
#######################################################
#                                                     #
#                        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 T0372TS249_2_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_2_2-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
 ERROR! 0 0 9 126
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    K     290      L      77          2.832
LGA    Y     291      R      78          1.667
LGA    M     292      K      79          1.734
LGA    A     293      L      80          1.617
LGA    C     294      I      81          3.871
LGA    L     295      E      82          1.547
LGA    K     296      D      83          3.989
LGA    D     297      A      84          2.162
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    H     298      F      91          2.266
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.57     0.00      5.517     0.337

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.901452 * X  +  -0.430103 * Y  +   0.048948 * Z  +  34.138260
  Y_new =   0.199986 * X  +  -0.313504 * Y  +   0.928289 * Z  +  58.869488
  Z_new =  -0.383915 * X  +   0.846597 * Y  +   0.368623 * Z  +  -9.547715 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.160135   -1.981457  [ DEG:    66.4708   -113.5292 ]
  Theta =   0.394032    2.747561  [ DEG:    22.5764    157.4236 ]
  Phi   =   2.923280   -0.218313  [ DEG:   167.4916    -12.5084 ]
 
# 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: T0372TS249_2_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_2_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.57    0.00   5.517
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      31.184  59.695  -8.763  1.00  0.00
ATOM   1036  CA  LYS   290      31.069  58.688  -7.743  1.00  0.00
ATOM   1037  C   LYS   290      32.097  57.613  -7.942  1.00  0.00
ATOM   1038  O   LYS   290      32.032  56.548  -7.341  1.00  0.00
ATOM   1039  CB  LYS   290      29.666  58.065  -7.654  1.00  0.00
ATOM   1040  CG  LYS   290      29.467  57.263  -6.365  1.00  0.00
ATOM   1041  CD  LYS   290      28.003  57.081  -5.958  1.00  0.00
ATOM   1042  CE  LYS   290      27.376  58.369  -5.421  1.00  0.00
ATOM   1043  NZ  LYS   290      26.143  58.079  -4.656  1.00  0.00
ATOM   1044  N   TYR   291      32.911  57.792  -8.981  1.00  0.00
ATOM   1045  CA  TYR   291      33.966  56.974  -9.507  1.00  0.00
ATOM   1046  C   TYR   291      35.293  57.027  -8.812  1.00  0.00
ATOM   1047  O   TYR   291      36.275  56.540  -9.359  1.00  0.00
ATOM   1048  CB  TYR   291      34.070  57.102 -11.024  1.00  0.00
ATOM   1049  CG  TYR   291      32.732  56.530 -11.337  1.00  0.00
ATOM   1050  CD1 TYR   291      32.559  55.168 -11.404  1.00  0.00
ATOM   1051  CD2 TYR   291      31.637  57.351 -11.489  1.00  0.00
ATOM   1052  CE1 TYR   291      31.321  54.629 -11.662  1.00  0.00
ATOM   1053  CE2 TYR   291      30.397  56.819 -11.748  1.00  0.00
ATOM   1054  CZ  TYR   291      30.239  55.458 -11.838  1.00  0.00
ATOM   1055  OH  TYR   291      28.962  54.921 -12.102  1.00  0.00
ATOM   1056  N   MET   292      35.440  57.813  -7.743  1.00  0.00
ATOM   1057  CA  MET   292      36.692  57.926  -7.047  1.00  0.00
ATOM   1058  C   MET   292      37.137  56.668  -6.355  1.00  0.00
ATOM   1059  O   MET   292      38.332  56.539  -6.090  1.00  0.00
