
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS028_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         4.98     5.80
  LONGEST_CONTINUOUS_SEGMENT:     8       291 - 298         3.80     5.59
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       292 - 297         1.58     6.21
  LCS_AVERAGE:      4.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.39     6.72
  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    4    8     3    3    3    3    4    4    4    4    4    4    5    5    5    5    6    6    6    6    8    8 
LCS_GDT     Y     291     Y     291      3    4    8     3    3    3    3    4    4    4    4    5    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     M     292     M     292      3    6    8     3    3    4    4    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     293     A     293      4    6    8     4    4    5    5    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     294     C     294      4    6    8     4    4    5    5    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     295     L     295      4    6    8     4    4    5    5    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     K     296     K     296      4    6    8     4    4    5    5    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     297     D     297      3    6    8     0    3    5    5    6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     H     298     H     298      3    3    8     0    3    3    3    3    4    6    6    6    6    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.41  (   2.73    4.14    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      4      4      5      5      6      6      6      6      6      7      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   3.17   3.17   3.97   3.97   4.76   4.76   4.76   4.76   4.76   5.56   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.39   0.39   1.01   1.01   1.58   1.58   1.58   1.58   1.58   3.02   3.80   3.80   3.80   3.80   3.80   3.80   3.80   3.80   3.80   3.80
GDT RMS_ALL_CA   6.72   6.72   6.61   6.61   6.21   6.21   6.21   6.21   6.21   5.90   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         14.072
LGA    Y     291      Y     291          7.870
LGA    M     292      M     292          2.305
LGA    A     293      A     293          1.230
LGA    C     294      C     294          1.820
LGA    L     295      L     295          0.597
LGA    K     296      K     296          1.503
LGA    D     297      D     297          1.491
LGA    H     298      H     298          8.483

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    1.58     4.563     4.715     0.357

LGA_LOCAL      RMSD =  1.580  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.208  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  5.344  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.720769 * X  +  -0.219957 * Y  +   0.657351 * Z  +  27.222866
  Y_new =   0.483778 * X  +   0.519545 * Y  +   0.704295 * Z  + -17.036205
  Z_new =  -0.496439 * X  +   0.825646 * Y  +  -0.268062 * Z  + -53.836597 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.884729   -1.256864  [ DEG:   107.9870    -72.0130 ]
  Theta =   0.519491    2.622101  [ DEG:    29.7647    150.2353 ]
  Phi   =   2.550461   -0.591132  [ DEG:   146.1306    -33.8694 ]
 
