
#######################################################
#                                                     #
#                        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   34 (  140),  selected   34 , name T0353AL586_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   34 , name T0353.pdb
# PARAMETERS: T0353AL586_1.T0353.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:    15        22 - 54          4.97    14.44
  LCS_AVERAGE:     15.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        56 - 67          1.71    15.37
  LCS_AVERAGE:      6.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        61 - 67          0.70    14.70
  LONGEST_CONTINUOUS_SEGMENT:     5        62 - 71          0.95    15.05
  LCS_AVERAGE:      3.56

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:   85
LCS_GDT     D       7     D       7      3    5    6     1    3    3    4    5    5    5    6    6    6    7    8    9   11   13   17   18   19   19   20 
LCS_GDT     Y       9     Y       9      4    5   12     3    5    5    6    6    7    8    8   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     V      10     V      10      4    5   12     3    5    5    5    5    6    8    8   10   11   13   14   16   17   17   18   19   19   21   21 
LCS_GDT     K      11     K      11      4    5   12     3    5    5    5    5    5    5    6   10   10   12   13   14   15   17   18   18   19   21   21 
LCS_GDT     A      12     A      12      4    5   12     0    5    5    5    5    5    5    6    6    8   10   11   13   13   14   16   16   17   19   20 
LCS_GDT     V      17     V      17      0    3   12     0    1    2    4    4    5    5    6   10   10   12   12   13   13   16   18   18   18   21   21 
LCS_GDT     V      22     V      22      0    3   15     0    1    2    6    8   11   11   12   12   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     F      23     F      23      0    4   15     0    0    2    4    5    6    8    9    9   10   13   14   15   17   18   18   19   19   21   21 
LCS_GDT     A      32     A      32      3    4   15     2    4    4    6    7    8    9    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     F      35     F      35      3    4   15     1    4    4    6    6    7    8    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     A      36     A      36      3    4   15     2    4    4    6    6    7    8    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     Q      38     Q      38      3    3   15     0    3    3    3    4    7    8    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     L      40     L      40      0    3   15     2    5    5    5    5    5    8    8   10   10   12   12   13   16   17   18   19   19   21   21 
LCS_GDT     G      44     G      44      0    3   15     0    1    3    6    6    7    8    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     E      45     E      45      0    4   15     0    1    2    5    6    7    8    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     G      47     G      47      4    4   15     0    4    4    4    5    6    7    8    9   10   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     A      48     A      48      4    4   15     3    4    4    4    5    6    7    8    9   10   12   14   16   17   18   18   19   19   21   21 
LCS_GDT     T      49     T      49      4    4   15     3    4    4    4    5    6    7    8   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     V      50     V      50      4    4   15     3    4    4    4    5    5    7    7   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     S      52     S      52      3    4   15     1    3    4    6    6    7    7    9   10   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     E      54     E      54      3    3   15     1    3    3    3    5    6   10   10   11   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     R      56     R      56      4   10   14     3    4    6    7    9   11   11   12   12   12   13   14   16   17   18   18   19   19   21   21 
