
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0350TS383_2
# Molecule2: number of CA atoms  109 ( 1798),  selected   26 , name T0350.pdb
# PARAMETERS: T0350TS383_2.T0350.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:    18        61 - 78          4.82     7.45
  LCS_AVERAGE:     15.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        67 - 75          1.74    12.12
  LCS_AVERAGE:      6.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        69 - 75          0.86    12.48
  LCS_AVERAGE:      4.48

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:  109
LCS_GDT     E      61     E      61      5    5   18     3    4    5    6    6    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     L      62     L      62      5    5   18     3    4    5    6    6    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     H      63     H      63      5    5   18     3    4    5    6    6    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     D      64     D      64      5    5   18     3    4    5    6    6    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     K      65     K      65      5    6   18     3    4    5    6    6    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     L      66     L      66      5    8   18     3    5    5    6    7    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     N      67     N      67      5    9   18     3    5    6    6    9    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     E      68     E      68      5    9   18     3    5    6    6    9    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     Y      69     Y      69      7    9   18     3    5    7    7    9    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     Y      70     Y      70      7    9   18     5    5    7    7    9    9   10   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     V      71     V      71      7    9   18     5    5    7    7    9    9    9   11   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     K      72     K      72      7    9   18     5    5    7    7    9    9    9   10   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     V      73     V      73      7    9   18     5    5    7    7    9    9    9   10   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     I      74     I      74      7    9   18     5    5    7    7    9    9    9   10   10   11   14   16   17   20   22   24   24   25   25   25 
LCS_GDT     E      75     E      75      7    9   18     3    5    7    7    9    9    9   10   10   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     D      76     D      76      3    5   18     1    3    4    6    6    7    8   10   12   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     S      77     S      77      3    5   18     3    3    4    4    6    7    8   10   11   12   12   15   17   20   22   24   24   25   25   25 
LCS_GDT     T      78     T      78      3    5   18     3    3    4    4    4    5    7    8   11   12   12   13   14   18   22   24   24   25   25   25 
LCS_GDT     N      79     N      79      3    5   14     3    3    4    4    5    6    8   10   11   12   12   13   17   20   22   24   24   25   25   25 
LCS_GDT     E      80     E      80      3    5   14     3    3    4    4    4    6    7   10   11   12   12   13   15   18   22   24   24   25   25   25 
LCS_GDT     V      81     V      81      3    5   14     3    3    3    3    4    5    8   10   11   12   12   13   17   20   22   24   24   25   25   25 
