
#######################################################
#                                                     #
#                        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    6 (   53),  selected    6 , name T0372TS022_3_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected    6 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_3_1-D2.T0372_D2.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:     6       118 - 123         1.57     1.57
  LCS_AVERAGE:      3.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       118 - 123         1.57     1.57
  LCS_AVERAGE:      3.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       118 - 122         0.67     1.86
  LCS_AVERAGE:      2.71

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:  172
LCS_GDT     R     118     R     118      5    6    6     4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     119     A     119      5    6    6     4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y     120     Y     120      5    6    6     4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     121     A     121      5    6    6     4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     122     D     122      5    6    6     3    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y     123     Y     123      3    6    6     0    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.23  (   2.71    3.49    3.49 )

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      5      5      5      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.33   2.91   2.91   2.91   2.91   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49
GDT RMS_LOCAL    0.33   0.67   0.67   0.67   0.67   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57
GDT RMS_ALL_CA   2.40   1.86   1.86   1.86   1.86   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          1.132
LGA    A     119      A     119          1.923
LGA    Y     120      Y     120          0.293
LGA    A     121      A     121          0.761
LGA    D     122      D     122          0.412
LGA    Y     123      Y     123          3.010

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  172    4.0      6    1.57     3.198     3.320     0.358

LGA_LOCAL      RMSD =  1.574  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.574  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  1.574  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.278435 * X  +   0.229348 * Y  +  -0.932670 * Z  +  41.135838
  Y_new =   0.154558 * X  +   0.969115 * Y  +   0.192168 * Z  + -111.874779
  Z_new =   0.947938 * X  +  -0.090645 * Y  +  -0.305283 * Z  + -60.518234 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.852962    0.288631  [ DEG:  -163.4626     16.5374 ]
  Theta =  -1.246696   -1.894897  [ DEG:   -71.4304   -108.5696 ]
  Phi   =   2.634845   -0.506748  [ DEG:   150.9655    -29.0345 ]
 
# 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: T0372TS022_3_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_3_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  172   4.0    6   1.57   3.320     1.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1qso_A
ATOM    953  N   ARG   118      21.842  40.098  11.123  1.00  0.00
ATOM    954  CA  ARG   118      23.028  39.971  10.332  1.00  0.00
ATOM    955  C   ARG   118      24.191  39.802  11.250  1.00  0.00
ATOM    956  O   ARG   118      24.393  40.586  12.177  1.00  0.00
ATOM    957  CB  ARG   118      23.235  41.219   9.471  1.00  0.00
ATOM    958  CG  ARG   118      22.172  41.420   8.403  1.00  0.00
ATOM    959  CD  ARG   118      22.383  42.724   7.653  1.00  0.00
ATOM    960  NE  ARG   118      22.104  43.888   8.491  1.00  0.00
ATOM    961  CZ  ARG   118      22.423  45.137   8.165  1.00  0.00
ATOM    962  NH1 ARG   118      22.130  46.133   8.990  1.00  0.00
ATOM    963  NH2 ARG   118      23.034  45.387   7.015  1.00  0.00
ATOM    964  N   ALA   119      24.968  38.731  11.009  1.00  0.00
ATOM    965  CA  ALA   119      26.176  38.449  11.720  1.00  0.00
ATOM    966  C   ALA   119      27.137  39.522  11.346  1.00  0.00
ATOM    967  O   ALA   119      27.917  40.002  12.165  1.00  0.00
ATOM    968  CB  ALA   119      26.716  37.083  11.328  1.00  0.00
ATOM    969  N   TYR   120      27.065  39.933  10.067  1.00  0.00
ATOM    970  CA  TYR   120      27.948  40.900   9.489  1.00  0.00
ATOM    971  C   TYR   120      27.839  42.152  10.284  1.00  0.00
ATOM    972  O   TYR   120      28.843  42.790  10.595  1.00  0.00
ATOM    973  CB  TYR   120      27.563  41.176   8.034  1.00  0.00
ATOM    974  CG  TYR   120      28.432  42.210   7.356  1.00  0.00
ATOM    975  CD1 TYR   120      29.698  41.880   6.889  1.00  0.00
ATOM    976  CD2 TYR   120      27.984  43.514   7.184  1.00  0.00
ATOM    977  CE1 TYR   120      30.499  42.819   6.268  1.00  0.00
ATOM    978  CE2 TYR   120      28.771  44.466   6.565  1.00  0.00
ATOM    979  CZ  TYR   120      30.038  44.108   6.106  1.00  0.00
ATOM    980  OH  TYR   120      30.834  45.045   5.488  1.00  0.00
ATOM    981  N   ALA   121      26.607  42.519  10.674  1.00  0.00
ATOM    982  CA  ALA   121      26.421  43.706  11.447  1.00  0.00
ATOM    983  C   ALA   121      27.226  43.547  12.695  1.00  0.00
ATOM    984  O   ALA   121      27.717  42.458  12.995  1.00  0.00
ATOM    985  CB  ALA   121      24.951  43.890  11.790  1.00  0.00
ATOM    986  N   ASP   122      27.390  44.654  13.446  1.00  0.00
ATOM    987  CA  ASP   122      28.206  44.637  14.624  1.00  0.00
ATOM    988  C   ASP   122      27.667  43.554  15.492  1.00  0.00
ATOM    989  O   ASP   122      28.440  42.815  16.101  1.00  0.00
ATOM    990  CB  ASP   122      28.138  45.985  15.343  1.00  0.00
ATOM    991  CG  ASP   122      28.893  47.076  14.608  1.00  0.00
ATOM    992  OD1 ASP   122      29.660  46.746  13.680  1.00  0.00
ATOM    993  OD2 ASP   122      28.718  48.261  14.962  1.00  0.00
ATOM    994  N   TYR   123      26.320  43.451  15.529  1.00  0.00
ATOM    995  CA  TYR   123      25.550  42.434  16.193  1.00  0.00
ATOM    996  C   TYR   123      24.492  43.153  17.013  1.00  0.00
ATOM    997  O   TYR   123      24.880  43.906  17.944  1.00  0.00
ATOM    998  CB  TYR   123      26.447  41.592  17.103  1.00  0.00
ATOM    999  CG  TYR   123      25.714  40.489  17.835  1.00  0.00
ATOM   1000  CD1 TYR   123      25.359  39.316  17.181  1.00  0.00
ATOM   1001  CD2 TYR   123      25.380  40.627  19.175  1.00  0.00
ATOM   1002  CE1 TYR   123      24.690  38.303  17.842  1.00  0.00
ATOM   1003  CE2 TYR   123      24.710  39.625  19.852  1.00  0.00
ATOM   1004  CZ  TYR   123      24.367  38.457  19.172  1.00  0.00
ATOM   1005  OH  TYR   123      23.699  37.450  19.833  1.00  0.00
TER
END
