
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_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:     9       290 - 298         4.27     4.27
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.44     4.91
  LCS_AVERAGE:      4.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.35    11.42
  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    3    9     0    3    3    3    3    4    4    4    6    6    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     3    4    5    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     M     292     M     292      3    6    9     3    4    5    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     A     293     A     293      3    6    9     3    4    5    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     C     294     C     294      3    6    9     3    3    4    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     4    4    5    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     4    4    5    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     D     297     D     297      4    5    9     4    4    4    5    5    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     H     298     H     298      4    5    9     4    4    4    4    4    6    6    7    7    7    8    8    8    8    8    8    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.73  (   2.73    4.32    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      5      5      5      6      6      7      7      7      8      8      8      8      8      8      9      9      9      9 
GDT PERCENT_CA   3.17   3.17   3.97   3.97   3.97   4.76   4.76   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.35   0.35   0.79   0.79   0.79   1.44   1.44   2.22   2.22   2.22   3.18   3.18   3.18   3.18   3.18   3.18   4.27   4.27   4.27   4.27
GDT RMS_ALL_CA  11.42  11.42   5.11   5.11   5.11   4.91   4.91   4.60   4.60   4.60   4.58   4.58   4.58   4.58   4.58   4.58   4.27   4.27   4.27   4.27

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          8.877
LGA    Y     291      Y     291          2.111
LGA    M     292      M     292          1.386
LGA    A     293      A     293          0.282
LGA    C     294      C     294          2.099
LGA    L     295      L     295          0.723
LGA    K     296      K     296          3.216
LGA    D     297      D     297          3.567
LGA    H     298      H     298          8.795

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      7    2.22     4.762     4.808     0.302

LGA_LOCAL      RMSD =  2.219  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.602  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.272  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.436265 * X  +  -0.284622 * Y  +  -0.853618 * Z  +  47.524536
  Y_new =  -0.847592 * X  +   0.188505 * Y  +  -0.496038 * Z  +  83.221344
  Z_new =   0.302095 * X  +   0.939923 * Y  +  -0.159005 * Z  + -45.094856 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.738378   -1.403214  [ DEG:    99.6017    -80.3983 ]
  Theta =  -0.306890   -2.834703  [ DEG:   -17.5835   -162.4165 ]
  Phi   =  -1.095450    2.046143  [ DEG:   -62.7646    117.2354 ]
 
