
#######################################################
#                                                     #
#                        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 T0372TS174_1u-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS174_1u-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         4.33     4.33
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         1.32     9.02
  LCS_AVERAGE:      2.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.79    11.55
  LONGEST_CONTINUOUS_SEGMENT:     3       292 - 294         0.53     6.93
  LONGEST_CONTINUOUS_SEGMENT:     3       293 - 295         0.60     7.05
  LONGEST_CONTINUOUS_SEGMENT:     3       294 - 296         0.46     8.64
  LONGEST_CONTINUOUS_SEGMENT:     3       295 - 297         0.20    10.74
  LONGEST_CONTINUOUS_SEGMENT:     3       296 - 298         0.28    13.49
  LCS_AVERAGE:      2.38

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    3    4    4    6    7    7    8    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    3    9     3    3    3    3    3    3    4    5    6    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      3    3    9     3    3    3    3    3    3    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      3    3    9     3    3    3    3    4    5    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      3    3    9     3    3    3    3    4    5    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      3    4    9     3    3    4    4    4    5    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      3    4    9     3    3    4    4    4    5    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      3    4    9     3    3    4    4    4    4    5    5    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    4    9     3    3    4    4    4    5    6    6    7    7    8    8    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.09  (   2.38    2.73    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      4      5      6      6      7      7      8      8      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   2.38   3.17   3.17   3.17   3.97   4.76   4.76   5.56   5.56   6.35   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.20   0.20   1.32   1.32   1.32   2.31   2.84   2.84   3.26   3.26   3.83   3.83   4.33   4.33   4.33   4.33   4.33   4.33   4.33   4.33
GDT RMS_ALL_CA  10.74  10.74   9.02   9.02   9.02   5.30   4.89   4.89   4.86   4.86   4.50   4.50   4.33   4.33   4.33   4.33   4.33   4.33   4.33   4.33

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          7.471
LGA    Y     291      Y     291          7.407
LGA    M     292      M     292          3.428
LGA    A     293      A     293          1.572
LGA    C     294      C     294          2.773
LGA    L     295      L     295          2.897
LGA    K     296      K     296          3.008
LGA    D     297      D     297          6.619
LGA    H     298      H     298          3.282

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    2.84     4.365     4.168     0.204

LGA_LOCAL      RMSD =  2.837  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.768  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.333  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.162530 * X  +  -0.116202 * Y  +  -0.979837 * Z  +  48.537689
  Y_new =  -0.824543 * X  +   0.561429 * Y  +   0.070189 * Z  +  49.690624
  Z_new =   0.541952 * X  +   0.819326 * Y  +  -0.187063 * Z  + -35.629986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.795262   -1.346331  [ DEG:   102.8609    -77.1391 ]
  Theta =  -0.572759   -2.568834  [ DEG:   -32.8167   -147.1833 ]
  Phi   =  -1.765417    1.376176  [ DEG:  -101.1509     78.8491 ]
 
