
#######################################################
#                                                     #
#                        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 T0363AL509_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   28 , name T0363_D1.pdb
# PARAMETERS: T0363AL509_1-D1.T0363_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:    28        13 - 45          1.48     1.48
  LCS_AVERAGE:     60.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28        13 - 45          1.48     1.48
  LCS_AVERAGE:     60.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        27 - 43          1.00     1.53
  LCS_AVERAGE:     28.96

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:   46
LCS_GDT     I      13     I      13      7   28   28     6   13   16   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     N      14     N      14      7   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     I      15     I      15      7   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      16     E      16      7   28   28     6   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     I      17     I      17      7   28   28     4   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     A      18     A      18      7   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Y      19     Y      19      7   28   28     4    8   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     F      21     F      21      4   28   28     0    4    5    9   17   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     P      22     P      22      4   28   28     1    4    5    9   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      27     L      27     17   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     K      28     K      28     17   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     S      29     S      29     17   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     F      30     F      30     17   28   28     7   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Q      31     Q      31     17   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     V      32     V      32     17   28   28     8   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     D      33     D      33     17   28   28     7   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      34     E      34     17   28   28     3   11   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     G      35     G      35     17   28   28     7   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     I      36     I      36     17   28   28     5   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     T      37     T      37     17   28   28     7   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     V      38     V      38     17   28   28     5   12   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Q      39     Q      39     17   28   28     5   12   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     T      40     T      40     17   28   28     6   12   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     A      41     A      41     17   28   28     7   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     I      42     I      42     17   28   28     6   12   19   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     T      43     T      43     17   28   28     6   10   19   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Q      44     Q      44     16   28   28     6   10   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     S      45     S      45     11   28   28     4   13   20   26   27   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_AVERAGE  LCS_A:  50.23  (  28.96   60.87   60.87 )

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      8     13     20     26     27     28     28     28     28     28     28     28     28     28     28     28     28     28     28     28 
GDT PERCENT_CA  17.39  28.26  43.48  56.52  58.70  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87  60.87
GDT RMS_LOCAL    0.32   0.56   0.97   1.22   1.34   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48
GDT RMS_ALL_CA   2.33   2.61   1.63   1.53   1.50   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48   1.48

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13          1.931
LGA    N      14      N      14          0.845
LGA    I      15      I      15          0.962
LGA    E      16      E      16          1.672
LGA    I      17      I      17          1.587
LGA    A      18      A      18          1.611
LGA    Y      19      Y      19          2.174
LGA    F      21      F      21          3.300
LGA    P      22      P      22          2.946
LGA    L      27      L      27          1.083
LGA    K      28      K      28          0.935
LGA    S      29      S      29          0.474
LGA    F      30      F      30          1.222
LGA    Q      31      Q      31          1.308
LGA    V      32      V      32          1.232
LGA    D      33      D      33          0.583
LGA    E      34      E      34          1.269
LGA    G      35      G      35          0.311
LGA    I      36      I      36          0.801
LGA    T      37      T      37          0.305
LGA    V      38      V      38          0.604
LGA    Q      39      Q      39          1.221
LGA    T      40      T      40          0.987
LGA    A      41      A      41          0.654
LGA    I      42      I      42          1.480
LGA    T      43      T      43          1.764
LGA    Q      44      Q      44          1.436
LGA    S      45      S      45          1.776

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   46    4.0     28    1.48    51.630    56.550     1.775

LGA_LOCAL      RMSD =  1.478  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.478  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  1.478  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.590545 * X  +  -0.794036 * Y  +  -0.144095 * Z  +  45.872631
  Y_new =   0.719559 * X  +   0.437254 * Y  +   0.539484 * Z  + -27.025511
  Z_new =  -0.365364 * X  +  -0.422275 * Y  +   0.829574 * Z  +  36.204777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.470842    2.670750  [ DEG:   -26.9773    153.0227 ]
  Theta =   0.374023    2.767569  [ DEG:    21.4300    158.5700 ]
  Phi   =   0.883558   -2.258035  [ DEG:    50.6241   -129.3759 ]
 
