
#######################################################
#                                                     #
#                        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   44 (   44),  selected   44 , name T0321TS464_2_2
# Molecule2: number of CA atoms  244 ( 1840),  selected   44 , name T0321.pdb
# PARAMETERS: T0321TS464_2_2.T0321.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:    16       203 - 218         3.63    15.92
  LCS_AVERAGE:      5.64

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       206 - 216         1.81    15.08
  LCS_AVERAGE:      2.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        88 - 95          0.34    20.33
  LONGEST_CONTINUOUS_SEGMENT:     8       206 - 213         0.84    15.80
  LCS_AVERAGE:      2.41

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:  244
LCS_GDT     E       3     E       3      5    5   11     5    6    6    6    6    6    6    7    8    8   17   18   19   19   20   20   21   22   24   24 
LCS_GDT     I       4     I       4      5    5   11     5    6    6    6    6    6    6   14   16   17   17   18   19   19   20   20   22   23   24   24 
LCS_GDT     Y       5     Y       5      5    5   12     5    6    6    6    6   12   12   14   16   17   17   18   19   19   21   21   22   23   24   24 
LCS_GDT     D       6     D       6      5    5   12     5    6    9   10   10   11   12   13   16   17   17   18   19   19   20   20   21   23   24   24 
LCS_GDT     A       7     A       7      5    5   12     5    6    6    6    6    6    6    7    8    9   14   16   16   17   20   20   21   22   22   23 
LCS_GDT     V      18     V      18      7    7   12     5    6    7    7    7    7    7   10   10   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     D      19     D      19      7    7   12     5    6    7    7    7    7    7    7    8    9   13   15   16   18   19   21   22   24   24   25 
LCS_GDT     E      20     E      20      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   13   15   19   21   22   24   24   25 
LCS_GDT     L      21     L      21      7    7   12     5    6    7    7    7    7    7    7    8    9   10   12   15   17   19   21   22   24   24   25 
LCS_GDT     V      22     V      22      7    7   12     3    5    7    7    7    7    7    7    7    8   10   11   13   15   16   16   18   20   22   25 
LCS_GDT     C      23     C      23      7    7   12     3    6    7    7    7    7    7    7    8    9   10   12   13   15   16   21   22   24   24   25 
LCS_GDT     G      24     G      24      7    7   13     5    6    7    7    7    7    7    7    7    8   10   12   13   15   16   16   18   24   24   25 
LCS_GDT     N      87     N      87      3    3   13     3    3    3    4    5    6    9   10   11   14   14   17   18   18   20   21   22   24   24   25 
LCS_GDT     N      88     N      88      8    8   13     7    8    8    8    8    8    8   10   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     P      89     P      89      8    8   13     7    8    8    8    8    8    9    9   11   12   13   17   18   18   19   21   22   24   24   25 
LCS_GDT     Q      90     Q      90      8    8   13     7    8    8    8    8    8    9   10   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     V      91     V      91      8    8   13     7    8    8    8    8    8    9   10   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     A      92     A      92      8    8   13     7    8    8    8    8    8    9    9   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     R      93     R      93      8    8   13     7    8    8    8    8    8    9    9   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     E      94     E      94      8    8   13     7    8    8    8    8    8    9   10   11   12   14   17   18   18   19   21   22   24   24   25 
LCS_GDT     H      95     H      95      8    8   13     5    8    8    8    8    8    9    9   11   11   11   13   16   17   19   20   21   24   24   25 
LCS_GDT     N     110     N     110      4    4   13     3    4    4    4    6   11   11   12   13   14   16   17   18   20   21   21   22   23   24   24 
LCS_GDT     D     111     D     111      4    4   13     3    4    5    9   12   12   13   13   14   15   16   18   18   20   21   21   22   23   24   24 
LCS_GDT     P     112     P     112      4    4   13     3    4    5    5    9   10   11   13   14   15   16   17   18   20   21   21   22   23   24   24 
LCS_GDT     F     113     F     113      4    4    9     3    4    5    8    9    9    9   10   12   14   14   16   17   20   21   21   22   23   24   24 
LCS_GDT     I     114     I     114      3    3   13     0    3    3    3    3    3    4    6    9   11   14   16   17   17   18   19   20   22   22   23 
LCS_GDT     M     115     M     115      3    3   14     0    3    3    3    3    4    7    7    8   11   13   14   16   17   18   19   20   22   22   23 
LCS_GDT     S     116     S     116      3    3   14     0    3    3    3    3    3    4    7    7    8   11   13   14   16   18   19   20   21   22   23 
LCS_GDT     T     203     T     203      3    3   16     0    3    3    3    4    5    8   10   12   15   15   17   18   20   21   21   22   24   24   25 
LCS_GDT     P     204     P     204      3    4   16     3    3    3    3    4    6    8   12   13   15   15   18   19   20   21   21   22   24   24   25 
LCS_GDT     L     205     L     205      3   10   16     3    3    3    4    5    7   13   13   14   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     A     206     A     206      8   11   16     3    4    8   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     P     207     P     207      8   11   16     3    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   23   24   25 
LCS_GDT     V     208     V     208      8   11   16     3    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     L     209     L     209      8   11   16     4    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     F     210     F     210      8   11   16     4    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     E     211     E     211      8   11   16     4    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     H     212     H     212      8   11   16     4    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   24   24   25 
LCS_GDT     G     213     G     213      8   11   16     4    7    9   10   12   12   13   14   16   17   17   18   19   20   21   21   22   23   24   25 
LCS_GDT     L     214     L     214      4   11   16     3    4    5    9   12   12   13   14   16   17   17   18   19   20   21   21   22   23   24   24 
LCS_GDT     Q     215     Q     215      4   11   16     4    4    5    8   12   12   13   14   16   17   17   18   19   20   21   21   22   23   24   24 
LCS_GDT     E     216     E     216      4   11   16     4    4    5    9   12   12   13   14   16   17   17   18   19   20   21   21   22   23   24   24 
LCS_GDT     L     217     L     217      4    7   16     4    4    4    8    9    9   13   14   16   17   17   18   19   20   21   21   22   23   24   24 
LCS_GDT     S     218     S     218      4    7   16     4    7    9   10   10   12   13   14   16   17   17   18   19   20   21   21   22   23   24   24 
LCS_AVERAGE  LCS_A:   3.67  (   2.41    2.96    5.64 )

