
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_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         2.95     2.95
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       291 - 297         1.89     3.59
  LONGEST_CONTINUOUS_SEGMENT:     7       292 - 298         1.97     3.99
  LCS_AVERAGE:      5.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       294 - 298         0.81     6.19
  LCS_AVERAGE:      3.53

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    5    9     3    3    3    4    5    5    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      4    7    9     4    4    5    5    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    7    9     4    4    5    5    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    7    9     3    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      5    7    9     4    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      5    7    9     3    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      5    7    9     4    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      5    7    9     3    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      5    7    9     3    4    5    6    6    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.35  (   3.53    5.38    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      7      8      8      8      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   3.17   3.17   3.97   4.76   4.76   5.56   6.35   6.35   6.35   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    0.16   0.16   0.64   1.43   1.43   1.89   2.37   2.37   2.37   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95
GDT RMS_ALL_CA   4.17   4.17   4.46   5.46   5.46   3.59   3.25   3.25   3.25   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95   2.95

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          7.089
LGA    Y     291      Y     291          2.946
LGA    M     292      M     292          1.516
LGA    A     293      A     293          2.915
LGA    C     294      C     294          1.961
LGA    L     295      L     295          1.847
LGA    K     296      K     296          2.228
LGA    D     297      D     297          1.922
LGA    H     298      H     298          3.080

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      8    2.37     5.357     5.605     0.324

LGA_LOCAL      RMSD =  2.368  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.251  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.953  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.769342 * X  +  -0.299608 * Y  +   0.564223 * Z  +  47.066528
  Y_new =  -0.396564 * X  +   0.916411 * Y  +  -0.054109 * Z  +   3.701454
  Z_new =  -0.500849 * X  +  -0.265379 * Y  +  -0.823848 * Z  +  33.555641 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.829967    0.311626  [ DEG:  -162.1452     17.8548 ]
  Theta =   0.524579    2.617014  [ DEG:    30.0562    149.9438 ]
  Phi   =  -2.665655    0.475938  [ DEG:  -152.7308     27.2692 ]
 
