
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS393_1-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:    44        13 - 56          4.84     5.41
  LCS_AVERAGE:     94.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        36 - 47          1.77    10.64
  LCS_AVERAGE:     21.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        37 - 46          0.72    12.23
  LCS_AVERAGE:     11.77

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      3   11   35     3    3    3    7   11   11   14   16   21   26   29   30   34   35   40   41   41   42   45   45 
LCS_GDT     Q      12     Q      12      4   11   35     3    4    5    7   11   12   19   21   25   28   29   33   34   35   40   41   43   44   45   45 
LCS_GDT     I      13     I      13      4   11   44     3    3    5   10   12   16   19   22   26   30   32   35   37   40   40   42   43   44   45   45 
LCS_GDT     N      14     N      14      4   11   44     3    5    6    8   11   13   19   21   25   28   29   33   34   38   40   42   43   44   45   45 
LCS_GDT     I      15     I      15      4   11   44     3    4    6   10   12   17   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     E      16     E      16      4   11   44     3    4    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     I      17     I      17      4   11   44     3    4    5   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     A      18     A      18      4   11   44     3    4    5    8   11   15   19   23   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Y      19     Y      19      4   11   44     3    4    5    8   11   13   19   22   25   28   29   31   35   40   41   42   43   44   45   45 
LCS_GDT     A      20     A      20      4   11   44     3    3    4    8   11   13   19   22   25   28   30   37   39   40   41   42   43   44   45   45 
LCS_GDT     F      21     F      21      5   11   44     3    3    5    8   11   13   21   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     P      22     P      22      5    7   44     3    4    5    7   10   13   18   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     E      23     E      23      5    7   44     3    4    6   10   12   17   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     R      24     R      24      5    9   44     3    4    5    7   12   17   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Y      25     Y      25      5   11   44     3    4    6    7   12   16   19   23   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Y      26     Y      26      4   11   44     3    4    5    7   12   16   19   23   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     L      27     L      27      4   11   44     3    4    6   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     K      28     K      28      4   11   44     3    4    6   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     S      29     S      29      4   11   44     3    4    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     F      30     F      30      4   11   44     3    4    6   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Q      31     Q      31      4   11   44     3    3    5    7   12   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     V      32     V      32      5   11   44     3    4    6   10   12   18   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     D      33     D      33      5   11   44     3    5    6   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     E      34     E      34      5   11   44     3    5    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     G      35     G      35      5   11   44     3    5    6   10   12   16   19   24   27   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     I      36     I      36      5   12   44     3    5    6   10   12   16   21   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     T      37     T      37     10   12   44     4    9   10   10   13   15   19   22   25   28   29   31   35   40   41   42   43   44   45   45 
LCS_GDT     V      38     V      38     10   12   44     7    9   10   10   13   13   17   22   27   30   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Q      39     Q      39     10   12   44     7    9   10   10   13   13   19   24   27   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     T      40     T      40     10   12   44     7    9   10   10   13   19   21   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     A      41     A      41     10   12   44     7    9   10   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     I      42     I      42     10   12   44     7    9   10   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     T      43     T      43     10   12   44     7    9   10   10   13   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Q      44     Q      44     10   12   44     7    9   10   10   13   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     S      45     S      45     10   12   44     5    9   10   10   13   13   17   23   27   30   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     G      46     G      46     10   12   44     3    6   10   10   13   13   14   17   20   24   27   31   33   36   41   42   43   44   44   45 
LCS_GDT     I      47     I      47      3   12   44     3    3    3   10   13   13   18   23   27   29   33   37   39   40   41   42   43   44   45   45 
LCS_GDT     L      48     L      48      3    5   44     3    4    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     S      49     S      49      3    5   44     3    3    7    9   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     Q      50     Q      50      4    6   44     3    4    4    6    9   10   16   21   27   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     F      51     F      51      4    6   44     3    4    4    5    7    9   13   15   16   21   28   36   39   40   41   42   43   44   45   45 
LCS_GDT     P      52     P      52      4    6   44     3    4    5    6   11   15   19   24   27   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     E      53     E      53      4    6   44     3    4    5    7   11   15   19   24   27   30   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     I      54     I      54      4    6   44     3    4    5    6   13   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     D      55     D      55      4    6   44     3    4    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     L      56     L      56      3    5   44     3    3    7   10   14   19   22   24   29   31   36   37   39   40   41   42   43   44   45   45 
LCS_AVERAGE  LCS_A:  42.77  (  11.77   21.74   94.80 )

