
#######################################################
#                                                     #
#                        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   20 (  153),  selected   20 , name T0298TS022_4_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   20 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_4_2-D1.T0298_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:    16       317 - 332         4.83     7.49
  LONGEST_CONTINUOUS_SEGMENT:    16       318 - 333         4.93     7.21
  LCS_AVERAGE:     10.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       325 - 334         1.69    10.93
  LCS_AVERAGE:      4.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       325 - 333         0.93    10.41
  LCS_AVERAGE:      4.12

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:  148
LCS_GDT     V     316     V     316      3    3   15     3    3    4    4    4    4    6    6    6    8    8    8   11   11   11   17   18   19   19   19 
LCS_GDT     R     317     R     317      4    5   16     3    4    4    4    5    5    6    6    9   10   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     K     318     K     318      4    5   16     3    4    4    4    5    6    8    8    9   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     G     319     G     319      4    5   16     3    4    4    4    5    5    6    8    9   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     A     320     A     320      4    5   16     3    4    4    4    5    6    6    8    9   11   11   13   15   16   17   17   18   19   19   19 
LCS_GDT     A     321     A     321      4    5   16     3    4    4    4    5    6    8    8    9   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     L     322     L     322      4    4   16     3    3    4    4    4    6    6    8    9   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     N     323     N     323      4    4   16     3    3    4    4    4    6    6    7    9   11   11   13   15   16   17   17   18   19   19   19 
LCS_GDT     A     324     A     324      4    4   16     3    3    4    4    6    8    9   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     V     325     V     325      9   10   16     3    6    9    9    9   10   10   10   11   11   11   13   15   16   17   17   18   19   19   19 
LCS_GDT     L     326     L     326      9   10   16     3    5    9    9    9   10   10   10   11   11   11   13   15   16   17   17   18   19   19   19 
LCS_GDT     L     327     L     327      9   10   16     3    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     G     328     G     328      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     E     329     E     329      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     L     330     L     330      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     L     331     L     331      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     I     332     I     332      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     K     333     K     333      9   10   16     6    6    9    9    9   10   10   10   11   11   12   13   15   16   17   17   18   19   19   19 
LCS_GDT     H     334     H     334      3   10   14     3    5    5    6    8   10   10   10   11   11   11   12   12   14   16   17   17   19   19   19 
