
#######################################################
#                                                     #
#                        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 T0372TS671_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_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:     9       290 - 298         2.74     2.74
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 297         1.84     3.35
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.79     3.69
  LCS_AVERAGE:      3.62

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      4    8    9     3    4    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      5    8    9     3    5    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      5    8    9     3    5    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      5    8    9     3    5    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      5    8    9     3    5    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      5    8    9     3    5    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    8    9     3    4    5    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    8    9     3    4    6    6    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    6    9     3    4    4    4    5    6    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.64  (   3.62    6.17    7.14 )

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      5      6      6      7      8      8      8      8      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.97   4.76   4.76   5.56   6.35   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.05   0.79   1.07   1.07   1.51   1.84   1.84   1.84   1.84   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74
GDT RMS_ALL_CA   9.51   3.69   4.20   4.20   3.30   3.35   3.35   3.35   3.35   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          2.630
LGA    Y     291      Y     291          0.365
LGA    M     292      M     292          1.440
LGA    A     293      A     293          1.286
LGA    C     294      C     294          1.634
LGA    L     295      L     295          1.532
LGA    K     296      K     296          2.598
LGA    D     297      D     297          2.158
LGA    H     298      H     298          8.592

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      8    1.84     5.556     6.027     0.412

LGA_LOCAL      RMSD =  1.844  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.350  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.745  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.152148 * X  +   0.275042 * Y  +  -0.949317 * Z  +  42.793228
  Y_new =  -0.987725 * X  +   0.007950 * Y  +  -0.156001 * Z  +  56.718967
  Z_new =  -0.035359 * X  +   0.961399 * Y  +   0.272876 * Z  +  -6.588535 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.294238   -1.847355  [ DEG:    74.1544   -105.8456 ]
  Theta =   0.035367    3.106226  [ DEG:     2.0264    177.9736 ]
  Phi   =  -1.417958    1.723634  [ DEG:   -81.2430     98.7570 ]
 
