
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_4_2-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       290 - 297         4.31     5.80
  LONGEST_CONTINUOUS_SEGMENT:     8       291 - 298         4.32     5.68
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       290 - 294         1.33     9.86
  LONGEST_CONTINUOUS_SEGMENT:     5       293 - 297         1.84     7.09
  LONGEST_CONTINUOUS_SEGMENT:     5       294 - 298         1.50     8.89
  LCS_AVERAGE:      3.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.90    10.47
  LONGEST_CONTINUOUS_SEGMENT:     4       291 - 294         0.67     9.20
  LCS_AVERAGE:      2.82

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    5    8     0    3    4    5    5    5    5    5    5    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     Y     291     Y     291      4    5    8     3    4    4    5    5    5    5    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     M     292     M     292      4    5    8     3    4    4    5    5    5    5    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     A     293     A     293      4    5    8     3    4    4    5    5    5    6    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     C     294     C     294      4    5    8     3    4    4    5    5    5    6    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     L     295     L     295      3    5    8     3    3    4    5    5    5    6    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     K     296     K     296      3    5    8     3    3    4    5    5    5    6    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     D     297     D     297      3    5    8     3    3    4    5    5    5    6    6    6    6    7    7    7    8    8    8    8    9    9    9 
LCS_GDT     H     298     H     298      3    5    8     0    3    3    5    5    5    6    6    6    6    7    7    7    7    8    8    8    9    9    9 
LCS_AVERAGE  LCS_A:   4.38  (   2.82    3.97    6.35 )

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      5      5      5      6      6      6      6      7      7      7      8      8      8      8      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.17   3.97   3.97   3.97   4.76   4.76   4.76   4.76   5.56   5.56   5.56   6.35   6.35   6.35   6.35   7.14   7.14   7.14
GDT RMS_LOCAL    0.02   0.67   0.67   1.33   1.33   1.33   2.23   2.23   2.23   2.23   3.13   3.13   3.13   4.31   4.31   4.31   4.31   5.27   5.27   5.27
GDT RMS_ALL_CA  10.35   9.20   9.20   9.86   9.86   9.86   7.79   7.79   7.79   7.79   6.75   6.75   6.75   5.80   5.80   5.80   5.80   5.27   5.27   5.27

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         17.305
LGA    Y     291      Y     291         12.761
LGA    M     292      M     292          7.371
LGA    A     293      A     293          3.154
LGA    C     294      C     294          3.197
LGA    L     295      L     295          1.286
LGA    K     296      K     296          1.829
LGA    D     297      D     297          1.217
LGA    H     298      H     298          1.765

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    2.23     4.563     4.403     0.258

LGA_LOCAL      RMSD =  2.227  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.792  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  5.267  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.558218 * X  +   0.780129 * Y  +   0.282474 * Z  +  34.425785
  Y_new =   0.697264 * X  +   0.625616 * Y  +  -0.349895 * Z  +  50.162613
  Z_new =  -0.449684 * X  +   0.001641 * Y  +  -0.893186 * Z  +   3.612671 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.139755   -0.001837  [ DEG:   179.8947     -0.1053 ]
  Theta =   0.466411    2.675182  [ DEG:    26.7234    153.2766 ]
  Phi   =   2.245893   -0.895700  [ DEG:   128.6802    -51.3198 ]
 
