
#######################################################
#                                                     #
#                        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 (   86),  selected    9 , name T0372TS277_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_3-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         3.33     3.33
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.95     4.93
  LONGEST_CONTINUOUS_SEGMENT:     6       292 - 297         1.91     4.76
  LCS_AVERAGE:      4.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.87     4.68
  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    9     3    3    3    4    4    6    6    6    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     3    3    4    4    5    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      3    6    9     3    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      4    6    9     3    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     3    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     3    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      3    6    9     0    3    4    4    6    6    7    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    4    9     0    3    4    4    5    6    6    8    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.76  (   2.73    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      3      3      4      4      6      6      7      8      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   2.38   3.17   3.17   4.76   4.76   5.56   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.04   0.04   0.87   0.87   1.91   1.91   2.28   3.08   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33
GDT RMS_ALL_CA  11.51  11.51   4.68   4.68   4.76   4.76   4.27   3.49   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          5.803
LGA    Y     291      Y     291          3.802
LGA    M     292      M     292          2.636
LGA    A     293      A     293          3.361
LGA    C     294      C     294          3.482
LGA    L     295      L     295          3.782
LGA    K     296      K     296          2.083
LGA    D     297      D     297          2.847
LGA    H     298      H     298          2.067

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      8    3.08     4.762     5.074     0.252

LGA_LOCAL      RMSD =  3.079  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.488  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  3.326  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.477541 * X  +  -0.664001 * Y  +   0.575376 * Z  +  18.587671
  Y_new =  -0.251149 * X  +   0.524385 * Y  +   0.813600 * Z  +  13.975558
  Z_new =  -0.841949 * X  +  -0.533032 * Y  +   0.083652 * Z  +  42.396267 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.415129    1.726463  [ DEG:   -81.0809     98.9191 ]
  Theta =   1.000886    2.140707  [ DEG:    57.3465    122.6535 ]
  Phi   =  -0.484169    2.657424  [ DEG:   -27.7408    152.2592 ]
 