ATOM   1060  CB  MET   292      36.717  59.062  -6.015  1.00  0.00
ATOM   1061  CG  MET   292      36.695  60.440  -6.676  1.00  0.00
ATOM   1062  SD  MET   292      36.810  61.833  -5.517  1.00  0.00
ATOM   1063  CE  MET   292      36.872  63.097  -6.818  1.00  0.00
ATOM   1064  N   ALA   293      36.225  55.745  -5.965  1.00  0.00
ATOM   1065  CA  ALA   293      36.691  54.580  -5.255  1.00  0.00
ATOM   1066  C   ALA   293      37.675  53.894  -6.137  1.00  0.00
ATOM   1067  O   ALA   293      38.799  53.605  -5.733  1.00  0.00
ATOM   1068  CB  ALA   293      35.588  53.553  -4.965  1.00  0.00
ATOM   1069  N   CYS   294      37.283  53.666  -7.395  1.00  0.00
ATOM   1070  CA  CYS   294      38.213  53.147  -8.335  1.00  0.00
ATOM   1071  C   CYS   294      37.924  53.907  -9.565  1.00  0.00
ATOM   1072  O   CYS   294      36.758  54.141  -9.878  1.00  0.00
ATOM   1073  CB  CYS   294      38.016  51.661  -8.665  1.00  0.00
ATOM   1074  SG  CYS   294      38.263  50.589  -7.217  1.00  0.00
ATOM   1075  N   LEU   295      38.978  54.320 -10.283  1.00  0.00
ATOM   1076  CA  LEU   295      38.735  55.056 -11.477  1.00  0.00
ATOM   1077  C   LEU   295      37.956  54.106 -12.324  1.00  0.00
ATOM   1078  O   LEU   295      36.964  54.485 -12.950  1.00  0.00
ATOM   1079  CB  LEU   295      40.045  55.394 -12.204  1.00  0.00
ATOM   1080  CG  LEU   295      39.861  56.200 -13.497  1.00  0.00
ATOM   1081  CD1 LEU   295      39.315  57.605 -13.203  1.00  0.00
ATOM   1082  CD2 LEU   295      41.148  56.219 -14.334  1.00  0.00
ATOM   1083  N   LYS   296      38.422  52.841 -12.393  1.00  0.00
ATOM   1084  CA  LYS   296      37.680  51.848 -13.115  1.00  0.00
ATOM   1085  C   LYS   296      36.451  51.361 -12.390  1.00  0.00
ATOM   1086  O   LYS   296      35.328  51.735 -12.727  1.00  0.00
ATOM   1087  CB  LYS   296      38.518  50.593 -13.429  1.00  0.00
ATOM   1088  CG  LYS   296      39.650  50.836 -14.431  1.00  0.00
ATOM   1089  CD  LYS   296      40.693  49.714 -14.478  1.00  0.00
ATOM   1090  CE  LYS   296      40.493  48.702 -15.610  1.00  0.00
ATOM   1091  NZ  LYS   296      39.528  47.656 -15.203  1.00  0.00
ATOM   1092  N   ASP   297      36.654  50.574 -11.305  1.00  0.00
ATOM   1093  CA  ASP   297      35.573  49.866 -10.656  1.00  0.00
ATOM   1094  C   ASP   297      35.157  50.495  -9.364  1.00  0.00
ATOM   1095  O   ASP   297      35.315  51.693  -9.143  1.00  0.00
ATOM   1096  CB  ASP   297      35.895  48.400 -10.320  1.00  0.00
ATOM   1097  CG  ASP   297      35.980  47.603 -11.610  1.00  0.00
ATOM   1098  OD1 ASP   297      35.941  48.236 -12.697  1.00  0.00
ATOM   1099  OD2 ASP   297      36.083  46.349 -11.527  1.00  0.00
ATOM   1100  N   HIS   298      34.567  49.651  -8.482  1.00  0.00
ATOM   1101  CA  HIS   298      34.113  50.054  -7.178  1.00  0.00
ATOM   1102  C   HIS   298      34.978  49.366  -6.172  1.00  0.00
ATOM   1103  O   HIS   298      35.935  48.687  -6.531  1.00  0.00
ATOM   1104  CB  HIS   298      32.662  49.654  -6.864  1.00  0.00
ATOM   1105  CG  HIS   298      31.662  50.386  -7.707  1.00  0.00
ATOM   1106  ND1 HIS   298      31.111  51.601  -7.368  1.00  0.00
ATOM   1107  CD2 HIS   298      31.120  50.050  -8.908  1.00  0.00
ATOM   1108  CE1 HIS   298      30.265  51.939  -8.375  1.00  0.00
ATOM   1109  NE2 HIS   298      30.238  51.030  -9.332  1.00  0.00
TER
END
