
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS028_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS028_4-D1.T0372_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:     8       291 - 298         4.96     7.17
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       290 - 294         1.93    12.04
  LONGEST_CONTINUOUS_SEGMENT:     5       294 - 298         1.91     9.63
  LCS_AVERAGE:      3.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       294 - 297         0.56     9.50
  LCS_AVERAGE:      2.73

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:  126
LCS_GDT     K     290     K     290      3    5    7     3    3    4    4    4    5    5    5    5    5    5    5    6    6    6    6    7    7    7    8 
LCS_GDT     Y     291     Y     291      3    5    8     3    3    4    4    4    5    5    5    5    5    6    6    6    7    7    8    8    8    8    8 
LCS_GDT     M     292     M     292      3    5    8     3    3    4    4    4    5    5    5    5    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     A     293     A     293      3    5    8     3    3    4    4    4    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     C     294     C     294      4    5    8     3    4    4    4    4    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     L     295     L     295      4    5    8     3    4    4    4    4    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     K     296     K     296      4    5    8     3    4    4    4    4    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     D     297     D     297      4    5    8     3    4    4    4    4    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_GDT     H     298     H     298      3    5    8     0    3    3    3    3    5    6    6    6    6    7    7    7    7    7    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.32  (   2.73    3.97    6.26 )

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      5      6      6      6      6      7      7      7      7      7      8      8      8      8      8 
GDT PERCENT_CA   2.38   3.17   3.17   3.17   3.17   3.97   4.76   4.76   4.76   4.76   5.56   5.56   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.20   0.56   0.56   0.56   0.56   1.93   2.50   2.50   2.50   2.50   3.53   3.53   3.53   3.53   3.53   4.96   4.96   4.96   4.96   4.96
GDT RMS_ALL_CA   9.14   9.50   9.50   9.50   9.50  12.04   8.83   8.83   8.83   8.83   8.01   8.01   8.01   8.01   8.01   7.17   7.17   7.17   7.17   7.17

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         20.477
LGA    Y     291      Y     291         13.399
LGA    M     292      M     292          8.028
LGA    A     293      A     293          2.967
LGA    C     294      C     294          3.006
LGA    L     295      L     295          2.479
LGA    K     296      K     296          0.660
LGA    D     297      D     297          2.590
LGA    H     298      H     298          2.551

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    2.50     4.365     4.247     0.230

LGA_LOCAL      RMSD =  2.505  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.825  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  6.718  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.106835 * X  +   0.078566 * Y  +   0.991168 * Z  +  32.967026
  Y_new =   0.528925 * X  +  -0.839625 * Y  +   0.123565 * Z  +  27.904402
  Z_new =   0.841917 * X  +   0.537455 * Y  +   0.048146 * Z  + -56.515369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.481453   -1.660140  [ DEG:    84.8810    -95.1190 ]
  Theta =  -1.000826   -2.140767  [ DEG:   -57.3431   -122.6569 ]
  Phi   =   1.770100   -1.371493  [ DEG:   101.4193    -78.5807 ]
 