# 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_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_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    8   2.37   5.605     2.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_2-D1
PFRMAT TS 
TARGET T0372
MODEL 2
PARENT 1QSM_A
ATOM   2963  H   LYS   290      20.697  49.840   4.281  1.00  0.00                              
ATOM   2965  N   LYS   290      20.933  49.879   3.361  1.00  0.00                              
ATOM   2967  CA  LYS   290      22.128  50.602   2.947  1.00  0.00                              
ATOM   2969  CB  LYS   290      22.112  52.019   3.518  1.00  0.00                              
ATOM   2971  C   LYS   290      23.433  49.888   3.289  1.00  0.00                              
ATOM   2973  O   LYS   290      23.507  49.141   4.269  1.00  0.00                              
ATOM   2975  CG  LYS   290      21.004  52.904   2.975  1.00  0.00                              
ATOM   2977  CD  LYS   290      21.094  54.304   3.568  1.00  0.00                              
ATOM   2979  CE  LYS   290      19.934  55.177   3.109  1.00  0.00                              
ATOM   2981  NZ  LYS   290      20.002  56.547   3.699  1.00  0.00                              
ATOM   2983  H   TYR   291      24.282  50.617   1.671  1.00  0.00                              
ATOM   2985  N   TYR   291      24.440  50.093   2.439  1.00  0.00                              
ATOM   2987  CA  TYR   291      25.786  49.557   2.641  1.00  0.00                              
ATOM   2989  CB  TYR   291      26.207  49.603   4.117  1.00  0.00                              
ATOM   2991  C   TYR   291      25.960  48.162   2.038  1.00  0.00                              
ATOM   2993  O   TYR   291      26.246  47.201   2.757  1.00  0.00                              
ATOM   2995  CG  TYR   291      26.097  50.979   4.738  1.00  0.00                              
ATOM   2997  CD1 TYR   291      25.828  52.106   3.960  1.00  0.00                              
ATOM   2999  CE1 TYR   291      25.787  53.376   4.529  1.00  0.00                              
ATOM   3001  CZ  TYR   291      26.039  53.523   5.883  1.00  0.00                              
ATOM   3003  CD2 TYR   291      26.225  51.145   6.114  1.00  0.00                              
ATOM   3005  CE2 TYR   291      26.179  52.410   6.692  1.00  0.00                              
ATOM   3007  OH  TYR   291      26.017  54.778   6.447  1.00  0.00                              
ATOM   3009  H   MET   292      25.537  48.827   0.236  1.00  0.00                              
ATOM   3011  N   MET   292      25.811  48.058   0.715  1.00  0.00                              
ATOM   3013  CA  MET   292      26.023  46.803  -0.013  1.00  0.00                              
ATOM   3015  CB  MET   292      24.855  46.491  -0.969  1.00  0.00                              
ATOM   3017  C   MET   292      27.340  46.847  -0.793  1.00  0.00                              
ATOM   3019  O   MET   292      28.382  47.223  -0.253  1.00  0.00                              
ATOM   3021  CG  MET   292      23.498  46.285  -0.301  1.00  0.00                              
ATOM   3023  SD  MET   292      23.387  44.718   0.597  1.00  0.00                              
ATOM   3025  CE  MET   292      22.858  43.606  -0.701  1.00  0.00                              
ATOM   3027  H   ALA   293      26.555  46.030  -2.404  1.00  0.00                              
ATOM   3029  N   ALA   293      27.330  46.411  -2.048  1.00  0.00                              
ATOM   3031  CA  ALA   293      28.537  46.498  -2.867  1.00  0.00                              
ATOM   3033  CB  ALA   293      29.602  45.517  -2.382  1.00  0.00                              
ATOM   3035  C   ALA   293      28.242  46.272  -4.344  1.00  0.00                              
ATOM   3037  O   ALA   293      29.069  46.601  -5.199  1.00  0.00                              
ATOM   3039  H   CYS   294      26.453  45.569  -3.961  1.00  0.00                              
ATOM   3041  N   CYS   294      27.057  45.748  -4.646  1.00  0.00                              
ATOM   3043  CA  CYS   294      26.655  45.505  -6.028  1.00  0.00                              
ATOM   3045  CB  CYS   294      25.470  44.541  -6.058  1.00  0.00                              
ATOM   3047  C   CYS   294      26.248  46.815  -6.686  1.00  0.00                              
ATOM   3049  O   CYS   294      26.006  47.799  -5.984  1.00  0.00                              
ATOM   3051  SG  CYS   294      25.836  42.911  -5.363  1.00  0.00                              
ATOM   3053  H   LEU   295      26.425  46.122  -8.534  1.00  0.00                              
ATOM   3055  N   LEU   295      26.227  46.884  -8.011  1.00  0.00                              
ATOM   3057  CA  LEU   295      25.893  48.149  -8.657  1.00  0.00                              
ATOM   3059  CB  LEU   295      26.886  49.246  -8.254  1.00  0.00                              
ATOM   3061  C   LEU   295      25.720  48.050 -10.171  1.00  0.00                              
ATOM   3063  O   LEU   295      25.631  49.073 -10.852  1.00  0.00                              
ATOM   3065  CG  LEU   295      28.337  49.139  -8.743  1.00  0.00                              
ATOM   3067  CD1 LEU   295      29.248  48.772  -7.578  1.00  0.00                              
ATOM   3069  CD2 LEU   295      28.472  48.119  -9.865  1.00  0.00                              
ATOM   3071  H   LYS   296      25.702  46.083 -10.105  1.00  0.00                              
ATOM   3073  N   LYS   296      25.617  46.829 -10.684  1.00  0.00                              
ATOM   3075  CA  LYS   296      25.373  46.592 -12.104  1.00  0.00                              
ATOM   3077  CB  LYS   296      23.877  46.673 -12.433  1.00  0.00                              
ATOM   3079  C   LYS   296      26.173  47.492 -13.044  1.00  0.00                              
ATOM   3081  O   LYS   296      27.309  47.157 -13.396  1.00  0.00                              
ATOM   3083  CG  LYS   296      23.357  48.080 -12.686  1.00  0.00                              
ATOM   3085  CD  LYS   296      21.841  48.148 -12.553  1.00  0.00                              
ATOM   3087  CE  LYS   296      21.357  49.589 -12.415  1.00  0.00                              
ATOM   3089  NZ  LYS   296      22.343  50.558 -12.978  1.00  0.00                              
ATOM   3091  H   ASP   297      24.822  48.918 -12.935  1.00  0.00                              
ATOM   3093  N   ASP   297      25.601  48.649 -13.391  1.00  0.00                              
ATOM   3095  CA  ASP   297      26.172  49.553 -14.393  1.00  0.00                              
ATOM   3097  CB  ASP   297      25.138  49.812 -15.498  1.00  0.00                              
ATOM   3099  C   ASP   297      26.704  50.879 -13.837  1.00  0.00                              
ATOM   3101  O   ASP   297      26.752  51.874 -14.563  1.00  0.00                              
ATOM   3103  CG  ASP   297      25.740  50.264 -16.817  1.00  0.00                              
ATOM   3105  OD1 ASP   297      26.961  50.087 -17.014  1.00  0.00                              
ATOM   3107  OD2 ASP   297      24.992  50.785 -17.673  1.00  0.00                              
ATOM   3109  H   HIS   298      27.023  50.118 -12.043  1.00  0.00                              
ATOM   3111  N   HIS   298      27.109  50.901 -12.569  1.00  0.00                              
ATOM   3113  CA  HIS   298      27.711  52.095 -11.974  1.00  0.00                              
ATOM   3115  CB  HIS   298      27.237  53.385 -12.661  1.00  0.00                              
ATOM   3117  C   HIS   298      27.477  52.146 -10.467  1.00  0.00                              
ATOM   3119  O   HIS   298      26.463  51.632  -9.998  1.00  0.00                              
ATOM   3121  CG  HIS   298      25.779  53.715 -12.511  1.00  0.00                              
ATOM   3123  ND1 HIS   298      25.225  54.850 -13.064  1.00  0.00                              
ATOM   3125  HD1 HIS   298      25.681  55.491 -13.598  1.00  0.00                              
ATOM   3127  CE1 HIS   298      23.928  54.870 -12.805  1.00  0.00                              
ATOM   3129  NE2 HIS   298      23.612  53.757 -12.165  1.00  0.00                              
ATOM   3131  HE2 HIS   298      22.727  53.496 -11.936  1.00  0.00                              
ATOM   3133  CD2 HIS   298      24.746  52.997 -12.005  1.00  0.00                              
TER 
END
