
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0312AL381_2-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected   28 , name T0312_D1.pdb
# PARAMETERS: T0312AL381_2-D1.T0312_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:    21        41 - 61          4.71     8.42
  LONGEST_CONTINUOUS_SEGMENT:    21        42 - 62          4.82     8.36
  LCS_AVERAGE:     14.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        46 - 55          1.58     9.62
  LCS_AVERAGE:      5.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        46 - 52          0.72    10.23
  LONGEST_CONTINUOUS_SEGMENT:     7        47 - 53          0.95    11.04
  LCS_AVERAGE:      3.95

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:  132
LCS_GDT     I      40     I      40      5    6    9     3    4    5    5    6    6    6    7    7    8    8   15   16   17   19   21   23   24   27   28 
LCS_GDT     S      41     S      41      5    6   21     3    4    5    5    6    6    6    7    7    9   10   15   16   21   22   22   23   24   27   28 
LCS_GDT     A      42     A      42      5    6   21     3    4    5    5    6    6    6    7   11   13   16   18   20   21   22   22   23   24   27   28 
LCS_GDT     I      43     I      43      5    6   21     3    4    5    5    6    6   11   11   12   13   16   18   20   21   22   22   23   24   27   28 
LCS_GDT     G      44     G      44      5    6   21     3    4    5    7    7    9   11   11   13   16   16   18   20   21   22   22   23   24   27   28 
LCS_GDT     A      45     A      45      4    8   21     3    4    5    7    8    9   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     V      46     V      46      7   10   21     5    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     R      47     R      47      7   10   21     3    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   25   28 
LCS_GDT     S      48     S      48      7   10   21     5    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     A      49     A      49      7   10   21     5    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     V      50     V      50      7   10   21     5    7    7    8    9   10   11   12   13   15   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     I      51     I      51      7   10   21     5    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     G      52     G      52      7   10   21     4    7    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     Y      53     Y      53      7   10   21     4    5    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     Y      54     Y      54      5   10   21     4    5    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     D      55     D      55      5   10   21     4    5    7    8    9   10   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     Q      56     Q      56      5    9   21     3    5    5    7    8    8   11   12   13   15   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     E      57     E      57      4    7   21     3    4    5    7    8    9   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     K      58     K      58      4    5   21     3    4    4    6    7    9   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     K      59     K      59      4    5   21     3    4    4    6    7    9   11   12   13   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     E      60     E      60      3    5   21     0    3    3    4    4    6    9    9   12   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     Y      61     Y      61      3    5   21     3    3    3    4    4    6    9    9   12   16   17   18   20   21   22   23   23   24   27   28 
LCS_GDT     V      62     V      62      3    6   21     3    3    3    5    5    6    6    8    8   10   12   15   17   19   22   23   23   24   27   28 
LCS_GDT     K      63     K      63      5    6   13     4    5    5    5    5    6    6    8    8    9   11   15   16   17   20   23   23   24   27   28 
LCS_GDT     K      64     K      64      5    6   13     4    5    5    5    5    6    6    8    8    8   11   15   16   17   20   23   23   24   27   28 
