
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_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         4.41     4.41
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       290 - 296         1.89     5.80
  LCS_AVERAGE:      5.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.85     5.72
  LONGEST_CONTINUOUS_SEGMENT:     5       292 - 296         0.62     5.27
  LCS_AVERAGE:      3.62

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      4    7    9     3    3    4    5    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     Y     291     Y     291      5    7    9     3    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     M     292     M     292      5    7    9     4    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     A     293     A     293      5    7    9     4    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     C     294     C     294      5    7    9     3    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     L     295     L     295      5    7    9     4    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     K     296     K     296      5    7    9     4    4    5    6    6    6    7    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     D     297     D     297      4    6    9     0    3    4    5    6    6    6    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     H     298     H     298      3    5    9     0    3    3    4    4    5    5    7    7    7    7    7    7    8    8    8    8    9    9    9 
LCS_AVERAGE  LCS_A:   5.35  (   3.62    5.29    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      6      6      6      7      7      7      7      8      8      8      8      8      8      8      9      9      9 
GDT PERCENT_CA   3.17   3.17   3.97   4.76   4.76   4.76   5.56   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35   6.35   7.14   7.14   7.14
GDT RMS_LOCAL    0.16   0.16   0.62   1.06   1.06   1.06   1.89   1.89   1.89   1.89   2.90   2.90   2.90   2.90   2.90   2.90   2.90   4.41   4.41   4.41
GDT RMS_ALL_CA   5.08   5.08   5.27   5.33   5.33   5.33   5.80   5.80   5.80   5.80   4.86   4.86   4.86   4.86   4.86   4.86   4.86   4.41   4.41   4.41

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          3.175
LGA    Y     291      Y     291          1.199
LGA    M     292      M     292          1.479
LGA    A     293      A     293          1.737
LGA    C     294      C     294          1.193
LGA    L     295      L     295          1.085
LGA    K     296      K     296          2.385
LGA    D     297      D     297          8.171
LGA    H     298      H     298         14.518

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      7    1.89     4.960     5.194     0.352

LGA_LOCAL      RMSD =  1.890  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.798  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.406  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.055770 * X  +  -0.492467 * Y  +  -0.868542 * Z  +  38.480103
  Y_new =  -0.594000 * X  +   0.715571 * Y  +  -0.367591 * Z  +  39.676929
  Z_new =   0.802530 * X  +   0.495414 * Y  +  -0.332432 * Z  +   0.016846 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.161807   -0.979786  [ DEG:   123.8624    -56.1376 ]
  Theta =  -0.931524   -2.210069  [ DEG:   -53.3724   -126.6276 ]
  Phi   =  -1.664410    1.477183  [ DEG:   -95.3637     84.6363 ]
 
