
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0312AL381_3
# Molecule2: number of CA atoms  140 ( 1114),  selected   35 , name T0312.pdb
# PARAMETERS: T0312AL381_3.T0312.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        69 - 92          4.96     9.57
  LONGEST_CONTINUOUS_SEGMENT:    24        71 - 94          4.86    10.45
  LONGEST_CONTINUOUS_SEGMENT:    24        72 - 95          4.94    11.55
  LCS_AVERAGE:     15.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        84 - 95          1.85    12.15
  LCS_AVERAGE:      7.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        86 - 93          0.98    12.16
  LCS_AVERAGE:      3.78

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:  140
LCS_GDT     V      62     V      62      5    9   13     3    5    6    7    9    9    9   10   11   11   13   13   14   14   15   15   16   16   17   19 
LCS_GDT     K      63     K      63      6    9   13     3    5    6    7    9    9    9   10   11   11   13   13   14   14   15   15   16   26   27   27 
LCS_GDT     K      64     K      64      6    9   13     4    5    6    7    9    9    9   10   11   11   13   13   14   14   15   15   16   24   27   27 
LCS_GDT     E      65     E      65      6    9   13     4    5    5    7    9    9    9   10   11   11   13   13   14   14   15   19   25   27   29   30 
LCS_GDT     L      66     L      66      6    9   13     4    5    6    7    9    9    9   10   11   11   13   13   15   21   24   26   27   29   29   30 
LCS_GDT     M      67     M      67      6    9   18     3    5    6    7    9    9    9   10   11   11   13   13   14   14   15   26   26   29   29   30 
LCS_GDT     E      68     E      68      6    9   23     4    5    6    7    9    9    9   10   11   11   14   17   25   25   26   26   27   29   29   30 
LCS_GDT     P      69     P      69      4    9   24     3    4    4    7    9    9    9   10   12   14   18   21   25   25   26   26   27   29   29   30 
LCS_GDT     L      70     L      70      4    9   24     4    4    4    5    9    9    9   11   12   14   17   21   25   25   26   26   27   29   29   30 
LCS_GDT     E      71     E      71      4   10   24     4    4    4    5    8   10   10   12   15   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     I      72     I      72      4   10   24     4    5    6    7    9   10   11   12   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     L      73     L      73      4   10   24     4    4    4    6    9   10   10   12   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     S      74     S      74      4   10   24     3    4    6    7    9   10   10   13   15   17   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     L      75     L      75      4   10   24     3    4    6    7    9   10   10   13   15   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     S      76     S      76      4   10   24     3    4    6    7    9   10   10   11   12   15   18   21   23   24   26   26   27   29   29   30 
LCS_GDT     G      77     G      77      4   10   24     3    4    5    7    9   10   10   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     N      78     N      78      4   10   24     4    4    6    7    9   10   10   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     V      79     V      79      4   10   24     4    4    6    7    9   10   11   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     S      80     S      80      4   10   24     4    4    6    7    9   10   10   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     M      81     M      81      4    4   24     3    3    4    4    4    6    8   11   14   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     K      82     K      82      4    5   24     3    3    4    4    5    8    8    9   12   17   18   20   25   25   26   26   27   29   29   30 
LCS_GDT     D      83     D      83      4    5   24     3    3    4    4    5    5    8   12   12   14   16   21   25   25   26   26   27   29   29   30 