# 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: T0372TS671_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_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    8   1.84   6.027     2.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 1NE9_A
ATOM   1245  N   LYS   290      26.983  44.295   6.721  1.00  0.00
ATOM   1246  CA  LYS   290      27.651  45.001   5.589  1.00  0.00
ATOM   1247  C   LYS   290      26.603  45.281   4.470  1.00  0.00
ATOM   1248  O   LYS   290      26.242  44.415   3.659  1.00  0.00
ATOM   1249  CB  LYS   290      28.772  44.137   4.934  1.00  0.00
ATOM   1250  CG  LYS   290      30.132  44.417   5.445  1.00  0.00
ATOM   1251  CD  LYS   290      31.013  44.406   4.154  1.00  0.00
ATOM   1252  CE  LYS   290      32.468  44.732   4.485  1.00  0.00
ATOM   1253  NZ  LYS   290      33.047  43.540   5.214  1.00  0.00
ATOM   1254  N   TYR   291      26.179  46.557   4.463  1.00  0.00
ATOM   1255  CA  TYR   291      25.261  47.144   3.505  1.00  0.00
ATOM   1256  C   TYR   291      26.034  47.450   2.203  1.00  0.00
ATOM   1257  O   TYR   291      26.895  48.349   2.157  1.00  0.00
ATOM   1258  CB  TYR   291      24.659  48.383   4.094  1.00  0.00
ATOM   1259  CG  TYR   291      23.590  48.231   5.139  1.00  0.00
ATOM   1260  CD1 TYR   291      22.329  47.780   4.801  1.00  0.00
ATOM   1261  CD2 TYR   291      23.857  48.507   6.482  1.00  0.00
ATOM   1262  CE1 TYR   291      21.355  47.614   5.761  1.00  0.00
ATOM   1263  CE2 TYR   291      22.891  48.330   7.459  1.00  0.00
ATOM   1264  CZ  TYR   291      21.643  47.886   7.090  1.00  0.00
ATOM   1265  OH  TYR   291      20.635  47.733   8.056  1.00  0.00
ATOM   1266  N   MET   292      25.611  46.788   1.125  1.00  0.00
ATOM   1267  CA  MET   292      26.292  46.920  -0.132  1.00  0.00
ATOM   1268  C   MET   292      25.605  47.821  -1.142  1.00  0.00
ATOM   1269  O   MET   292      24.428  47.635  -1.438  1.00  0.00
ATOM   1270  CB  MET   292      26.475  45.495  -0.756  1.00  0.00
ATOM   1271  CG  MET   292      27.375  45.532  -2.026  1.00  0.00
ATOM   1272  SD  MET   292      27.974  43.813  -2.274  1.00  0.00
ATOM   1273  CE  MET   292      28.225  43.804  -4.109  1.00  0.00
ATOM   1274  N   ALA   293      26.399  48.782  -1.557  1.00  0.00
ATOM   1275  CA  ALA   293      26.041  49.672  -2.603  1.00  0.00
ATOM   1276  C   ALA   293      26.396  48.902  -3.906  1.00  0.00
ATOM   1277  O   ALA   293      27.574  48.937  -4.305  1.00  0.00
ATOM   1278  CB  ALA   293      26.795  51.020  -2.454  1.00  0.00
ATOM   1279  N   CYS   294      25.538  47.876  -4.186  1.00  0.00
ATOM   1280  CA  CYS   294      25.802  47.043  -5.391  1.00  0.00
ATOM   1281  C   CYS   294      26.465  47.862  -6.564  1.00  0.00
ATOM   1282  O   CYS   294      27.390  47.382  -7.233  1.00  0.00
ATOM   1283  CB  CYS   294      24.376  46.711  -5.799  1.00  0.00
ATOM   1284  SG  CYS   294      24.088  45.743  -7.210  1.00  0.00
ATOM   1285  N   LEU   295      25.703  48.875  -6.955  1.00  0.00
ATOM   1286  CA  LEU   295      26.074  49.972  -7.833  1.00  0.00
ATOM   1287  C   LEU   295      26.101  49.745  -9.407  1.00  0.00
ATOM   1288  O   LEU   295      25.069  50.222  -9.973  1.00  0.00
ATOM   1289  CB  LEU   295      27.459  50.473  -7.340  1.00  0.00
ATOM   1290  CG  LEU   295      28.032  51.873  -7.616  1.00  0.00
ATOM   1291  CD1 LEU   295      29.505  51.915  -7.324  1.00  0.00
ATOM   1292  CD2 LEU   295      27.995  52.225  -9.067  1.00  0.00
ATOM   1293  N   LYS   296      26.911  48.874 -10.054  1.00  0.00
ATOM   1294  CA  LYS   296      26.809  49.004 -11.479  1.00  0.00
ATOM   1295  C   LYS   296      26.001  47.900 -12.165  1.00  0.00
ATOM   1296  O   LYS   296      24.878  48.158 -12.623  1.00  0.00
ATOM   1297  CB  LYS   296      28.035  49.352 -12.216  1.00  0.00
ATOM   1298  CG  LYS   296      28.846  50.506 -11.954  1.00  0.00
ATOM   1299  CD  LYS   296      30.142  50.327 -12.733  1.00  0.00
ATOM   1300  CE  LYS   296      30.848  49.057 -12.234  1.00  0.00
ATOM   1301  NZ  LYS   296      31.944  48.631 -13.080  1.00  0.00
ATOM   1302  N   ASP   297      26.733  46.938 -12.558  1.00  0.00
ATOM   1303  CA  ASP   297      26.167  45.817 -13.239  1.00  0.00
ATOM   1304  C   ASP   297      26.430  44.509 -12.376  1.00  0.00
ATOM   1305  O   ASP   297      26.178  43.412 -12.977  1.00  0.00
ATOM   1306  CB  ASP   297      26.964  45.703 -14.597  1.00  0.00
ATOM   1307  CG  ASP   297      26.564  46.941 -15.480  1.00  0.00
ATOM   1308  OD1 ASP   297      25.414  47.411 -15.349  1.00  0.00
ATOM   1309  OD2 ASP   297      27.353  47.348 -16.351  1.00  0.00
ATOM   1310  N   HIS   298      26.915  44.613 -11.102  1.00  0.00
ATOM   1311  CA  HIS   298      27.090  43.364 -10.461  1.00  0.00
ATOM   1312  C   HIS   298      25.659  42.690 -10.528  1.00  0.00
ATOM   1313  O   HIS   298      24.665  43.444 -10.476  1.00  0.00
ATOM   1314  CB  HIS   298      27.548  43.479  -8.979  1.00  0.00
ATOM   1315  CG  HIS   298      27.476  42.329  -8.066  1.00  0.00
ATOM   1316  ND1 HIS   298      28.064  41.099  -8.274  1.00  0.00
ATOM   1317  CD2 HIS   298      26.820  42.222  -6.881  1.00  0.00
ATOM   1318  CE1 HIS   298      27.768  40.281  -7.275  1.00  0.00
ATOM   1319  NE2 HIS   298      27.004  40.935  -6.417  1.00  0.00
TER
END