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     10     10     14     19     22     24     29     31     36     37     39     40     41     42     43     44     45     45 
GDT PERCENT_CA  15.22  19.57  21.74  21.74  30.43  41.30  47.83  52.17  63.04  67.39  78.26  80.43  84.78  86.96  89.13  91.30  93.48  95.65  97.83  97.83
GDT RMS_LOCAL    0.32   0.50   0.72   0.72   1.91   2.24   2.61   2.80   3.24   3.51   3.89   3.98   4.18   4.30   4.43   4.56   4.70   4.84   5.16   5.04
GDT RMS_ALL_CA  11.20  12.01  12.23  12.23   5.98   5.86   5.45   5.42   5.47   5.38   5.52   5.53   5.52   5.41   5.63   5.35   5.36   5.41   5.28   5.31

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         15.647
LGA    Q      12      Q      12         12.331
LGA    I      13      I      13          7.629
LGA    N      14      N      14          8.517
LGA    I      15      I      15          3.411
LGA    E      16      E      16          0.833
LGA    I      17      I      17          3.120
LGA    A      18      A      18          6.666
LGA    Y      19      Y      19         10.721
LGA    A      20      A      20          9.704
LGA    F      21      F      21          7.726
LGA    P      22      P      22          9.250
LGA    E      23      E      23          7.933
LGA    R      24      R      24          7.822
LGA    Y      25      Y      25          9.205
LGA    Y      26      Y      26          7.416
LGA    L      27      L      27          3.224
LGA    K      28      K      28          3.477
LGA    S      29      S      29          1.463
LGA    F      30      F      30          3.039
LGA    Q      31      Q      31          3.600
LGA    V      32      V      32          4.635
LGA    D      33      D      33          1.935
LGA    E      34      E      34          2.455
LGA    G      35      G      35          3.930
LGA    I      36      I      36          2.966
LGA    T      37      T      37          7.521
LGA    V      38      V      38          5.636
LGA    Q      39      Q      39          4.085
LGA    T      40      T      40          1.907
LGA    A      41      A      41          2.037
LGA    I      42      I      42          1.322
LGA    T      43      T      43          2.191
LGA    Q      44      Q      44          3.165
LGA    S      45      S      45          4.636
LGA    G      46      G      46          7.820
LGA    I      47      I      47          4.933
LGA    L      48      L      48          3.615
LGA    S      49      S      49          2.834
LGA    Q      50      Q      50          5.007
LGA    F      51      F      51          6.500
LGA    P      52      P      52          3.580
LGA    E      53      E      53          3.760
LGA    I      54      I      54          2.736
LGA    D      55      D      55          2.832
LGA    L      56      L      56          2.368

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     24    2.79    46.196    42.992     0.831

LGA_LOCAL      RMSD =  2.787  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.057  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.274  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.196486 * X  +   0.946429 * Y  +   0.256252 * Z  +  22.837801
  Y_new =   0.265505 * X  +  -0.302939 * Y  +   0.915279 * Z  +  12.886621
  Z_new =   0.943875 * X  +  -0.111803 * Y  +  -0.310804 * Z  +   5.510016 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.796283    0.345309  [ DEG:  -160.2152     19.7848 ]
  Theta =  -1.234173   -1.907420  [ DEG:   -70.7129   -109.2871 ]
  Phi   =   0.933695   -2.207897  [ DEG:    53.4968   -126.5032 ]
 