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      9     10     12     12     13     14     16     17     17     18     19     20     21     21     22     24     24     25 
GDT PERCENT_CA   2.87   3.28   3.69   4.10   4.92   4.92   5.33   5.74   6.56   6.97   6.97   7.38   7.79   8.20   8.61   8.61   9.02   9.84   9.84  10.25
GDT RMS_LOCAL    0.19   0.34   0.89   1.06   1.78   1.78   2.00   2.32   2.80   3.06   3.06   3.33   3.71   4.30   4.51   4.51   4.79   6.32   6.32   6.82
GDT RMS_ALL_CA  20.18  20.33  15.12  15.18  15.22  15.22  15.34  15.09  15.12  15.13  15.13  15.30  15.59  15.81  15.66  15.66  15.55  14.89  14.89  15.03

#      Molecule1      Molecule2       DISTANCE
LGA    E       3      E       3          6.982
LGA    I       4      I       4          5.091
LGA    Y       5      Y       5          3.364
LGA    D       6      D       6          6.194
LGA    A       7      A       7         10.372
LGA    V      18      V      18         26.831
LGA    D      19      D      19         27.567
LGA    E      20      E      20         22.528
LGA    L      21      L      21         18.102
LGA    V      22      V      22         16.403
LGA    C      23      C      23         14.766
LGA    G      24      G      24         16.157
LGA    N      87      N      87         12.127
LGA    N      88      N      88         16.311
LGA    P      89      P      89         18.860
LGA    Q      90      Q      90         23.440
LGA    V      91      V      91         22.431
LGA    A      92      A      92         19.981
LGA    R      93      R      93         24.180
LGA    E      94      E      94         27.655
LGA    H      95      H      95         25.428
LGA    N     110      N     110         11.731
LGA    D     111      D     111          7.730
LGA    P     112      P     112         10.814
LGA    F     113      F     113         15.096
LGA    I     114      I     114         20.404
LGA    M     115      M     115         23.469
LGA    S     116      S     116         27.719
LGA    T     203      T     203         10.935
LGA    P     204      P     204          8.725
LGA    L     205      L     205          6.228
LGA    A     206      A     206          1.376
LGA    P     207      P     207          2.716
LGA    V     208      V     208          1.789
LGA    L     209      L     209          0.896
LGA    F     210      F     210          1.678
LGA    E     211      E     211          1.005
LGA    H     212      H     212          0.930
LGA    G     213      G     213          2.759
LGA    L     214      L     214          0.897
LGA    Q     215      Q     215          3.570
LGA    E     216      E     216          2.746
LGA    L     217      L     217          3.772
LGA    S     218      S     218          2.167

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   44  244    4.0     14    2.32     5.430     4.992     0.578