LCS_GDT     Y     335     Y     335      3    4   13     3    5    5    5    6    6    6    6    8    8    8   12   12   12   12   12   15   17   18   18 
LCS_AVERAGE  LCS_A:   6.53  (   4.12    4.86   10.61 )

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      6      6      9      9      9     10     10     10     11     11     12     13     15     16     17     17     18     19     19     19 
GDT PERCENT_CA   4.05   4.05   6.08   6.08   6.08   6.76   6.76   6.76   7.43   7.43   8.11   8.78  10.14  10.81  11.49  11.49  12.16  12.84  12.84  12.84
GDT RMS_LOCAL    0.20   0.20   0.93   0.93   0.93   1.69   1.69   1.69   2.70   2.70   4.04   4.18   4.64   4.82   5.04   5.04   5.37   5.82   5.82   5.82
GDT RMS_ALL_CA  11.52  11.52  10.41  10.41  10.41  10.93  10.93  10.93   9.91   9.91   6.94   8.57   7.82   7.15   7.13   7.13   7.02   6.66   6.66   6.66

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316         14.401
LGA    R     317      R     317         14.303
LGA    K     318      K     318         15.378
LGA    G     319      G     319         21.814
LGA    A     320      A     320         21.646
LGA    A     321      A     321         15.856
LGA    L     322      L     322         14.381
LGA    N     323      N     323         12.304
LGA    A     324      A     324          8.402
LGA    V     325      V     325          1.304
LGA    L     326      L     326          1.425
LGA    L     327      L     327          1.580
LGA    G     328      G     328          1.010
LGA    E     329      E     329          1.622
LGA    L     330      L     330          1.560
LGA    L     331      L     331          0.677
LGA    I     332      I     332          0.751
LGA    K     333      K     333          1.469
LGA    H     334      H     334          3.608
LGA    Y     335      Y     335          9.391

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  148    4.0     10    1.69     7.095     6.663     0.559

LGA_LOCAL      RMSD =  1.689  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.931  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  6.530  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.092724 * X  +   0.112534 * Y  +   0.989312 * Z  + -21.915480
  Y_new =   0.390583 * X  +  -0.909844 * Y  +   0.140102 * Z  +  59.091557
  Z_new =   0.915886 * X  +   0.399399 * Y  +   0.040410 * Z  +  -8.821907 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.469962   -1.671631  [ DEG:    84.2226    -95.7774 ]
  Theta =  -1.157709   -1.983883  [ DEG:   -66.3319   -113.6681 ]
  Phi   =   1.803880   -1.337713  [ DEG:   103.3547    -76.6453 ]
 
# 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: T0298TS022_4_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_4_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  148   4.0   10   1.69   6.663     6.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1ojg_A
ATOM   1934  N   VAL   316     -27.832  67.918   0.342  1.00  0.00
ATOM   1935  CA  VAL   316     -28.176  68.547   1.571  1.00  0.00
ATOM   1936  C   VAL   316     -29.646  68.756   1.489  1.00  0.00
ATOM   1937  O   VAL   316     -30.126  69.588   0.720  1.00  0.00
ATOM   1938  CB  VAL   316     -27.439  69.888   1.744  1.00  0.00
