
#######################################################
#                                                     #
#                        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 T0356AL381_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   12 , name T0356_D1.pdb
# PARAMETERS: T0356AL381_3-D1.T0356_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        85 - 96          2.88     2.88
  LCS_AVERAGE:      9.68

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        87 - 96          1.28     3.88
  LCS_AVERAGE:      7.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        88 - 96          0.34     4.16
  LCS_AVERAGE:      6.05

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:  124
LCS_GDT     L      85     L      85      3    3   12     3    3    3    3    3    4    4    8   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     R      86     R      86      3    3   12     3    3    3    3    3    4    5   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E      87     E      87      3   10   12     3    3    3    3    4   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     V      88     V      88      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     G      89     G      89      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     K      90     K      90      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      91     L      91      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      92     L      92      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     A      93     A      93      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     F      94     F      94      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      95     L      95      9   10   12     8    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     K      96     K      96      9   10   12     3    9    9    9    9   10   10   10   11   12   12   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   7.62  (   6.05    7.12    9.68 )

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      9      9      9      9     10     10     10     11     12     12     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   6.45   7.26   7.26   7.26   7.26   8.06   8.06   8.06   8.87   9.68   9.68   9.68   9.68   9.68   9.68   9.68   9.68   9.68   9.68   9.68
GDT RMS_LOCAL    0.19   0.34   0.34   0.34   0.34   1.28   1.28   1.28   2.42   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88
GDT RMS_ALL_CA   4.23   4.16   4.16   4.16   4.16   3.88   3.88   3.88   3.15   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88   2.88

#      Molecule1      Molecule2       DISTANCE
LGA    L      85      L      85          9.820
LGA    R      86      R      86          8.207
LGA    E      87      E      87          3.512
LGA    V      88      V      88          0.713
LGA    G      89      G      89          0.836
LGA    K      90      K      90          0.891
LGA    L      91      L      91          0.817
LGA    L      92      L      92          0.386
LGA    A      93      A      93          0.712
LGA    F      94      F      94          0.264
LGA    L      95      L      95          0.219
LGA    K      96      K      96          0.818

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  124    4.0     10    1.28     8.065     8.024     0.723

LGA_LOCAL      RMSD =  1.282  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.875  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  2.878  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.882944 * X  +   0.214836 * Y  +   0.417438 * Z  +  80.435104
  Y_new =   0.170767 * X  +  -0.681284 * Y  +   0.711822 * Z  + 108.060555
  Z_new =   0.437319 * X  +   0.699784 * Y  +   0.564849 * Z  +  60.403412 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.891695   -2.249898  [ DEG:    51.0904   -128.9096 ]
  Theta =  -0.452615   -2.688977  [ DEG:   -25.9330   -154.0670 ]
  Phi   =   2.950546   -0.191047  [ DEG:   169.0538    -10.9462 ]
 
# 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: T0356AL381_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL381_3-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  124   4.0   10   1.28   8.024     2.88
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL381_3-D1
REMARK Aligment from pdb entry: 1om2A
ATOM      1  N   LEU    85      69.028  84.305  68.795  1.00  0.00              
ATOM      2  CA  LEU    85      68.825  85.529  68.046  1.00  0.00              
ATOM      3  C   LEU    85      68.207  85.243  66.680  1.00  0.00              
ATOM      4  O   LEU    85      67.660  86.157  66.068  1.00  0.00              
ATOM      5  N   ARG    86      68.273  83.992  66.202  1.00  0.00              
ATOM      6  CA  ARG    86      67.686  83.645  64.912  1.00  0.00              
ATOM      7  C   ARG    86      66.204  83.305  65.072  1.00  0.00              
ATOM      8  O   ARG    86      65.364  83.844  64.354  1.00  0.00              
ATOM      9  N   GLU    87      65.875  82.411  66.011  1.00  0.00              
ATOM     10  CA  GLU    87      64.503  81.997  66.277  1.00  0.00              
ATOM     11  C   GLU    87      63.986  80.960  65.274  1.00  0.00              
ATOM     12  O   GLU    87      62.816  80.588  65.328  1.00  0.00              
ATOM     13  N   VAL    88      65.785  77.701  64.552  1.00  0.00              
ATOM     14  CA  VAL    88      66.835  76.715  64.720  1.00  0.00              
ATOM     15  C   VAL    88      66.914  75.718  63.576  1.00  0.00              
ATOM     16  O   VAL    88      67.977  75.536  63.004  1.00  0.00              
ATOM     17  N   GLY    89      65.794  75.067  63.272  1.00  0.00              
ATOM     18  CA  GLY    89      65.694  74.022  62.260  1.00  0.00              
ATOM     19  C   GLY    89      66.239  74.449  60.900  1.00  0.00              
ATOM     20  O   GLY    89      66.907  73.653  60.239  1.00  0.00              
ATOM     21  N   LYS    90      65.985  75.691  60.476  1.00  0.00              
ATOM     22  CA  LYS    90      66.521  76.162  59.204  1.00  0.00              
ATOM     23  C   LYS    90      68.039  76.142  59.289  1.00  0.00              
ATOM     24  O   LYS    90      68.716  75.612  58.410  1.00  0.00              
ATOM     25  N   LEU    91      68.567  76.712  60.373  1.00  0.00              
ATOM     26  CA  LEU    91      69.996  76.747  60.581  1.00  0.00              
ATOM     27  C   LEU    91      70.561  75.327  60.706  1.00  0.00              
ATOM     28  O   LEU    91      71.638  75.056  60.194  1.00  0.00              
ATOM     29  N   LEU    92      69.863  74.399  61.362  1.00  0.00              
ATOM     30  CA  LEU    92      70.372  73.037  61.494  1.00  0.00              
ATOM     31  C   LEU    92      70.526  72.382  60.121  1.00  0.00              
ATOM     32  O   LEU    92      71.520  71.698  59.875  1.00  0.00              
ATOM     33  N   ALA    93      69.575  72.609  59.211  1.00  0.00              
ATOM     34  CA  ALA    93      69.668  72.070  57.863  1.00  0.00              
ATOM     35  C   ALA    93      70.865  72.708  57.156  1.00  0.00              
ATOM     36  O   ALA    93      71.604  72.033  56.439  1.00  0.00              
ATOM     37  N   PHE    94      71.059  74.013  57.368  1.00  0.00              
ATOM     38  CA  PHE    94      72.155  74.771  56.779  1.00  0.00              
ATOM     39  C   PHE    94      73.517  74.315  57.312  1.00  0.00              
ATOM     40  O   PHE    94      74.499  74.304  56.573  1.00  0.00              
ATOM     41  N   LEU    95      73.569  73.902  58.581  1.00  0.00              
ATOM     42  CA  LEU    95      74.788  73.425  59.222  1.00  0.00              
ATOM     43  C   LEU    95      75.061  71.984  58.799  1.00  0.00              
ATOM     44  O   LEU    95      76.223  71.601  58.718  1.00  0.00              
ATOM     45  N   LYS    96      74.025  71.181  58.535  1.00  0.00              
ATOM     46  CA  LYS    96      74.217  69.786  58.154  1.00  0.00              
ATOM     47  C   LYS    96      74.692  69.654  56.705  1.00  0.00              
ATOM     48  O   LYS    96      75.340  68.668  56.360  1.00  0.00              
END
