
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS599_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:    46        11 - 56          4.08     4.08
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        28 - 53          1.93     5.78
  LONGEST_CONTINUOUS_SEGMENT:    26        29 - 54          1.91     5.96
  LCS_AVERAGE:     54.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        30 - 46          0.89     6.75
  LCS_AVERAGE:     32.04

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      6   24   46     4    6   10   18   23   25   28   32   36   38   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Q      12     Q      12      9   24   46     4   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      13     I      13     14   24   46     8   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     N      14     N      14     14   24   46     5   13   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      15     I      15     14   24   46     4   12   18   21   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     E      16     E      16     14   24   46     5   12   18   21   22   23   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      17     I      17     14   24   46     5   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     A      18     A      18     14   24   46     4   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Y      19     Y      19     14   24   46     4    9   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     A      20     A      20     14   24   46     5   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     F      21     F      21     14   24   46     3   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     P      22     P      22     14   24   46     3    9   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     E      23     E      23     14   24   46     4    9   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     R      24     R      24     14   24   46     4   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Y      25     Y      25     14   24   46     4   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Y      26     Y      26     14   24   46     4    7   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     L      27     L      27     12   24   46     3   12   18   21   22   23   27   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     K      28     K      28      8   26   46     4    9   18   21   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     S      29     S      29      8   26   46     4   12   18   21   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     F      30     F      30     17   26   46     8   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Q      31     Q      31     17   26   46     4   12   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     V      32     V      32     17   26   46     3    7   18   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     D      33     D      33     17   26   46     3   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     E      34     E      34     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     G      35     G      35     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      36     I      36     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     T      37     T      37     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     V      38     V      38     17   26   46     9   13   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Q      39     Q      39     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     T      40     T      40     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     A      41     A      41     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      42     I      42     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     T      43     T      43     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Q      44     Q      44     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     S      45     S      45     17   26   46    10   14   19   24   25   28   31   33   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     G      46     G      46     17   26   46     7   13   19   24   25   28   31   32   36   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     I      47     I      47     15   26   46     7   11   17   24   25   28   31   32   34   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     L      48     L      48     15   26   46     7   11   17   24   25   28   31   32   34   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     S      49     S      49     15   26   46     7   11   17   24   25   28   31   32   35   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     Q      50     Q      50     15   26   46     7   11   17   24   25   28   31   32   34   39   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     F      51     F      51     15   26   46     7   11   15   21   25   28   31   32   34   37   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     P      52     P      52     15   26   46     7   11   15   19   25   28   31   32   34   37   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     E      53     E      53     15   26   46     4   11   15   17   21   28   31   32   34   37   38   42   46   46   46   46   46   46   46   46 
LCS_GDT     I      54     I      54     15   26   46     5   11   15   18   23   28   31   32   34   37   41   44   46   46   46   46   46   46   46   46 
LCS_GDT     D      55     D      55     15   23   46     3   11   13   16   18   22   28   32   34   37   39   43   46   46   46   46   46   46   46   46 
LCS_GDT     L      56     L      56     15   23   46     4    5   10   15   17   21   28   32   34   37   41   44   46   46   46   46   46   46   46   46 
LCS_AVERAGE  LCS_A:  62.22  (  32.04   54.63  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     14     19     24     25     28     31     33     36     39     41     44     46     46     46     46     46     46     46     46 
GDT PERCENT_CA  21.74  30.43  41.30  52.17  54.35  60.87  67.39  71.74  78.26  84.78  89.13  95.65 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.57   0.88   1.31   1.44   1.80   2.11   3.03   3.14   3.54   3.66   3.90   4.08   4.08   4.08   4.08   4.08   4.08   4.08   4.08
GDT RMS_ALL_CA   5.65   6.90   6.59   6.86   6.82   6.18   5.81   5.03   4.92   4.33   4.26   4.11   4.08   4.08   4.08   4.08   4.08   4.08   4.08   4.08

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          4.078
LGA    Q      12      Q      12          2.990
LGA    I      13      I      13          2.727
LGA    N      14      N      14          2.072
LGA    I      15      I      15          2.326
LGA    E      16      E      16          2.443
LGA    I      17      I      17          3.420
LGA    A      18      A      18          3.820
LGA    Y      19      Y      19          3.963
LGA    A      20      A      20          3.991
LGA    F      21      F      21          4.185
LGA    P      22      P      22          3.999
LGA    E      23      E      23          3.134
LGA    R      24      R      24          2.293
LGA    Y      25      Y      25          3.365
LGA    Y      26      Y      26          2.880
LGA    L      27      L      27          2.283
LGA    K      28      K      28          2.591
LGA    S      29      S      29          2.445
LGA    F      30      F      30          3.667
LGA    Q      31      Q      31          3.420
LGA    V      32      V      32          2.979
LGA    D      33      D      33          1.658
LGA    E      34      E      34          1.110
LGA    G      35      G      35          2.279
LGA    I      36      I      36          2.273
LGA    T      37      T      37          3.294
LGA    V      38      V      38          3.455
LGA    Q      39      Q      39          3.989
LGA    T      40      T      40          3.345
LGA    A      41      A      41          2.966
LGA    I      42      I      42          3.763
LGA    T      43      T      43          3.865
LGA    Q      44      Q      44          2.690
LGA    S      45      S      45          3.358
LGA    G      46      G      46          5.408
LGA    I      47      I      47          6.607
LGA    L      48      L      48          7.396
LGA    S      49      S      49          7.602
LGA    Q      50      Q      50          8.356
LGA    F      51      F      51          9.077
LGA    P      52      P      52          9.973
LGA    E      53      E      53         11.472
LGA    I      54      I      54          9.191
LGA    D      55      D      55         10.367
LGA    L      56      L      56          8.458