ATOM   1939  CG1 VAL   316     -27.847  70.555   3.048  1.00  0.00
ATOM   1940  CG2 VAL   316     -25.934  69.671   1.764  1.00  0.00
ATOM   1941  N   ARG   317     -30.408  67.982   2.274  1.00  0.00
ATOM   1942  CA  ARG   317     -31.818  68.185   2.217  1.00  0.00
ATOM   1943  C   ARG   317     -32.294  68.383   3.614  1.00  0.00
ATOM   1944  O   ARG   317     -32.106  67.527   4.476  1.00  0.00
ATOM   1945  CB  ARG   317     -32.509  66.970   1.594  1.00  0.00
ATOM   1946  CG  ARG   317     -34.014  67.123   1.438  1.00  0.00
ATOM   1947  CD  ARG   317     -34.624  65.912   0.753  1.00  0.00
ATOM   1948  NE  ARG   317     -34.572  64.721   1.597  1.00  0.00
ATOM   1949  CZ  ARG   317     -34.816  63.488   1.167  1.00  0.00
ATOM   1950  NH1 ARG   317     -34.744  62.465   2.008  1.00  0.00
ATOM   1951  NH2 ARG   317     -35.132  63.281  -0.104  1.00  0.00
ATOM   1952  N   LYS   318     -32.895  69.548   3.896  1.00  0.00
ATOM   1953  CA  LYS   318     -33.502  69.661   5.181  1.00  0.00
ATOM   1954  C   LYS   318     -34.945  69.617   4.861  1.00  0.00
ATOM   1955  O   LYS   318     -35.422  70.373   4.016  1.00  0.00
ATOM   1956  CB  LYS   318     -33.095  70.975   5.852  1.00  0.00
ATOM   1957  CG  LYS   318     -31.617  71.062   6.200  1.00  0.00
ATOM   1958  CD  LYS   318     -31.285  72.383   6.873  1.00  0.00
ATOM   1959  CE  LYS   318     -29.799  72.490   7.178  1.00  0.00
ATOM   1960  NZ  LYS   318     -29.457  73.789   7.819  1.00  0.00
ATOM   1961  N   GLY   319     -35.691  68.726   5.527  1.00  0.00
ATOM   1962  CA  GLY   319     -37.009  68.555   5.019  1.00  0.00
ATOM   1963  C   GLY   319     -36.751  67.897   3.705  1.00  0.00
ATOM   1964  O   GLY   319     -36.037  66.896   3.643  1.00  0.00
ATOM   1965  N   ALA   320     -37.305  68.443   2.610  1.00  0.00
ATOM   1966  CA  ALA   320     -37.054  67.828   1.343  1.00  0.00
ATOM   1967  C   ALA   320     -36.288  68.801   0.504  1.00  0.00
ATOM   1968  O   ALA   320     -36.596  69.991   0.490  1.00  0.00
ATOM   1969  CB  ALA   320     -38.365  67.476   0.656  1.00  0.00
ATOM   1970  N   ALA   321     -35.239  68.319  -0.196  1.00  0.00
ATOM   1971  CA  ALA   321     -34.516  69.208  -1.054  1.00  0.00
ATOM   1972  C   ALA   321     -34.126  68.461  -2.292  1.00  0.00
ATOM   1973  O   ALA   321     -33.464  67.425  -2.228  1.00  0.00
ATOM   1974  CB  ALA   321     -33.267  69.721  -0.355  1.00  0.00
ATOM   1975  N   LEU   322     -34.561  68.972  -3.460  1.00  0.00
ATOM   1976  CA  LEU   322     -34.182  68.414  -4.725  1.00  0.00
ATOM   1977  C   LEU   322     -32.739  68.738  -4.959  1.00  0.00
ATOM   1978  O   LEU   322     -31.996  67.946  -5.538  1.00  0.00
ATOM   1979  CB  LEU   322     -35.034  69.008  -5.848  1.00  0.00
ATOM   1980  CG  LEU   322     -36.512  68.612  -5.861  1.00  0.00
ATOM   1981  CD1 LEU   322     -37.273  69.406  -6.912  1.00  0.00
ATOM   1982  CD2 LEU   322     -36.670  67.132  -6.177  1.00  0.00
ATOM   1983  N   ASN   323     -32.301  69.930  -4.513  1.00  0.00
ATOM   1984  CA  ASN   323     -30.932  70.316  -4.687  1.00  0.00
ATOM   1985  C   ASN   323     -30.081  69.367  -3.925  1.00  0.00
ATOM   1986  O   ASN   323     -30.478  68.879  -2.870  1.00  0.00
ATOM   1987  CB  ASN   323     -30.705  71.738  -4.169  1.00  0.00
ATOM   1988  CG  ASN   323     -30.780  71.826  -2.657  1.00  0.00
