
#######################################################
#                                                     #
#                        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 (   32),  selected    4 , name T0298TS021_1_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS021_1_2-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         0.48     0.48
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.48     0.48
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.48     0.48
  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    0.09   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48
GDT RMS_ALL_CA   0.61   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.368
LGA    R     317      R     317          0.322
LGA    K     318      K     318          0.298
LGA    G     319      G     319          0.765

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.48     2.703     2.703     0.692

LGA_LOCAL      RMSD =  0.478  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.478  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.478  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.944088 * X  +   0.100377 * Y  +  -0.314043 * Z  + -41.110008
  Y_new =  -0.248979 * X  +  -0.841461 * Y  +   0.479534 * Z  + 133.296158
  Z_new =  -0.216121 * X  +   0.530912 * Y  +   0.819404 * Z  +  -5.341223 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.574915   -2.566678  [ DEG:    32.9402   -147.0598 ]
  Theta =   0.217840    2.923753  [ DEG:    12.4813    167.5187 ]
  Phi   =  -2.883739    0.257853  [ DEG:  -165.2261     14.7739 ]
 
# 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: T0298TS021_1_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS021_1_2-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   0.48   2.703     0.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS021_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT N/A
ATOM   1384  N   VAL   316     -13.511  65.926   4.270  1.00108.75       1SG1385
ATOM   1385  CA  VAL   316     -14.172  65.585   3.044  1.00108.75       1SG1386
ATOM   1386  CB  VAL   316     -13.978  64.142   2.645  1.00108.75       1SG1387
ATOM   1387  CG1 VAL   316     -14.676  63.208   3.647  1.00108.75       1SG1388
ATOM   1388  CG2 VAL   316     -14.466  63.971   1.197  1.00108.75       1SG1389
ATOM   1389  C   VAL   316     -15.640  65.897   3.062  1.00108.75       1SG1390
ATOM   1390  O   VAL   316     -16.135  66.581   2.168  1.00108.75       1SG1391
ATOM   1391  N   ARG   317     -16.389  65.412   4.074  1.00190.23       1SG1392
ATOM   1392  CA  ARG   317     -17.810  65.591   3.973  1.00190.23       1SG1393
ATOM   1393  CB  ARG   317     -18.588  64.809   5.047  1.00190.23       1SG1394
ATOM   1394  CG  ARG   317     -20.104  64.936   4.899  1.00190.23       1SG1395
ATOM   1395  CD  ARG   317     -20.615  64.422   3.552  1.00190.23       1SG1396
ATOM   1396  NE  ARG   317     -20.053  63.055   3.350  1.00190.23       1SG1397
ATOM   1397  CZ  ARG   317     -20.494  62.283   2.314  1.00190.23       1SG1398
ATOM   1398  NH1 ARG   317     -21.463  62.757   1.476  1.00190.23       1SG1399
ATOM   1399  NH2 ARG   317     -19.967  61.041   2.111  1.00190.23       1SG1400
ATOM   1400  C   ARG   317     -18.225  67.024   4.079  1.00190.23       1SG1401
ATOM   1401  O   ARG   317     -18.756  67.609   3.136  1.00190.23       1SG1402
ATOM   1402  N   LYS   318     -17.951  67.630   5.244  1.00 73.33       1SG1403
ATOM   1403  CA  LYS   318     -18.359  68.969   5.545  1.00 73.33       1SG1404
ATOM   1404  CB  LYS   318     -18.113  69.257   7.025  1.00 73.33       1SG1405
ATOM   1405  CG  LYS   318     -18.752  68.157   7.869  1.00 73.33       1SG1406
ATOM   1406  CD  LYS   318     -18.109  67.993   9.240  1.00 73.33       1SG1407
ATOM   1407  CE  LYS   318     -18.297  66.594   9.821  1.00 73.33       1SG1408
ATOM   1408  NZ  LYS   318     -17.210  66.297  10.778  1.00 73.33       1SG1409
ATOM   1409  C   LYS   318     -17.541  69.905   4.728  1.00 73.33       1SG1410
ATOM   1410  O   LYS   318     -18.049  70.871   4.159  1.00 73.33       1SG1411
ATOM   1411  N   GLY   319     -16.231  69.618   4.649  1.00 22.67       1SG1412
ATOM   1412  CA  GLY   319     -15.349  70.474   3.926  1.00 22.67       1SG1413
ATOM   1413  C   GLY   319     -15.579  70.206   2.444  1.00 22.67       1SG1414
ATOM   1414  O   GLY   319     -14.568  70.187   1.692  1.00 22.67       1SG1415
ATOM   1415  OXT GLY   319     -16.758  70.019   2.046  1.00 22.67       1SG1416
TER
END
