
#######################################################
#                                                     #
#                        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    4 (   16),  selected    4 , name T0298AL242_3-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298AL242_3-D1.T0298_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:     4       316 - 319         0.56     0.56
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.56     0.56
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.56     0.56
  LCS_AVERAGE:      2.70

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:  148
LCS_GDT     V     316     V     316      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     R     317     R     317      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     K     318     K     318      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     G     319     G     319      4    4    4     0    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   2.70  (   2.70    2.70    2.70 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   2.03   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70
GDT RMS_LOCAL    0.35   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56
GDT RMS_ALL_CA   0.71   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.274
LGA    R     317      R     317          0.532
LGA    K     318      K     318          0.557
LGA    G     319      G     319          0.759

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.56     2.703     2.703     0.608

LGA_LOCAL      RMSD =  0.558  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.558  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.558  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.866984 * X  +  -0.498181 * Y  +   0.012386 * Z  + -41.160358
  Y_new =  -0.264274 * X  +  -0.438560 * Y  +   0.858967 * Z  +  87.311981
  Z_new =  -0.422489 * X  +  -0.747984 * Y  +  -0.511881 * Z  +  59.532078 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.170940    0.970653  [ DEG:  -124.3857     55.6143 ]
  Theta =   0.436190    2.705403  [ DEG:    24.9918    155.0082 ]
  Phi   =  -0.295873    2.845720  [ DEG:   -16.9523    163.0477 ]
 
# 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: T0298AL242_3-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298AL242_3-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  148   4.0    4   0.56   2.703     0.56
REMARK  ---------------------------------------------------------- 
MOLECULE T0298AL242_3-D1
REMARK Aligment from pdb entry: 1brm_A
ATOM    745  N   VAL   316     -13.408  65.846   3.980  1.00  0.00              
ATOM    746  CA  VAL   316     -14.089  65.320   2.808  1.00  0.00              
ATOM    747  C   VAL   316     -15.600  65.487   2.843  1.00  0.00              
ATOM    748  O   VAL   316     -16.240  65.570   1.794  1.00  0.00              
ATOM    749  N   ARG   317     -16.170  65.546   4.041  1.00  0.00              
ATOM    750  CA  ARG   317     -17.611  65.696   4.176  1.00  0.00              
ATOM    751  C   ARG   317     -18.046  67.157   4.156  1.00  0.00              
ATOM    752  O   ARG   317     -18.234  67.737   3.087  1.00  0.00              
ATOM    753  N   LYS   318     -18.200  67.753   5.331  1.00  0.00              
ATOM    754  CA  LYS   318     -18.632  69.140   5.423  1.00  0.00              
ATOM    755  C   LYS   318     -17.635  70.069   4.752  1.00  0.00              
ATOM    756  O   LYS   318     -17.991  71.156   4.300  1.00  0.00              
ATOM    757  N   GLY   319     -16.382  69.637   4.689  1.00  0.00              
ATOM    758  CA  GLY   319     -15.359  70.462   4.080  1.00  0.00              
ATOM    759  C   GLY   319     -15.322  70.362   2.573  1.00  0.00              
ATOM    760  O   GLY   319     -14.650  71.158   1.921  1.00  0.00              
END