LCS_GDT     S      84     S      84      4   12   24     0    3    5    5    9   11   12   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     K      85     K      85      7   12   24     4    5    9    9   10   11   12   12   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     P      86     P      86      8   12   24     5    5    9    9   10   11   12   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     F      87     F      87      8   12   24     5    5    9    9   10   11   12   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     C      88     C      88      8   12   24     4    5    9    9   10   11   12   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     H      89     H      89      8   12   24     5    5    9    9   10   11   12   12   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     I      90     I      90      8   12   24     5    5    9    9   10   11   12   13   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     H      91     H      91      8   12   24     5    5    9    9   10   11   12   12   16   19   19   21   25   25   26   26   27   29   29   30 
LCS_GDT     V      92     V      92      8   12   24     3    4    7    9   10   11   12   13   16   19   19   20   25   25   26   26   27   29   29   30 
LCS_GDT     L      93     L      93      8   12   24     3    3    9    9   10   11   12   13   16   19   19   20   25   25   26   26   27   29   29   30 
LCS_GDT     L      94     L      94      3   12   24     3    3    6    7   10   11   12   12   13   17   18   19   21   22   26   26   27   29   29   30 
LCS_GDT     G      95     G      95      3   12   24     0    3    9    9   10   11   12   12   12   17   18   19   20   22   23   24   25   26   28   30 
LCS_GDT     K      96     K      96      3    4   18     0    2    3    3    4    4    5    7    9    9   13   13   18   20   23   23   25   26   28   30 
LCS_AVERAGE  LCS_A:   8.84  (   3.78    7.00   15.76 )

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      9      9     10     11     12     13     16     19     19     21     25     25     26     26     27     29     29     30 
GDT PERCENT_CA   3.57   3.57   6.43   6.43   7.14   7.86   8.57   9.29  11.43  13.57  13.57  15.00  17.86  17.86  18.57  18.57  19.29  20.71  20.71  21.43
GDT RMS_LOCAL    0.30   0.30   1.04   1.04   1.25   1.54   1.85   3.23   3.58   3.94   3.94   4.60   5.05   5.05   5.17   5.17   5.40   5.87   5.87   6.30
GDT RMS_ALL_CA  11.39  11.39  12.47  12.47  12.41  12.13  12.15  12.25  10.57  10.21  10.21   9.66   9.31   9.31   9.38   9.38   9.32   9.04   9.04   8.86

#      Molecule1      Molecule2       DISTANCE
LGA    V      62      V      62         24.397
LGA    K      63      K      63         24.099
LGA    K      64      K      64         23.273
LGA    E      65      E      65         23.878
LGA    L      66      L      66         21.057
LGA    M      67      M      67         19.213
LGA    E      68      E      68         18.878
LGA    P      69      P      69         19.494
LGA    L      70      L      70         18.380
LGA    E      71      E      71         12.166
LGA    I      72      I      72          9.866
LGA    L      73      L      73          5.821
LGA    S      74      S      74          3.808
LGA    L      75      L      75          3.542
LGA    S      76      S      76          5.881
LGA    G      77      G      77          2.397
LGA    N      78      N      78          3.185
LGA    V      79      V      79          3.452
LGA    S      80      S      80          2.523
LGA    M      81      M      81          7.099
LGA    K      82      K      82          5.565
LGA    D      83      D      83          6.482
LGA    S      84      S      84          3.726
LGA    K      85      K      85          4.429
LGA    P      86      P      86          3.912
LGA    F      87      F      87          3.423
LGA    C      88      C      88          3.096
LGA    H      89      H      89          6.053
LGA    I      90      I      90          3.181
LGA    H      91      H      91          4.177
LGA    V      92      V      92          3.749
LGA    L      93      L      93          3.243
LGA    L      94      L      94          7.697
LGA    G      95      G      95         11.821
LGA    K      96      K      96         15.482

