
#######################################################
#                                                     #
#                        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   30 (  150),  selected   30 , name T0297TS239_2_2
# Molecule2: number of CA atoms  211 ( 1703),  selected   30 , name T0297.pdb
# PARAMETERS: T0297TS239_2_2.T0297.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:    24         7 - 30          4.63    11.07
  LCS_AVERAGE:     10.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        12 - 28          1.94    13.60
  LCS_AVERAGE:      5.58

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        14 - 28          0.75    12.46
  LCS_AVERAGE:      4.39

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:  211
LCS_GDT     M       1     M       1      4    4   11     3    3    4    4    4    4    6    7    8   10   11   12   13   15   15   16   18   19   19   21 
LCS_GDT     A       2     A       2      4    4   11     3    3    4    4    4    4    5    7    8   10   11   11   13   15   15   16   18   19   19   22 
LCS_GDT     V       3     V       3      4    4   13     3    3    4    4    4    4    7    7    8   10   10   12   13   15   15   16   19   19   21   22 
LCS_GDT     Q       4     Q       4      4    4   13     3    3    4    4    4    4    7    7    7    9   10   12   13   15   15   16   18   19   19   21 
LCS_GDT     L       5     L       5      3    3   13     0    3    3    3    4    4    7    7    8   10   11   12   13   15   15   18   19   22   23   23 
LCS_GDT     L       6     L       6      3    3   13     0    3    3    3    4    4    7    7    8   10   11   12   13   15   17   18   20   23   23   24 
LCS_GDT     E       7     E       7      3    3   24     3    3    3    3    4    6    7    7    8   10   11   12   15   17   19   21   22   23   23   24 
LCS_GDT     N       8     N       8      3    5   24     3    3    3    3    5    6    7   12   16   18   20   20   20   22   22   22   23   23   23   24 
LCS_GDT     W       9     W       9      4    5   24     4    4    4    4    5    7   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     L      10     L      10      4    5   24     4    4    4    4   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     L      11     L      11      4    5   24     4    4    4    4    7   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     K      12     K      12      4   17   24     4    4    4    4    7    9   10   16   18   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     E      13     E      13      3   17   24     3    3    4    4    7    9   11   14   17   18   20   21   21   21   22   22   23   23   23   24 
LCS_GDT     Q      14     Q      14     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     E      15     E      15     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     K      16     K      16     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     I      17     I      17     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     Q      18     Q      18     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     T      19     T      19     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     K      20     K      20     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     Y      21     Y      21     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     R      22     R      22     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     H      23     H      23     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     