ATOM   1989  OD1 ASN   323     -29.880  71.367  -1.954  1.00  0.00
ATOM   1990  ND2 ASN   323     -31.856  72.419  -2.153  1.00  0.00
ATOM   1991  N   ALA   324     -28.878  69.079  -4.451  1.00  0.00
ATOM   1992  CA  ALA   324     -27.963  68.233  -3.749  1.00  0.00
ATOM   1993  C   ALA   324     -26.736  69.053  -3.556  1.00  0.00
ATOM   1994  O   ALA   324     -26.451  69.926  -4.375  1.00  0.00
ATOM   1995  CB  ALA   324     -27.664  66.984  -4.563  1.00  0.00
ATOM   1996  N   VAL   325     -26.015  68.811  -2.441  1.00  0.00
ATOM   1997  CA  VAL   325     -24.813  69.512  -2.085  1.00  0.00
ATOM   1998  C   VAL   325     -25.226  70.705  -1.298  1.00  0.00
ATOM   1999  O   VAL   325     -26.330  71.217  -1.482  1.00  0.00
ATOM   2000  CB  VAL   325     -24.028  69.955  -3.333  1.00  0.00
ATOM   2001  CG1 VAL   325     -22.818  70.787  -2.934  1.00  0.00
ATOM   2002  CG2 VAL   325     -23.541  68.745  -4.115  1.00  0.00
ATOM   2003  N   LEU   326     -24.371  71.163  -0.363  1.00  0.00
ATOM   2004  CA  LEU   326     -24.732  72.348   0.355  1.00  0.00
ATOM   2005  C   LEU   326     -24.743  73.421  -0.676  1.00  0.00
ATOM   2006  O   LEU   326     -25.684  74.204  -0.782  1.00  0.00
ATOM   2007  CB  LEU   326     -23.709  72.641   1.455  1.00  0.00
ATOM   2008  CG  LEU   326     -23.960  73.892   2.298  1.00  0.00
ATOM   2009  CD1 LEU   326     -25.288  73.788   3.032  1.00  0.00
ATOM   2010  CD2 LEU   326     -22.859  74.073   3.331  1.00  0.00
ATOM   2011  N   LEU   327     -23.683  73.449  -1.499  1.00  0.00
ATOM   2012  CA  LEU   327     -23.617  74.427  -2.532  1.00  0.00
ATOM   2013  C   LEU   327     -24.602  73.977  -3.555  1.00  0.00
ATOM   2014  O   LEU   327     -24.956  72.801  -3.606  1.00  0.00
ATOM   2015  CB  LEU   327     -22.205  74.494  -3.118  1.00  0.00
ATOM   2016  CG  LEU   327     -21.097  74.944  -2.164  1.00  0.00
ATOM   2017  CD1 LEU   327     -19.736  74.844  -2.836  1.00  0.00
ATOM   2018  CD2 LEU   327     -21.310  76.388  -1.735  1.00  0.00
ATOM   2019  N   GLY   328     -25.110  74.916  -4.370  1.00  0.00
ATOM   2020  CA  GLY   328     -26.063  74.560  -5.381  1.00  0.00
ATOM   2021  C   GLY   328     -27.424  74.860  -4.848  1.00  0.00
ATOM   2022  O   GLY   328     -28.393  74.969  -5.599  1.00  0.00
ATOM   2023  N   GLU   329     -27.534  75.016  -3.519  1.00  0.00
ATOM   2024  CA  GLU   329     -28.810  75.344  -2.961  1.00  0.00
ATOM   2025  C   GLU   329     -29.180  76.677  -3.518  1.00  0.00
ATOM   2026  O   GLU   329     -30.323  76.911  -3.908  1.00  0.00
ATOM   2027  CB  GLU   329     -28.728  75.403  -1.434  1.00  0.00
ATOM   2028  CG  GLU   329     -30.057  75.684  -0.752  1.00  0.00
ATOM   2029  CD  GLU   329     -29.948  75.678   0.760  1.00  0.00
ATOM   2030  OE1 GLU   329     -28.837  75.434   1.274  1.00  0.00
ATOM   2031  OE2 GLU   329     -30.975  75.916   1.430  1.00  0.00
ATOM   2032  N   LEU   330     -28.190  77.585  -3.578  1.00  0.00
ATOM   2033  CA  LEU   330     -28.414  78.920  -4.042  1.00  0.00
ATOM   2034  C   LEU   330     -28.807  78.869  -5.479  1.00  0.00
ATOM   2035  O   LEU   330     -29.723  79.575  -5.903  1.00  0.00
ATOM   2036  CB  LEU   330     -27.143  79.758  -3.895  1.00  0.00
ATOM   2037  CG  LEU   330     -26.716  80.097  -2.466  1.00  0.00