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35  140    4.0     13    3.23     9.464     9.378     0.391

LGA_LOCAL      RMSD =  3.226  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.271  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  8.478  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.915891 * X  +   0.391682 * Y  +  -0.087912 * Z  +  65.136086
  Y_new =   0.401267 * X  +   0.899469 * Y  +  -0.173031 * Z  +  -2.114491
  Z_new =   0.011301 * X  +  -0.193754 * Y  +  -0.980985 * Z  +  27.890316 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.946593    0.194999  [ DEG:  -168.8274     11.1726 ]
  Theta =  -0.011301   -3.130291  [ DEG:    -0.6475   -179.3525 ]
  Phi   =   2.728665   -0.412928  [ DEG:   156.3410    -23.6590 ]
 
# 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_3                                  
REMARK     2: T0312.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_3.T0312.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35  140   4.0   13   3.23   9.378     8.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_3
REMARK Aligment from pdb entry: 1fxtA
ATOM      1  N   VAL    62      64.179   6.324  27.828  1.00  0.00              
ATOM      2  CA  VAL    62      63.078   6.533  26.835  1.00  0.00              
ATOM      3  C   VAL    62      62.914   8.057  26.502  1.00  0.00              
ATOM      4  O   VAL    62      62.876   8.898  27.406  1.00  0.00              
ATOM      5  N   LYS    63      62.708   8.412  25.224  1.00  0.00              
ATOM      6  CA  LYS    63      61.987   9.674  24.852  1.00  0.00              
ATOM      7  C   LYS    63      60.553   9.328  24.333  1.00  0.00              
ATOM      8  O   LYS    63      60.391   8.514  23.417  1.00  0.00              
ATOM      9  N   LYS    64      59.508   9.957  24.893  1.00  0.00              
ATOM     10  CA  LYS    64      58.153   9.967  24.264  1.00  0.00              
ATOM     11  C   LYS    64      57.935  11.332  23.525  1.00  0.00              
ATOM     12  O   LYS    64      57.301  12.256  24.045  1.00  0.00              
ATOM     13  N   GLU    65      58.500  11.455  22.312  1.00  0.00              
ATOM     14  CA  GLU    65      58.555  12.734  21.550  1.00  0.00              
ATOM     15  C   GLU    65      57.435  12.794  20.450  1.00  0.00              
ATOM     16  O   GLU    65      57.347  11.937  19.564  1.00  0.00              
ATOM     17  N   LEU    66      56.533  13.787  20.541  1.00  0.00              
ATOM     18  CA  LEU    66      55.283  13.839  19.727  1.00  0.00              
ATOM     19  C   LEU    66      55.467  14.055  18.187  1.00  0.00              
ATOM     20  O   LEU    66      56.327  14.809  17.725  1.00  0.00              
ATOM     21  N   MET    67      54.586  13.419  17.401  1.00  0.00              
ATOM     22  CA  MET    67      54.527  13.606  15.915  1.00  0.00              
ATOM     23  C   MET    67      53.787  14.924  15.463  1.00  0.00              
ATOM     24  O   MET    67      54.198  15.503  14.452  1.00  0.00              
ATOM     25  N   GLU    68      52.731  15.400  16.160  1.00  0.00              
ATOM     26  CA  GLU    68      52.138  16.748  15.911  1.00  0.00              
ATOM     27  C   GLU    68      52.942  17.907  16.612  1.00  0.00              
ATOM     28  O   GLU    68      53.914  18.405  16.039  1.00  0.00              
ATOM     29  N   PRO    69      52.560  18.314  17.834  1.00  0.00              
ATOM     30  CA  PRO    69      53.299  19.316  18.659  1.00  0.00              
ATOM     31  C   PRO    69      53.361  18.815  20.147  1.00  0.00              
ATOM     32  O   PRO    69      54.409  18.358  20.614  1.00  0.00              
ATOM     33  N   LEU    70      52.238  18.872  20.890  1.00  0.00              
ATOM     34  CA  LEU    70      52.084  18.192  22.206  1.00  0.00              
ATOM     35  C   LEU    70      50.610  17.706  22.413  1.00  0.00              
ATOM     36  O   LEU    70      49.854  18.298  23.192  1.00  0.00              
ATOM     37  N   GLU    71      50.209  16.618  21.732  1.00  0.00              