# 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: T0372TS028_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS028_4-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    6   2.50   4.247     6.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS028_4-D1
PFRMAT TS
TARGET T0372
MODEL 4
PARENT 1s7f-A
ATOM   1236  N   LYS   290      27.508  44.637 -14.310  1.00  9.00
ATOM   1237  CA  LYS   290      28.219  44.162 -13.114  1.00  9.00
ATOM   1238  C   LYS   290      27.672  44.753 -11.825  1.00  9.00
ATOM   1239  O   LYS   290      27.658  45.976 -11.652  1.00  9.00
ATOM   1240  CB  LYS   290      29.699  44.504 -13.241  1.00  9.00
ATOM   1241  CG  LYS   290      30.347  43.731 -14.383  1.00  9.00
ATOM   1242  CD  LYS   290      30.217  42.225 -14.171  1.00  9.00
ATOM   1243  CE  LYS   290      30.813  41.447 -15.337  1.00  9.00
ATOM   1244  NZ  LYS   290      30.666  39.998 -15.126  1.00  9.00
ATOM   1245  N   TYR   291      27.237  43.887 -10.927  1.00  9.00
ATOM   1246  CA  TYR   291      26.786  44.353  -9.614  1.00  9.00
ATOM   1247  C   TYR   291      27.975  44.462  -8.661  1.00  9.00
ATOM   1248  O   TYR   291      28.620  43.464  -8.319  1.00  9.00
ATOM   1249  CB  TYR   291      25.742  43.391  -9.056  1.00  9.00
ATOM   1250  CG  TYR   291      25.098  43.870  -7.757  1.00  9.00
ATOM   1251  CD1 TYR   291      24.123  44.858  -7.796  1.00  9.00
ATOM   1252  CD2 TYR   291      25.492  43.327  -6.539  1.00  9.00
ATOM   1253  CE1 TYR   291      23.540  45.304  -6.620  1.00  9.00
ATOM   1254  CE2 TYR   291      24.908  43.774  -5.359  1.00  9.00
ATOM   1255  CZ  TYR   291      23.934  44.763  -5.405  1.00  9.00
ATOM   1256  OH  TYR   291      23.385  45.238  -4.233  1.00  9.00
ATOM   1257  N   MET   292      28.232  45.682  -8.224  1.00  9.00
ATOM   1258  CA  MET   292      29.359  45.959  -7.333  1.00  9.00
ATOM   1259  C   MET   292      28.985  47.036  -6.317  1.00  9.00
ATOM   1260  O   MET   292      28.570  48.144  -6.682  1.00  9.00
ATOM   1261  CB  MET   292      30.552  46.397  -8.186  1.00  9.00
ATOM   1262  CG  MET   292      31.805  46.673  -7.356  1.00  9.00
ATOM   1263  SD  MET   292      32.432  45.288  -6.376  1.00  9.00
ATOM   1264  CE  MET   292      32.806  44.121  -7.706  1.00  9.00
ATOM   1265  N   ALA   293      29.085  46.659  -5.049  1.00  9.00
ATOM   1266  CA  ALA   293      28.813  47.550  -3.906  1.00  9.00
ATOM   1267  C   ALA   293      27.506  48.323  -4.049  1.00  9.00
ATOM   1268  O   ALA   293      27.513  49.523  -4.351  1.00  9.00
ATOM   1269  CB  ALA   293      29.980  48.519  -3.742  1.00  9.00
ATOM   1270  N   CYS   294      26.416  47.568  -3.999  1.00  9.00
ATOM   1271  CA  CYS   294      25.024  48.063  -4.064  1.00  9.00
ATOM   1272  C   CYS   294      24.529  48.571  -5.429  1.00  9.00
ATOM   1273  O   CYS   294      23.311  48.695  -5.599  1.00  9.00
ATOM   1274  CB  CYS   294      24.830  49.171  -3.030  1.00  9.00
ATOM   1275  SG  CYS   294      25.147  48.710  -1.310  1.00  9.00
ATOM   1276  N   LEU   295      25.403  48.799  -6.397  1.00  9.00
ATOM   1277  CA  LEU   295      24.935  49.304  -7.695  1.00  9.00
ATOM   1278  C   LEU   295      25.280  48.398  -8.867  1.00  9.00
ATOM   1279  O   LEU   295      26.055  47.442  -8.750  1.00  9.00
ATOM   1280  CB  LEU   295      25.553  50.673  -7.946  1.00  9.00
ATOM   1281  CG  LEU   295      24.996  51.728  -7.000  1.00  9.00
ATOM   1282  CD1 LEU   295      25.703  53.063  -7.202  1.00  9.00
ATOM   1283  CD2 LEU   295      23.491  51.886  -7.193  1.00  9.00
ATOM   1284  N   LYS   296      24.568  48.629  -9.956  1.00  9.00
ATOM   1285  CA  LYS   296      24.892  47.990 -11.232  1.00  9.00
ATOM   1286  C   LYS   296      25.712  48.956 -12.083  1.00  9.00
ATOM   1287  O   LYS   296      25.341  50.117 -12.272  1.00  9.00
ATOM   1288  CB  LYS   296      23.604  47.643 -11.963  1.00  9.00
ATOM   1289  CG  LYS   296      22.723  46.686 -11.173  1.00  9.00
ATOM   1290  CD  LYS   296      21.433  46.412 -11.939  1.00  9.00
ATOM   1291  CE  LYS   296      20.502  45.478 -11.177  1.00  9.00
ATOM   1292  NZ  LYS   296      19.257  45.256 -11.932  1.00  9.00
ATOM   1293  N   ASP   297      26.853  48.483 -12.544  1.00  9.00
ATOM   1294  CA  ASP   297      27.780  49.329 -13.307  1.00  9.00
ATOM   1295  C   ASP   297      27.812  48.979 -14.793  1.00  9.00
ATOM   1296  O   ASP   297      27.564  47.830 -15.177  1.00  9.00
ATOM   1297  CB  ASP   297      29.174  49.135 -12.720  1.00  9.00
ATOM   1298  CG  ASP   297      29.206  49.535 -11.246  1.00  9.00
ATOM   1299  OD1 ASP   297      28.582  50.534 -10.913  1.00  9.00
ATOM   1300  OD2 ASP   297      29.932  48.893 -10.500  1.00  9.00
ATOM   1301  N   HIS   298      28.023  49.998 -15.614  1.00  9.00
ATOM   1302  CA  HIS   298      28.247  49.811 -17.063  1.00  9.00
ATOM   1303  C   HIS   298      29.709  49.490 -17.365  1.00  9.00
ATOM   1304  O   HIS   298      30.560  50.339 -17.089  1.00  9.00
ATOM   1305  CB  HIS   298      27.976  51.129 -17.784  1.00  9.00
ATOM   1306  CG  HIS   298      26.572  51.686 -17.735  1.00  9.00
ATOM   1307  ND1 HIS   298      25.583  51.411 -18.602  1.00  9.00
ATOM   1308  CD2 HIS   298      26.071  52.591 -16.828  1.00  9.00
ATOM   1309  CE1 HIS   298      24.478  52.102 -18.254  1.00  9.00
ATOM   1310  NE2 HIS   298      24.782  52.832 -17.157  1.00  9.00
TER
END