L      24     L      24     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     N      25     N      25     15   17   24    12   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     H      26     H      26     15   17   24     3   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     I      27     I      27     15   17   24     6   14   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     S      28     S      28     15   17   24     3    8   15   15   16   17   18   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     V      29     V      29      3   16   24     3    3    3    4    9   10   14   19   19   19   20   21   21   22   22   22   23   23   23   24 
LCS_GDT     V      30     V      30      3    3   24     3    3    3    4    7    9   10   12   16   17   19   20   20   22   22   22   23   23   23   24 
LCS_AVERAGE  LCS_A:   6.75  (   4.39    5.58   10.27 )

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     12     14     15     15     16     17     18     19     19     19     20     21     21     22     22     22     23     23     23     24 
GDT PERCENT_CA   5.69   6.64   7.11   7.11   7.58   8.06   8.53   9.00   9.00   9.00   9.48   9.95   9.95  10.43  10.43  10.43  10.90  10.90  10.90  11.37
GDT RMS_LOCAL    0.21   0.40   0.75   0.75   1.08   1.24   1.60   2.09   2.09   2.09   2.47   2.84   2.84   3.54   3.35   3.35   3.81   3.81   3.81   4.63
GDT RMS_ALL_CA  12.93  12.77  12.46  12.46  12.11  12.04  11.90  11.61  11.61  11.61  11.94  12.32  12.32  11.43  12.32  12.32  11.83  11.83  11.83  11.07

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         26.792
LGA    A       2      A       2         27.088
LGA    V       3      V       3         26.416
LGA    Q       4      Q       4         25.415
LGA    L       5      L       5         18.226
LGA    L       6      L       6         15.492
LGA    E       7      E       7         13.613
LGA    N       8      N       8          8.594
LGA    W       9      W       9          3.361
LGA    L      10      L      10          3.935
LGA    L      11      L      11          2.896
LGA    K      12      K      12          6.246
LGA    E      13      E      13          7.235
LGA    Q      14      Q      14          0.708
LGA    E      15      E      15          1.008
LGA    K      16      K      16          1.202
LGA    I      17      I      17          1.333
LGA    Q      18      Q      18          1.127
LGA    T      19      T      19          0.466
LGA    K      20      K      20          1.582
LGA    Y      21      Y      21          2.460
LGA    R      22      R      22          2.356
LGA    H      23      H      23          2.160
LGA    L      24      L      24          3.213
LGA    N      25      N      25          3.680
LGA    H      26      H      26          2.977
LGA    I      27      I      27          3.111
LGA    S      28      S      28          2.196
LGA    V      29      V      29          3.649
LGA    V      30      V      30          9.653

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  211    4.0     19    2.09     8.294     7.732     0.869

LGA_LOCAL      RMSD =  2.086  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.448  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  8.500  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.769978 * X  +   0.112543 * Y  +   0.628067 * Z  + -23.198408
  Y_new =  -0.160170 * X  +  -0.918714 * Y  +   0.360985 * Z  +  88.709320
  Z_new =   0.617641 * X  +  -0.378548 * Y  +  -0.689363 * Z  + -18.606380 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.639420    0.502173  [ DEG:  -151.2276     28.7724 ]