# 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: T0372TS277_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_3-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    8   3.08   5.074     3.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_3-D1
PFRMAT TS 
TARGET T0372
MODEL 3
PARENT 1YR0_A
ATOM   2945  H   LYS   290      21.846  51.154   2.718  1.00  0.00                              
ATOM   2947  N   LYS   290      22.535  51.048   3.363  1.00  0.00                              
ATOM   2949  CA  LYS   290      23.428  49.896   3.257  1.00  0.00                              
ATOM   2951  CB  LYS   290      22.680  48.692   2.676  1.00  0.00                              
ATOM   2953  C   LYS   290      24.630  50.222   2.373  1.00  0.00                              
ATOM   2955  O   LYS   290      24.550  51.094   1.504  1.00  0.00                              
ATOM   2957  CG  LYS   290      21.625  48.096   3.597  1.00  0.00                              
ATOM   2959  CD  LYS   290      20.926  46.908   2.944  1.00  0.00                              
ATOM   2961  CE  LYS   290      19.928  46.247   3.887  1.00  0.00                              
ATOM   2963  NZ  LYS   290      19.244  45.087   3.244  1.00  0.00                              
ATOM   2965  H   TYR   291      25.752  48.851   3.246  1.00  0.00                              
ATOM   2967  N   TYR   291      25.735  49.508   2.567  1.00  0.00                              
ATOM   2969  CA  TYR   291      26.939  49.747   1.781  1.00  0.00                              
ATOM   2971  CB  TYR   291      28.121  50.058   2.697  1.00  0.00                              
ATOM   2973  C   TYR   291      27.306  48.547   0.926  1.00  0.00                              
ATOM   2975  O   TYR   291      27.189  47.403   1.368  1.00  0.00                              
ATOM   2977  CG  TYR   291      29.402  50.309   1.940  1.00  0.00                              
ATOM   2979  CD1 TYR   291      29.552  51.457   1.165  1.00  0.00                              
ATOM   2981  CE1 TYR   291      30.746  51.726   0.504  1.00  0.00                              
ATOM   2983  CZ  TYR   291      31.812  50.855   0.644  1.00  0.00                              
ATOM   2985  CD2 TYR   291      30.463  49.409   1.998  1.00  0.00                              
ATOM   2987  CE2 TYR   291      31.673  49.686   1.371  1.00  0.00                              
ATOM   2989  OH  TYR   291      33.006  51.130   0.013  1.00  0.00                              
ATOM   2991  H   MET   292      27.888  49.719  -0.544  1.00  0.00                              
ATOM   2993  N   MET   292      27.810  48.816  -0.275  1.00  0.00                              
ATOM   2995  CA  MET   292      28.216  47.760  -1.193  1.00  0.00                              
ATOM   2997  CB  MET   292      29.662  47.336  -0.929  1.00  0.00                              
ATOM   2999  C   MET   292      27.307  46.549  -1.060  1.00  0.00                              
ATOM   3001  O   MET   292      27.760  45.465  -0.685  1.00  0.00                              
ATOM   3003  CG  MET   292      30.696  48.301  -1.488  1.00  0.00                              
ATOM   3005  SD  MET   292      30.343  48.794  -3.191  1.00  0.00                              
ATOM   3007  CE  MET   292      29.729  50.452  -2.937  1.00  0.00                              
ATOM   3009  H   ALA   293      25.732  47.545  -1.692  1.00  0.00                              
ATOM   3011  N   ALA   293      26.035  46.703  -1.425  1.00  0.00                              
ATOM   3013  CA  ALA   293      25.092  45.586  -1.402  1.00  0.00                              
ATOM   3015  CB  ALA   293      23.858  45.947  -0.581  1.00  0.00                              
ATOM   3017  C   ALA   293      24.681  45.178  -2.815  1.00  0.00                              
ATOM   3019  O   ALA   293      24.394  44.005  -3.071  1.00  0.00                              
ATOM   3021  H   CYS   294      24.971  46.990  -3.511  1.00  0.00                              
ATOM   3023  N   CYS   294      24.682  46.135  -3.739  1.00  0.00                              
ATOM   3025  CA  CYS   294      24.272  45.867  -5.113  1.00  0.00                              
ATOM   3027  CB  CYS   294      22.937  46.555  -5.415  1.00  0.00                              
ATOM   3029  C   CYS   294      25.329  46.343  -6.100  1.00  0.00                              
ATOM   3031  O   CYS   294      25.836  47.461  -5.984  1.00  0.00                              
ATOM   3033  SG  CYS   294      21.569  45.986  -4.377  1.00  0.00                              
ATOM   3035  H   LEU   295      25.242  44.650  -7.102  1.00  0.00                              
ATOM   3037  N   LEU   295      25.645  45.505  -7.080  1.00  0.00                              
ATOM   3039  CA  LEU   295      26.618  45.854  -8.108  1.00  0.00                              
ATOM   3041  CB  LEU   295      27.675  44.749  -8.194  1.00  0.00                              
ATOM   3043  C   LEU   295      25.922  45.987  -9.457  1.00  0.00                              
ATOM   3045  O   LEU   295      24.914  45.323  -9.706  1.00  0.00                              
ATOM   3047  CG  LEU   295      27.120  43.323  -8.248  1.00  0.00                              
ATOM   3049  CD1 LEU   295      26.916  42.878  -9.690  1.00  0.00                              
ATOM   3051  CD2 LEU   295      28.041  42.361  -7.509  1.00  0.00                              
ATOM   3053  H   LYS   296      27.185  47.381 -10.053  1.00  0.00                              
ATOM   3055  N   LYS   296      26.434  46.861 -10.315  1.00  0.00                              
ATOM   3057  CA  LYS   296      25.880  47.024 -11.655  1.00  0.00                              
ATOM   3059  CB  LYS   296      24.581  46.225 -11.783  1.00  0.00                              
ATOM   3061  C   LYS   296      25.629  48.491 -11.997  1.00  0.00                              
ATOM   3063  O   LYS   296      24.873  49.175 -11.303  1.00  0.00                              
ATOM   3065  CG  LYS   296      23.942  46.299 -13.162  1.00  0.00                              
ATOM   3067  CD  LYS   296      24.878  45.759 -14.235  1.00  0.00                              
ATOM   3069  CE  LYS   296      24.241  45.824 -15.617  1.00  0.00                              
ATOM   3071  NZ  LYS   296      25.103  45.185 -16.655  1.00  0.00                              
ATOM   3073  H   ASP   297      26.886  48.426 -13.511  1.00  0.00                              
ATOM   3075  N   ASP   297      26.267  48.974 -13.059  1.00  0.00                              
ATOM   3077  CA  ASP   297      26.058  50.339 -13.535  1.00  0.00                              
ATOM   3079  CB  ASP   297      24.800  50.957 -12.920  1.00  0.00                              
ATOM   3081  C   ASP   297      27.270  51.225 -13.255  1.00  0.00                              
ATOM   3083  O   ASP   297      27.640  51.430 -12.098  1.00  0.00                              
ATOM   3085  CG  ASP   297      24.355  52.207 -13.655  1.00  0.00                              
ATOM   3087  OD1 ASP   297      24.773  52.397 -14.818  1.00  0.00                              
ATOM   3089  OD2 ASP   297      23.606  53.018 -13.069  1.00  0.00                              
ATOM   3091  H   HIS   298      27.518  51.604 -15.176  1.00  0.00                              
ATOM   3093  N   HIS   298      27.868  51.765 -14.311  1.00  0.00                              
ATOM   3095  CA  HIS   298      29.075  52.574 -14.170  1.00  0.00                              
ATOM   3097  CB  HIS   298      29.837  52.147 -12.910  1.00  0.00                              
ATOM   3099  C   HIS   298      29.963  52.384 -15.397  1.00  0.00                              
ATOM   3101  O   HIS   298      30.068  51.272 -15.919  1.00  0.00                              
ATOM   3103  CG  HIS   298      30.558  53.263 -12.216  1.00  0.00                              
ATOM   3105  ND1 HIS   298      31.742  53.075 -11.539  1.00  0.00                              
ATOM   3107  HD1 HIS   298      32.222  52.257 -11.471  1.00  0.00                              
ATOM   3109  CE1 HIS   298      32.162  54.238 -11.073  1.00  0.00                              
ATOM   3111  NE2 HIS   298      31.227  55.141 -11.305  1.00  0.00                              
ATOM   3113  HE2 HIS   298      31.243  56.036 -10.982  1.00  0.00                              
ATOM   3115  CD2 HIS   298      30.195  54.549 -11.991  1.00  0.00                              
TER 
END
