
#######################################################
#                                                     #
#                        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    8 (   68),  selected    8 , name T0316TS186_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected    8 , name T0316_D2.pdb
# PARAMETERS: T0316TS186_1-D2.T0316_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:     8       276 - 283         4.41     4.41
  LCS_AVERAGE:     13.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       278 - 282         1.68     6.60
  LCS_AVERAGE:      7.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       276 - 279         0.31     7.52
  LCS_AVERAGE:      6.25

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:   60
LCS_GDT     Q     276     Q     276      4    4    8     4    4    4    4    4    4    5    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     G     277     G     277      4    4    8     4    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     F     278     F     278      4    5    8     4    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     Y     279     Y     279      4    5    8     4    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     H     280     H     280      4    5    8     3    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     D     281     D     281      4    5    8     3    4    4    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     S     282     S     282      3    5    8     0    3    3    4    4    5    6    6    6    7    7    7    7    7    7    7    8    8    8    8 
LCS_GDT     L     283     L     283      3    3    8     0    3    3    3    3    4    4    4    4    5    5    5    7    7    7    7    8    8    8    8 
LCS_AVERAGE  LCS_A:   9.03  (   6.25    7.50   13.33 )

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      4      4      4      5      6      6      6      7      7      7      7      7      7      7      8      8      8      8 
GDT PERCENT_CA   6.67   6.67   6.67   6.67   6.67   8.33  10.00  10.00  10.00  11.67  11.67  11.67  11.67  11.67  11.67  11.67  13.33  13.33  13.33  13.33
GDT RMS_LOCAL    0.31   0.31   0.31   0.31   0.31   1.68   2.63   2.57   2.57   3.20   3.20   3.20   3.20   3.20   3.20   3.20   4.41   4.41   4.41   4.41
GDT RMS_ALL_CA   7.52   7.52   7.52   7.52   7.52   6.60   4.85   5.49   5.49   4.77   4.77   4.77   4.77   4.77   4.77   4.77   4.41   4.41   4.41   4.41

#      Molecule1      Molecule2       DISTANCE
LGA    Q     276      Q     276          3.267
LGA    G     277      G     277          1.670
LGA    F     278      F     278          1.098
LGA    Y     279      Y     279          2.441
LGA    H     280      H     280          3.770
LGA    D     281      D     281          2.170
LGA    S     282      S     282          7.163
LGA    L     283      L     283         12.276

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8   60    4.0      6    2.57     8.750     8.754     0.225

LGA_LOCAL      RMSD =  2.567  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.495  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.406  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.641213 * X  +   0.584993 * Y  +  -0.496618 * Z  +  40.784145
  Y_new =  -0.681244 * X  +  -0.731847 * Y  +   0.017513 * Z  +  38.865536
  Z_new =  -0.353203 * X  +   0.349548 * Y  +   0.867792 * Z  + -24.806738 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.382919   -2.758674  [ DEG:    21.9396   -158.0604 ]
  Theta =   0.360993    2.780600  [ DEG:    20.6834    159.3166 ]
  Phi   =  -2.325933    0.815660  [ DEG:  -133.2661     46.7339 ]
 
