
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0363AL381_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   19 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_4-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:    19        31 - 56          1.96     1.96
  LCS_AVERAGE:     41.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        31 - 56          1.96     1.96
  LCS_AVERAGE:     41.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        33 - 46          0.96     2.34
  LONGEST_CONTINUOUS_SEGMENT:    14        34 - 47          0.80     2.32
  LCS_AVERAGE:     24.71

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     Q      31     Q      31      3   19   19     4   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      32     V      32      3   19   19     3    3    3    3   14   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      33     D      33     14   19   19     4    5    6   12   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      34     E      34     14   19   19     6   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     G      35     G      35     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I      36     I      36     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     T      37     T      37     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      38     V      38     14   19   19     8   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q      39     Q      39     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     T      40     T      40     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A      41     A      41     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I      42     I      42     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     T      43     T      43     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q      44     Q      44     14   19   19     9   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     S      45     S      45     14   19   19     5   13   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     G      46     G      46     14   19   19     4    9   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I      47     I      47     14   19   19     4    8   14   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      55     D      55      0   19   19     0    0    0    0    0    0    7   17   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      56     L      56      0   19   19     0    0    1   13   15   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  35.77  (  24.71   41.30   41.30 )

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      9     13     14     15     16     17     18     18     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA  19.57  28.26  30.43  32.61  34.78  36.96  39.13  39.13  41.30  41.30  41.30  41.30  41.30  41.30  41.30  41.30  41.30  41.30  41.30  41.30
GDT RMS_LOCAL    0.29   0.57   0.75   0.86   1.06   1.28   1.59   1.59   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96
GDT RMS_ALL_CA   2.06   2.06   2.15   2.26   2.32   2.25   2.03   2.03   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96

#      Molecule1      Molecule2       DISTANCE
LGA    Q      31      Q      31          0.980
LGA    V      32      V      32          2.790
LGA    D      33      D      33          2.920
LGA    E      34      E      34          0.684
LGA    G      35      G      35          0.665
LGA    I      36      I      36          0.793
LGA    T      37      T      37          0.465
LGA    V      38      V      38          0.889
LGA    Q      39      Q      39          0.161
LGA    T      40      T      40          0.513
LGA    A      41      A      41          0.748
LGA    I      42      I      42          0.376
LGA    T      43      T      43          0.345
LGA    Q      44      Q      44          0.308
LGA    S      45      S      45          0.880
LGA    G      46      G      46          2.081
LGA    I      47      I      47          2.434
LGA    D      55      D      55          5.741
LGA    L      56      L      56          3.632

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   46    4.0     18    1.59    35.326    37.920     1.068

LGA_LOCAL      RMSD =  1.585  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.029  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  1.957  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.430375 * X  +  -0.124775 * Y  +  -0.893985 * Z  +  49.170269
  Y_new =   0.762985 * X  +   0.478920 * Y  +  -0.434154 * Z  +  -8.787760
  Z_new =   0.482319 * X  +  -0.868946 * Y  +  -0.110914 * Z  +  19.930279 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.697752    1.443841  [ DEG:   -97.2740     82.7260 ]
  Theta =  -0.503300   -2.638293  [ DEG:   -28.8370   -151.1630 ]
  Phi   =   2.084376   -1.057217  [ DEG:   119.4259    -60.5741 ]
 