LCS_GDT     F      57     F      57      4   10   14     3    3    7    8    9   11   11   12   12   12   13   14   14   15   18   18   19   19   21   21 
LCS_GDT     C      58     C      58      4   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     H      59     H      59      4   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     S      60     S      60      4   10   14     3    3    4    6    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     Q      61     Q      61      5   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     K      62     K      62      5   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     A      63     A      63      5   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     P      64     P      64      5   10   14     3    4    7    8    9   11   11   12   12   12   13   14   14   15   15   15   18   18   19   20 
LCS_GDT     V      67     V      67      5   10   14     3    4    6    8    9   11   11   12   12   12   13   14   14   15   18   18   18   19   20   20 
LCS_GDT     I      71     I      71      5    7   14     0    4    5    6    7    8    9   12   12   12   13   14   14   15   15   15   16   17   19   20 
LCS_GDT     K      72     K      72      0    7   14     0    0    3    5    7    8    9    9    9   10   13   14   14   15   15   15   16   17   18   18 
LCS_GDT     C      84     C      84      0    0    0     0    0    0    0    1    2    2    5    6    8    9    9   11   12   13   14   15   15   18   18 
LCS_AVERAGE  LCS_A:   8.75  (   3.56    6.82   15.88 )

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      3      5      7      8      9     11     11     12     12     12     13     14     16     17     18     18     19     19     21     21 
GDT PERCENT_CA   3.53   5.88   8.24   9.41  10.59  12.94  12.94  14.12  14.12  14.12  15.29  16.47  18.82  20.00  21.18  21.18  22.35  22.35  24.71  24.71
GDT RMS_LOCAL    0.08   0.57   1.15   1.27   1.50   1.88   1.88   2.25   2.25   2.25   3.05   3.38   4.66   4.85   5.66   5.08   5.34   5.34   6.29   6.29
GDT RMS_ALL_CA  14.56  16.10  15.66  15.60  15.62  15.36  15.36  15.29  15.29  15.29  15.05  15.12  14.73  14.62  13.43  14.70  14.58  14.58  15.92  15.92

#      Molecule1      Molecule2       DISTANCE
LGA    D       7      D       7         15.628
LGA    Y       9      Y       9         15.470
LGA    V      10      V      10         16.213
LGA    K      11      K      11         17.853
LGA    A      12      A      12         17.218
LGA    V      17      V      17         18.223
LGA    V      22      V      22          2.274
LGA    F      23      F      23          6.555
LGA    A      32      A      32         10.873
LGA    F      35      F      35         20.026
LGA    A      36      A      36         16.378
LGA    Q      38      Q      38         21.354
LGA    L      40      L      40         21.469
LGA    G      44      G      44         32.455
LGA    E      45      E      45         29.218
LGA    G      47      G      47         27.529
LGA    A      48      A      48         21.363
LGA    T      49      T      49         19.951
LGA    V      50      V      50         14.424
LGA    S      52      S      52          9.812
LGA    E      54      E      54         10.529
LGA    R      56      R      56          2.441
LGA    F      57      F      57          2.699
LGA    C      58      C      58          3.346
LGA    H      59      H      59          3.246
LGA    S      60      S      60          2.843
LGA    Q      61      Q      61          1.530
LGA    K      62      K      62          1.305
LGA    A      63      A      63          1.365
LGA    P      64      P      64          1.218
LGA    V      67      V      67          0.961
LGA    I      71      I      71          3.768
LGA    K      72      K      72          7.631
LGA    C      84      C      84         20.575

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   85    4.0     12    2.25    12.647    11.436     0.512

LGA_LOCAL      RMSD =  2.245  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.270  Number of atoms =   34 