LCS_GDT     E      65     E      65      5    6   13     4    5    5    5    5    6    6    8    8    8   10   13   15   17   20   23   23   24   27   28 
LCS_GDT     L      66     L      66      5    6   12     4    5    5    5    5    6    6    7    8    8   10   11   15   16   20   23   23   24   27   28 
LCS_GDT     M      67     M      67      5    6   11     3    5    5    5    5    6    6    6    8    8   10   10   10   15   20   23   23   24   27   28 
LCS_AVERAGE  LCS_A:   8.02  (   3.95    5.68   14.42 )

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      7      7      8      9     10     11     12     13     16     17     18     20     21     22     23     23     24     27     28 
GDT PERCENT_CA   3.79   5.30   5.30   6.06   6.82   7.58   8.33   9.09   9.85  12.12  12.88  13.64  15.15  15.91  16.67  17.42  17.42  18.18  20.45  21.21
GDT RMS_LOCAL    0.29   0.72   0.72   1.03   1.30   1.58   2.11   2.33   2.80   3.74   3.77   4.01   4.45   4.71   5.03   6.21   6.06   6.33   6.91   7.11
GDT RMS_ALL_CA   9.59  10.23  10.23   9.47   9.51   9.62   9.34   9.39   8.73   8.69   8.42   8.80   8.55   8.42   8.22   8.25   7.88   7.61   7.17   7.11

#      Molecule1      Molecule2       DISTANCE
LGA    I      40      I      40         12.751
LGA    S      41      S      41         15.296
LGA    A      42      A      42         13.282
LGA    I      43      I      43         16.207
LGA    G      44      G      44         14.049
LGA    A      45      A      45          7.151
LGA    V      46      V      46          0.534
LGA    R      47      R      47          3.398
LGA    S      48      S      48          1.197
LGA    A      49      A      49          0.389
LGA    V      50      V      50          0.223
LGA    I      51      I      51          1.559
LGA    G      52      G      52          3.855
LGA    Y      53      Y      53          2.662
LGA    Y      54      Y      54          1.592
LGA    D      55      D      55          1.104
LGA    Q      56      Q      56          3.444
LGA    E      57      E      57          3.457
LGA    K      58      K      58          8.066
LGA    K      59      K      59          9.837
LGA    E      60      E      60         10.971
LGA    Y      61      Y      61          9.024
LGA    V      62      V      62          9.838
LGA    K      63      K      63         13.026
LGA    K      64      K      64         13.068
LGA    E      65      E      65         13.432
LGA    L      66      L      66         13.210
LGA    M      67      M      67         12.817

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28  132    4.0     12    2.33     9.470     8.554     0.493

LGA_LOCAL      RMSD =  2.335  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.392  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  7.111  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.322796 * X  +   0.588619 * Y  +  -0.741168 * Z  +  -3.285229
  Y_new =   0.216002 * X  +  -0.808237 * Y  +  -0.547810 * Z  +  62.945133
  Z_new =  -0.921491 * X  +   0.016737 * Y  +  -0.388039 * Z  +  52.797916 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.098487   -0.043105  [ DEG:   177.5302     -2.4698 ]
  Theta =   1.171902    1.969690  [ DEG:    67.1451    112.8549 ]
  Phi   =   0.589727   -2.551866  [ DEG:    33.7889   -146.2111 ]
 
# 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: T0312AL381_2-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_2-D1.T0312_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28  132   4.0   12   2.33   8.554     7.11
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_2-D1
REMARK Aligment from pdb entry: 1yh6A
ATOM      1  N   ILE    40      55.171   2.305  14.070  1.00  0.00              
ATOM      2  CA  ILE    40      54.382   2.783  12.938  1.00  0.00              
ATOM      3  C   ILE    40      55.199   3.239  11.710  1.00  0.00              
ATOM      4  O   ILE    40      56.114   4.059  11.841  1.00  0.00              
ATOM      5  N   SER    41      54.817   2.742  10.526  1.00  0.00              
ATOM      6  CA  SER    41      55.321   3.194   9.220  1.00  0.00              
ATOM      7  C   SER    41      54.209   3.914   8.445  1.00  0.00              
ATOM      8  O   SER    41      53.111   3.373   8.251  1.00  0.00              