# 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_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_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    7   1.89   5.194     4.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_4-D1
PFRMAT TS 
TARGET T0372
MODEL 4
PARENT 1KUV_A
ATOM   2963  H   LYS   290      21.604  45.311   5.643  1.00  0.00                              
ATOM   2965  N   LYS   290      22.121  46.021   5.282  1.00  0.00                              
ATOM   2967  CA  LYS   290      23.583  45.979   5.424  1.00  0.00                              
ATOM   2969  CB  LYS   290      24.049  44.582   5.858  1.00  0.00                              
ATOM   2971  C   LYS   290      24.222  46.362   4.094  1.00  0.00                              
ATOM   2973  O   LYS   290      23.738  45.958   3.032  1.00  0.00                              
ATOM   2975  CG  LYS   290      25.408  44.522   6.547  1.00  0.00                              
ATOM   2977  CD  LYS   290      25.611  43.196   7.270  1.00  0.00                              
ATOM   2979  CE  LYS   290      25.523  43.359   8.781  1.00  0.00                              
ATOM   2981  NZ  LYS   290      25.189  42.072   9.460  1.00  0.00                              
ATOM   2983  H   TYR   291      25.759  47.301   4.932  1.00  0.00                              
ATOM   2985  N   TYR   291      25.330  47.104   4.114  1.00  0.00                              
ATOM   2987  CA  TYR   291      25.895  47.596   2.858  1.00  0.00                              
ATOM   2989  CB  TYR   291      25.933  49.118   2.836  1.00  0.00                              
ATOM   2991  C   TYR   291      27.269  47.053   2.484  1.00  0.00                              
ATOM   2993  O   TYR   291      28.199  47.034   3.294  1.00  0.00                              
ATOM   2995  CG  TYR   291      26.570  49.715   4.062  1.00  0.00                              
ATOM   2997  CD1 TYR   291      27.928  50.012   4.102  1.00  0.00                              
ATOM   2999  CE1 TYR   291      28.501  50.591   5.227  1.00  0.00                              
ATOM   3001  CZ  TYR   291      27.703  50.901   6.313  1.00  0.00                              
ATOM   3003  CD2 TYR   291      25.811  49.942   5.204  1.00  0.00                              
ATOM   3005  CE2 TYR   291      26.366  50.548   6.321  1.00  0.00                              
ATOM   3007  OH  TYR   291      28.273  51.434   7.451  1.00  0.00                              
ATOM   3009  H   MET   292      26.608  46.701   0.671  1.00  0.00                              
ATOM   3011  N   MET   292      27.383  46.666   1.212  1.00  0.00                              
ATOM   3013  CA  MET   292      28.627  46.196   0.607  1.00  0.00                              
ATOM   3015  CB  MET   292      28.643  44.663   0.606  1.00  0.00                              
ATOM   3017  C   MET   292      28.680  46.717  -0.834  1.00  0.00                              
ATOM   3019  O   MET   292      28.992  45.978  -1.770  1.00  0.00                              
ATOM   3021  CG  MET   292      29.997  44.038   0.300  1.00  0.00                              
ATOM   3023  SD  MET   292      29.859  42.283  -0.116  1.00  0.00                              
ATOM   3025  CE  MET   292      30.413  41.538   1.409  1.00  0.00                              
ATOM   3027  H   ALA   293      28.134  48.480  -0.215  1.00  0.00                              
ATOM   3029  N   ALA   293      28.336  47.995  -0.986  1.00  0.00                              
ATOM   3031  CA  ALA   293      28.214  48.703  -2.267  1.00  0.00                              
ATOM   3033  CB  ALA   293      28.733  50.129  -2.103  1.00  0.00                              
ATOM   3035  C   ALA   293      28.878  48.058  -3.489  1.00  0.00                              
ATOM   3037  O   ALA   293      30.102  47.915  -3.549  1.00  0.00                              
ATOM   3039  H   CYS   294      27.144  47.832  -4.374  1.00  0.00                              
ATOM   3041  N   CYS   294      28.062  47.737  -4.497  1.00  0.00                              
ATOM   3043  CA  CYS   294      28.546  47.221  -5.781  1.00  0.00                              
ATOM   3045  CB  CYS   294      28.134  45.764  -6.012  1.00  0.00                              
ATOM   3047  C   CYS   294      28.075  48.107  -6.938  1.00  0.00                              
ATOM   3049  O   CYS   294      28.812  49.013  -7.340  1.00  0.00                              
ATOM   3051  SG  CYS   294      28.441  44.665  -4.606  1.00  0.00                              
ATOM   3053  H   LEU   295      26.382  47.111  -7.256  1.00  0.00                              
ATOM   3055  N   LEU   295      26.898  47.858  -7.524  1.00  0.00                              
ATOM   3057  CA  LEU   295      26.397  48.761  -8.567  1.00  0.00                              
ATOM   3059  CB  LEU   295      27.484  49.064  -9.607  1.00  0.00                              
ATOM   3061  C   LEU   295      25.126  48.313  -9.293  1.00  0.00                              
ATOM   3063  O   LEU   295      25.212  47.652 -10.330  1.00  0.00                              
ATOM   3065  CG  LEU   295      27.101  50.056 -10.710  1.00  0.00                              
ATOM   3067  CD1 LEU   295      26.743  51.405 -10.100  1.00  0.00                              
ATOM   3069  CD2 LEU   295      28.241  50.206 -11.706  1.00  0.00                              
ATOM   3071  H   LYS   296      23.970  49.189  -7.961  1.00  0.00                              
ATOM   3073  N   LYS   296      23.960  48.726  -8.789  1.00  0.00                              
ATOM   3075  CA  LYS   296      22.673  48.485  -9.450  1.00  0.00                              
ATOM   3077  CB  LYS   296      22.720  49.011 -10.886  1.00  0.00                              
ATOM   3079  C   LYS   296      22.158  47.040  -9.442  1.00  0.00                              
ATOM   3081  O   LYS   296      22.910  46.097  -9.692  1.00  0.00                              
ATOM   3083  CG  LYS   296      23.084  50.486 -11.001  1.00  0.00                              
ATOM   3085  CD  LYS   296      23.140  50.935 -12.457  1.00  0.00                              
ATOM   3087  CE  LYS   296      23.221  52.452 -12.584  1.00  0.00                              
ATOM   3089  NZ  LYS   296      23.216  52.890 -14.011  1.00  0.00                              
ATOM   3091  H   ASP   297      20.338  47.644  -8.993  1.00  0.00                              
ATOM   3093  N   ASP   297      20.852  46.882  -9.204  1.00  0.00                              
ATOM   3095  CA  ASP   297      20.169  45.582  -9.244  1.00  0.00                              
ATOM   3097  CB  ASP   297      21.062  44.456  -9.775  1.00  0.00                              
ATOM   3099  C   ASP   297      19.607  45.167  -7.890  1.00  0.00                              
ATOM   3101  O   ASP   297      19.413  46.002  -7.003  1.00  0.00                              
ATOM   3103  CG  ASP   297      21.046  44.372 -11.287  1.00  0.00                              
ATOM   3105  OD1 ASP   297      20.307  45.154 -11.920  1.00  0.00                              
ATOM   3107  OD2 ASP   297      21.759  43.516 -11.855  1.00  0.00                              
ATOM   3109  H   HIS   298      19.361  43.310  -8.509  1.00  0.00                              
ATOM   3111  N   HIS   298      19.297  43.880  -7.758  1.00  0.00                              
ATOM   3113  CA  HIS   298      18.853  43.334  -6.482  1.00  0.00                              
ATOM   3115  CB  HIS   298      18.302  41.919  -6.691  1.00  0.00                              
ATOM   3117  C   HIS   298      20.037  43.291  -5.520  1.00  0.00                              
ATOM   3119  O   HIS   298      21.168  43.099  -5.966  1.00  0.00                              
ATOM   3121  CG  HIS   298      17.093  41.884  -7.574  1.00  0.00                              
ATOM   3123  ND1 HIS   298      15.827  42.175  -7.114  1.00  0.00                              
ATOM   3125  HD1 HIS   298      15.596  42.392  -6.216  1.00  0.00                              
ATOM   3127  CE1 HIS   298      14.959  42.016  -8.099  1.00  0.00                              
ATOM   3129  NE2 HIS   298      15.618  41.630  -9.179  1.00  0.00                              
ATOM   3131  HE2 HIS   298      15.214  41.407 -10.010  1.00  0.00                              
ATOM   3133  CD2 HIS   298      16.950  41.508  -8.870  1.00  0.00                              
TER 
END