# 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_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_1-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   24   2.79  42.992     5.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_1-D1
PFRMAT TS
TARGET T0363
MODEL 1
PARENT N/A
ATOM     11  CA  ASN    11      15.196  12.706  19.999  1.00 25.00           C
ATOM     12  CA  GLN    12      16.071  11.260  16.615  1.00 25.00           C
ATOM     13  CA  ILE    13      18.042  11.634  13.365  1.00 25.00           C
ATOM     14  CA  ASN    14      21.276  13.113  12.058  1.00 25.00           C
ATOM     15  CA  ILE    15      22.541  12.390   8.526  1.00 25.00           C
ATOM     16  CA  GLU    16      21.485  14.029   5.204  1.00 25.00           C
ATOM     17  CA  ILE    17      22.679  15.807   2.018  1.00 25.00           C
ATOM     18  CA  ALA    18      24.722  13.501  -0.229  1.00 25.00           C
ATOM     19  CA  TYR    19      26.092  12.704  -3.729  1.00 25.00           C
ATOM     20  CA  ALA    20      28.619  15.540  -3.914  1.00 25.00           C
ATOM     21  CA  PHE    21      27.597  18.563  -5.999  1.00 25.00           C
ATOM     22  CA  PRO    22      26.181  21.060  -8.452  1.00 25.00           C
ATOM     23  CA  GLU    23      26.262  21.657 -12.165  1.00 25.00           C
ATOM     24  CA  ARG    24      28.130  18.518 -13.177  1.00 25.00           C
ATOM     25  CA  TYR    25      25.636  16.726 -10.988  1.00 25.00           C
ATOM     26  CA  TYR    26      23.216  16.832  -8.003  1.00 25.00           C
ATOM     27  CA  LEU    27      23.198  16.815  -4.166  1.00 25.00           C
ATOM     28  CA  LYS    28      20.424  14.931  -2.370  1.00 25.00           C
ATOM     29  CA  SER    29      19.871  11.953  -0.023  1.00 25.00           C
ATOM     30  CA  PHE    30      19.454   9.865   3.138  1.00 25.00           C
ATOM     31  CA  GLN    31      20.923   8.094   6.131  1.00 25.00           C
ATOM     32  CA  VAL    32      19.643   7.368   9.693  1.00 25.00           C
ATOM     33  CA  ASP    33      20.717   3.782  10.335  1.00 25.00           C
ATOM     34  CA  GLU    34      22.029   4.674  13.797  1.00 25.00           C
ATOM     35  CA  GLY    35      24.140   1.450  13.700  1.00 25.00           C
ATOM     36  CA  ILE    36      26.752   3.767  12.178  1.00 25.00           C
ATOM     37  CA  THR    37      25.612   4.723   8.696  1.00 25.00           C
ATOM     38  CA  VAL    38      25.129   8.232  10.046  1.00 25.00           C
ATOM     39  CA  GLN    39      28.186   8.959  12.234  1.00 25.00           C
ATOM     40  CA  THR    40      30.332   6.670  10.037  1.00 25.00           C
ATOM     41  CA  ALA    41      29.073   8.464   6.896  1.00 25.00           C
ATOM     42  CA  ILE    42      29.909  11.855   8.467  1.00 25.00           C
ATOM     43  CA  THR    43      33.422  10.610   9.346  1.00 25.00           C
ATOM     44  CA  GLN    44      33.911   9.377   5.754  1.00 25.00           C
ATOM     45  CA  SER    45      32.772  12.776   4.405  1.00 25.00           C
ATOM     46  CA  GLY    46      33.930  16.101   5.814  1.00 25.00           C
ATOM     47  CA  ILE    47      33.294  18.463   2.930  1.00 25.00           C
ATOM     48  CA  LEU    48      35.138  16.385   0.318  1.00 25.00           C
ATOM     49  CA  SER    49      38.115  15.030  -1.673  1.00 25.00           C
ATOM     50  CA  GLN    50      38.517  12.162   0.833  1.00 25.00           C
ATOM     51  CA  PHE    51      38.076  13.642   4.279  1.00 25.00           C
ATOM     52  CA  PRO    52      41.625  15.026   3.702  1.00 25.00           C
ATOM     53  CA  GLU    53      41.299  18.451   5.293  1.00 25.00           C
ATOM     54  CA  ILE    54      39.100  21.060   3.529  1.00 25.00           C
ATOM     55  CA  ASP    55      37.845  21.571   7.127  1.00 25.00           C
ATOM     56  CA  LEU    56      37.091  18.368   8.970  1.00 25.00           C
TER
END