Std_ALL_ATOMS  RMSD = 12.684  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.918222 * X  +  -0.071464 * Y  +   0.389566 * Z  +   8.892311
  Y_new =  -0.210739 * X  +   0.920951 * Y  +  -0.327778 * Z  +   0.381685
  Z_new =  -0.335347 * X  +  -0.383069 * Y  +  -0.860698 * Z  +   2.342797 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.722847    0.418745  [ DEG:  -156.0077     23.9923 ]
  Theta =   0.341973    2.799620  [ DEG:    19.5936    160.4064 ]
  Phi   =  -2.915992    0.225601  [ DEG:  -167.0740     12.9260 ]
 
# 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: T0353AL586_1                                  
REMARK     2: T0353.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0353AL586_1.T0353.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   85   4.0   12   2.25  11.436    12.68
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL586_1
REMARK Aligment from pdb entry: 1aho
ATOM      1  N   ASP     7      13.215   1.665  -7.460  1.00  0.00              
ATOM      2  CA  ASP     7      12.411   2.663  -6.794  1.00  0.00              
ATOM      3  C   ASP     7      10.925   2.358  -6.970  1.00  0.00              
ATOM      4  O   ASP     7      10.583   1.731  -8.004  1.00  0.00              
ATOM      5  N   TYR     9       6.493   2.522  -5.307  1.00  0.00              
ATOM      6  CA  TYR     9       5.511   2.540  -4.220  1.00  0.00              
ATOM      7  C   TYR     9       5.506   1.211  -3.523  1.00  0.00              
ATOM      8  O   TYR     9       5.149   0.182  -4.126  1.00  0.00              
ATOM      9  N   VAL    10       5.843   1.188  -2.241  1.00  0.00              
ATOM     10  CA  VAL    10       5.858  -0.056  -1.465  1.00  0.00              
ATOM     11  C   VAL    10       4.425  -0.511  -1.215  1.00  0.00              
ATOM     12  O   VAL    10       3.507   0.257  -1.054  1.00  0.00              
ATOM     13  N   LYS    11       4.273  -1.849  -1.160  1.00  0.00              
ATOM     14  CA  LYS    11       2.962  -2.452  -0.896  1.00  0.00              
ATOM     15  C   LYS    11       3.070  -3.599   0.083  1.00  0.00              
ATOM     16  O   LYS    11       4.163  -4.129   0.330  1.00  0.00              
ATOM     17  N   ALA    12       1.948  -3.980   0.684  1.00  0.00              
ATOM     18  CA  ALA    12       1.814  -5.164   1.539  1.00  0.00              
ATOM     19  C   ALA    12       1.751  -6.376   0.581  1.00  0.00              
ATOM     20  O   ALA    12       1.945  -6.320  -0.631  1.00  0.00              
ATOM     21  N   VAL    17      -0.740  -8.008  -0.419  1.00  0.00              
ATOM     22  CA  VAL    17      -1.899  -8.098  -1.296  1.00  0.00              
ATOM     23  C   VAL    17      -2.015  -6.858  -2.210  1.00  0.00              
ATOM     24  O   VAL    17      -3.031  -6.501  -2.660  1.00  0.00              
ATOM     25  N   VAL    22      -0.962  -0.142  -1.094  1.00  0.00              
ATOM     26  CA  VAL    22       0.026   0.899  -0.746  1.00  0.00              
ATOM     27  C   VAL    22      -0.104   1.357   0.690  1.00  0.00              
ATOM     28  O   VAL    22      -1.102   1.130   1.383  1.00  0.00              
ATOM     29  N   PHE    23       0.953   2.036   1.168  1.00  0.00              
ATOM     30  CA  PHE    23       1.059   2.558   2.522  1.00  0.00              
ATOM     31  C   PHE    23       0.526   3.993   2.584  1.00  0.00              
ATOM     32  O   PHE    23       1.153   4.918   2.029  1.00  0.00              
ATOM     33  N   ALA    32      -0.102   7.637   4.028  1.00  0.00              
ATOM     34  CA  ALA    32       0.791   8.504   4.763  1.00  0.00              
ATOM     35  C   ALA    32       0.274   9.943   4.738  1.00  0.00              
ATOM     36  O   ALA    32      -0.496  10.323   3.896  1.00  0.00              
ATOM     37  N   PHE    35       7.584   9.769   8.099  1.00  0.00              
ATOM     38  CA  PHE    35       6.978   8.450   8.309  1.00  0.00              
ATOM     39  C   PHE    35       7.373   7.537   7.179  1.00  0.00              
