
#######################################################
#                                                     #
#                        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    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_2_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     5.65
  LONGEST_CONTINUOUS_SEGMENT:     8       291 - 298         4.68     5.57
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         1.80     9.97
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.58     7.88
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.99    10.05
  LCS_AVERAGE:      3.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.58     7.88
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.99    10.05
  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    8     0    3    3    3    3    5    5    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    4    8     3    3    3    3    3    5    5    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     M     292     M     292      3    4    8     3    3    3    3    3    5    5    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     A     293     A     293      4    4    8     3    4    4    4    4    5    5    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     C     294     C     294      4    4    8     3    4    4    4    4    5    5    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     L     295     L     295      4    4    8     3    4    4    4    4    4    4    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     K     296     K     296      4    4    8     3    4    4    4    4    4    4    6    7    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     D     297     D     297      4    4    8     3    3    4    4    4    4    4    6    6    7    7    7    7    8    8    8    9    9    9    9 
LCS_GDT     H     298     H     298      4    4    8     0    3    4    4    4    4    4    4    5    7    7    7    7    7    7    8    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.14  (   2.91    3.17    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      4      4      5      5      6      7      7      7      7      7      8      8      8      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.17   3.17   3.17   3.97   3.97   4.76   5.56   5.56   5.56   5.56   5.56   6.35   6.35   6.35   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.05   0.58   0.58   0.58   0.58   2.30   2.30   2.97   3.59   3.59   3.59   3.59   3.59   4.31   4.31   4.31   5.23   5.23   5.23   5.23
GDT RMS_ALL_CA   8.08   7.88   7.88   7.88   7.88   8.35   8.35   6.08   6.37   6.37   6.37   6.37   6.37   5.65   5.65   5.65   5.23   5.23   5.23   5.23

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         10.905
LGA    Y     291      Y     291          8.445
LGA    M     292      M     292          3.527
LGA    A     293      A     293          3.740
LGA    C     294      C     294          1.480
LGA    L     295      L     295          2.900
LGA    K     296      K     296          1.249
LGA    D     297      D     297          3.809
LGA    H     298      H     298          9.430

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    2.97     4.365     4.135     0.195

LGA_LOCAL      RMSD =  2.975  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.076  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  5.234  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.809726 * X  +   0.552185 * Y  +  -0.198586 * Z  +  22.098606
  Y_new =  -0.579839 * X  +  -0.804903 * Y  +   0.126166 * Z  +  46.532219
  Z_new =  -0.090175 * X  +   0.217308 * Y  +   0.971929 * Z  +  -3.086684 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.219967   -2.921626  [ DEG:    12.6032   -167.3968 ]
  Theta =   0.090298    3.051295  [ DEG:     5.1737    174.8263 ]
  Phi   =  -2.520148    0.621445  [ DEG:  -144.3938     35.6062 ]
 