LCS_GDT     I      82     I      82      4    5   14     3    4    5    5    5    6    7    7    9   12   12   12   13   13   19   22   24   25   25   25 
LCS_GDT     R      83     R      83      4    5   14     3    4    5    5    5    6    7    8    8   12   12   15   17   20   22   24   24   25   25   25 
LCS_GDT     E      84     E      84      4    5   14     3    4    5    5    5    6    7    8    8    9   11   12   15   19   22   24   24   25   25   25 
LCS_GDT     I      85     I      85      4    5   14     3    4    5    5    5    6    7    8    8    9   11   12   17   19   22   24   24   25   25   25 
LCS_GDT     P      86     P      86      4    5   14     3    3    5    5    5    6    7    7    8    9   11   12   13   14   15   16   17   18   19   20 
LCS_AVERAGE  LCS_A:   8.62  (   4.48    6.00   15.38 )

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      5      5      7      7      9      9     10     11     12     14     15     16     17     20     22     24     24     25     25     25 
GDT PERCENT_CA   4.59   4.59   6.42   6.42   8.26   8.26   9.17  10.09  11.01  12.84  13.76  14.68  15.60  18.35  20.18  22.02  22.02  22.94  22.94  22.94
GDT RMS_LOCAL    0.33   0.33   0.86   0.86   1.74   1.74   2.65   2.88   3.34   3.81   3.97   4.13   4.72   5.21   5.58   5.87   5.87   6.03   6.03   6.03
GDT RMS_ALL_CA  12.63  12.63  12.48  12.48  12.12  12.12  14.09  12.74  11.05   8.60   8.16   8.01   6.89   6.77   6.67   6.62   6.62   6.64   6.64   6.64

#      Molecule1      Molecule2       DISTANCE
LGA    E      61      E      61          3.204
LGA    L      62      L      62          3.639
LGA    H      63      H      63          3.801
LGA    D      64      D      64          3.445
LGA    K      65      K      65          3.263
LGA    L      66      L      66          1.348
LGA    N      67      N      67          2.391
LGA    E      68      E      68          1.563
LGA    Y      69      Y      69          2.279
LGA    Y      70      Y      70          2.358
LGA    V      71      V      71          3.807
LGA    K      72      K      72          7.387
LGA    V      73      V      73          9.932
LGA    I      74      I      74         14.256
LGA    E      75      E      75         15.175
LGA    D      76      D      76         13.391
LGA    S      77      S      77         16.749
LGA    T      78      T      78         16.451
LGA    N      79      N      79         18.323
LGA    E      80      E      80         16.248
LGA    V      81      V      81         15.990
LGA    I      82      I      82         21.625
LGA    R      83      R      83         20.534
LGA    E      84      E      84         20.094
LGA    I      85      I      85         17.307
LGA    P      86      P      86         19.727

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  109    4.0     11    2.88    10.780     9.431     0.369

LGA_LOCAL      RMSD =  2.882  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.785  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  6.587  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.398110 * X  +   0.124986 * Y  +   0.908783 * Z  +   4.649017
  Y_new =  -0.706191 * X  +   0.590545 * Y  +  -0.390579 * Z  +   4.158242
  Z_new =  -0.585494 * X  +  -0.797267 * Y  +  -0.146838 * Z  + -27.860926 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.752931    1.388661  [ DEG:  -100.4356     79.5644 ]
  Theta =   0.625489    2.516103  [ DEG:    35.8379    144.1621 ]
  Phi   =  -2.084130    1.057463  [ DEG:  -119.4118     60.5882 ]
 