ATOM   2038  CD1 LEU   330     -25.353  80.771  -2.457  1.00  0.00
ATOM   2039  CD2 LEU   330     -27.717  81.039  -1.814  1.00  0.00
ATOM   2040  N   LEU   331     -28.129  78.018  -6.271  1.00  0.00
ATOM   2041  CA  LEU   331     -28.419  78.002  -7.670  1.00  0.00
ATOM   2042  C   LEU   331     -29.848  77.622  -7.829  1.00  0.00
ATOM   2043  O   LEU   331     -30.610  78.307  -8.509  1.00  0.00
ATOM   2044  CB  LEU   331     -27.527  76.988  -8.390  1.00  0.00
ATOM   2045  CG  LEU   331     -27.740  76.850  -9.899  1.00  0.00
ATOM   2046  CD1 LEU   331     -27.446  78.164 -10.606  1.00  0.00
ATOM   2047  CD2 LEU   331     -26.823  75.784 -10.477  1.00  0.00
ATOM   2048  N   ILE   332     -30.272  76.532  -7.171  1.00  0.00
ATOM   2049  CA  ILE   332     -31.650  76.214  -7.345  1.00  0.00
ATOM   2050  C   ILE   332     -32.335  76.749  -6.138  1.00  0.00
ATOM   2051  O   ILE   332     -32.903  76.006  -5.339  1.00  0.00
ATOM   2052  CB  ILE   332     -31.868  74.694  -7.461  1.00  0.00
ATOM   2053  CG1 ILE   332     -31.112  74.137  -8.668  1.00  0.00
ATOM   2054  CG2 ILE   332     -33.347  74.379  -7.631  1.00  0.00
ATOM   2055  CD1 ILE   332     -30.982  72.629  -8.666  1.00  0.00
ATOM   2056  N   LYS   333     -32.308  78.088  -6.011  1.00  0.00
ATOM   2057  CA  LYS   333     -32.902  78.787  -4.917  1.00  0.00
ATOM   2058  C   LYS   333     -34.368  78.587  -5.037  1.00  0.00
ATOM   2059  O   LYS   333     -35.089  78.466  -4.047  1.00  0.00
ATOM   2060  CB  LYS   333     -32.558  80.277  -4.984  1.00  0.00
ATOM   2061  CG  LYS   333     -33.088  81.089  -3.813  1.00  0.00
ATOM   2062  CD  LYS   333     -32.627  82.535  -3.891  1.00  0.00
ATOM   2063  CE  LYS   333     -33.152  83.347  -2.718  1.00  0.00
ATOM   2064  NZ  LYS   333     -32.695  84.762  -2.772  1.00  0.00
ATOM   2065  N   HIS   334     -34.833  78.520  -6.291  1.00  0.00
ATOM   2066  CA  HIS   334     -36.227  78.377  -6.547  1.00  0.00
ATOM   2067  C   HIS   334     -36.577  76.967  -6.221  1.00  0.00
ATOM   2068  O   HIS   334     -35.708  76.111  -6.062  1.00  0.00
ATOM   2069  CB  HIS   334     -36.536  78.678  -8.015  1.00  0.00
ATOM   2070  CG  HIS   334     -36.285  80.102  -8.406  1.00  0.00
ATOM   2071  ND1 HIS   334     -37.097  81.139  -8.001  1.00  0.00
ATOM   2072  CD2 HIS   334     -35.287  80.798  -9.204  1.00  0.00
ATOM   2073  CE1 HIS   334     -36.621  82.290  -8.507  1.00  0.00
ATOM   2074  NE2 HIS   334     -35.535  82.094  -9.229  1.00  0.00
ATOM   2075  N   TYR   335     -37.883  76.703  -6.077  1.00  0.00
ATOM   2076  CA  TYR   335     -38.315  75.378  -5.767  1.00  0.00
ATOM   2077  C   TYR   335     -38.159  74.567  -7.046  1.00  0.00
ATOM   2078  O   TYR   335     -37.021  74.103  -7.320  1.00  0.00
ATOM   2079  CB  TYR   335     -39.775  75.383  -5.308  1.00  0.00
ATOM   2080  CG  TYR   335     -39.994  76.051  -3.969  1.00  0.00
ATOM   2081  CD1 TYR   335     -40.343  77.394  -3.892  1.00  0.00
ATOM   2082  CD2 TYR   335     -39.851  75.336  -2.786  1.00  0.00
ATOM   2083  CE1 TYR   335     -40.545  78.012  -2.673  1.00  0.00
ATOM   2084  CE2 TYR   335     -40.049  75.939  -1.559  1.00  0.00
ATOM   2085  CZ  TYR   335     -40.399  77.288  -1.510  1.00  0.00
ATOM   2086  OH  TYR   335     -40.600  77.901  -0.295  1.00  0.00
TER
END