ATOM     40  O   PHE    35       7.799   6.376   7.390  1.00  0.00              
ATOM     41  N   ALA    36       7.258   7.984   5.918  1.00  0.00              
ATOM     42  CA  ALA    36       7.636   7.135   4.808  1.00  0.00              
ATOM     43  C   ALA    36       9.126   6.866   4.773  1.00  0.00              
ATOM     44  O   ALA    36       9.541   5.769   4.412  1.00  0.00              
ATOM     45  N   GLN    38       9.520   3.948   7.039  1.00  0.00              
ATOM     46  CA  GLN    38       8.999   2.709   6.511  1.00  0.00              
ATOM     47  C   GLN    38       9.884   2.194   5.391  1.00  0.00              
ATOM     48  O   GLN    38      10.098   0.967   5.227  1.00  0.00              
ATOM     49  N   LEU    40      12.552  -1.492   5.264  1.00  0.00              
ATOM     50  CA  LEU    40      12.634  -2.422   4.151  1.00  0.00              
ATOM     51  C   LEU    40      13.978  -2.400   3.451  1.00  0.00              
ATOM     52  O   LEU    40      14.150  -3.074   2.409  1.00  0.00              
ATOM     53  N   GLY    44      16.905   3.135   0.617  1.00  0.00              
ATOM     54  CA  GLY    44      17.737   4.285   0.939  1.00  0.00              
ATOM     55  C   GLY    44      16.993   5.352   1.712  1.00  0.00              
ATOM     56  O   GLY    44      17.443   5.876   2.729  1.00  0.00              
ATOM     57  N   GLU    45      15.794   5.729   1.213  1.00  0.00              
ATOM     58  CA  GLU    45      15.035   6.864   1.712  1.00  0.00              
ATOM     59  C   GLU    45      13.675   6.831   1.052  1.00  0.00              
ATOM     60  O   GLU    45      13.418   5.979   0.181  1.00  0.00              
ATOM     61  N   GLY    47       9.525   9.185   0.750  1.00  0.00              
ATOM     62  CA  GLY    47       8.711  10.335   1.109  1.00  0.00              
ATOM     63  C   GLY    47       7.254   9.981   0.875  1.00  0.00              
ATOM     64  O   GLY    47       6.936   8.925   0.311  1.00  0.00              
ATOM     65  N   ALA    48       6.356  10.831   1.352  1.00  0.00              
ATOM     66  CA  ALA    48       4.916  10.645   1.189  1.00  0.00              
ATOM     67  C   ALA    48       4.465  11.370  -0.062  1.00  0.00              
ATOM     68  O   ALA    48       4.491  12.606  -0.120  1.00  0.00              
ATOM     69  N   THR    49       4.073  10.600  -1.091  1.00  0.00              
ATOM     70  CA  THR    49       3.544  11.194  -2.301  1.00  0.00              
ATOM     71  C   THR    49       2.056  11.487  -2.053  1.00  0.00              
ATOM     72  O   THR    49       1.223  10.575  -2.037  1.00  0.00              
ATOM     73  N   VAL    50       1.723  12.766  -1.867  1.00  0.00              
ATOM     74  CA  VAL    50       0.334  13.135  -1.735  1.00  0.00              
ATOM     75  C   VAL    50      -0.279  13.039  -3.127  1.00  0.00              
ATOM     76  O   VAL    50       0.289  13.353  -4.150  1.00  0.00              
ATOM     77  N   SER    52      -1.091  10.609  -5.197  1.00  0.00              
ATOM     78  CA  SER    52      -0.691   9.630  -6.191  1.00  0.00              
ATOM     79  C   SER    52      -2.011   9.047  -6.738  1.00  0.00              
ATOM     80  O   SER    52      -3.085   9.285  -6.202  1.00  0.00              
ATOM     81  N   GLU    54      -3.124   6.352  -6.178  1.00  0.00              
ATOM     82  CA  GLU    54      -3.595   5.474  -5.112  1.00  0.00              
ATOM     83  C   GLU    54      -3.914   6.255  -3.872  1.00  0.00              
ATOM     84  O   GLU    54      -4.091   5.685  -2.782  1.00  0.00              
ATOM     85  N   ARG    56      -2.747   9.210  -1.036  1.00  0.00              
ATOM     86  CA  ARG    56      -1.427   9.447  -0.440  1.00  0.00              
ATOM     87  C   ARG    56      -0.739   8.093  -0.253  1.00  0.00              
ATOM     88  O   ARG    56      -1.339   7.162   0.307  1.00  0.00              
ATOM     89  N   PHE    57       0.507   7.992  -0.697  1.00  0.00              
ATOM     90  CA  PHE    57       1.216   6.708  -0.615  1.00  0.00              