# 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: T0350TS383_2                                  
REMARK     2: T0350.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0350TS383_2.T0350.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  109   4.0   11   2.88   9.431     6.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS383_2
PFRMAT TS
TARGET T0350
MODEL 2
PARENT 1g5vA
ATOM      1  N   GLU    61      11.586   6.213 -26.639  1.00  0.00
ATOM      2  CA  GLU    61      12.516   6.300 -27.761  1.00  0.00
ATOM      3  C   GLU    61      11.812   5.995 -29.076  1.00  0.00
ATOM      4  O   GLU    61      10.785   5.319 -29.101  1.00  0.00
ATOM      5  N   LEU    62      12.367   6.504 -30.172  1.00  0.00
ATOM      6  CA  LEU    62      11.788   6.289 -31.494  1.00  0.00
ATOM      7  C   LEU    62      12.870   6.067 -32.544  1.00  0.00
ATOM      8  O   LEU    62      13.952   6.648 -32.468  1.00  0.00
ATOM      9  N   HIS    63      12.565   5.226 -33.529  1.00  0.00
ATOM     10  CA  HIS    63      13.506   4.933 -34.601  1.00  0.00
ATOM     11  C   HIS    63      12.849   5.139 -35.964  1.00  0.00
ATOM     12  O   HIS    63      12.236   4.224 -36.514  1.00  0.00
ATOM     13  N   ASP    64      12.975   6.352 -36.494  1.00  0.00
ATOM     14  CA  ASP    64      12.388   6.695 -37.787  1.00  0.00
ATOM     15  C   ASP    64      12.840   5.736 -38.886  1.00  0.00
ATOM     16  O   ASP    64      12.176   5.604 -39.915  1.00  0.00
ATOM     17  N   LYS    65      13.972   5.070 -38.667  1.00  0.00
ATOM     18  CA  LYS    65      14.505   4.127 -39.647  1.00  0.00
ATOM     19  C   LYS    65      13.460   3.080 -40.028  1.00  0.00
ATOM     20  O   LYS    65      12.990   3.045 -41.163  1.00  0.00
ATOM     21  N   LEU    66      13.103   2.230 -39.068  1.00  0.00
ATOM     22  CA  LEU    66      12.116   1.182 -39.303  1.00  0.00
ATOM     23  C   LEU    66      10.728   1.624 -38.846  1.00  0.00
ATOM     24  O   LEU    66       9.865   0.792 -38.559  1.00  0.00
ATOM     25  N   ASN    67      10.522   2.939 -38.791  1.00  0.00
ATOM     26  CA  ASN    67       9.240   3.509 -38.377  1.00  0.00
ATOM     27  C   ASN    67       8.676   2.783 -37.157  1.00  0.00
ATOM     28  O   ASN    67       7.590   2.202 -37.214  1.00  0.00
ATOM     29  N   GLU    68       9.419   2.819 -36.055  1.00  0.00
ATOM     30  CA  GLU    68       8.991   2.163 -34.825  1.00  0.00
ATOM     31  C   GLU    68       9.272   3.043 -33.611  1.00  0.00
ATOM     32  O   GLU    68       9.771   4.159 -33.744  1.00  0.00
ATOM     33  N   TYR    69       8.949   2.529 -32.427  1.00  0.00
ATOM     34  CA  TYR    69       9.168   3.266 -31.188  1.00  0.00
ATOM     35  C   TYR    69       9.045   2.350 -29.976  1.00  0.00
ATOM     36  O   TYR    69       8.627   1.199 -30.096  1.00  0.00
ATOM     37  N   TYR    70       9.409   2.872 -28.810  1.00  0.00
ATOM     38  CA  TYR    70       9.342   2.112 -27.569  1.00  0.00
ATOM     39  C   TYR    70       8.450   2.820 -26.556  1.00  0.00
ATOM     40  O   TYR    70       8.636   4.004 -26.275  1.00  0.00
ATOM     41  N   VAL    71       7.475   2.095 -26.013  1.00  0.00
ATOM     42  CA  VAL    71       6.557   2.669 -25.040  1.00  0.00
ATOM     43  C   VAL    71       6.779   2.089 -23.648  1.00  0.00
ATOM     44  O   VAL    71       7.056   0.898 -23.495  1.00  0.00
ATOM     45  N   LYS    72       6.640   2.940 -22.637  1.00  0.00
ATOM     46  CA  LYS    72       6.810   2.526 -21.251  1.00  0.00
ATOM     47  C   LYS    72       5.457   2.420 -20.557  1.00  0.00
ATOM     48  O   LYS    72       4.648   3.346 -20.612  1.00  0.00
ATOM     49  N   VAL    73       5.213   1.288 -19.906  1.00  0.00
ATOM     50  CA  VAL    73       3.952   1.066 -19.208  1.00  0.00
