
#######################################################
#                                                     #
#                        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 T0372TS298_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS298_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         4.45     4.45
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.73     5.14
  LCS_AVERAGE:      4.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.45     5.80
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.20    11.03
  LCS_AVERAGE:      2.91

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    9     0    3    3    3    3    4    4    5    6    6    7    7    7    8    8    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     3    3    4    5    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     M     292     M     292      3    6    9     3    3    4    5    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    4    4    5    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     C     294     C     294      4    6    9     3    4    4    4    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     4    4    4    5    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     4    4    4    5    6    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    5    9     4    4    4    4    4    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    5    9     4    4    4    4    4    6    6    6    7    7    8    8    8    8    8    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.82  (   2.91    4.41    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      4      4      4      5      6      6      6      6      7      7      8      8      8      8      8      9      9      9      9      9 
GDT PERCENT_CA   3.17   3.17   3.17   3.97   4.76   4.76   4.76   4.76   5.56   5.56   6.35   6.35   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.20   0.20   0.20   1.48   1.73   1.73   1.73   1.73   2.49   2.49   3.42   3.42   3.42   3.42   3.42   4.45   4.45   4.45   4.45   4.45
GDT RMS_ALL_CA  11.03  11.03  11.03   5.37   5.14   5.14   5.14   5.14   4.79   4.79   4.80   4.80   4.80   4.80   4.80   4.45   4.45   4.45   4.45   4.45

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          7.482
LGA    Y     291      Y     291          1.604
LGA    M     292      M     292          1.605
LGA    A     293      A     293          1.505
LGA    C     294      C     294          2.344
LGA    L     295      L     295          1.976
LGA    K     296      K     296          1.059
LGA    D     297      D     297          6.514
LGA    H     298      H     298         11.000

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    1.73     4.762     4.796     0.328

LGA_LOCAL      RMSD =  1.729  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.135  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.452  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.139080 * X  +  -0.001176 * Y  +  -0.990280 * Z  +  51.101524
  Y_new =  -0.954661 * X  +   0.265634 * Y  +  -0.134393 * Z  +  72.619087
  Z_new =   0.263210 * X  +   0.964073 * Y  +   0.035822 * Z  + -49.537922 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.533656   -1.607936  [ DEG:    87.8720    -92.1280 ]
  Theta =  -0.266348   -2.875244  [ DEG:   -15.2606   -164.7394 ]
  Phi   =  -1.426129    1.715464  [ DEG:   -81.7111     98.2889 ]
 