# 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: T0316TS186_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS186_1-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8   60   4.0    6   2.57   8.754     4.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS186_1-D2
PFRMAT TS
TARGET T0316
MODEL  1
PARENT 1vl2_A
ATOM   1352  N   GLN   276      25.724  22.588 -26.116  1.00  0.00
ATOM   1353  CA  GLN   276      24.912  23.634 -25.544  1.00  0.00
ATOM   1354  C   GLN   276      23.555  23.216 -24.975  1.00  0.00
ATOM   1355  O   GLN   276      22.558  23.939 -25.151  1.00  0.00
ATOM   1356  CB  GLN   276      24.595  24.701 -26.594  1.00  0.00
ATOM   1357  CG  GLN   276      25.805  25.491 -27.063  1.00  0.00
ATOM   1358  CD  GLN   276      25.466  26.478 -28.162  1.00  0.00
ATOM   1359  OE1 GLN   276      24.322  26.559 -28.606  1.00  0.00
ATOM   1360  NE2 GLN   276      26.466  27.233 -28.606  1.00  0.00
ATOM   1361  N   GLY   277      23.528  22.059 -24.334  1.00  0.00
ATOM   1362  CA  GLY   277      22.345  21.552 -23.634  1.00  0.00
ATOM   1363  C   GLY   277      22.787  20.983 -22.288  1.00  0.00
ATOM   1364  O   GLY   277      23.959  20.595 -22.145  1.00  0.00
ATOM   1365  N   PHE   278      21.862  20.945 -21.331  1.00  0.00
ATOM   1366  CA  PHE   278      22.072  20.205 -20.073  1.00  0.00
ATOM   1367  C   PHE   278      21.737  18.746 -20.333  1.00  0.00
ATOM   1368  O   PHE   278      20.617  18.454 -20.671  1.00  0.00
ATOM   1369  CB  PHE   278      21.166  20.757 -18.969  1.00  0.00
ATOM   1370  CG  PHE   278      21.346  20.078 -17.642  1.00  0.00
ATOM   1371  CD1 PHE   278      22.468  20.322 -16.870  1.00  0.00
ATOM   1372  CD2 PHE   278      20.393  19.194 -17.165  1.00  0.00
ATOM   1373  CE1 PHE   278      22.634  19.697 -15.648  1.00  0.00
ATOM   1374  CE2 PHE   278      20.559  18.569 -15.944  1.00  0.00
ATOM   1375  CZ  PHE   278      21.673  18.817 -15.186  1.00  0.00
ATOM   1376  N   TYR   279      22.701  17.838 -20.165  1.00  0.00
ATOM   1377  CA  TYR   279      22.508  16.447 -20.552  1.00  0.00
ATOM   1378  C   TYR   279      22.869  15.542 -19.378  1.00  0.00
ATOM   1379  O   TYR   279      23.819  15.851 -18.643  1.00  0.00
ATOM   1380  CB  TYR   279      23.397  16.094 -21.746  1.00  0.00
ATOM   1381  CG  TYR   279      23.074  16.873 -23.001  1.00  0.00
ATOM   1382  CD1 TYR   279      23.690  18.089 -23.263  1.00  0.00
ATOM   1383  CD2 TYR   279      22.152  16.388 -23.921  1.00  0.00
ATOM   1384  CE1 TYR   279      23.401  18.807 -24.408  1.00  0.00
ATOM   1385  CE2 TYR   279      21.850  17.092 -25.071  1.00  0.00
ATOM   1386  CZ  TYR   279      22.485  18.311 -25.309  1.00  0.00
ATOM   1387  OH  TYR   279      22.195  19.024 -26.449  1.00  0.00
ATOM   1388  N   HIS   280      22.054  14.513 -19.161  1.00  0.00
ATOM   1389  CA  HIS   280      22.328  13.462 -18.147  1.00  0.00
ATOM   1390  C   HIS   280      22.311  12.164 -18.902  1.00  0.00
ATOM   1391  O   HIS   280      21.417  11.952 -19.681  1.00  0.00
ATOM   1392  CB  HIS   280      21.255  13.477 -17.057  1.00  0.00
ATOM   1393  CG  HIS   280      21.486  12.477 -15.968  1.00  0.00
ATOM   1394  ND1 HIS   280      21.009  11.186 -16.027  1.00  0.00
ATOM   1395  CD2 HIS   280      22.170  12.482 -14.681  1.00  0.00
ATOM   1396  CE1 HIS   280      21.374  10.531 -14.910  1.00  0.00
ATOM   1397  NE2 HIS   280      22.071  11.303 -14.099  1.00  0.00
ATOM   1398  N   ASP   281      23.230  11.261 -18.628  1.00  0.00
ATOM   1399  CA  ASP   281      23.236   9.999 -19.352  1.00  0.00
ATOM   1400  C   ASP   281      23.491   8.805 -18.422  1.00  0.00
ATOM   1401  O   ASP   281      24.282   8.894 -17.467  1.00  0.00
ATOM   1402  CB  ASP   281      24.333   9.999 -20.418  1.00  0.00
ATOM   1403  CG  ASP   281      24.228   8.817 -21.361  1.00  0.00
ATOM   1404  OD1 ASP   281      23.243   8.057 -21.254  1.00  0.00
ATOM   1405  OD2 ASP   281      25.130   8.651 -22.209  1.00  0.00
ATOM   1406  N   SER   282      22.805   7.717 -18.683  1.00  0.00
ATOM   1407  CA  SER   282      23.051   6.470 -17.952  1.00  0.00
ATOM   1408  C   SER   282      22.670   5.341 -18.871  1.00  0.00
ATOM   1409  O   SER   282      22.330   5.572 -20.069  1.00  0.00
ATOM   1410  CB  SER   282      22.208   6.422 -16.676  1.00  0.00
ATOM   1411  OG  SER   282      20.826   6.342 -16.981  1.00  0.00
ATOM   1412  N   LEU   283      22.691   4.117 -18.355  1.00  0.00
ATOM   1413  CA  LEU   283      22.365   2.968 -19.154  1.00  0.00
ATOM   1414  C   LEU   283      20.953   2.964 -19.698  1.00  0.00
ATOM   1415  O   LEU   283      20.663   2.280 -20.660  1.00  0.00
ATOM   1416  CB  LEU   283      22.554   1.687 -18.294  1.00  0.00
ATOM   1417  CG  LEU   283      22.805   0.403 -19.028  1.00  0.00
ATOM   1418  CD1 LEU   283      24.185   0.389 -19.688  1.00  0.00
ATOM   1419  CD2 LEU   283      22.644  -0.746 -17.995  1.00  0.00
TER
END