ATOM     38  CA  GLU    71      48.824  16.072  21.809  1.00  0.00              
ATOM     39  C   GLU    71      48.579  15.115  23.044  1.00  0.00              
ATOM     40  O   GLU    71      49.052  15.364  24.157  1.00  0.00              
ATOM     41  N   ILE    72      47.793  14.044  22.863  1.00  0.00              
ATOM     42  CA  ILE    72      47.571  12.984  23.909  1.00  0.00              
ATOM     43  C   ILE    72      47.659  11.501  23.372  1.00  0.00              
ATOM     44  O   ILE    72      47.087  10.585  23.974  1.00  0.00              
ATOM     45  N   LEU    73      48.363  11.227  22.255  1.00  0.00              
ATOM     46  CA  LEU    73      48.315   9.912  21.557  1.00  0.00              
ATOM     47  C   LEU    73      49.530   9.604  20.622  1.00  0.00              
ATOM     48  O   LEU    73      50.143   8.545  20.795  1.00  0.00              
ATOM     49  N   SER    74      49.841  10.436  19.606  1.00  0.00              
ATOM     50  CA  SER    74      50.691   9.999  18.460  1.00  0.00              
ATOM     51  C   SER    74      52.207  10.320  18.680  1.00  0.00              
ATOM     52  O   SER    74      52.661  11.471  18.628  1.00  0.00              
ATOM     53  N   LEU    75      52.976   9.268  18.986  1.00  0.00              
ATOM     54  CA  LEU    75      54.308   9.400  19.630  1.00  0.00              
ATOM     55  C   LEU    75      55.422   8.660  18.837  1.00  0.00              
ATOM     56  O   LEU    75      55.279   7.492  18.467  1.00  0.00              
ATOM     57  N   SER    76      56.598   9.290  18.712  1.00  0.00              
ATOM     58  CA  SER    76      57.871   8.544  18.537  1.00  0.00              
ATOM     59  C   SER    76      58.378   8.044  19.934  1.00  0.00              
ATOM     60  O   SER    76      58.992   8.793  20.703  1.00  0.00              
ATOM     61  N   GLY    77      58.102   6.776  20.272  1.00  0.00              
ATOM     62  CA  GLY    77      58.657   6.134  21.494  1.00  0.00              
ATOM     63  C   GLY    77      60.048   5.531  21.256  1.00  0.00              
ATOM     64  O   GLY    77      60.168   4.523  20.557  1.00  0.00              
ATOM     65  N   ASN    78      61.098   6.177  21.770  1.00  0.00              
ATOM     66  CA  ASN    78      62.497   5.890  21.326  1.00  0.00              
ATOM     67  C   ASN    78      63.371   5.390  22.519  1.00  0.00              
ATOM     68  O   ASN    78      63.560   6.114  23.499  1.00  0.00              
ATOM     69  N   VAL    79      63.909   4.163  22.439  1.00  0.00              
ATOM     70  CA  VAL    79      64.826   3.601  23.479  1.00  0.00              
ATOM     71  C   VAL    79      66.343   3.649  23.080  1.00  0.00              
ATOM     72  O   VAL    79      66.704   3.753  21.902  1.00  0.00              
ATOM     73  N   SER    80      67.239   3.541  24.075  1.00  0.00              
ATOM     74  CA  SER    80      68.706   3.420  23.829  1.00  0.00              
ATOM     75  C   SER    80      69.167   1.930  23.637  1.00  0.00              
ATOM     76  O   SER    80      68.710   1.014  24.328  1.00  0.00              
ATOM     77  N   MET    81      72.815  -4.928  18.740  1.00  0.00              
ATOM     78  CA  MET    81      71.894  -3.754  18.918  1.00  0.00              
ATOM     79  C   MET    81      72.373  -2.647  19.938  1.00  0.00              
ATOM     80  O   MET    81      71.601  -1.753  20.283  1.00  0.00              
ATOM     81  N   LYS    82      73.657  -2.647  20.333  1.00  0.00              
ATOM     82  CA  LYS    82      74.291  -1.658  21.248  1.00  0.00              
ATOM     83  C   LYS    82      74.275  -0.162  20.789  1.00  0.00              
ATOM     84  O   LYS    82      74.570   0.148  19.632  1.00  0.00              
ATOM     85  N   ASP    83      74.061   0.776  21.729  1.00  0.00              
ATOM     86  CA  ASP    83      74.426   2.214  21.541  1.00  0.00              
ATOM     87  C   ASP    83      73.798   2.978  20.353  1.00  0.00              
ATOM     88  O   ASP    83      74.451   3.171  19.326  1.00  0.00              
ATOM     89  N   SER    84      72.540   3.398  20.503  1.00  0.00              