LGA_LOCAL      RMSD =  2.320  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.143  Number of atoms =   44 
Std_ALL_ATOMS  RMSD = 12.394  (standard rmsd on all 44 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.491346 * X  +  -0.319250 * Y  +  -0.810345 * Z  +  28.958805
  Y_new =  -0.768337 * X  +   0.279276 * Y  +  -0.575901 * Z  + 107.614037
  Z_new =   0.410166 * X  +   0.905585 * Y  +  -0.108070 * Z  +  30.368017 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.689572   -1.452020  [ DEG:    96.8054    -83.1946 ]
  Theta =  -0.422637   -2.718956  [ DEG:   -24.2153   -155.7847 ]
  Phi   =  -1.001843    2.139750  [ DEG:   -57.4014    122.5986 ]
 
# 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: T0321TS464_2_2                                
REMARK     2: T0321.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_2_2.T0321.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   44  244   4.0   14   2.32   4.992    12.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3      -5.754  42.377  57.780  1.00  0.00
ATOM      2  CA  ILE     4      -3.770  42.451  61.036  1.00  0.00
ATOM      3  CA  TYR     5      -4.111  38.741  61.866  1.00  0.00
ATOM      4  CA  ASP     6      -3.885  37.738  58.187  1.00  0.00
ATOM      5  CA  ALA     7      -0.920  39.976  57.548  1.00  0.00
ATOM      6  CA  VAL    18       7.385  45.620  75.570  1.00  0.00
ATOM      7  CA  ASP    19       8.089  46.076  71.849  1.00  0.00
ATOM      8  CA  GLU    20       4.906  47.628  70.492  1.00  0.00
ATOM      9  CA  LEU    21       1.544  48.864  71.601  1.00  0.00
ATOM     10  CA  VAL    22      -1.807  48.420  70.035  1.00  0.00
ATOM     11  CA  CYS    23      -4.150  51.190  71.150  1.00  0.00
ATOM     12  CA  GLY    24      -7.626  50.792  69.692  1.00  0.00
ATOM     13  CA  ASN    87      -0.258  46.865  63.487  1.00  0.00
ATOM     14  CA  ASN    88       2.564  45.312  65.553  1.00  0.00
ATOM     15  CA  PRO    89       0.944  41.901  65.009  1.00  0.00
ATOM     16  CA  GLN    90       0.851  42.226  61.212  1.00  0.00
ATOM     17  CA  VAL    91       4.420  43.518  61.290  1.00  0.00
ATOM     18  CA  ALA    92       5.608  40.541  63.392  1.00  0.00
ATOM     19  CA  ARG    93       3.746  37.903  61.382  1.00  0.00
ATOM     20  CA  GLU    94       5.011  39.217  58.041  1.00  0.00
ATOM     21  CA  HIS    95       8.597  39.879  59.180  1.00  0.00
ATOM     22  CA  ASN   110      10.777  54.206  71.232  1.00  0.00
ATOM     23  CA  ASP   111       7.997  51.597  71.075  1.00  0.00
ATOM     24  CA  PRO   112       6.240  50.606  67.846  1.00  0.00
ATOM     25  CA  PHE   113       2.686  51.960  67.923  1.00  0.00
ATOM     26  CA  ILE   114      -0.457  50.609  66.226  1.00  0.00
ATOM     27  CA  MET   115      -3.759  52.465  66.306  1.00  0.00
ATOM     28  CA  SER   116      -7.308  51.716  65.186  1.00  0.00
ATOM     29  CA  THR   203      -8.038  42.823  73.917  1.00  0.00
ATOM     30  CA  PRO   204     -10.046  40.956  71.294  1.00  0.00
ATOM     31  CA  LEU   205      -7.169  41.574  68.813  1.00  0.00
ATOM     32  CA  ALA   206      -4.584  40.008  71.135  1.00  0.00
ATOM     33  CA  PRO   207      -6.775  36.995  71.752  1.00  0.00
ATOM     34  CA  VAL   208      -5.922  36.814  68.030  1.00  0.00
ATOM     35  CA  LEU   209      -2.172  36.999  68.759  1.00  0.00
ATOM     36  CA  PHE   210      -2.431  34.031  71.118  1.00  0.00
ATOM     37  CA  GLU   211      -4.075  31.860  68.422  1.00  0.00
ATOM     38  CA  HIS   212      -1.615  32.938  65.721  1.00  0.00
ATOM     39  CA  GLY   213       1.497  32.308  67.849  1.00  0.00
ATOM     40  CA  LEU   214       2.530  35.932  67.251  1.00  0.00
ATOM     41  CA  GLN   215       5.799  36.895  68.953  1.00  0.00
ATOM     42  CA  GLU   216       4.674  40.108  70.651  1.00  0.00
ATOM     43  CA  LEU   217       6.476  41.881  73.483  1.00  0.00
ATOM     44  CA  SER   218       3.870  44.005  75.240  1.00  0.00
TER
END