ATOM     91  C   PHE    57       2.695   6.933  -0.480  1.00  0.00              
ATOM     92  O   PHE    57       3.274   7.844  -1.132  1.00  0.00              
ATOM     93  N   CYS    58       3.372   6.098   0.303  1.00  0.00              
ATOM     94  CA  CYS    58       4.812   6.191   0.427  1.00  0.00              
ATOM     95  C   CYS    58       5.523   5.683  -0.870  1.00  0.00              
ATOM     96  O   CYS    58       5.187   4.648  -1.447  1.00  0.00              
ATOM     97  N   HIS    59       6.533   6.459  -1.264  1.00  0.00              
ATOM     98  CA  HIS    59       7.390   6.151  -2.419  1.00  0.00              
ATOM     99  C   HIS    59       8.816   6.030  -1.876  1.00  0.00              
ATOM    100  O   HIS    59       9.259   6.902  -1.118  1.00  0.00              
ATOM    101  N   SER    60       9.516   4.966  -2.251  1.00  0.00              
ATOM    102  CA  SER    60      10.848   4.699  -1.753  1.00  0.00              
ATOM    103  C   SER    60      11.869   4.654  -2.879  1.00  0.00              
ATOM    104  O   SER    60      11.594   4.237  -4.015  1.00  0.00              
ATOM    105  N   GLN    61      13.108   5.030  -2.553  1.00  0.00              
ATOM    106  CA  GLN    61      14.249   4.948  -3.456  1.00  0.00              
ATOM    107  C   GLN    61      15.183   3.801  -3.045  1.00  0.00              
ATOM    108  O   GLN    61      15.444   3.624  -1.860  1.00  0.00              
ATOM    109  N   LYS    62      15.684   3.125  -4.039  1.00  0.00              
ATOM    110  CA  LYS    62      16.737   2.118  -3.854  1.00  0.00              
ATOM    111  C   LYS    62      16.377   1.003  -2.889  1.00  0.00              
ATOM    112  O   LYS    62      17.171   0.576  -2.057  1.00  0.00              
ATOM    113  N   ALA    63      15.179   0.454  -3.081  1.00  0.00              
ATOM    114  CA  ALA    63      14.809  -0.761  -2.399  1.00  0.00              
ATOM    115  C   ALA    63      15.547  -1.955  -2.978  1.00  0.00              
ATOM    116  O   ALA    63      15.862  -2.010  -4.149  1.00  0.00              
ATOM    117  N   PRO    64      15.780  -2.989  -2.161  1.00  0.00              
ATOM    118  CA  PRO    64      16.296  -4.232  -2.721  1.00  0.00              
ATOM    119  C   PRO    64      15.300  -4.785  -3.765  1.00  0.00              
ATOM    120  O   PRO    64      14.080  -4.642  -3.684  1.00  0.00              
ATOM    121  N   VAL    67      11.952  -6.735  -2.808  1.00  0.00              
ATOM    122  CA  VAL    67      10.775  -6.087  -2.201  1.00  0.00              
ATOM    123  C   VAL    67       9.689  -5.888  -3.223  1.00  0.00              
ATOM    124  O   VAL    67       9.989  -5.439  -4.347  1.00  0.00              
ATOM    125  N   ILE    71       6.811  -3.966  -5.058  1.00  0.00              
ATOM    126  CA  ILE    71       6.272  -2.631  -5.279  1.00  0.00              
ATOM    127  C   ILE    71       4.953  -2.781  -6.067  1.00  0.00              
ATOM    128  O   ILE    71       4.634  -3.842  -6.602  1.00  0.00              
ATOM    129  N   LYS    72       4.212  -1.682  -6.146  1.00  0.00              
ATOM    130  CA  LYS    72       2.885  -1.736  -6.718  1.00  0.00              
ATOM    131  C   LYS    72       2.837  -2.243  -8.131  1.00  0.00              
ATOM    132  O   LYS    72       3.590  -1.835  -9.022  1.00  0.00              
ATOM    133  N  ACYS    84      -6.317  -1.847  -4.921  1.00  0.00              
ATOM    134  N  BCYS    84      -6.209  -1.877  -4.977  1.00  0.00              
ATOM    135  CA ACYS    84      -6.366  -2.253  -3.504  1.00  0.00              
ATOM    136  CA BCYS    84      -6.393  -1.958  -3.548  1.00  0.00              
ATOM    137  C  ACYS    84      -6.389  -0.915  -2.805  1.00  0.00              
ATOM    138  C  BCYS    84      -6.551  -0.547  -2.979  1.00  0.00              
ATOM    139  O  ACYS    84      -5.477  -0.085  -3.055  1.00  0.00              
ATOM    140  O  BCYS    84      -5.812   0.410  -3.232  1.00  0.00              
END