# 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_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS028_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   1.58   4.715     5.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS028_2-D1
PFRMAT TS
TARGET T0372
MODEL 2
PARENT 1yvo-A
ATOM   1061  N   LYS   290      22.037  49.666  -7.336  1.00  9.00
ATOM   1062  CA  LYS   290      23.039  49.308  -6.315  1.00  9.00
ATOM   1063  C   LYS   290      22.648  48.071  -5.498  1.00  9.00
ATOM   1064  O   LYS   290      21.468  47.833  -5.218  1.00  9.00
ATOM   1065  CB  LYS   290      23.208  50.465  -5.334  1.00  9.00
ATOM   1066  CG  LYS   290      23.792  51.714  -5.979  1.00  9.00
ATOM   1067  CD  LYS   290      23.911  52.842  -4.963  1.00  9.00
ATOM   1068  CE  LYS   290      24.434  54.121  -5.604  1.00  9.00
ATOM   1069  NZ  LYS   290      24.540  55.203  -4.613  1.00  9.00
ATOM   1070  N   TYR   291      23.660  47.317  -5.100  1.00  9.00
ATOM   1071  CA  TYR   291      23.488  46.188  -4.167  1.00  9.00
ATOM   1072  C   TYR   291      24.824  45.875  -3.494  1.00  9.00
ATOM   1073  O   TYR   291      25.886  46.047  -4.105  1.00  9.00
ATOM   1074  CB  TYR   291      22.954  44.942  -4.878  1.00  9.00
ATOM   1075  CG  TYR   291      23.941  44.201  -5.779  1.00  9.00
ATOM   1076  CD1 TYR   291      24.610  43.077  -5.308  1.00  9.00
ATOM   1077  CD2 TYR   291      24.158  44.637  -7.078  1.00  9.00
ATOM   1078  CE1 TYR   291      25.506  42.404  -6.128  1.00  9.00
ATOM   1079  CE2 TYR   291      25.051  43.965  -7.900  1.00  9.00
ATOM   1080  CZ  TYR   291      25.723  42.851  -7.424  1.00  9.00
ATOM   1081  OH  TYR   291      26.564  42.154  -8.265  1.00  9.00
ATOM   1082  N   MET   292      24.758  45.489  -2.226  1.00  9.00
ATOM   1083  CA  MET   292      25.944  45.186  -1.397  1.00  9.00
ATOM   1084  C   MET   292      26.944  46.343  -1.419  1.00  9.00
ATOM   1085  O   MET   292      28.145  46.139  -1.636  1.00  9.00
ATOM   1086  CB  MET   292      26.608  43.911  -1.915  1.00  9.00
ATOM   1087  CG  MET   292      25.662  42.712  -1.895  1.00  9.00
ATOM   1088  SD  MET   292      25.137  42.124  -0.268  1.00  9.00
ATOM   1089  CE  MET   292      26.735  41.561   0.364  1.00  9.00
ATOM   1090  N   ALA   293      26.411  47.542  -1.227  1.00  9.00
ATOM   1091  CA  ALA   293      27.143  48.821  -1.331  1.00  9.00
ATOM   1092  C   ALA   293      27.947  49.053  -2.625  1.00  9.00
ATOM   1093  O   ALA   293      28.958  49.764  -2.581  1.00  9.00
ATOM   1094  CB  ALA   293      28.068  48.956  -0.126  1.00  9.00
ATOM   1095  N   CYS   294      27.510  48.499  -3.749  1.00  9.00
ATOM   1096  CA  CYS   294      28.194  48.740  -5.030  1.00  9.00
ATOM   1097  C   CYS   294      27.214  48.955  -6.189  1.00  9.00
ATOM   1098  O   CYS   294      26.052  48.540  -6.126  1.00  9.00
ATOM   1099  CB  CYS   294      29.081  47.540  -5.349  1.00  9.00
ATOM   1100  SG  CYS   294      30.422  47.200  -4.184  1.00  9.00
ATOM   1101  N   LEU   295      27.694  49.643  -7.215  1.00  9.00
ATOM   1102  CA  LEU   295      26.924  49.907  -8.453  1.00  9.00
ATOM   1103  C   LEU   295      26.822  48.680  -9.370  1.00  9.00
ATOM   1104  O   LEU   295      27.680  47.791  -9.319  1.00  9.00
ATOM   1105  CB  LEU   295      27.634  51.023  -9.212  1.00  9.00
ATOM   1106  CG  LEU   295      27.502  52.373  -8.517  1.00  9.00
ATOM   1107  CD1 LEU   295      28.517  53.373  -9.062  1.00  9.00
ATOM   1108  CD2 LEU   295      26.083  52.910  -8.654  1.00  9.00
ATOM   1109  N   LYS   296      25.761  48.622 -10.169  1.00  9.00
ATOM   1110  CA  LYS   296      25.567  47.478 -11.094  1.00  9.00
ATOM   1111  C   LYS   296      24.964  47.818 -12.480  1.00  9.00
ATOM   1112  O   LYS   296      24.221  48.796 -12.656  1.00  9.00
ATOM   1113  CB  LYS   296      24.663  46.478 -10.394  1.00  9.00
ATOM   1114  CG  LYS   296      23.245  47.019 -10.281  1.00  9.00
ATOM   1115  CD  LYS   296      22.327  46.059  -9.542  1.00  9.00
ATOM   1116  CE  LYS   296      22.366  44.669 -10.157  1.00  9.00
ATOM   1117  NZ  LYS   296      21.948  44.697 -11.561  1.00  9.00
ATOM   1118  N   ASP   297      25.215  46.916 -13.430  1.00  9.00
ATOM   1119  CA  ASP   297      24.854  47.088 -14.873  1.00  9.00
ATOM   1120  C   ASP   297      23.714  46.135 -15.336  1.00  9.00
ATOM   1121  O   ASP   297      23.506  45.122 -14.664  1.00  9.00
ATOM   1122  CB  ASP   297      26.106  46.813 -15.710  1.00  9.00
ATOM   1123  CG  ASP   297      27.308  47.710 -15.385  1.00  9.00
ATOM   1124  OD1 ASP   297      27.116  48.712 -14.711  1.00  9.00
ATOM   1125  OD2 ASP   297      28.337  47.488 -15.999  1.00  9.00
ATOM   1126  N   HIS   298      23.089  46.385 -16.499  1.00  9.00
ATOM   1127  CA  HIS   298      21.798  45.711 -16.903  1.00  9.00
ATOM   1128  C   HIS   298      21.467  45.538 -18.433  1.00  9.00
ATOM   1129  O   HIS   298      21.286  46.557 -19.113  1.00  9.00
ATOM   1130  CB  HIS   298      20.659  46.605 -16.394  1.00  9.00
ATOM   1131  CG  HIS   298      20.408  46.777 -14.900  1.00  9.00
ATOM   1132  ND1 HIS   298      21.000  47.659 -14.073  1.00  9.00
ATOM   1133  CD2 HIS   298      19.485  46.085 -14.153  1.00  9.00
ATOM   1134  CE1 HIS   298      20.487  47.522 -12.833  1.00  9.00
ATOM   1135  NE2 HIS   298      19.547  46.554 -12.885  1.00  9.00
TER
END