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     33    3.03    63.587    64.382     1.054

LGA_LOCAL      RMSD =  3.032  Number of atoms =   33  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.064  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  4.076  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.041948 * X  +   0.022630 * Y  +  -0.998863 * Z  +  24.031466
  Y_new =  -0.980835 * X  +  -0.191324 * Y  +   0.036856 * Z  +  17.477842
  Z_new =  -0.190272 * X  +   0.981266 * Y  +   0.030222 * Z  +   4.437046 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.540007   -1.601585  [ DEG:    88.2359    -91.7641 ]
  Theta =   0.191439    2.950153  [ DEG:    10.9687    169.0313 ]
  Phi   =  -1.613538    1.528055  [ DEG:   -92.4489     87.5511 ]
 
# 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_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_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   33   3.03  64.382     4.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_4-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM     11  CA  ASN    11      14.857   3.508  11.483  1.00  0.00              
ATOM     12  CA  GLN    12      16.409   5.025   8.386  1.00  0.00              
ATOM     13  CA  ILE    13      17.531   8.567   8.749  1.00  0.00              
ATOM     14  CA  ASN    14      18.249  10.581   5.714  1.00  0.00              
ATOM     15  CA  ILE    15      20.486  13.652   5.838  1.00  0.00              
ATOM     16  CA  GLU    16      20.639  16.083   2.998  1.00  0.00              
ATOM     17  CA  ILE    17      23.461  18.553   2.633  1.00  0.00              
ATOM     18  CA  ALA    18      23.501  21.116  -0.022  1.00  0.00              
ATOM     19  CA  TYR    19      26.562  23.005  -0.952  1.00  0.00              
ATOM     20  CA  ALA    20      26.406  26.040  -3.029  1.00  0.00              
ATOM     21  CA  PHE    21      29.634  27.562  -4.370  1.00  0.00              
ATOM     22  CA  PRO    22      29.636  30.173  -6.937  1.00  0.00              
ATOM     23  CA  GLU    23      27.668  28.351  -9.673  1.00  0.00              
ATOM     24  CA  ARG    24      28.488  24.759  -8.886  1.00  0.00              
ATOM     25  CA  TYR    25      25.919  22.751  -7.054  1.00  0.00              
ATOM     26  CA  TYR    26      27.025  19.979  -4.976  1.00  0.00              
ATOM     27  CA  LEU    27      24.546  17.684  -3.410  1.00  0.00              
ATOM     28  CA  LYS    28      25.594  15.458  -0.655  1.00  0.00              
ATOM     29  CA  SER    29      23.215  12.680   0.677  1.00  0.00              
ATOM     30  CA  PHE    30      23.967  11.039   3.889  1.00  0.00              
ATOM     31  CA  GLN    31      22.210   7.975   4.966  1.00  0.00              
ATOM     32  CA  VAL    32      22.095   7.030   8.520  1.00  0.00              
ATOM     33  CA  ASP    33      20.953   3.563   9.637  1.00  0.00              
ATOM     34  CA  GLU    34      18.887   3.445  12.741  1.00  0.00              
ATOM     35  CA  GLY    35      21.134   2.686  15.528  1.00  0.00              
ATOM     36  CA  ILE    36      24.377   4.032  13.984  1.00  0.00              
ATOM     37  CA  THR    37      26.385   6.381  16.185  1.00  0.00              
ATOM     38  CA  VAL    38      27.351   9.711  14.790  1.00  0.00              
ATOM     39  CA  GLN    39      31.049   8.856  15.314  1.00  0.00              
ATOM     40  CA  THR    40      30.661   5.648  13.258  1.00  0.00              
ATOM     41  CA  ALA    41      28.897   7.452  10.449  1.00  0.00              
ATOM     42  CA  ILE    42      31.628  10.100  10.381  1.00  0.00              
ATOM     43  CA  THR    43      34.370   7.487  10.283  1.00  0.00              
ATOM     44  CA  GLN    44      32.794   5.543   7.480  1.00  0.00              
ATOM     45  CA  SER    45      32.181   8.554   5.377  1.00  0.00              
ATOM     46  CA  GLY    46      35.630  10.091   5.734  1.00  0.00              
ATOM     47  CA  ILE    47      34.065  13.036   7.656  1.00  0.00              
ATOM     48  CA  LEU    48      36.922  13.072  10.201  1.00  0.00              
ATOM     49  CA  SER    49      39.324  13.093   7.275  1.00  0.00              
ATOM     50  CA  GLN    50      37.560  16.056   5.621  1.00  0.00              
ATOM     51  CA  PHE    51      36.863  18.206   8.704  1.00  0.00              
ATOM     52  CA  PRO    52      39.398  17.294  11.404  1.00  0.00              
ATOM     53  CA  GLU    53      37.880  19.526  13.985  1.00  0.00              
ATOM     54  CA  ILE    54      34.263  18.516  13.826  1.00  0.00              
ATOM     55  CA  ASP    55      33.120  16.752  17.004  1.00  0.00              
ATOM     56  CA  LEU    56      30.486  14.162  15.983  1.00  0.00              
TER                                                                             
END
