
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0361AL586_1-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected   12 , name T0361_D1.pdb
# PARAMETERS: T0361AL586_1-D1.T0361_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:    12       157 - 168         2.83     2.83
  LCS_AVERAGE:      7.59

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       159 - 168         0.88     3.83
  LCS_AVERAGE:      5.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       159 - 168         0.88     3.83
  LCS_AVERAGE:      5.43

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:  158
LCS_GDT     T     157     T     157      0    0   12     0    0    0    0    2    3    4    6    6   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     158     L     158      3    3   12     0    0    3    3    3    3    5    9   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     A     159     A     159     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     V     160     V     160     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     T     161     T     161     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     T     162     T     162     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     T     163     T     163     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     164     L     164     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     K     165     K     165     10   10   12     7    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E     166     E     166     10   10   12     4    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     167     L     167     10   10   12     3    9    9   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     T     168     T     168     10   10   12     3    3    4   10   10   10   10   10   10   11   12   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   6.15  (   5.43    5.43    7.59 )

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      7      9      9     10     10     10     10     10     10     11     12     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   4.43   5.70   5.70   6.33   6.33   6.33   6.33   6.33   6.33   6.96   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59
GDT RMS_LOCAL    0.23   0.51   0.51   0.88   0.88   0.88   0.88   0.88   0.88   2.35   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83
GDT RMS_ALL_CA   3.81   3.82   3.82   3.83   3.83   3.83   3.83   3.83   3.83   3.01   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83

#      Molecule1      Molecule2       DISTANCE
LGA    T     157      T     157          9.557
LGA    L     158      L     158          8.750
LGA    A     159      A     159          0.586
LGA    V     160      V     160          0.555
LGA    T     161      T     161          0.507
LGA    T     162      T     162          0.526
LGA    T     163      T     163          0.513
LGA    L     164      L     164          0.485
LGA    K     165      K     165          0.443
LGA    E     166      E     166          0.855
LGA    L     167      L     167          1.118
LGA    T     168      T     168          1.961

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  158    4.0     10    0.88     6.487     6.285     1.023

LGA_LOCAL      RMSD =  0.878  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.826  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  2.833  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.532359 * X  +  -0.622048 * Y  +  -0.574151 * Z  +  56.322945
  Y_new =   0.556774 * X  +   0.253602 * Y  +  -0.791005 * Z  +  -8.521317
  Z_new =   0.637649 * X  +  -0.740771 * Y  +   0.211333 * Z  +   5.560243 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.292891    1.848702  [ DEG:   -74.0772    105.9228 ]
  Theta =  -0.691442   -2.450150  [ DEG:   -39.6167   -140.3833 ]
  Phi   =   2.333781   -0.807811  [ DEG:   133.7158    -46.2842 ]
 
# 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: T0361AL586_1-D1                               
REMARK     2: T0361_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361AL586_1-D1.T0361_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  158   4.0   10   0.88   6.285     2.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL586_1-D1
REMARK Aligment from pdb entry: 1h97_A
ATOM      1  N   THR   157       5.641  -8.299  27.806  1.00  0.00              
ATOM      2  CA  THR   157       6.182  -7.077  27.172  1.00  0.00              
ATOM      3  C   THR   157       7.585  -6.926  27.741  1.00  0.00              
ATOM      4  O   THR   157       7.810  -7.320  28.930  1.00  0.00              
ATOM      5  N   LEU   158       8.591  -6.440  27.032  1.00  0.00              
ATOM      6  CA  LEU   158       9.926  -6.227  27.556  1.00  0.00              
ATOM      7  C   LEU   158       9.822  -5.248  28.725  1.00  0.00              
ATOM      8  O   LEU   158       8.945  -4.418  28.703  1.00  0.00              
ATOM      9  N   ALA   159      15.064  -3.551  30.372  1.00  0.00              
ATOM     10  CA  ALA   159      15.547  -4.053  29.101  1.00  0.00              
ATOM     11  C   ALA   159      15.572  -2.966  28.019  1.00  0.00              
ATOM     12  O   ALA   159      16.563  -2.912  27.260  1.00  0.00              
ATOM     13  N   VAL   160      14.540  -2.115  27.992  1.00  0.00              
ATOM     14  CA  VAL   160      14.544  -0.968  27.063  1.00  0.00              
ATOM     15  C   VAL   160      15.784  -0.104  27.336  1.00  0.00              
ATOM     16  O   VAL   160      16.491   0.316  26.377  1.00  0.00              
ATOM     17  N   THR   161      16.069   0.121  28.618  1.00  0.00              
ATOM     18  CA  THR   161      17.194   1.015  29.004  1.00  0.00              
ATOM     19  C   THR   161      18.501   0.373  28.620  1.00  0.00              
ATOM     20  O   THR   161      19.404   1.077  28.089  1.00  0.00              
ATOM     21  N   THR   162      18.655  -0.947  28.810  1.00  0.00              
ATOM     22  CA  THR   162      19.889  -1.617  28.443  1.00  0.00              
ATOM     23  C   THR   162      20.114  -1.551  26.936  1.00  0.00              
ATOM     24  O   THR   162      21.207  -1.260  26.454  1.00  0.00              
ATOM     25  N   THR   163      19.075  -1.800  26.159  1.00  0.00              
ATOM     26  CA  THR   163      19.173  -1.772  24.697  1.00  0.00              
ATOM     27  C   THR   163      19.567  -0.352  24.239  1.00  0.00              
ATOM     28  O   THR   163      20.395  -0.241  23.345  1.00  0.00              
ATOM     29  N   LEU   164      18.807   0.646  24.709  1.00  0.00              
ATOM     30  CA  LEU   164      19.132   2.011  24.243  1.00  0.00              
ATOM     31  C   LEU   164      20.553   2.362  24.616  1.00  0.00              
ATOM     32  O   LEU   164      21.290   3.007  23.821  1.00  0.00              
ATOM     33  N   LYS   165      21.032   2.042  25.828  1.00  0.00              
ATOM     34  CA  LYS   165      22.393   2.361  26.261  1.00  0.00              
ATOM     35  C   LYS   165      23.428   1.626  25.443  1.00  0.00              
ATOM     36  O   LYS   165      24.355   2.279  24.919  1.00  0.00              
ATOM     37  N   GLU   166      23.218   0.315  25.175  1.00  0.00              
ATOM     38  CA  GLU   166      24.288  -0.402  24.495  1.00  0.00              
ATOM     39  C   GLU   166      24.274  -0.187  22.984  1.00  0.00              
ATOM     40  O   GLU   166      25.346  -0.359  22.359  1.00  0.00              
ATOM     41  N   LEU   167      23.156   0.127  22.378  1.00  0.00              
ATOM     42  CA  LEU   167      23.126   0.405  20.953  1.00  0.00              
ATOM     43  C   LEU   167      23.343   1.898  20.662  1.00  0.00              
ATOM     44  O   LEU   167      23.595   2.240  19.507  1.00  0.00              
ATOM     45  N   THR   168      23.341   2.746  21.685  1.00  0.00              
ATOM     46  CA  THR   168      23.489   4.168  21.502  1.00  0.00              
ATOM     47  C   THR   168      24.611   4.599  20.590  1.00  0.00              
ATOM     48  O   THR   168      24.398   5.405  19.674  1.00  0.00              
END
