
#######################################################
#                                                     #
#                        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 (   39),  selected    5 , name T0298TS671_3-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    5 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_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:     5       129 - 319         0.87     0.87
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       129 - 319         0.87     0.87
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       129 - 319         0.87     0.87
  LCS_AVERAGE:      3.38

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      5    5    5     0    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     316     V     316      5    5    5     4    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      5    5    5     4    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      5    5    5     4    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      5    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.38  (   3.38    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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.70   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    0.30   0.30   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87
GDT RMS_ALL_CA   1.66   1.66   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87

#      Molecule1      Molecule2       DISTANCE
LGA    P     129      P     129          1.111
LGA    V     316      V     316          0.613
LGA    R     317      R     317          0.480
LGA    K     318      K     318          0.924
LGA    G     319      G     319          1.065

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  148    4.0      5    0.87     3.209     3.325     0.513

LGA_LOCAL      RMSD =  0.875  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.875  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.875  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.319202 * X  +   0.935706 * Y  +   0.150216 * Z  + -45.430798
  Y_new =   0.005123 * X  +   0.160210 * Y  +  -0.987070 * Z  +  54.601307
  Z_new =  -0.947673 * X  +  -0.314305 * Y  +  -0.055933 * Z  + -28.518391 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.746911    1.394682  [ DEG:  -100.0906     79.9094 ]
  Theta =   1.245866    1.895727  [ DEG:    71.3829    108.6171 ]
  Phi   =   3.125544   -0.016049  [ DEG:   179.0805     -0.9195 ]
 
# 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: T0298TS671_3-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_3-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   0.87   3.325     0.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_3-D1
PFRMAT TS
TARGET T0298
MODEL  3  REFINED
PARENT 1PQP_A 1MB4_B 1T4B_B
ATOM      1  N   PRO   129     -13.969  77.248  -0.590  1.00  0.00
ATOM      2  CA  PRO   129     -13.989  75.929  -0.998  1.00  0.00
ATOM      3  C   PRO   129     -12.987  75.032  -0.285  1.00  0.00
ATOM      4  O   PRO   129     -13.304  73.867  -0.073  1.00  0.00
ATOM      5  CB  PRO   129     -13.735  75.998  -2.528  1.00  0.00
ATOM      6  CG  PRO   129     -14.379  77.289  -2.846  1.00  0.00
ATOM      7  CD  PRO   129     -13.829  78.074  -1.689  1.00  0.00
ATOM   1402  N   VAL   316     -13.602  65.515   4.757  1.00  0.00
ATOM   1403  CA  VAL   316     -14.140  64.922   3.540  1.00  0.00
ATOM   1404  C   VAL   316     -15.603  65.369   3.208  1.00  0.00
ATOM   1405  O   VAL   316     -15.904  65.389   2.009  1.00  0.00
ATOM   1406  CB  VAL   316     -14.065  63.385   3.621  1.00  0.00
ATOM   1407  CG1 VAL   316     -14.444  62.755   2.246  1.00  0.00
ATOM   1408  CG2 VAL   316     -12.647  62.968   4.009  1.00  0.00
ATOM   1409  N   ARG   317     -16.553  65.449   4.176  1.00  0.00
ATOM   1410  CA  ARG   317     -17.964  65.762   3.914  1.00  0.00
ATOM   1411  C   ARG   317     -18.285  67.281   3.786  1.00  0.00
ATOM   1412  O   ARG   317     -18.530  67.683   2.659  1.00  0.00
ATOM   1413  CB  ARG   317     -18.827  65.187   5.029  1.00  0.00
ATOM   1414  CG  ARG   317     -18.985  63.723   5.137  1.00  0.00
ATOM   1415  CD  ARG   317     -20.118  63.199   4.347  1.00  0.00
ATOM   1416  NE  ARG   317     -21.168  62.569   5.165  1.00  0.00
ATOM   1417  CZ  ARG   317     -22.363  63.136   5.324  1.00  0.00
ATOM   1418  NH1 ARG   317     -22.762  64.232   4.700  1.00  0.00
ATOM   1419  NH2 ARG   317     -23.142  62.629   6.289  1.00  0.00
ATOM   1420  N   LYS   318     -17.922  68.147   4.755  1.00  0.00
ATOM   1421  CA  LYS   318     -18.152  69.571   4.747  1.00  0.00
ATOM   1422  C   LYS   318     -17.087  70.334   3.928  1.00  0.00
ATOM   1423  O   LYS   318     -17.414  71.127   3.050  1.00  0.00
ATOM   1424  CB  LYS   318     -18.050  70.111   6.191  1.00  0.00
ATOM   1425  CG  LYS   318     -19.266  69.768   7.028  1.00  0.00
ATOM   1426  CD  LYS   318     -20.439  70.687   6.756  1.00  0.00
ATOM   1427  CE  LYS   318     -21.339  70.817   7.988  1.00  0.00
ATOM   1428  NZ  LYS   318     -22.747  70.885   7.469  1.00  0.00
ATOM   1429  N   GLY   319     -15.808  70.085   4.195  1.00  0.00
ATOM   1430  CA  GLY   319     -14.693  70.648   3.508  1.00  0.00
ATOM   1431  C   GLY   319     -14.394  69.831   2.233  1.00  0.00
ATOM   1432  O   GLY   319     -13.363  70.000   1.588  1.00  0.00
ATOM   1433  OXT GLY   319     -15.292  69.050   1.828  1.00  0.00
TER
END