# 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: T0372TS174_1u-D1                              
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS174_1u-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   2.84   4.168     4.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS174_1u-D1
PFRMAT TS
TARGET T0372
MODEL 1  UNREFINED
PARENT 1ew6_A 
ATOM    927  N   LYS   290      29.638  48.543   1.547  1.00  1.00
ATOM    928  CA  LYS   290      28.698  49.115   0.556  1.00  1.00
ATOM    929  C   LYS   290      28.719  48.295  -0.739  1.00  1.00
ATOM    930  O   LYS   290      27.691  48.148  -1.415  1.00  1.00
ATOM    931  CB  LYS   290      29.038  50.589   0.292  1.00  1.00
ATOM    932  CG  LYS   290      28.780  51.343   1.434  1.00  1.00
ATOM    933  CD  LYS   290      29.091  52.820   1.201  1.00  1.00
ATOM    934  CE  LYS   290      28.100  53.431   0.207  1.00  1.00
ATOM    935  NZ  LYS   290      28.405  54.866  -0.031  1.00  1.00
ATOM    936  N   TYR   291      29.700  47.425  -0.822  1.00  1.00
ATOM    937  CA  TYR   291      30.161  46.810  -2.088  1.00  1.00
ATOM    938  C   TYR   291      28.963  46.412  -2.958  1.00  1.00
ATOM    939  O   TYR   291      28.994  46.565  -4.189  1.00  1.00
ATOM    940  CB  TYR   291      31.065  45.605  -1.793  1.00  1.00
ATOM    941  CG  TYR   291      31.651  44.946  -3.026  1.00  1.00
ATOM    942  CD1 TYR   291      32.763  45.487  -3.656  1.00  1.00
ATOM    943  CD2 TYR   291      31.110  43.790  -3.551  1.00  1.00
ATOM    944  CE1 TYR   291      33.318  44.900  -4.782  1.00  1.00
ATOM    945  CE2 TYR   291      31.652  43.185  -4.673  1.00  1.00
ATOM    946  CZ  TYR   291      32.757  43.747  -5.293  1.00  1.00
ATOM    947  OH  TYR   291      33.276  43.118  -6.413  1.00  1.00
ATOM    948  N   MET   292      27.920  45.943  -2.273  1.00  1.00
ATOM    949  CA  MET   292      26.677  45.545  -2.972  1.00  1.00
ATOM    950  C   MET   292      25.979  46.773  -3.566  1.00  1.00
ATOM    951  O   MET   292      25.403  46.709  -4.662  1.00  1.00
ATOM    952  CB  MET   292      25.751  44.782  -2.015  1.00  1.00
ATOM    953  CG  MET   292      24.439  44.260  -2.711  1.00  1.00
ATOM    954  SD  MET   292      23.435  43.402  -1.583  1.00  1.00
ATOM    955  CE  MET   292      22.802  44.672  -0.690  1.00  1.00
ATOM    956  N   ALA   293      26.041  47.875  -2.829  1.00  1.00
ATOM    957  CA  ALA   293      25.435  49.143  -3.295  1.00  1.00
ATOM    958  C   ALA   293      26.213  49.701  -4.492  1.00  1.00
ATOM    959  O   ALA   293      25.623  50.267  -5.425  1.00  1.00
ATOM    960  CB  ALA   293      25.375  50.156  -2.143  1.00  1.00
ATOM    961  N   CYS   294      27.545  49.427  -4.436  1.00  1.00
ATOM    962  CA  CYS   294      28.444  49.858  -5.531  1.00  1.00
ATOM    963  C   CYS   294      28.182  49.033  -6.795  1.00  1.00
ATOM    964  O   CYS   294      28.242  49.555  -7.918  1.00  1.00
ATOM    965  CB  CYS   294      29.910  49.754  -5.086  1.00  1.00
ATOM    966  SG  CYS   294      30.243  50.939  -3.724  1.00  1.00
ATOM    967  N   LEU   295      27.977  47.796  -6.644  1.00  1.00
ATOM    968  CA  LEU   295      27.749  46.910  -7.808  1.00  1.00
ATOM    969  C   LEU   295      26.448  47.289  -8.524  1.00  1.00
ATOM    970  O   LEU   295      26.390  47.320  -9.762  1.00  1.00
ATOM    971  CB  LEU   295      27.736  45.441  -7.361  1.00  1.00
ATOM    972  CG  LEU   295      29.106  44.773  -7.284  1.00  1.00
ATOM    973  CD1 LEU   295      30.033  45.317  -6.204  1.00  1.00
ATOM    974  CD2 LEU   295      28.869  43.260  -7.136  1.00  1.00
ATOM    975  N   LYS   296      25.467  47.667  -7.653  1.00  1.00
ATOM    976  CA  LYS   296      24.159  48.133  -8.167  1.00  1.00
ATOM    977  C   LYS   296      24.340  49.377  -9.043  1.00  1.00
ATOM    978  O   LYS   296      23.907  49.405 -10.204  1.00  1.00
ATOM    979  CB  LYS   296      23.198  48.403  -7.000  1.00  1.00
ATOM    980  CG  LYS   296      22.873  47.204  -6.370  1.00  1.00
ATOM    981  CD  LYS   296      21.901  47.435  -5.215  1.00  1.00
ATOM    982  CE  LYS   296      21.543  46.122  -4.517  1.00  1.00
ATOM    983  NZ  LYS   296      20.607  46.348  -3.402  1.00  1.00
ATOM    984  N   ASP   297      24.989  50.373  -8.480  1.00  1.00
ATOM    985  CA  ASP   297      25.233  51.634  -9.217  1.00  1.00
ATOM    986  C   ASP   297      26.115  51.377 -10.444  1.00  1.00
ATOM    987  O   ASP   297      26.131  52.173 -11.393  1.00  1.00
ATOM    988  CB  ASP   297      25.861  52.679  -8.283  1.00  1.00
ATOM    989  CG  ASP   297      24.891  53.209  -7.237  1.00  1.00
ATOM    990  OD1 ASP   297      23.757  53.010  -7.188  1.00  1.00
ATOM    991  OD2 ASP   297      25.520  53.928  -6.381  1.00  1.00
ATOM    992  N   HIS   298      26.844  50.315 -10.417  1.00  1.00
ATOM    993  CA  HIS   298      27.743  49.974 -11.544  1.00  1.00
ATOM    994  C   HIS   298      26.966  49.251 -12.650  1.00  1.00
ATOM    995  O   HIS   298      27.540  48.861 -13.678  1.00  1.00
ATOM    996  CB  HIS   298      28.922  49.128 -11.042  1.00  1.00
ATOM    997  CG  HIS   298      29.889  48.786 -11.968  1.00  1.00
ATOM    998  ND1 HIS   298      30.668  49.670 -12.706  1.00  1.00
ATOM    999  CD2 HIS   298      30.257  47.494 -12.322  1.00  1.00
ATOM   1000  CE1 HIS   298      31.516  48.919 -13.524  1.00  1.00
ATOM   1001  NE2 HIS   298      31.262  47.580 -13.282  1.00  1.00
TER
END