ATOM     90  CA  SER    84      71.773   4.001  19.380  1.00  0.00              
ATOM     91  C   SER    84      70.322   4.391  19.724  1.00  0.00              
ATOM     92  O   SER    84      69.701   3.788  20.601  1.00  0.00              
ATOM     93  N   LYS    85      69.756   5.383  19.020  1.00  0.00              
ATOM     94  CA  LYS    85      68.336   5.795  19.229  1.00  0.00              
ATOM     95  C   LYS    85      67.356   4.938  18.351  1.00  0.00              
ATOM     96  O   LYS    85      67.267   5.116  17.132  1.00  0.00              
ATOM     97  N   PRO    86      66.625   4.006  18.980  1.00  0.00              
ATOM     98  CA  PRO    86      65.709   3.061  18.278  1.00  0.00              
ATOM     99  C   PRO    86      64.260   3.639  18.168  1.00  0.00              
ATOM    100  O   PRO    86      63.469   3.545  19.109  1.00  0.00              
ATOM    101  N   PHE    87      63.936   4.262  17.024  1.00  0.00              
ATOM    102  CA  PHE    87      62.723   5.127  16.868  1.00  0.00              
ATOM    103  C   PHE    87      61.452   4.300  16.452  1.00  0.00              
ATOM    104  O   PHE    87      61.437   3.674  15.389  1.00  0.00              
ATOM    105  N   CYS    88      60.386   4.343  17.274  1.00  0.00              
ATOM    106  CA  CYS    88      59.117   3.583  17.022  1.00  0.00              
ATOM    107  C   CYS    88      57.915   4.582  16.895  1.00  0.00              
ATOM    108  O   CYS    88      57.564   5.244  17.875  1.00  0.00              
ATOM    109  N   HIS    89      57.240   4.646  15.738  1.00  0.00              
ATOM    110  CA  HIS    89      55.940   5.367  15.590  1.00  0.00              
ATOM    111  C   HIS    89      54.744   4.595  16.268  1.00  0.00              
ATOM    112  O   HIS    89      54.631   3.366  16.160  1.00  0.00              
ATOM    113  N   ILE    90      53.905   5.307  17.040  1.00  0.00              
ATOM    114  CA  ILE    90      52.910   4.685  17.970  1.00  0.00              
ATOM    115  C   ILE    90      51.528   5.426  17.852  1.00  0.00              
ATOM    116  O   ILE    90      51.361   6.538  18.365  1.00  0.00              
ATOM    117  N   HIS    91      50.514   4.734  17.307  1.00  0.00              
ATOM    118  CA  HIS    91      49.086   4.966  17.669  1.00  0.00              
ATOM    119  C   HIS    91      48.696   4.013  18.856  1.00  0.00              
ATOM    120  O   HIS    91      48.530   2.804  18.680  1.00  0.00              
ATOM    121  N   VAL    92      48.561   4.564  20.075  1.00  0.00              
ATOM    122  CA  VAL    92      47.895   3.881  21.235  1.00  0.00              
ATOM    123  C   VAL    92      46.335   3.993  21.075  1.00  0.00              
ATOM    124  O   VAL    92      45.816   5.044  21.458  1.00  0.00              
ATOM    125  N   LEU    93      45.533   3.043  20.501  1.00  0.00              
ATOM    126  CA  LEU    93      44.218   3.384  19.877  1.00  0.00              
ATOM    127  C   LEU    93      43.114   4.023  20.778  1.00  0.00              
ATOM    128  O   LEU    93      43.214   3.999  22.005  1.00  0.00              
ATOM    129  N   LEU    94      42.085   4.622  20.157  1.00  0.00              
ATOM    130  CA  LEU    94      41.040   5.455  20.848  1.00  0.00              
ATOM    131  C   LEU    94      40.543   5.062  22.288  1.00  0.00              
ATOM    132  O   LEU    94      40.500   5.921  23.174  1.00  0.00              
ATOM    133  N   GLY    95      40.241   3.780  22.526  1.00  0.00              
ATOM    134  CA  GLY    95      39.818   3.246  23.852  1.00  0.00              
ATOM    135  C   GLY    95      40.971   2.971  24.914  1.00  0.00              
ATOM    136  O   GLY    95      40.754   2.249  25.890  1.00  0.00              
ATOM    137  N   LYS    96      42.181   3.558  24.778  1.00  0.00              
ATOM    138  CA  LYS    96      43.284   3.492  25.788  1.00  0.00              
ATOM    139  C   LYS    96      42.883   4.161  27.160  1.00  0.00              
ATOM    140  O   LYS    96      42.505   5.336  27.128  1.00  0.00              
END