# 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   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_2_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   2.97   4.135     5.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      20.797  43.833  -2.065  1.00  0.00
ATOM   1036  CA  LYS   290      21.984  43.056  -2.302  1.00  0.00
ATOM   1037  C   LYS   290      22.898  43.766  -3.258  1.00  0.00
ATOM   1038  O   LYS   290      23.844  43.191  -3.783  1.00  0.00
ATOM   1039  CB  LYS   290      21.693  41.634  -2.809  1.00  0.00
ATOM   1040  CG  LYS   290      22.922  40.725  -2.727  1.00  0.00
ATOM   1041  CD  LYS   290      22.597  39.230  -2.692  1.00  0.00
ATOM   1042  CE  LYS   290      22.005  38.787  -1.354  1.00  0.00
ATOM   1043  NZ  LYS   290      22.099  37.319  -1.193  1.00  0.00
ATOM   1044  N   TYR   291      22.466  44.952  -3.683  1.00  0.00
ATOM   1045  CA  TYR   291      23.028  45.884  -4.616  1.00  0.00
ATOM   1046  C   TYR   291      24.132  46.772  -4.125  1.00  0.00
ATOM   1047  O   TYR   291      24.473  47.733  -4.803  1.00  0.00
ATOM   1048  CB  TYR   291      21.943  46.633  -5.383  1.00  0.00
ATOM   1049  CG  TYR   291      21.373  45.447  -6.078  1.00  0.00
ATOM   1050  CD1 TYR   291      21.950  44.977  -7.234  1.00  0.00
ATOM   1051  CD2 TYR   291      20.311  44.759  -5.535  1.00  0.00
ATOM   1052  CE1 TYR   291      21.450  43.864  -7.867  1.00  0.00
ATOM   1053  CE2 TYR   291      19.806  43.646  -6.162  1.00  0.00
ATOM   1054  CZ  TYR   291      20.374  43.199  -7.330  1.00  0.00
ATOM   1055  OH  TYR   291      19.849  42.056  -7.966  1.00  0.00
ATOM   1056  N   MET   292      24.548  46.659  -2.862  1.00  0.00
ATOM   1057  CA  MET   292      25.585  47.497  -2.324  1.00  0.00
ATOM   1058  C   MET   292      26.941  47.281  -2.935  1.00  0.00
ATOM   1059  O   MET   292      27.772  48.186  -2.846  1.00  0.00
ATOM   1060  CB  MET   292      25.734  47.381  -0.801  1.00  0.00
ATOM   1061  CG  MET   292      24.542  47.984  -0.058  1.00  0.00
ATOM   1062  SD  MET   292      24.691  47.960   1.752  1.00  0.00
ATOM   1063  CE  MET   292      23.148  48.870   2.034  1.00  0.00
ATOM   1064  N   ALA   293      27.255  46.089  -3.496  1.00  0.00
ATOM   1065  CA  ALA   293      28.586  45.909  -4.021  1.00  0.00
ATOM   1066  C   ALA   293      28.795  46.960  -5.054  1.00  0.00
ATOM   1067  O   ALA   293      29.773  47.704  -5.018  1.00  0.00
ATOM   1068  CB  ALA   293      28.791  44.563  -4.730  1.00  0.00
ATOM   1069  N   CYS   294      27.837  47.078  -5.980  1.00  0.00
ATOM   1070  CA  CYS   294      27.893  48.147  -6.913  1.00  0.00
ATOM   1071  C   CYS   294      26.492  48.594  -7.013  1.00  0.00
ATOM   1072  O   CYS   294      25.586  47.762  -7.043  1.00  0.00
ATOM   1073  CB  CYS   294      28.337  47.734  -8.323  1.00  0.00
ATOM   1074  SG  CYS   294      30.034  47.082  -8.354  1.00  0.00
ATOM   1075  N   LEU   295      26.279  49.917  -7.052  1.00  0.00
ATOM   1076  CA  LEU   295      24.938  50.384  -7.149  1.00  0.00
ATOM   1077  C   LEU   295      24.458  49.810  -8.440  1.00  0.00
ATOM   1078  O   LEU   295      23.341  49.296  -8.527  1.00  0.00
ATOM   1079  CB  LEU   295      24.882  51.915  -7.246  1.00  0.00
ATOM   1080  CG  LEU   295      23.462  52.491  -7.341  1.00  0.00
ATOM   1081  CD1 LEU   295      22.677  52.248  -6.044  1.00  0.00
ATOM   1082  CD2 LEU   295      23.484  53.967  -7.763  1.00  0.00
ATOM   1083  N   LYS   296      25.291  49.926  -9.496  1.00  0.00
ATOM   1084  CA  LYS   296      24.940  49.322 -10.750  1.00  0.00
ATOM   1085  C   LYS   296      25.111  47.824 -10.772  1.00  0.00
ATOM   1086  O   LYS   296      24.137  47.076 -10.701  1.00  0.00
ATOM   1087  CB  LYS   296      25.774  49.867 -11.925  1.00  0.00
ATOM   1088  CG  LYS   296      25.488  51.332 -12.265  1.00  0.00
ATOM   1089  CD  LYS   296      26.541  51.980 -13.170  1.00  0.00
ATOM   1090  CE  LYS   296      26.172  52.015 -14.656  1.00  0.00
ATOM   1091  NZ  LYS   296      26.537  50.737 -15.309  1.00  0.00
ATOM   1092  N   ASP   297      26.382  47.355 -10.781  1.00  0.00
ATOM   1093  CA  ASP   297      26.685  45.962 -11.023  1.00  0.00
ATOM   1094  C   ASP   297      27.070  45.225  -9.778  1.00  0.00
ATOM   1095  O   ASP   297      26.679  45.576  -8.668  1.00  0.00
ATOM   1096  CB  ASP   297      27.840  45.734 -12.013  1.00  0.00
ATOM   1097  CG  ASP   297      27.386  46.138 -13.406  1.00  0.00
ATOM   1098  OD1 ASP   297      26.271  46.712 -13.518  1.00  0.00
ATOM   1099  OD2 ASP   297      28.145  45.876 -14.377  1.00  0.00
ATOM   1100  N   HIS   298      27.845  44.131  -9.980  1.00  0.00
ATOM   1101  CA  HIS   298      28.336  43.298  -8.915  1.00  0.00
ATOM   1102  C   HIS   298      29.821  43.466  -8.865  1.00  0.00
ATOM   1103  O   HIS   298      30.381  44.280  -9.592  1.00  0.00
ATOM   1104  CB  HIS   298      28.065  41.798  -9.112  1.00  0.00
ATOM   1105  CG  HIS   298      26.608  41.456  -9.036  1.00  0.00
ATOM   1106  ND1 HIS   298      25.949  41.142  -7.868  1.00  0.00
ATOM   1107  CD2 HIS   298      25.674  41.392 -10.022  1.00  0.00
ATOM   1108  CE1 HIS   298      24.656  40.903  -8.203  1.00  0.00
ATOM   1109  NE2 HIS   298      24.440  41.043  -9.498  1.00  0.00
TER
END