ATOM      9  N   ALA    42      54.505   5.144   8.012  1.00  0.00              
ATOM     10  CA  ALA    42      53.511   6.003   7.388  1.00  0.00              
ATOM     11  C   ALA    42      53.653   5.772   5.922  1.00  0.00              
ATOM     12  O   ALA    42      54.780   5.729   5.444  1.00  0.00              
ATOM     13  N   ILE    43      52.537   5.582   5.208  1.00  0.00              
ATOM     14  CA  ILE    43      52.590   5.337   3.755  1.00  0.00              
ATOM     15  C   ILE    43      52.421   6.632   2.940  1.00  0.00              
ATOM     16  O   ILE    43      53.308   7.484   2.968  1.00  0.00              
ATOM     17  N   GLY    44      51.299   6.805   2.250  1.00  0.00              
ATOM     18  CA  GLY    44      51.009   8.067   1.536  1.00  0.00              
ATOM     19  C   GLY    44      50.854   9.319   2.400  1.00  0.00              
ATOM     20  O   GLY    44      51.105  10.438   1.945  1.00  0.00              
ATOM     21  N   ALA    45      50.466   9.141   3.649  1.00  0.00              
ATOM     22  CA  ALA    45      50.206  10.254   4.543  1.00  0.00              
ATOM     23  C   ALA    45      49.611   9.649   5.800  1.00  0.00              
ATOM     24  O   ALA    45      49.595   8.438   5.945  1.00  0.00              
ATOM     25  N   VAL    46      49.084  10.477   6.684  1.00  0.00              
ATOM     26  CA  VAL    46      48.579   9.962   7.975  1.00  0.00              
ATOM     27  C   VAL    46      47.288   9.132   7.890  1.00  0.00              
ATOM     28  O   VAL    46      46.932   8.458   8.842  1.00  0.00              
ATOM     29  N   ARG    47      46.616   9.148   6.748  1.00  0.00              
ATOM     30  CA  ARG    47      45.483   8.239   6.530  1.00  0.00              
ATOM     31  C   ARG    47      45.866   6.824   6.096  1.00  0.00              
ATOM     32  O   ARG    47      44.992   6.036   5.816  1.00  0.00              
ATOM     33  N   SER    48      47.160   6.494   6.032  1.00  0.00              
ATOM     34  CA  SER    48      47.572   5.111   5.731  1.00  0.00              
ATOM     35  C   SER    48      48.868   4.826   6.407  1.00  0.00              
ATOM     36  O   SER    48      49.858   5.489   6.154  1.00  0.00              
ATOM     37  N   ALA    49      48.873   3.836   7.270  1.00  0.00              
ATOM     38  CA  ALA    49      50.084   3.491   7.989  1.00  0.00              
ATOM     39  C   ALA    49      50.066   1.996   8.247  1.00  0.00              
ATOM     40  O   ALA    49      49.022   1.357   8.118  1.00  0.00              
ATOM     41  N   VAL    50      51.213   1.456   8.632  1.00  0.00              
ATOM     42  CA  VAL    50      51.361   0.054   8.897  1.00  0.00              
ATOM     43  C   VAL    50      52.012  -0.031  10.257  1.00  0.00              
ATOM     44  O   VAL    50      52.912   0.754  10.571  1.00  0.00              
ATOM     45  N   ILE    51      51.552  -0.986  11.057  1.00  0.00              
ATOM     46  CA  ILE    51      52.042  -1.205  12.393  1.00  0.00              
ATOM     47  C   ILE    51      52.530  -2.653  12.508  1.00  0.00              
ATOM     48  O   ILE    51      51.846  -3.585  12.087  1.00  0.00              
ATOM     49  N   GLY    52      53.702  -2.836  13.110  1.00  0.00              
ATOM     50  CA  GLY    52      54.165  -4.165  13.482  1.00  0.00              
ATOM     51  C   GLY    52      53.350  -4.672  14.660  1.00  0.00              
ATOM     52  O   GLY    52      53.239  -4.017  15.676  1.00  0.00              
ATOM     53  N   TYR    53      52.771  -5.847  14.504  1.00  0.00              
ATOM     54  CA  TYR    53      51.875  -6.414  15.491  1.00  0.00              
ATOM     55  C   TYR    53      52.338  -7.833  15.806  1.00  0.00              
ATOM     56  O   TYR    53      52.624  -8.643  14.899  1.00  0.00              
ATOM     57  N   TYR    54      52.380  -8.124  17.095  1.00  0.00              
ATOM     58  CA  TYR    54      52.865  -9.386  17.624  1.00  0.00              
ATOM     59  C   TYR    54      51.707 -10.238  18.117  1.00  0.00              
ATOM     60  O   TYR    54      50.835  -9.741  18.843  1.00  0.00              