# 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: T0363AL381_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_4-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   46   4.0   18   1.59  37.920     1.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_4-D1
REMARK Aligment from pdb entry: 2cu3A
ATOM      1  N   GLN    31      18.299   6.376   4.170  1.00  0.00              
ATOM      2  CA  GLN    31      19.452   5.512   4.392  1.00  0.00              
ATOM      3  C   GLN    31      19.426   4.879   5.785  1.00  0.00              
ATOM      4  O   GLN    31      19.087   5.503   6.782  1.00  0.00              
ATOM      5  N   VAL    32      19.768   3.577   5.826  1.00  0.00              
ATOM      6  CA  VAL    32      19.798   2.831   7.077  1.00  0.00              
ATOM      7  C   VAL    32      20.974   3.266   7.951  1.00  0.00              
ATOM      8  O   VAL    32      22.014   2.622   8.017  1.00  0.00              
ATOM      9  N   ASP    33      20.794   4.423   8.614  1.00  0.00              
ATOM     10  CA  ASP    33      21.905   5.011   9.352  1.00  0.00              
ATOM     11  C   ASP    33      21.677   4.988  10.867  1.00  0.00              
ATOM     12  O   ASP    33      22.517   5.399  11.656  1.00  0.00              
ATOM     13  N   GLU    34      20.478   4.523  11.265  1.00  0.00              
ATOM     14  CA  GLU    34      20.165   4.488  12.689  1.00  0.00              
ATOM     15  C   GLU    34      21.275   3.810  13.494  1.00  0.00              
ATOM     16  O   GLU    34      21.798   2.766  13.125  1.00  0.00              
ATOM     17  N   GLY    35      21.644   4.422  14.616  1.00  0.00              
ATOM     18  CA  GLY    35      22.679   3.859  15.462  1.00  0.00              
ATOM     19  C   GLY    35      24.067   4.413  15.211  1.00  0.00              
ATOM     20  O   GLY    35      24.927   4.360  16.094  1.00  0.00              
ATOM     21  N   ILE    36      24.291   4.937  14.009  1.00  0.00              
ATOM     22  CA  ILE    36      25.583   5.510  13.643  1.00  0.00              
ATOM     23  C   ILE    36      25.639   6.974  14.062  1.00  0.00              
ATOM     24  O   ILE    36      24.606   7.630  14.184  1.00  0.00              
ATOM     25  N   THR    37      26.845   7.480  14.294  1.00  0.00              
ATOM     26  CA  THR    37      27.020   8.880  14.666  1.00  0.00              
ATOM     27  C   THR    37      27.302   9.672  13.396  1.00  0.00              
ATOM     28  O   THR    37      27.712   9.106  12.381  1.00  0.00              
ATOM     29  N   VAL    38      27.091  10.983  13.454  1.00  0.00              
ATOM     30  CA  VAL    38      27.344  11.830  12.297  1.00  0.00              
ATOM     31  C   VAL    38      28.797  11.733  11.832  1.00  0.00              
ATOM     32  O   VAL    38      29.064  11.686  10.633  1.00  0.00              
ATOM     33  N   GLN    39      29.734  11.695  12.773  1.00  0.00              
ATOM     34  CA  GLN    39      31.144  11.585  12.405  1.00  0.00              
ATOM     35  C   GLN    39      31.384  10.323  11.591  1.00  0.00              
ATOM     36  O   GLN    39      32.092  10.345  10.589  1.00  0.00              
ATOM     37  N   THR    40      30.799   9.218  12.038  1.00  0.00              
ATOM     38  CA  THR    40      30.953   7.951  11.342  1.00  0.00              
ATOM     39  C   THR    40      30.380   8.080   9.940  1.00  0.00              
ATOM     40  O   THR    40      31.002   7.665   8.967  1.00  0.00              
ATOM     41  N   ALA    41      29.194   8.672   9.838  1.00  0.00              
ATOM     42  CA  ALA    41      28.548   8.855   8.546  1.00  0.00              
ATOM     43  C   ALA    41      29.373   9.741   7.616  1.00  0.00              
ATOM     44  O   ALA    41      29.538   9.428   6.434  1.00  0.00              
ATOM     45  N   ILE    42      29.893  10.844   8.148  1.00  0.00              
ATOM     46  CA  ILE    42      30.687  11.765   7.339  1.00  0.00              
ATOM     47  C   ILE    42      31.958  11.107   6.800  1.00  0.00              
ATOM     48  O   ILE    42      32.379  11.384   5.672  1.00  0.00              
ATOM     49  N   THR    43      32.564  10.237   7.601  1.00  0.00              
ATOM     50  CA  THR    43      33.777   9.550   7.174  1.00  0.00              
ATOM     51  C   THR    43      33.445   8.559   6.067  1.00  0.00              
ATOM     52  O   THR    43      34.235   8.361   5.150  1.00  0.00              
ATOM     53  N   GLN    44      32.266   7.946   6.151  1.00  0.00              
ATOM     54  CA  GLN    44      31.843   6.978   5.147  1.00  0.00              
ATOM     55  C   GLN    44      31.473   7.676   3.843  1.00  0.00              
ATOM     56  O   GLN    44      31.378   7.036   2.799  1.00  0.00              
ATOM     57  N   SER    45      31.265   8.990   3.917  1.00  0.00              
ATOM     58  CA  SER    45      30.914   9.801   2.753  1.00  0.00              
ATOM     59  C   SER    45      32.179  10.396   2.128  1.00  0.00              
ATOM     60  O   SER    45      32.139  10.915   1.016  1.00  0.00              
ATOM     61  N   GLY    46      33.291  10.331   2.856  1.00  0.00              
ATOM     62  CA  GLY    46      34.540  10.883   2.355  1.00  0.00              
ATOM     63  C   GLY    46      34.507  12.400   2.413  1.00  0.00              
ATOM     64  O   GLY    46      35.191  13.081   1.658  1.00  0.00              
ATOM     65  N   ILE    47      33.698  12.929   3.325  1.00  0.00              
ATOM     66  CA  ILE    47      33.547  14.368   3.490  1.00  0.00              
ATOM     67  C   ILE    47      34.684  15.054   4.247  1.00  0.00              
ATOM     68  O   ILE    47      35.267  14.488   5.164  1.00  0.00              
ATOM     69  N   ASP    55      34.999  16.274   3.826  1.00  0.00              
ATOM     70  CA  ASP    55      36.028  17.091   4.457  1.00  0.00              
ATOM     71  C   ASP    55      35.280  17.842   5.555  1.00  0.00              
ATOM     72  O   ASP    55      34.519  18.765   5.271  1.00  0.00              
ATOM     73  N   LEU    56      35.487  17.441   6.804  1.00  0.00              
ATOM     74  CA  LEU    56      34.789  18.057   7.929  1.00  0.00              
ATOM     75  C   LEU    56      34.911  19.568   8.023  1.00  0.00              
ATOM     76  O   LEU    56      33.918  20.250   8.258  1.00  0.00              
END