# 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: T0363AL509_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL509_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   46   4.0   28   1.48  56.550     1.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL509_1-D1
REMARK Aligment from pdb entry: 1vjkA_
ATOM      1  N   ILE    13      18.498   5.492   8.966  1.00  0.00              
ATOM      2  CA  ILE    13      18.382   6.937   9.174  1.00  0.00              
ATOM      3  C   ILE    13      18.848   7.595   7.862  1.00  0.00              
ATOM      4  O   ILE    13      19.994   7.387   7.454  1.00  0.00              
ATOM      5  N   ASN    14      17.972   8.351   7.200  1.00  0.00              
ATOM      6  CA  ASN    14      18.339   8.997   5.948  1.00  0.00              
ATOM      7  C   ASN    14      18.554  10.473   6.185  1.00  0.00              
ATOM      8  O   ASN    14      17.624  11.179   6.638  1.00  0.00              
ATOM      9  N   ILE    15      19.760  10.947   5.908  1.00  0.00              
ATOM     10  CA  ILE    15      20.091  12.354   6.105  1.00  0.00              
ATOM     11  C   ILE    15      20.339  13.012   4.764  1.00  0.00              
ATOM     12  O   ILE    15      20.757  12.352   3.783  1.00  0.00              
ATOM     13  N   GLU    16      20.087  14.302   4.685  1.00  0.00              
ATOM     14  CA  GLU    16      20.333  15.082   3.499  1.00  0.00              
ATOM     15  C   GLU    16      21.622  15.824   3.718  1.00  0.00              
ATOM     16  O   GLU    16      21.706  16.667   4.622  1.00  0.00              
ATOM     17  N   ILE    17      22.629  15.539   2.915  1.00  0.00              
ATOM     18  CA  ILE    17      23.918  16.206   3.004  1.00  0.00              
ATOM     19  C   ILE    17      24.001  17.311   1.980  1.00  0.00              
ATOM     20  O   ILE    17      23.745  17.058   0.801  1.00  0.00              
ATOM     21  N   ALA    18      24.325  18.531   2.425  1.00  0.00              
ATOM     22  CA  ALA    18      24.477  19.674   1.519  1.00  0.00              
ATOM     23  C   ALA    18      25.935  20.075   1.526  1.00  0.00              
ATOM     24  O   ALA    18      26.496  20.414   2.583  1.00  0.00              
ATOM     25  N   TYR    19      26.556  20.034   0.358  1.00  0.00              
ATOM     26  CA  TYR    19      27.951  20.453   0.202  1.00  0.00              
ATOM     27  C   TYR    19      28.020  21.888  -0.232  1.00  0.00              
ATOM     28  O   TYR    19      27.169  22.364  -1.005  1.00  0.00              
ATOM     29  N   PHE    21      29.070  22.572   0.238  1.00  0.00              
ATOM     30  CA  PHE    21      29.266  23.974  -0.074  1.00  0.00              
ATOM     31  C   PHE    21      30.613  24.247  -0.684  1.00  0.00              
ATOM     32  O   PHE    21      31.595  23.573  -0.383  1.00  0.00              
ATOM     33  N   PRO    22      30.659  25.283  -1.521  1.00  0.00              
ATOM     34  CA  PRO    22      31.911  25.797  -2.069  1.00  0.00              
ATOM     35  C   PRO    22      32.713  24.666  -2.731  1.00  0.00              
ATOM     36  O   PRO    22      32.142  23.907  -3.525  1.00  0.00              
ATOM     37  N   LEU    27      24.228  18.201  -3.320  1.00  0.00              
ATOM     38  CA  LEU    27      23.573  17.572  -2.183  1.00  0.00              
ATOM     39  C   LEU    27      23.365  16.115  -2.482  1.00  0.00              
ATOM     40  O   LEU    27      23.344  15.699  -3.646  1.00  0.00              
ATOM     41  N   LYS    28      23.204  15.324  -1.429  1.00  0.00              
ATOM     42  CA  LYS    28      22.962  13.903  -1.574  1.00  0.00              
ATOM     43  C   LYS    28      22.314  13.348  -0.338  1.00  0.00              
ATOM     44  O   LYS    28      22.591  13.812   0.775  1.00  0.00              
ATOM     45  N   SER    29      21.437  12.383  -0.522  1.00  0.00              
ATOM     46  CA  SER    29      20.823  11.667   0.569  1.00  0.00              
ATOM     47  C   SER    29      21.673  10.492   0.942  1.00  0.00              
ATOM     48  O   SER    29      22.042   9.679   0.067  1.00  0.00              
ATOM     49  N   PHE    30      21.960  10.340   2.223  1.00  0.00              
ATOM     50  CA  PHE    30      22.774   9.243   2.688  1.00  0.00              
ATOM     51  C   PHE    30      22.015   8.438   3.730  1.00  0.00              
ATOM     52  O   PHE    30      21.646   8.951   4.806  1.00  0.00              
ATOM     53  N   GLN    31      21.750   7.184   3.405  1.00  0.00              
ATOM     54  CA  GLN    31      21.108   6.250   4.321  1.00  0.00              