  Theta =  -0.665739   -2.475853  [ DEG:   -38.1440   -141.8560 ]
  Phi   =  -0.205095    2.936498  [ DEG:   -11.7511    168.2489 ]
 
# 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: T0297TS239_2_2                                
REMARK     2: T0297.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0297TS239_2_2.T0297.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  211   4.0   19   2.09   7.732     8.50
REMARK  ---------------------------------------------------------- 
MOLECULE T0297TS239_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0297
PARENT 1wab
ATOM      1  N   MET     1      19.233 105.365  -2.681  1.00  9.99
ATOM      2  CA  MET     1      20.362 105.133  -1.736  1.00  9.99
ATOM      3  C   MET     1      19.965 105.390  -0.274  1.00  9.99
ATOM      4  O   MET     1      20.704 104.930   0.617  1.00  9.99
ATOM      5  CB  MET     1      21.548 106.005  -2.149  1.00  9.99
ATOM      6  N   ALA     2      18.851 106.118  -0.092  1.00  9.99
ATOM      7  CA  ALA     2      18.455 106.471   1.290  1.00  9.99
ATOM      8  C   ALA     2      17.108 105.847   1.615  1.00  9.99
ATOM      9  O   ALA     2      16.595 106.242   2.689  1.00  9.99
ATOM     10  CB  ALA     2      18.520 107.989   1.477  1.00  9.99
ATOM     11  N   VAL     3      16.604 104.974   0.763  1.00  9.99
ATOM     12  CA  VAL     3      15.323 104.286   1.122  1.00  9.99
ATOM     13  C   VAL     3      15.747 102.945   1.698  1.00  9.99
ATOM     14  O   VAL     3      16.170 102.081   0.937  1.00  9.99
ATOM     15  CB  VAL     3      14.516 104.124  -0.148  1.00  9.99
ATOM     16  N   GLN     4      15.524 102.734   2.985  1.00  9.99
ATOM     17  CA  GLN     4      16.049 101.493   3.606  1.00  9.99
ATOM     18  C   GLN     4      15.388 100.278   3.002  1.00  9.99
ATOM     19  O   GLN     4      14.157 100.266   2.866  1.00  9.99
ATOM     20  CB  GLN     4      15.814 101.667   5.111  1.00  9.99
ATOM     21  N   LEU     5      16.199  99.283   2.659  1.00  9.99
ATOM     22  CA  LEU     5      15.642  98.062   2.072  1.00  9.99
ATOM     23  C   LEU     5      16.627  96.945   2.319  1.00  9.99
ATOM     24  O   LEU     5      17.858  97.208   2.326  1.00  9.99
ATOM     25  CB  LEU     5      15.339  98.252   0.544  1.00  9.99
ATOM     26  N   LEU     6      16.121  95.777   2.616  1.00  9.99
ATOM     27  CA  LEU     6      16.993  94.635   2.832  1.00  9.99
ATOM     28  C   LEU     6      17.450  94.091   1.491  1.00  9.99
ATOM     29  O   LEU     6      16.853  94.416   0.450  1.00  9.99
ATOM     30  CB  LEU     6      16.142  93.624   3.608  1.00  9.99
ATOM     31  N   GLU     7      18.503  93.281   1.533  1.00  9.99
ATOM     32  CA  GLU     7      18.851  92.558   0.263  1.00  9.99
ATOM     33  C   GLU     7      17.876  91.408   0.094  1.00  9.99
ATOM     34  O   GLU     7      17.715  90.527   0.966  1.00  9.99
ATOM     35  CB  GLU     7      20.320  92.162   0.318  1.00  9.99
ATOM     36  N   ASN     8      17.322  91.359  -1.111  1.00  9.99
ATOM     37  CA  ASN     8      16.365  90.282  -1.473  1.00  9.99
ATOM     38  C   ASN     8      17.168  89.022  -1.793  1.00  9.99
ATOM     39  O   ASN     8      18.148  89.138  -2.567  1.00  9.99
ATOM     40  CB  ASN     8      15.606  90.725  -2.731  1.00  9.99
ATOM     41  N   TRP     9      16.711  87.893  -1.271  1.00  9.99
ATOM     42  CA  TRP     9      17.433  86.637  -1.503  1.00  9.99
ATOM     43  C   TRP     9      17.017  86.112  -2.898  1.00  9.99
ATOM     44  O   TRP     9      15.823  85.692  -3.003  1.00  9.99