# 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_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_4_2-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   2.23   4.403     5.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      35.854  47.875  -6.989  1.00  0.00
ATOM   1036  CA  LYS   290      34.976  48.786  -7.628  1.00  0.00
ATOM   1037  C   LYS   290      33.685  48.064  -7.682  1.00  0.00
ATOM   1038  O   LYS   290      32.741  48.498  -8.341  1.00  0.00
ATOM   1039  CB  LYS   290      35.430  49.170  -9.023  1.00  0.00
ATOM   1040  CG  LYS   290      36.467  50.292  -9.016  1.00  0.00
ATOM   1041  CD  LYS   290      37.727  49.963  -8.221  1.00  0.00
ATOM   1042  CE  LYS   290      38.785  51.064  -8.272  1.00  0.00
ATOM   1043  NZ  LYS   290      38.214  52.337  -7.782  1.00  0.00
ATOM   1044  N   TYR   291      33.694  46.846  -7.100  1.00  0.00
ATOM   1045  CA  TYR   291      32.510  46.069  -7.009  1.00  0.00
ATOM   1046  C   TYR   291      31.744  46.828  -5.993  1.00  0.00
ATOM   1047  O   TYR   291      31.836  46.624  -4.782  1.00  0.00
ATOM   1048  CB  TYR   291      32.760  44.634  -6.507  1.00  0.00
ATOM   1049  CG  TYR   291      31.510  43.842  -6.706  1.00  0.00
ATOM   1050  CD1 TYR   291      31.128  43.461  -7.973  1.00  0.00
ATOM   1051  CD2 TYR   291      30.732  43.457  -5.639  1.00  0.00
ATOM   1052  CE1 TYR   291      29.984  42.726  -8.177  1.00  0.00
ATOM   1053  CE2 TYR   291      29.585  42.722  -5.836  1.00  0.00
ATOM   1054  CZ  TYR   291      29.210  42.357  -7.106  1.00  0.00
ATOM   1055  OH  TYR   291      28.036  41.603  -7.312  1.00  0.00
ATOM   1056  N   MET   292      31.016  47.815  -6.528  1.00  0.00
ATOM   1057  CA  MET   292      30.174  48.653  -5.767  1.00  0.00
ATOM   1058  C   MET   292      28.949  47.836  -5.725  1.00  0.00
ATOM   1059  O   MET   292      28.258  47.678  -6.731  1.00  0.00
ATOM   1060  CB  MET   292      29.833  49.968  -6.484  1.00  0.00
ATOM   1061  CG  MET   292      31.025  50.914  -6.637  1.00  0.00
ATOM   1062  SD  MET   292      30.675  52.335  -7.707  1.00  0.00
ATOM   1063  CE  MET   292      30.764  51.334  -9.217  1.00  0.00
ATOM   1064  N   ALA   293      28.685  47.251  -4.552  1.00  0.00
ATOM   1065  CA  ALA   293      27.534  46.425  -4.457  1.00  0.00
ATOM   1066  C   ALA   293      26.398  47.337  -4.739  1.00  0.00
ATOM   1067  O   ALA   293      25.421  46.970  -5.387  1.00  0.00
ATOM   1068  CB  ALA   293      27.333  45.831  -3.053  1.00  0.00
ATOM   1069  N   CYS   294      26.521  48.578  -4.244  1.00  0.00
ATOM   1070  CA  CYS   294      25.533  49.582  -4.470  1.00  0.00
ATOM   1071  C   CYS   294      25.426  49.851  -5.939  1.00  0.00
ATOM   1072  O   CYS   294      24.315  49.993  -6.446  1.00  0.00
ATOM   1073  CB  CYS   294      25.835  50.930  -3.794  1.00  0.00
ATOM   1074  SG  CYS   294      25.489  50.921  -2.012  1.00  0.00
ATOM   1075  N   LEU   295      26.558  49.926  -6.674  1.00  0.00
ATOM   1076  CA  LEU   295      26.433  50.271  -8.071  1.00  0.00
ATOM   1077  C   LEU   295      26.692  49.067  -8.938  1.00  0.00
ATOM   1078  O   LEU   295      27.830  48.633  -9.107  1.00  0.00
ATOM   1079  CB  LEU   295      27.403  51.386  -8.500  1.00  0.00
ATOM   1080  CG  LEU   295      27.253  51.809  -9.972  1.00  0.00
ATOM   1081  CD1 LEU   295      25.863  52.413 -10.236  1.00  0.00
ATOM   1082  CD2 LEU   295      28.394  52.746 -10.399  1.00  0.00
ATOM   1083  N   LYS   296      25.601  48.483  -9.485  1.00  0.00
ATOM   1084  CA  LYS   296      25.589  47.306 -10.317  1.00  0.00
ATOM   1085  C   LYS   296      26.040  47.498 -11.751  1.00  0.00
ATOM   1086  O   LYS   296      26.737  46.639 -12.285  1.00  0.00
ATOM   1087  CB  LYS   296      24.199  46.648 -10.364  1.00  0.00
ATOM   1088  CG  LYS   296      23.706  46.192  -8.989  1.00  0.00
ATOM   1089  CD  LYS   296      24.633  45.191  -8.294  1.00  0.00
ATOM   1090  CE  LYS   296      24.192  44.839  -6.871  1.00  0.00
ATOM   1091  NZ  LYS   296      25.143  43.879  -6.268  1.00  0.00
ATOM   1092  N   ASP   297      25.639  48.596 -12.434  1.00  0.00
ATOM   1093  CA  ASP   297      25.870  48.680 -13.863  1.00  0.00
ATOM   1094  C   ASP   297      27.121  49.409 -14.266  1.00  0.00
ATOM   1095  O   ASP   297      27.689  50.204 -13.522  1.00  0.00
ATOM   1096  CB  ASP   297      24.694  49.317 -14.625  1.00  0.00
ATOM   1097  CG  ASP   297      24.502  50.736 -14.114  1.00  0.00
ATOM   1098  OD1 ASP   297      25.278  51.154 -13.213  1.00  0.00
ATOM   1099  OD2 ASP   297      23.567  51.419 -14.612  1.00  0.00
ATOM   1100  N   HIS   298      27.562  49.165 -15.521  1.00  0.00
ATOM   1101  CA  HIS   298      28.731  49.783 -16.087  1.00  0.00
ATOM   1102  C   HIS   298      29.953  49.193 -15.446  1.00  0.00
ATOM   1103  O   HIS   298      29.876  48.516 -14.422  1.00  0.00
ATOM   1104  CB  HIS   298      28.774  51.320 -15.968  1.00  0.00
ATOM   1105  CG  HIS   298      27.787  52.005 -16.869  1.00  0.00
ATOM   1106  ND1 HIS   298      27.963  52.149 -18.228  1.00  0.00
ATOM   1107  CD2 HIS   298      26.595  52.599 -16.585  1.00  0.00
ATOM   1108  CE1 HIS   298      26.878  52.816 -18.696  1.00  0.00
ATOM   1109  NE2 HIS   298      26.020  53.110 -17.735  1.00  0.00
TER
END