ATOM     55  C   GLN    31      22.174   5.627   5.220  1.00  0.00              
ATOM     56  O   GLN    31      23.192   5.123   4.738  1.00  0.00              
ATOM     57  N   VAL    32      21.935   5.687   6.528  1.00  0.00              
ATOM     58  CA  VAL    32      22.871   5.224   7.528  1.00  0.00              
ATOM     59  C   VAL    32      22.178   4.218   8.428  1.00  0.00              
ATOM     60  O   VAL    32      20.967   4.275   8.580  1.00  0.00              
ATOM     61  N   ASP    33      22.923   3.283   9.027  1.00  0.00              
ATOM     62  CA  ASP    33      22.319   2.323   9.948  1.00  0.00              
ATOM     63  C   ASP    33      21.801   2.988  11.213  1.00  0.00              
ATOM     64  O   ASP    33      22.272   4.057  11.618  1.00  0.00              
ATOM     65  N   GLU    34      20.823   2.336  11.827  1.00  0.00              
ATOM     66  CA  GLU    34      20.318   2.713  13.128  1.00  0.00              
ATOM     67  C   GLU    34      21.473   3.048  14.080  1.00  0.00              
ATOM     68  O   GLU    34      22.465   2.329  14.136  1.00  0.00              
ATOM     69  N   GLY    35      21.326   4.158  14.802  1.00  0.00              
ATOM     70  CA  GLY    35      22.306   4.566  15.800  1.00  0.00              
ATOM     71  C   GLY    35      23.442   5.400  15.235  1.00  0.00              
ATOM     72  O   GLY    35      24.373   5.781  15.964  1.00  0.00              
ATOM     73  N   ILE    36      23.387   5.695  13.944  1.00  0.00              
ATOM     74  CA  ILE    36      24.469   6.440  13.325  1.00  0.00              
ATOM     75  C   ILE    36      24.708   7.761  13.992  1.00  0.00              
ATOM     76  O   ILE    36      23.768   8.475  14.377  1.00  0.00              
ATOM     77  N   THR    37      25.994   8.092  14.085  1.00  0.00              
ATOM     78  CA  THR    37      26.457   9.341  14.658  1.00  0.00              
ATOM     79  C   THR    37      27.109  10.212  13.587  1.00  0.00              
ATOM     80  O   THR    37      27.461   9.742  12.493  1.00  0.00              
ATOM     81  N   VAL    38      27.331  11.485  13.895  1.00  0.00              
ATOM     82  CA  VAL    38      28.041  12.376  12.977  1.00  0.00              
ATOM     83  C   VAL    38      29.358  11.755  12.472  1.00  0.00              
ATOM     84  O   VAL    38      29.657  11.791  11.257  1.00  0.00              
ATOM     85  N   GLN    39      30.142  11.147  13.372  1.00  0.00              
ATOM     86  CA  GLN    39      31.404  10.553  12.924  1.00  0.00              
ATOM     87  C   GLN    39      31.193   9.441  11.864  1.00  0.00              
ATOM     88  O   GLN    39      32.036   9.262  10.970  1.00  0.00              
ATOM     89  N   THR    40      30.081   8.703  11.970  1.00  0.00              
ATOM     90  CA  THR    40      29.796   7.630  10.991  1.00  0.00              
ATOM     91  C   THR    40      29.449   8.234   9.664  1.00  0.00              
ATOM     92  O   THR    40      29.852   7.704   8.620  1.00  0.00              
ATOM     93  N   ALA    41      28.728   9.343   9.681  1.00  0.00              
ATOM     94  CA  ALA    41      28.415  10.042   8.434  1.00  0.00              
ATOM     95  C   ALA    41      29.682  10.569   7.751  1.00  0.00              
ATOM     96  O   ALA    41      29.833  10.412   6.526  1.00  0.00              
ATOM     97  N   ILE    42      30.606  11.133   8.528  1.00  0.00              
ATOM     98  CA  ILE    42      31.865  11.604   7.964  1.00  0.00              
ATOM     99  C   ILE    42      32.609  10.445   7.304  1.00  0.00              
ATOM    100  O   ILE    42      33.136  10.585   6.170  1.00  0.00              
ATOM    101  N   THR    43      32.663   9.281   7.974  1.00  0.00              
ATOM    102  CA  THR    43      33.307   8.127   7.335  1.00  0.00              
ATOM    103  C   THR    43      32.635   7.686   6.056  1.00  0.00              
ATOM    104  O   THR    43      33.329   7.267   5.104  1.00  0.00              
ATOM    105  N   GLN    44      31.315   7.772   6.004  1.00  0.00              
ATOM    106  CA  GLN    44      30.599   7.394   4.800  1.00  0.00              
ATOM    107  C   GLN    44      30.849   8.394   3.671  1.00  0.00              
ATOM    108  O   GLN    44      30.974   7.974   2.515  1.00  0.00              
ATOM    109  N   SER    45      30.942   9.702   3.978  1.00  0.00              
ATOM    110  CA  SER    45      31.271  10.691   2.943  1.00  0.00              
ATOM    111  C   SER    45      32.632  10.361   2.325  1.00  0.00              
ATOM    112  O   SER    45      32.775  10.363   1.084  1.00  0.00              
END
