
#######################################################
#                                                     #
#                        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 T0319AL381_4
# Molecule2: number of CA atoms  135 ( 1055),  selected   12 , name T0319.pdb
# PARAMETERS: T0319AL381_4.T0319.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       107 - 118         2.80     2.80
  LCS_AVERAGE:      8.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       108 - 118         1.72     3.18
  LCS_AVERAGE:      7.72

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       109 - 118         0.76     3.91
  LCS_AVERAGE:      6.67

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:  135
LCS_GDT     E     107     E     107      4    4   12     3    4    4    4    4    6    6    6    8    9    9   11   12   12   12   12   12   12   12   12 
LCS_GDT     G     108     G     108      4   11   12     3    4    4    4    9    9   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     E     109     E     109     10   11   12     3    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     M     110     M     110     10   11   12     3    6   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     K     111     K     111     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     C     112     C     112     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     R     113     R     113     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     N     114     N     114     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     C     115     C     115     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     G     116     G     116     10   11   12     3    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     H     117     H     117     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_GDT     I     118     I     118     10   11   12     7    9   10   10   10   10   11   11   11   11   11   11   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   7.76  (   6.67    7.72    8.89 )

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     10     10     10     10     11     11     11     11     11     11     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   5.19   6.67   7.41   7.41   7.41   7.41   8.15   8.15   8.15   8.15   8.15   8.15   8.89   8.89   8.89   8.89   8.89   8.89   8.89   8.89
GDT RMS_LOCAL    0.24   0.65   0.76   0.76   0.76   0.76   1.72   1.72   1.72   1.72   1.72   1.72   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_ALL_CA   3.67   3.71   3.91   3.91   3.91   3.91   3.18   3.18   3.18   3.18   3.18   3.18   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80

#      Molecule1      Molecule2       DISTANCE
LGA    E     107      E     107          9.251
LGA    G     108      G     108          3.897
LGA    E     109      E     109          1.547
LGA    M     110      M     110          2.312
LGA    K     111      K     111          0.960
LGA    C     112      C     112          0.500
LGA    R     113      R     113          0.533
LGA    N     114      N     114          1.103
LGA    C     115      C     115          1.261
LGA    G     116      G     116          1.630
LGA    H     117      H     117          1.408
LGA    I     118      I     118          1.706

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  135    4.0     11    1.72     7.778     7.813     0.603

LGA_LOCAL      RMSD =  1.724  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.166  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  2.796  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.149634 * X  +   0.819551 * Y  +   0.553123 * Z  +  13.012361
  Y_new =   0.565363 * X  +   0.388025 * Y  +  -0.727874 * Z  +   7.143663
  Z_new =  -0.811156 * X  +   0.421631 * Y  +  -0.405282 * Z  +  14.659528 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.336427   -0.805166  [ DEG:   133.8674    -46.1326 ]
  Theta =   0.946126    2.195467  [ DEG:    54.2090    125.7910 ]
  Phi   =   1.312060   -1.829533  [ DEG:    75.1755   -104.8245 ]
 
# 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: T0319AL381_4                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_4.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  135   4.0   11   1.72   7.813     2.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_4
REMARK Aligment from pdb entry: 1rlyA
ATOM      1  N   GLU   107      14.694  12.180   4.115  1.00  0.00              
ATOM      2  CA  GLU   107      15.485  13.215   4.784  1.00  0.00              
ATOM      3  C   GLU   107      14.744  13.733   6.013  1.00  0.00              
ATOM      4  O   GLU   107      14.816  14.916   6.343  1.00  0.00              
ATOM      5  N   GLY   108      14.027  12.832   6.684  1.00  0.00              
ATOM      6  CA  GLY   108      13.277  13.212   7.868  1.00  0.00              
ATOM      7  C   GLY   108      13.400  12.202   8.997  1.00  0.00              
ATOM      8  O   GLY   108      14.503  11.786   9.352  1.00  0.00              
ATOM      9  N   GLU   109      12.260  11.824   9.570  1.00  0.00              
ATOM     10  CA  GLU   109      12.225  10.870  10.678  1.00  0.00              
ATOM     11  C   GLU   109      11.903   9.454  10.183  1.00  0.00              
ATOM     12  O   GLU   109      12.398   9.032   9.144  1.00  0.00              
ATOM     13  N   MET   110      11.093   8.713  10.936  1.00  0.00              
ATOM     14  CA  MET   110      10.741   7.344  10.572  1.00  0.00              
ATOM     15  C   MET   110       9.482   7.295   9.705  1.00  0.00              
ATOM     16  O   MET   110       8.394   7.625  10.146  1.00  0.00              
ATOM     17  N   LYS   111       9.666   6.946   8.451  1.00  0.00              
ATOM     18  CA  LYS   111       8.581   6.929   7.482  1.00  0.00              
ATOM     19  C   LYS   111       7.970   5.546   7.296  1.00  0.00              
ATOM     20  O   LYS   111       8.631   4.605   6.877  1.00  0.00              
ATOM     21  N   CYS   112       6.691   5.434   7.606  1.00  0.00              
ATOM     22  CA  CYS   112       5.994   4.175   7.461  1.00  0.00              
ATOM     23  C   CYS   112       5.589   3.963   6.004  1.00  0.00              
ATOM     24  O   CYS   112       4.660   4.590   5.524  1.00  0.00              
ATOM     25  N   ARG   113       6.260   3.058   5.285  1.00  0.00              
ATOM     26  CA  ARG   113       5.977   2.808   3.871  1.00  0.00              
ATOM     27  C   ARG   113       4.504   2.652   3.527  1.00  0.00              
ATOM     28  O   ARG   113       4.135   2.745   2.357  1.00  0.00              
ATOM     29  N   ASN   114       3.655   2.406   4.511  1.00  0.00              
ATOM     30  CA  ASN   114       2.238   2.222   4.223  1.00  0.00              
ATOM     31  C   ASN   114       1.412   3.452   4.535  1.00  0.00              
ATOM     32  O   ASN   114       0.722   3.948   3.655  1.00  0.00              
ATOM     33  N   CYS   115       1.537   4.032   5.722  1.00  0.00              
ATOM     34  CA  CYS   115       0.812   5.271   5.964  1.00  0.00              
ATOM     35  C   CYS   115       1.778   6.393   5.694  1.00  0.00              
ATOM     36  O   CYS   115       1.395   7.541   5.573  1.00  0.00              
ATOM     37  N   GLY   116       3.049   6.012   5.596  1.00  0.00              
ATOM     38  CA  GLY   116       4.126   6.931   5.319  1.00  0.00              
ATOM     39  C   GLY   116       4.336   7.966   6.404  1.00  0.00              
ATOM     40  O   GLY   116       4.885   9.043   6.169  1.00  0.00              
ATOM     41  N   HIS   117       3.870   7.624   7.586  1.00  0.00              
ATOM     42  CA  HIS   117       3.951   8.489   8.752  1.00  0.00              
ATOM     43  C   HIS   117       5.396   8.715   9.182  1.00  0.00              
ATOM     44  O   HIS   117       6.227   7.817   9.068  1.00  0.00              
ATOM     45  N   ILE   118       5.690   9.919   9.658  1.00  0.00              
ATOM     46  CA  ILE   118       7.029  10.260  10.085  1.00  0.00              
ATOM     47  C   ILE   118       7.090  10.469  11.592  1.00  0.00              
ATOM     48  O   ILE   118       6.360  11.291  12.144  1.00  0.00              
END