ATOM     45  CB  TRP     9      17.175  85.622  -0.399  1.00  9.99
ATOM     46  N   LEU    10      17.929  86.205  -3.861  1.00  9.99
ATOM     47  CA  LEU    10      17.567  85.562  -5.157  1.00  9.99
ATOM     48  C   LEU    10      18.397  84.307  -5.408  1.00  9.99
ATOM     49  O   LEU    10      18.437  83.871  -6.587  1.00  9.99
ATOM     50  CB  LEU    10      17.695  86.561  -6.305  1.00  9.99
ATOM     51  N   LEU    11      19.070  83.825  -4.368  1.00  9.99
ATOM     52  CA  LEU    11      19.998  82.669  -4.545  1.00  9.99
ATOM     53  C   LEU    11      19.349  81.509  -3.803  1.00  9.99
ATOM     54  O   LEU    11      19.368  80.340  -4.304  1.00  9.99
ATOM     55  CB  LEU    11      21.416  82.982  -4.072  1.00  9.99
ATOM     56  N   LYS    12      18.911  81.710  -2.559  1.00  9.99
ATOM     57  CA  LYS    12      18.075  80.688  -1.872  1.00  9.99
ATOM     58  C   LYS    12      18.623  80.237  -0.542  1.00  9.99
ATOM     59  O   LYS    12      17.876  79.509   0.194  1.00  9.99
ATOM     60  CB  LYS    12      17.900  79.473  -2.800  1.00  9.99
ATOM     61  N   GLU    13      19.801  80.697  -0.109  1.00  9.99
ATOM     62  CA  GLU    13      20.401  80.191   1.137  1.00  9.99
ATOM     63  C   GLU    13      20.240  81.197   2.303  1.00  9.99
ATOM     64  O   GLU    13      20.730  80.834   3.415  1.00  9.99
ATOM     65  CB  GLU    13      21.861  79.796   0.880  1.00  9.99
ATOM     66  N   GLN    14      19.651  82.349   2.052  1.00  9.99
ATOM     67  CA  GLN    14      19.270  83.245   3.188  1.00  9.99
ATOM     68  C   GLN    14      20.497  83.822   3.887  1.00  9.99
ATOM     69  O   GLN    14      20.335  84.272   5.070  1.00  9.99
ATOM     70  CB  GLN    14      18.395  82.470   4.187  1.00  9.99
ATOM     71  N   GLU    15      21.664  83.959   3.248  1.00  9.99
ATOM     72  CA  GLU    15      22.859  84.312   4.009  1.00  9.99
ATOM     73  C   GLU    15      22.809  85.752   4.528  1.00  9.99
ATOM     74  O   GLU    15      23.348  85.985   5.621  1.00  9.99
ATOM     75  CB  GLU    15      24.147  84.125   3.145  1.00  9.99
ATOM     76  N   LYS    16      22.278  86.660   3.705  1.00  9.99
ATOM     77  CA  LYS    16      22.287  88.073   4.167  1.00  9.99
ATOM     78  C   LYS    16      21.444  88.240   5.420  1.00  9.99
ATOM     79  O   LYS    16      21.912  88.892   6.388  1.00  9.99
ATOM     80  CB  LYS    16      21.767  88.942   3.015  1.00  9.99
ATOM     81  N   ILE    17      20.271  87.630   5.427  1.00  9.99
ATOM     82  CA  ILE    17      19.405  87.724   6.653  1.00  9.99
ATOM     83  C   ILE    17      20.056  86.959   7.802  1.00  9.99
ATOM     84  O   ILE    17      19.928  87.443   8.941  1.00  9.99
ATOM     85  CB  ILE    17      18.012  87.267   6.308  1.00  9.99
ATOM     86  N   GLN    18      20.774  85.867   7.564  1.00  9.99
ATOM     87  CA  GLN    18      21.500  85.208   8.647  1.00  9.99
ATOM     88  C   GLN    18      22.523  86.136   9.313  1.00  9.99
ATOM     89  O   GLN    18      22.696  86.127  10.540  1.00  9.99
ATOM     90  CB  GLN    18      22.168  83.923   8.170  1.00  9.99
ATOM     91  N   THR    19      23.266  86.833   8.443  1.00  9.99
ATOM     92  CA  THR    19      24.246  87.809   8.948  1.00  9.99
ATOM     93  C   THR    19      23.566  88.903   9.779  1.00  9.99
ATOM     94  O   THR    19      24.021  89.140  10.910  1.00  9.99
ATOM     95  CB  THR    19      24.996  88.391   7.736  1.00  9.99
ATOM     96  N   LYS    20      22.537  89.500   9.234  1.00  9.99
ATOM     97  CA  LYS    20      21.771  90.526   9.973  1.00  9.99