# 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: T0372TS298_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS298_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   1.73   4.796     4.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS298_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 2GE3_A
ATOM   1097  N   LYS   290      23.746  42.372   1.785  1.00  0.00
ATOM   1098  CA  LYS   290      23.480  43.477   0.876  1.00  0.00
ATOM   1099  C   LYS   290      24.117  44.806   1.443  1.00  0.00
ATOM   1100  O   LYS   290      23.638  45.902   1.075  1.00  0.00
ATOM   1101  CB  LYS   290      21.920  43.606   0.828  1.00  0.00
ATOM   1102  CG  LYS   290      21.164  42.373   0.319  1.00  0.00
ATOM   1103  CD  LYS   290      20.083  42.631  -0.701  1.00  0.00
ATOM   1104  CE  LYS   290      19.251  41.361  -0.732  1.00  0.00
ATOM   1105  NZ  LYS   290      18.411  41.301  -1.909  1.00  0.00
ATOM   1106  N   TYR   291      25.362  44.679   1.972  1.00  0.00
ATOM   1107  CA  TYR   291      26.068  45.826   2.462  1.00  0.00
ATOM   1108  C   TYR   291      26.598  46.617   1.235  1.00  0.00
ATOM   1109  O   TYR   291      26.608  47.866   1.346  1.00  0.00
ATOM   1110  CB  TYR   291      27.138  45.389   3.475  1.00  0.00
ATOM   1111  CG  TYR   291      27.586  46.434   4.412  1.00  0.00
ATOM   1112  CD1 TYR   291      26.731  46.877   5.422  1.00  0.00
ATOM   1113  CD2 TYR   291      28.851  47.019   4.322  1.00  0.00
ATOM   1114  CE1 TYR   291      27.091  47.877   6.315  1.00  0.00
ATOM   1115  CE2 TYR   291      29.250  48.006   5.221  1.00  0.00
ATOM   1116  CZ  TYR   291      28.353  48.435   6.204  1.00  0.00
ATOM   1117  OH  TYR   291      28.780  49.407   7.076  1.00  0.00
ATOM   1118  N   MET   292      27.107  45.960   0.163  1.00  0.00
ATOM   1119  CA  MET   292      27.509  46.719  -0.962  1.00  0.00
ATOM   1120  C   MET   292      26.346  47.637  -1.347  1.00  0.00
ATOM   1121  O   MET   292      25.184  47.197  -1.447  1.00  0.00
ATOM   1122  CB  MET   292      27.936  45.816  -2.118  1.00  0.00
ATOM   1123  CG  MET   292      28.312  46.597  -3.366  1.00  0.00
ATOM   1124  SD  MET   292      30.119  46.891  -3.310  1.00  0.00
ATOM   1125  CE  MET   292      30.094  48.658  -3.084  1.00  0.00
ATOM   1126  N   ALA   293      26.767  48.810  -1.749  1.00  0.00
ATOM   1127  CA  ALA   293      25.949  49.903  -2.253  1.00  0.00
ATOM   1128  C   ALA   293      25.445  49.592  -3.693  1.00  0.00
ATOM   1129  O   ALA   293      25.518  50.478  -4.556  1.00  0.00
ATOM   1130  CB  ALA   293      26.756  51.196  -2.153  1.00  0.00
ATOM   1131  N   CYS   294      25.542  48.283  -3.990  1.00  0.00
ATOM   1132  CA  CYS   294      25.116  47.550  -5.162  1.00  0.00
ATOM   1133  C   CYS   294      25.967  47.620  -6.461  1.00  0.00
ATOM   1134  O   CYS   294      25.676  46.735  -7.303  1.00  0.00
ATOM   1135  CB  CYS   294      23.637  48.045  -5.259  1.00  0.00
ATOM   1136  SG  CYS   294      22.899  47.079  -6.633  1.00  0.00
ATOM   1137  N   LEU   295      27.199  48.089  -6.451  1.00  0.00
ATOM   1138  CA  LEU   295      27.869  48.074  -7.774  1.00  0.00
ATOM   1139  C   LEU   295      26.765  48.586  -8.773  1.00  0.00
ATOM   1140  O   LEU   295      26.631  49.811  -8.839  1.00  0.00
ATOM   1141  CB  LEU   295      28.390  46.739  -8.173  1.00  0.00
ATOM   1142  CG  LEU   295      29.545  45.978  -7.716  1.00  0.00
ATOM   1143  CD1 LEU   295      29.833  44.879  -8.729  1.00  0.00
ATOM   1144  CD2 LEU   295      30.686  46.995  -7.691  1.00  0.00
ATOM   1145  N   LYS   296      26.329  47.829  -9.765  1.00  0.00
ATOM   1146  CA  LYS   296      25.225  48.299 -10.609  1.00  0.00
ATOM   1147  C   LYS   296      24.003  47.310 -10.523  1.00  0.00
ATOM   1148  O   LYS   296      23.957  46.324 -11.277  1.00  0.00
ATOM   1149  CB  LYS   296      25.802  48.400 -12.060  1.00  0.00
ATOM   1150  CG  LYS   296      26.874  49.452 -12.157  1.00  0.00
ATOM   1151  CD  LYS   296      27.751  49.115 -13.336  1.00  0.00
ATOM   1152  CE  LYS   296      28.838  50.206 -13.475  1.00  0.00
ATOM   1153  NZ  LYS   296      28.076  51.458 -13.846  1.00  0.00
ATOM   1154  N   ASP   297      23.027  47.708  -9.736  1.00  0.00
ATOM   1155  CA  ASP   297      21.847  46.955  -9.573  1.00  0.00
ATOM   1156  C   ASP   297      21.957  45.506  -8.984  1.00  0.00
ATOM   1157  O   ASP   297      20.909  44.859  -8.884  1.00  0.00
ATOM   1158  CB  ASP   297      20.997  47.028 -10.874  1.00  0.00
ATOM   1159  CG  ASP   297      20.608  48.401 -11.323  1.00  0.00
ATOM   1160  OD1 ASP   297      20.315  49.276 -10.466  1.00  0.00
ATOM   1161  OD2 ASP   297      20.602  48.638 -12.554  1.00  0.00
ATOM   1162  N   HIS   298      23.118  45.044  -8.508  1.00  0.00
ATOM   1163  CA  HIS   298      23.129  43.766  -7.912  1.00  0.00
ATOM   1164  C   HIS   298      23.625  43.821  -6.405  1.00  0.00
ATOM   1165  O   HIS   298      24.787  44.284  -6.225  1.00  0.00
ATOM   1166  CB  HIS   298      24.134  42.895  -8.714  1.00  0.00
ATOM   1167  CG  HIS   298      23.673  42.632 -10.120  1.00  0.00
ATOM   1168  ND1 HIS   298      22.350  42.398 -10.459  1.00  0.00
ATOM   1169  CD2 HIS   298      24.372  42.622 -11.287  1.00  0.00
ATOM   1170  CE1 HIS   298      22.251  42.251 -11.772  1.00  0.00
ATOM   1171  NE2 HIS   298      23.465  42.377 -12.296  1.00  0.00
TER
END