# 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_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_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    7   2.22   4.808     4.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_2-D1
PFRMAT TS
TARGET T0372
MODEL  2  REFINED
PARENT 2GE3_A 1YR0_D 1YVO_B
ATOM   1097  N   LYS   290      25.117  41.966   0.112  1.00  0.00
ATOM   1098  CA  LYS   290      24.464  42.934  -0.788  1.00  0.00
ATOM   1099  C   LYS   290      24.194  44.350  -0.126  1.00  0.00
ATOM   1100  O   LYS   290      23.555  45.224  -0.737  1.00  0.00
ATOM   1101  CB  LYS   290      23.149  42.283  -1.272  1.00  0.00
ATOM   1102  CG  LYS   290      23.384  41.001  -2.103  1.00  0.00
ATOM   1103  CD  LYS   290      22.142  40.276  -2.543  1.00  0.00
ATOM   1104  CE  LYS   290      22.296  39.474  -3.798  1.00  0.00
ATOM   1105  NZ  LYS   290      21.151  38.571  -4.059  1.00  0.00
ATOM   1106  N   TYR   291      24.963  44.625   0.878  1.00  0.00
ATOM   1107  CA  TYR   291      24.983  45.892   1.582  1.00  0.00
ATOM   1108  C   TYR   291      26.142  46.686   0.977  1.00  0.00
ATOM   1109  O   TYR   291      26.275  47.853   1.407  1.00  0.00
ATOM   1110  CB  TYR   291      25.104  45.678   3.095  1.00  0.00
ATOM   1111  CG  TYR   291      24.717  46.896   3.888  1.00  0.00
ATOM   1112  CD1 TYR   291      25.658  47.841   4.215  1.00  0.00
ATOM   1113  CD2 TYR   291      23.414  47.068   4.289  1.00  0.00
ATOM   1114  CE1 TYR   291      25.302  48.959   4.915  1.00  0.00
ATOM   1115  CE2 TYR   291      23.047  48.200   4.991  1.00  0.00
ATOM   1116  CZ  TYR   291      24.000  49.144   5.300  1.00  0.00
ATOM   1117  OH  TYR   291      23.664  50.333   5.945  1.00  0.00
ATOM   1118  N   MET   292      27.247  45.960   0.647  1.00  0.00
ATOM   1119  CA  MET   292      28.298  46.646  -0.016  1.00  0.00
ATOM   1120  C   MET   292      27.671  46.844  -1.395  1.00  0.00
ATOM   1121  O   MET   292      27.218  45.927  -2.075  1.00  0.00
ATOM   1122  CB  MET   292      29.550  45.852  -0.173  1.00  0.00
ATOM   1123  CG  MET   292      30.624  46.515  -0.985  1.00  0.00
ATOM   1124  SD  MET   292      31.662  47.542   0.119  1.00  0.00
ATOM   1125  CE  MET   292      31.173  49.149  -0.478  1.00  0.00
ATOM   1126  N   ALA   293      27.093  47.976  -1.401  1.00  0.00
ATOM   1127  CA  ALA   293      26.216  48.569  -2.337  1.00  0.00
ATOM   1128  C   ALA   293      26.600  48.362  -3.782  1.00  0.00
ATOM   1129  O   ALA   293      27.668  47.836  -4.133  1.00  0.00
ATOM   1130  CB  ALA   293      26.185  50.091  -2.006  1.00  0.00
ATOM   1131  N   CYS   294      25.504  48.141  -4.433  1.00  0.00
ATOM   1132  CA  CYS   294      25.366  47.983  -5.818  1.00  0.00
ATOM   1133  C   CYS   294      25.960  49.159  -6.586  1.00  0.00
ATOM   1134  O   CYS   294      25.893  50.336  -6.168  1.00  0.00
ATOM   1135  CB  CYS   294      23.875  47.885  -6.060  1.00  0.00
ATOM   1136  SG  CYS   294      23.587  47.614  -7.812  1.00  0.00
ATOM   1137  N   LEU   295      26.877  48.765  -7.418  1.00  0.00
ATOM   1138  CA  LEU   295      27.589  49.571  -8.342  1.00  0.00
ATOM   1139  C   LEU   295      27.738  48.698  -9.623  1.00  0.00
ATOM   1140  O   LEU   295      28.430  47.670  -9.587  1.00  0.00
ATOM   1141  CB  LEU   295      29.017  49.901  -7.808  1.00  0.00
ATOM   1142  CG  LEU   295      29.817  51.041  -8.456  1.00  0.00
ATOM   1143  CD1 LEU   295      31.278  50.644  -8.745  1.00  0.00
ATOM   1144  CD2 LEU   295      29.265  51.541  -9.788  1.00  0.00
ATOM   1145  N   LYS   296      27.422  49.308 -10.760  1.00  0.00
ATOM   1146  CA  LYS   296      27.385  48.663 -12.086  1.00  0.00
ATOM   1147  C   LYS   296      26.392  47.459 -12.148  1.00  0.00
ATOM   1148  O   LYS   296      26.610  46.516 -12.903  1.00  0.00
ATOM   1149  CB  LYS   296      28.776  48.254 -12.575  1.00  0.00
ATOM   1150  CG  LYS   296      28.798  47.966 -14.094  1.00  0.00
ATOM   1151  CD  LYS   296      30.173  47.541 -14.574  1.00  0.00
ATOM   1152  CE  LYS   296      30.252  47.293 -16.064  1.00  0.00
ATOM   1153  NZ  LYS   296      31.413  46.431 -16.401  1.00  0.00
ATOM   1154  N   ASP   297      25.143  47.650 -11.697  1.00  0.00
ATOM   1155  CA  ASP   297      24.059  46.677 -11.687  1.00  0.00
ATOM   1156  C   ASP   297      24.462  45.312 -11.000  1.00  0.00
ATOM   1157  O   ASP   297      23.720  44.330 -11.199  1.00  0.00
ATOM   1158  CB  ASP   297      23.589  46.497 -13.095  1.00  0.00
ATOM   1159  CG  ASP   297      22.853  47.667 -13.627  1.00  0.00
ATOM   1160  OD1 ASP   297      22.272  48.445 -12.863  1.00  0.00
ATOM   1161  OD2 ASP   297      22.919  47.871 -14.832  1.00  0.00
ATOM   1162  N   HIS   298      25.469  45.288 -10.136  1.00  0.00
ATOM   1163  CA  HIS   298      25.896  44.048  -9.507  1.00  0.00
ATOM   1164  C   HIS   298      26.146  44.215  -8.026  1.00  0.00
ATOM   1165  O   HIS   298      27.005  44.999  -7.670  1.00  0.00
ATOM   1166  CB  HIS   298      27.243  43.599 -10.187  1.00  0.00
ATOM   1167  CG  HIS   298      27.050  43.217 -11.632  1.00  0.00
ATOM   1168  ND1 HIS   298      25.918  42.583 -12.114  1.00  0.00
ATOM   1169  CD2 HIS   298      27.858  43.421 -12.707  1.00  0.00
ATOM   1170  CE1 HIS   298      26.032  42.407 -13.422  1.00  0.00
ATOM   1171  NE2 HIS   298      27.204  42.902 -13.804  1.00  0.00
TER
END