ATOM     98  C   LYS    20      21.318  89.983  11.331  1.00  9.99
ATOM     99  O   LYS    20      21.522  90.631  12.369  1.00  9.99
ATOM    100  CB  LYS    20      20.587  91.006   9.124  1.00  9.99
ATOM    101  N   TYR    21      20.743  88.791  11.284  1.00  9.99
ATOM    102  CA  TYR    21      20.257  88.184  12.571  1.00  9.99
ATOM    103  C   TYR    21      21.379  87.903  13.544  1.00  9.99
ATOM    104  O   TYR    21      21.189  88.105  14.781  1.00  9.99
ATOM    105  CB  TYR    21      19.389  86.934  12.337  1.00  9.99
ATOM    106  N   ARG    22      22.546  87.499  13.043  1.00  9.99
ATOM    107  CA  ARG    22      23.704  87.309  13.921  1.00  9.99
ATOM    108  C   ARG    22      24.061  88.621  14.620  1.00  9.99
ATOM    109  O   ARG    22      24.360  88.675  15.807  1.00  9.99
ATOM    110  CB  ARG    22      24.935  86.728  13.231  1.00  9.99
ATOM    111  N   HIS    23      24.105  89.712  13.826  1.00  9.99
ATOM    112  CA  HIS    23      24.470  91.031  14.357  1.00  9.99
ATOM    113  C   HIS    23      23.460  91.541  15.374  1.00  9.99
ATOM    114  O   HIS    23      23.880  92.134  16.387  1.00  9.99
ATOM    115  CB  HIS    23      24.586  91.993  13.149  1.00  9.99
ATOM    116  N   LEU    24      22.188  91.308  15.085  1.00  9.99
ATOM    117  CA  LEU    24      21.101  91.667  16.012  1.00  9.99
ATOM    118  C   LEU    24      21.389  90.937  17.337  1.00  9.99
ATOM    119  O   LEU    24      21.313  91.545  18.420  1.00  9.99
ATOM    120  CB  LEU    24      19.724  91.369  15.441  1.00  9.99
ATOM    121  N   ASN    25      21.681  89.666  17.217  1.00  9.99
ATOM    122  CA  ASN    25      21.979  88.869  18.445  1.00  9.99
ATOM    123  C   ASN    25      23.202  89.396  19.158  1.00  9.99
ATOM    124  O   ASN    25      23.255  89.425  20.408  1.00  9.99
ATOM    125  CB  ASN    25      22.058  87.380  18.084  1.00  9.99
ATOM    126  N   HIS    26      24.229  89.797  18.427  1.00  9.99
ATOM    127  CA  HIS    26      25.466  90.380  18.956  1.00  9.99
ATOM    128  C   HIS    26      25.144  91.613  19.801  1.00  9.99
ATOM    129  O   HIS    26      25.640  91.766  20.942  1.00  9.99
ATOM    130  CB  HIS    26      26.443  90.750  17.856  1.00  9.99
ATOM    131  N   ILE    27      24.316  92.477  19.200  1.00  9.99
ATOM    132  CA  ILE    27      23.961  93.728  19.907  1.00  9.99
ATOM    133  C   ILE    27      23.097  93.415  21.131  1.00  9.99
ATOM    134  O   ILE    27      23.239  94.152  22.139  1.00  9.99
ATOM    135  CB  ILE    27      23.252  94.715  18.973  1.00  9.99
ATOM    136  N   SER    28      22.260  92.413  21.051  1.00  9.99
ATOM    137  CA  SER    28      21.383  92.039  22.178  1.00  9.99
ATOM    138  C   SER    28      22.260  91.583  23.347  1.00  9.99
ATOM    139  O   SER    28      22.034  91.985  24.514  1.00  9.99
ATOM    140  CB  SER    28      20.339  91.014  21.820  1.00  9.99
ATOM    141  N   VAL    29      23.311  90.840  23.042  1.00  9.99
ATOM    142  CA  VAL    29      24.086  90.108  24.056  1.00  9.99
ATOM    143  C   VAL    29      25.337  90.856  24.473  1.00  9.99
ATOM    144  O   VAL    29      25.828  90.643  25.616  1.00  9.99
ATOM    145  CB  VAL    29      24.271  88.670  23.486  1.00  9.99
ATOM    146  N   VAL    30      25.856  91.836  23.740  1.00  9.99
ATOM    147  CA  VAL    30      27.121  92.488  24.018  1.00  9.99
ATOM    148  C   VAL    30      26.990  93.962  24.358  1.00  9.99
ATOM    149  O   VAL    30      25.923  94.552  24.146  1.00  9.99
ATOM    150  CB  VAL    30      28.089  92.424  22.819  1.00  9.99
TER
END
