =  2.480  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.910  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.618  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.540715 * X  +  -0.434403 * Y  +   0.720362 * Z  +  25.283674
  Y_new =   0.201326 * X  +  -0.898285 * Y  +  -0.390579 * Z  +  14.878347
  Z_new =   0.816759 * X  +  -0.066164 * Y  +   0.573173 * Z  +  -0.729688 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.114926    3.026666  [ DEG:    -6.5848    173.4152 ]
  Theta =  -0.955771   -2.185821  [ DEG:   -54.7617   -125.2383 ]
  Phi   =   2.785162   -0.356430  [ DEG:   159.5780    -20.4220 ]
 
# 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_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_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   28   2.48  53.405     5.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_5-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM     11  CA  ASN    11      20.337  10.814  16.678  1.00  0.00              
ATOM     12  CA  GLN    12      22.799  11.715  13.952  1.00  0.00              
ATOM     13  CA  ILE    13      20.546  11.682  10.839  1.00  0.00              
ATOM     14  CA  ASN    14      22.260  11.611   7.401  1.00  0.00              
ATOM     15  CA  ILE    15      20.900  13.523   4.462  1.00  0.00              
ATOM     16  CA  GLU    16      22.279  13.174   0.979  1.00  0.00              
ATOM     17  CA  ILE    17      20.944  15.290  -1.732  1.00  0.00              
ATOM     18  CA  ALA    18      21.916  14.858  -5.274  1.00  0.00              
ATOM     19  CA  TYR    19      21.030  17.536  -7.762  1.00  0.00              
ATOM     20  CA  ALA    20      21.537  17.049 -11.449  1.00  0.00              
ATOM     21  CA  PHE    21      21.688  20.007 -13.736  1.00  0.00              
ATOM     22  CA  PRO    22      20.467  19.744 -17.272  1.00  0.00              
ATOM     23  CA  GLU    23      16.817  20.594 -16.454  1.00  0.00              
ATOM     24  CA  ARG    24      15.928  17.592 -14.330  1.00  0.00              
ATOM     25  CA  TYR    25      16.279  17.690 -10.611  1.00  0.00              
ATOM     26  CA  TYR    26      17.027  14.555  -8.852  1.00  0.00              
ATOM     27  CA  LEU    27      16.785  14.373  -5.147  1.00  0.00              
ATOM     28  CA  LYS    28      18.026  11.461  -3.111  1.00  0.00              
ATOM     29  CA  SER    29      17.389  11.250   0.607  1.00  0.00              
ATOM     30  CA  PHE    30      19.568   9.073   2.783  1.00  0.00              
ATOM     31  CA  GLN    31      18.645   8.109   6.267  1.00  0.00              
ATOM     32  CA  VAL    32      21.098   6.391   8.363  1.00  0.00              
ATOM     33  CA  ASP    33      20.718   3.849  10.951  1.00  0.00              
ATOM     34  CA  GLU    34      20.671   3.874  14.534  1.00  0.00              
ATOM     35  CA  GLY    35      24.179   4.154  15.763  1.00  0.00              
ATOM     36  CA  ILE    36      25.841   5.697  12.768  1.00  0.00              
ATOM     37  CA  THR    37      27.399   9.155  13.283  1.00  0.00              
ATOM     38  CA  VAL    38      26.946  11.480  10.283  1.00  0.00              
ATOM     39  CA  GLN    39      30.730  11.969  10.505  1.00  0.00              
ATOM     40  CA  THR    40      31.206   8.187  10.044  1.00  0.00              
ATOM     41  CA  ALA    41      28.940   8.138   6.988  1.00  0.00              
ATOM     42  CA  ILE    42      30.795  11.144   5.513  1.00  0.00              
ATOM     43  CA  THR    43      34.107   9.367   6.110  1.00  0.00              
ATOM     44  CA  GLN    44      32.804   6.267   4.425  1.00  0.00              
ATOM     45  CA  SER    45      31.932   8.311   1.292  1.00  0.00              
ATOM     46  CA  GLY    46      35.369   9.931   1.188  1.00  0.00              
ATOM     47  CA  ILE    47      34.181  13.479   1.202  1.00  0.00              
ATOM     48  CA  LEU    48      36.138  14.702   4.178  1.00  0.00              
ATOM     49  CA  SER    49      39.352  13.254   2.870  1.00  0.00              
ATOM     50  CA  GLN    50      38.964  14.889  -0.572  1.00  0.00              
ATOM     51  CA  PHE    51      37.721  18.252   0.542  1.00  0.00              
ATOM     52  CA  PRO    52      39.351  19.119   3.904  1.00  0.00              
ATOM     53  CA  GLU    53      37.924  22.587   4.295  1.00  0.00              
ATOM     54  CA  ILE    54      34.346  21.653   3.592  1.00  0.00              
ATOM     55  CA  ASP    55      32.029  20.700   6.425  1.00  0.00              
ATOM     56  CA  LEU    56      29.721  18.091   4.861  1.00  0.00              
TER                                                                             
END
