
#######################################################
#                                                     #
#                        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    5 (   20),  selected    5 , name T0298AL333_1-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    5 , name T0298_D1.pdb
# PARAMETERS: T0298AL333_1-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:     5       129 - 319         1.05     1.05
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       129 - 319         1.05     1.05
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       129 - 318         0.86     1.14
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.60     1.90
  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     P     129     P     129      4    5    5     0    3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     316     V     316      4    5    5     3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     R     317     R     317      4    5    5     3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     318     K     318      4    5    5     3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     319     G     319      4    5    5     0    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.15  (   2.70    3.38    3.38 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.03   2.70   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38   3.38
GDT RMS_LOCAL    0.32   0.60   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05
GDT RMS_ALL_CA   1.72   1.90   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05   1.05

#      Molecule1      Molecule2       DISTANCE
LGA    P     129      P     129          1.170
LGA    V     316      V     316          0.528
LGA    R     317      R     317          0.733
LGA    K     318      K     318          1.223
LGA    G     319      G     319          1.339

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  148    4.0      5    1.05     3.209     3.325     0.436

LGA_LOCAL      RMSD =  1.047  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.047  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.047  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.924254 * X  +  -0.156687 * Y  +   0.348142 * Z  + -46.185219
  Y_new =   0.164586 * X  +   0.986338 * Y  +   0.006971 * Z  +  -0.633779
  Z_new =  -0.344478 * X  +   0.050856 * Y  +   0.937416 * Z  + -55.946281 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.054198   -3.087394  [ DEG:     3.1053   -176.8947 ]
  Theta =   0.351683    2.789910  [ DEG:    20.1499    159.8501 ]
  Phi   =   0.176227   -2.965365  [ DEG:    10.0971   -169.9029 ]
 
# 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: T0298AL333_1-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298AL333_1-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  148   4.0    5   1.05   3.325     1.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0298AL333_1-D1
REMARK Aligment from pdb entry: 1nwc_A
ATOM      1  N   PRO   129     -15.124  75.126  -1.635  1.00  0.00              
ATOM      2  CA  PRO   129     -14.072  75.901  -1.004  1.00  0.00              
ATOM      3  C   PRO   129     -13.064  75.089  -0.211  1.00  0.00              
ATOM      4  O   PRO   129     -13.239  73.884  -0.003  1.00  0.00              
ATOM    749  N   VAL   316     -13.624  65.541   4.716  1.00  0.00              
ATOM    750  CA  VAL   316     -14.139  64.977   3.472  1.00  0.00              
ATOM    751  C   VAL   316     -15.598  65.314   3.166  1.00  0.00              
ATOM    752  O   VAL   316     -16.018  65.268   2.009  1.00  0.00              
ATOM    753  N   ARG   317     -16.363  65.667   4.193  1.00  0.00              
ATOM    754  CA  ARG   317     -17.771  66.012   4.003  1.00  0.00              
ATOM    755  C   ARG   317     -17.956  67.516   3.740  1.00  0.00              
ATOM    756  O   ARG   317     -17.910  67.940   2.583  1.00  0.00              
ATOM    757  N   LYS   318     -18.160  68.328   4.776  1.00  0.00              
ATOM    758  CA  LYS   318     -18.316  69.769   4.538  1.00  0.00              
ATOM    759  C   LYS   318     -17.022  70.374   3.988  1.00  0.00              
ATOM    760  O   LYS   318     -17.034  71.444   3.377  1.00  0.00              
ATOM    761  N   GLY   319     -15.909  69.679   4.196  1.00  0.00              
ATOM    762  CA  GLY   319     -14.641  70.172   3.702  1.00  0.00              
ATOM    763  C   GLY   319     -14.354  69.800   2.256  1.00  0.00              
ATOM    764  O   GLY   319     -13.415  70.328   1.666  1.00  0.00              
END
