
#######################################################
#                                                     #
#                        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    6 (   24),  selected    6 , name T0295AL333_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected    6 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_5-D2.T0295_D2.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:     6       266 - 271         2.45     2.45
  LCS_AVERAGE:      6.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       267 - 271         1.31     3.23
  LCS_AVERAGE:      5.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       268 - 271         0.41     4.17
  LCS_AVERAGE:      3.86

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:   95
LCS_GDT     E     266     E     266      3    4    6     0    3    3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F     267     F     267      3    5    6     3    3    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     N     268     N     268      4    5    6     3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K     269     K     269      4    5    6     3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K     270     K     270      4    5    6     3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     271     G     271      4    5    6     3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   5.09  (   3.86    5.09    6.32 )

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      3      4      4      5      5      5      5      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   3.16   4.21   4.21   5.26   5.26   5.26   5.26   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32   6.32
GDT RMS_LOCAL    0.02   0.41   0.41   1.31   1.31   1.31   1.31   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45
GDT RMS_ALL_CA   3.94   4.17   4.17   3.23   3.23   3.23   3.23   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45   2.45

#      Molecule1      Molecule2       DISTANCE
LGA    E     266      E     266          3.501
LGA    F     267      F     267          1.382
LGA    N     268      N     268          1.542
LGA    K     269      K     269          2.700
LGA    K     270      K     270          1.776
LGA    G     271      G     271          3.028

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   95    4.0      6    2.45     5.526     5.418     0.235

LGA_LOCAL      RMSD =  2.455  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.455  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.455  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.926362 * X  +   0.169855 * Y  +  -0.336159 * Z  +  28.762764
  Y_new =   0.045159 * X  +   0.836003 * Y  +   0.546863 * Z  +  30.889046
  Z_new =   0.373918 * X  +  -0.521774 * Y  +   0.766771 * Z  + -22.372635 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.597507    2.544086  [ DEG:   -34.2346    145.7654 ]
  Theta =  -0.383229   -2.758363  [ DEG:   -21.9574   -158.0426 ]
  Phi   =   0.048710   -3.092882  [ DEG:     2.7909   -177.2091 ]
 
# 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: T0295AL333_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_5-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   95   4.0    6   2.45   5.418     2.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_5-D2
REMARK Aligment from pdb entry: 1dl5_A
ATOM    585  N   GLU   266      27.974  20.379  -4.086  1.00  0.00              
ATOM    586  CA  GLU   266      28.257  19.737  -2.801  1.00  0.00              
ATOM    587  C   GLU   266      27.390  20.166  -1.632  1.00  0.00              
ATOM    588  O   GLU   266      26.903  21.298  -1.569  1.00  0.00              
ATOM    589  N   PHE   267      27.211  19.237  -0.700  1.00  0.00              
ATOM    590  CA  PHE   267      26.455  19.512   0.509  1.00  0.00              
ATOM    591  C   PHE   267      27.480  19.613   1.623  1.00  0.00              
ATOM    592  O   PHE   267      28.683  19.683   1.348  1.00  0.00              
ATOM    593  N   ASN   268      27.030  19.621   2.874  1.00  0.00              
ATOM    594  CA  ASN   268      27.963  19.712   3.982  1.00  0.00              
ATOM    595  C   ASN   268      28.777  20.998   3.995  1.00  0.00              
ATOM    596  O   ASN   268      28.336  22.032   3.488  1.00  0.00              
ATOM    597  N   LYS   269      29.974  20.933   4.567  1.00  0.00              
ATOM    598  CA  LYS   269      30.846  22.101   4.655  1.00  0.00              
ATOM    599  C   LYS   269      31.459  22.505   3.316  1.00  0.00              
ATOM    600  O   LYS   269      32.193  23.486   3.241  1.00  0.00              
ATOM    601  N   LYS   270      31.167  21.753   2.257  1.00  0.00              
ATOM    602  CA  LYS   270      31.690  22.111   0.946  1.00  0.00              
ATOM    603  C   LYS   270      30.648  22.927   0.184  1.00  0.00              
ATOM    604  O   LYS   270      30.864  23.315  -0.961  1.00  0.00              
ATOM    605  N   GLY   271      29.520  23.202   0.835  1.00  0.00              
ATOM    606  CA  GLY   271      28.470  23.969   0.183  1.00  0.00              
ATOM    607  C   GLY   271      27.840  25.048   1.041  1.00  0.00              
ATOM    608  O   GLY   271      26.808  25.612   0.673  1.00  0.00              
END