ATOM     51  C   VAL    73       3.943   1.769 -17.855  1.00  0.00
ATOM     52  O   VAL    73       4.585   1.323 -16.907  1.00  0.00
ATOM     53  N   ILE    74       3.212   2.877 -17.784  1.00  0.00
ATOM     54  CA  ILE    74       3.115   3.658 -16.555  1.00  0.00
ATOM     55  C   ILE    74       2.591   2.813 -15.398  1.00  0.00
ATOM     56  O   ILE    74       1.404   2.491 -15.340  1.00  0.00
ATOM     57  N   GLU    75       3.485   2.458 -14.479  1.00  0.00
ATOM     58  CA  GLU    75       3.092   1.659 -13.332  1.00  0.00
ATOM     59  C   GLU    75       3.628   0.243 -13.390  1.00  0.00
ATOM     60  O   GLU    75       3.792  -0.407 -12.357  1.00  0.00
ATOM     61  N   ASP    76       6.421  -0.479 -15.589  1.00  0.00
ATOM     62  CA  ASP    76       7.844  -0.349 -15.849  1.00  0.00
ATOM     63  C   ASP    76       8.273  -1.025 -17.138  1.00  0.00
ATOM     64  O   ASP    76       9.190  -0.556 -17.812  1.00  0.00
ATOM     65  N   SER    77       7.616  -2.131 -17.477  1.00  0.00
ATOM     66  CA  SER    77       7.940  -2.878 -18.689  1.00  0.00
ATOM     67  C   SER    77       7.923  -1.977 -19.921  1.00  0.00
ATOM     68  O   SER    77       7.098  -1.070 -20.028  1.00  0.00
ATOM     69  N   THR    78       8.837  -2.242 -20.851  1.00  0.00
ATOM     70  CA  THR    78       8.931  -1.467 -22.083  1.00  0.00
ATOM     71  C   THR    78       8.852  -2.389 -23.295  1.00  0.00
ATOM     72  O   THR    78       9.619  -3.345 -23.407  1.00  0.00
ATOM     73  N   ASN    79       7.919  -2.103 -24.197  1.00  0.00
ATOM     74  CA  ASN    79       7.742  -2.922 -25.394  1.00  0.00
ATOM     75  C   ASN    79       7.765  -2.067 -26.658  1.00  0.00
ATOM     76  O   ASN    79       7.269  -0.938 -26.666  1.00  0.00
ATOM     77  N   GLU    80       8.341  -2.613 -27.724  1.00  0.00
ATOM     78  CA  GLU    80       8.428  -1.906 -28.998  1.00  0.00
ATOM     79  C   GLU    80       7.117  -2.020 -29.771  1.00  0.00
ATOM     80  O   GLU    80       6.574  -3.113 -29.936  1.00  0.00
ATOM     81  N   VAL    81       6.615  -0.884 -30.245  1.00  0.00
ATOM     82  CA  VAL    81       5.367  -0.850 -30.998  1.00  0.00
ATOM     83  C   VAL    81       5.500   0.033 -32.234  1.00  0.00
ATOM     84  O   VAL    81       6.530   0.678 -32.440  1.00  0.00
ATOM     85  N   ILE    82      -0.014   3.818 -32.342  1.00  0.00
ATOM     86  CA  ILE    82      -0.013   4.572 -31.094  1.00  0.00
ATOM     87  C   ILE    82      -1.362   5.251 -30.866  1.00  0.00
ATOM     88  O   ILE    82      -1.843   5.992 -31.722  1.00  0.00
ATOM     89  N   ARG    83      -1.963   4.992 -29.710  1.00  0.00
ATOM     90  CA  ARG    83      -3.255   5.579 -29.372  1.00  0.00
ATOM     91  C   ARG    83      -3.076   6.888 -28.608  1.00  0.00
ATOM     92  O   ARG    83      -2.075   7.085 -27.920  1.00  0.00
ATOM     93  N   GLU    84      -4.054   7.780 -28.736  1.00  0.00
ATOM     94  CA  GLU    84      -4.008   9.072 -28.060  1.00  0.00
ATOM     95  C   GLU    84      -4.264   8.912 -26.561  1.00  0.00
ATOM     96  O   GLU    84      -4.867   7.931 -26.130  1.00  0.00
ATOM     97  N   ILE    85      -3.806   9.880 -25.742  1.00  0.00
ATOM     98  CA  ILE    85      -3.992   9.836 -24.287  1.00  0.00
ATOM     99  C   ILE    85      -5.461   9.915 -23.885  1.00  0.00
ATOM    100  O   ILE    85      -6.345   9.997 -24.739  1.00  0.00
ATOM    101  N   PRO    86      -5.714   9.889 -22.579  1.00  0.00
ATOM    102  CA  PRO    86      -7.078   9.956 -22.064  1.00  0.00
ATOM    103  C   PRO    86      -7.267  11.175 -21.166  1.00  0.00
ATOM    104  O   PRO    86      -6.309  11.687 -20.586  1.00  0.00
TER
END