ATOM     61  N   ASP    55      51.697 -11.521  17.742  1.00  0.00              
ATOM     62  CA  ASP    55      50.598 -12.422  18.141  1.00  0.00              
ATOM     63  C   ASP    55      50.438 -12.471  19.656  1.00  0.00              
ATOM     64  O   ASP    55      51.432 -12.482  20.361  1.00  0.00              
ATOM     65  N   GLN    56      49.195 -12.416  20.167  1.00  0.00              
ATOM     66  CA  GLN    56      49.003 -12.402  21.629  1.00  0.00              
ATOM     67  C   GLN    56      49.423 -13.705  22.327  1.00  0.00              
ATOM     68  O   GLN    56      49.196 -14.813  21.810  1.00  0.00              
ATOM     69  N   GLU    57      50.049 -13.544  23.491  1.00  0.00              
ATOM     70  CA  GLU    57      50.583 -14.653  24.267  1.00  0.00              
ATOM     71  C   GLU    57      49.450 -15.537  24.687  1.00  0.00              
ATOM     72  O   GLU    57      48.359 -15.045  24.963  1.00  0.00              
ATOM     73  N   LYS    58      49.699 -16.844  24.661  1.00  0.00              
ATOM     74  CA  LYS    58      48.727 -17.831  25.100  1.00  0.00              
ATOM     75  C   LYS    58      47.630 -18.068  24.086  1.00  0.00              
ATOM     76  O   LYS    58      46.538 -18.501  24.451  1.00  0.00              
ATOM     77  N   LYS    59      47.906 -17.738  22.823  1.00  0.00              
ATOM     78  CA  LYS    59      47.013 -18.016  21.718  1.00  0.00              
ATOM     79  C   LYS    59      47.867 -18.766  20.703  1.00  0.00              
ATOM     80  O   LYS    59      49.099 -18.716  20.779  1.00  0.00              
ATOM     81  N   GLU    60      47.232 -19.456  19.740  1.00  0.00              
ATOM     82  CA  GLU    60      48.026 -20.086  18.689  1.00  0.00              
ATOM     83  C   GLU    60      48.853 -19.101  17.839  1.00  0.00              
ATOM     84  O   GLU    60      49.836 -19.509  17.230  1.00  0.00              
ATOM     85  N   TYR    61      48.465 -17.815  17.832  1.00  0.00              
ATOM     86  CA  TYR    61      49.229 -16.710  17.186  1.00  0.00              
ATOM     87  C   TYR    61      50.521 -16.265  17.902  1.00  0.00              
ATOM     88  O   TYR    61      51.315 -15.494  17.364  1.00  0.00              
ATOM     89  N   VAL    62      50.723 -16.733  19.122  1.00  0.00              
ATOM     90  CA  VAL    62      51.900 -16.341  19.865  1.00  0.00              
ATOM     91  C   VAL    62      53.144 -16.688  19.049  1.00  0.00              
ATOM     92  O   VAL    62      53.215 -17.751  18.430  1.00  0.00              
ATOM     93  N   LYS    63      54.094 -15.760  18.988  1.00  0.00              
ATOM     94  CA  LYS    63      55.284 -15.973  18.191  1.00  0.00              
ATOM     95  C   LYS    63      55.170 -15.360  16.807  1.00  0.00              
ATOM     96  O   LYS    63      56.178 -15.148  16.147  1.00  0.00              
ATOM     97  N   LYS    64      53.952 -15.077  16.337  1.00  0.00              
ATOM     98  CA  LYS    64      53.808 -14.503  15.006  1.00  0.00              
ATOM     99  C   LYS    64      54.092 -13.008  14.999  1.00  0.00              
ATOM    100  O   LYS    64      53.902 -12.310  16.010  1.00  0.00              
ATOM    101  N   GLU    65      54.541 -12.513  13.847  1.00  0.00              
ATOM    102  CA  GLU    65      54.743 -11.070  13.637  1.00  0.00              
ATOM    103  C   GLU    65      54.068 -10.693  12.323  1.00  0.00              
ATOM    104  O   GLU    65      54.177 -11.404  11.320  1.00  0.00              
ATOM    105  N   LEU    66      53.300  -9.611  12.357  1.00  0.00              
ATOM    106  CA  LEU    66      52.526  -9.198  11.189  1.00  0.00              
ATOM    107  C   LEU    66      52.710  -7.724  10.941  1.00  0.00              
ATOM    108  O   LEU    66      52.969  -6.941  11.878  1.00  0.00              
ATOM    109  N   MET    67      52.551  -7.363   9.672  1.00  0.00              
ATOM    110  CA  MET    67      52.462  -5.991   9.264  1.00  0.00              
ATOM    111  C   MET    67      50.989  -5.718   8.994  1.00  0.00              
ATOM    112  O   MET    67      50.364  -6.324   8.134  1.00  0.00              
END
