
#######################################################
#                                                     #
#                        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   11 (  109),  selected   11 , name T0320TS083_4-D2
# Molecule2: number of CA atoms   73 (  604),  selected   11 , name T0320_D2.pdb
# PARAMETERS: T0320TS083_4-D2.T0320_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:    11       228 - 238         3.40     3.40
  LCS_AVERAGE:     15.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       230 - 234         1.65     7.88
  LONGEST_CONTINUOUS_SEGMENT:     5       232 - 236         1.14     8.52
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       230 - 233         0.87     8.65
  LONGEST_CONTINUOUS_SEGMENT:     4       232 - 235         0.42    10.22
  LCS_AVERAGE:      4.86

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:   73
LCS_GDT     N     228     N     228      3    4   11     3    3    3    5    6    7    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     N     229     N     229      3    4   11     3    3    3    5    6    7    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     S     230     S     230      4    5   11     3    3    4    4    5    7    8    9    9   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     231     L     231      4    5   11     3    3    4    5    6    7    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P     232     P     232      4    5   11     3    4    4    5    5    6    7    8   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     N     233     N     233      4    5   11     3    4    4    5    5    6    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P     234     P     234      4    5   11     3    4    4    5    5    6    8    8   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     H     235     H     235      4    5   11     3    4    4    5    6    7    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     236     L     236      3    5   11     3    3    4    5    6    7    8    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     237     R     237      3    4   11     3    3    4    4    6    7    7    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     K     238     K     238      3    4   11     3    3    4    4    5    6    7    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   8.76  (   4.86    6.35   15.07 )

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      4      4      5      6      7      8      9     10     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   4.11   5.48   5.48   6.85   8.22   9.59  10.96  12.33  13.70  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07
GDT RMS_LOCAL    0.09   0.42   0.42   1.14   1.97   2.19   2.78   2.77   3.25   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40
GDT RMS_ALL_CA   8.99  10.22  10.22   8.52   3.73   3.85   4.17   3.57   3.44   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40   3.40

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          2.039
LGA    N     229      N     229          2.854
LGA    S     230      S     230          3.734
LGA    L     231      L     231          2.150
LGA    P     232      P     232          4.839
LGA    N     233      N     233          3.877
LGA    P     234      P     234          6.675
LGA    H     235      H     235          2.537
LGA    L     236      L     236          2.381
LGA    R     237      R     237          1.715
LGA    K     238      K     238          3.736

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   73    4.0      9    2.77     9.932     9.609     0.313

LGA_LOCAL      RMSD =  2.772  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.604  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  3.397  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.155753 * X  +   0.957784 * Y  +   0.241642 * Z  + -68.113884
  Y_new =  -0.549078 * X  +   0.119406 * Y  +  -0.827197 * Z  +  60.675144
  Z_new =  -0.821130 * X  +  -0.261519 * Y  +   0.507301 * Z  + -105.739944 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.475979    2.665613  [ DEG:   -27.2716    152.7284 ]
  Theta =   0.963387    2.178205  [ DEG:    55.1980    124.8020 ]
  Phi   =  -1.847199    1.294394  [ DEG:  -105.8367     74.1633 ]
 
# 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: T0320TS083_4-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS083_4-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   73   4.0    9   2.77   9.609     3.40
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS083_4-D2
PFRMAT TS
TARGET T0320
MODEL 4
PARENT 1bvp_1
ATOM   2117  H   ASN   228      30.590  19.680   3.216  1.00  1.00              
ATOM   2118  N   ASN   228      30.606  19.668   4.157  1.00  2.56              
ATOM   2119  CA  ASN   228      29.609  20.435   4.878  1.00  1.00              
ATOM   2120  CB  ASN   228      29.065  21.566   3.999  1.00  1.00              
ATOM   2121  C   ASN   228      28.475  19.495   5.279  1.00  1.03              
ATOM   2122  O   ASN   228      28.328  18.417   4.701  1.00  2.23              
ATOM   2123  CG  ASN   228      30.114  22.615   3.681  1.00  1.00              
ATOM   2124  ND2 ASN   228      30.066  23.157   2.470  1.00  1.00              
ATOM   2125 HD21 ASN   228      29.396  22.869   1.874  1.00  1.00              
ATOM   2126 HD22 ASN   228      30.700  23.812   2.228  1.00  1.00              
ATOM   2127  OD1 ASN   228      30.972  22.926   4.512  1.00  1.00              
ATOM   2128  H   ASN   229      27.761  20.772   6.586  1.00  1.00              
ATOM   2129  N   ASN   229      27.659  19.903   6.240  1.00  1.84              
ATOM   2130  CA  ASN   229      26.600  19.055   6.787  1.00  1.83              
ATOM   2131  CB  ASN   229      25.831  19.841   7.859  1.00  1.00              
ATOM   2132  C   ASN   229      25.608  18.584   5.732  1.00  2.29              
ATOM   2133  O   ASN   229      25.133  19.370   4.908  1.00  1.75              
ATOM   2134  CG  ASN   229      26.672  20.190   9.073  1.00  1.00              
ATOM   2135  ND2 ASN   229      26.245  21.204   9.822  1.00  1.00              
ATOM   2136 HD21 ASN   229      25.453  21.648   9.570  1.00  1.00              
ATOM   2137 HD22 ASN   229      26.734  21.454  10.588  1.00  1.00              
ATOM   2138  OD1 ASN   229      27.682  19.540   9.353  1.00  1.37              
ATOM   2139  H   SER   230      25.787  16.715   6.330  1.00  1.00              
ATOM   2140  N   SER   230      25.328  17.285   5.748  1.00  5.11              
ATOM   2141  CA  SER   230      24.317  16.711   4.871  1.00  3.57              
ATOM   2142  CB  SER   230      24.285  15.191   5.007  1.00  1.00              
ATOM   2143  C   SER   230      22.998  17.315   5.337  1.00  4.08              
ATOM   2144  O   SER   230      22.978  17.936   6.402  1.00  2.64              
ATOM   2145  OG  SER   230      23.933  14.833   6.333  1.00  3.54              
ATOM   2146  H   LEU   231      21.936  16.712   3.775  1.00  1.00              
ATOM   2147  N   LEU   231      21.916  17.217   4.573  1.00  3.88              
ATOM   2148  CA  LEU   231      20.701  17.922   4.970  1.00  2.99              
ATOM   2149  CB  LEU   231      19.528  17.529   4.064  1.00  1.01              
ATOM   2150  C   LEU   231      20.393  17.558   6.420  1.00  2.42              
ATOM   2151  O   LEU   231      20.530  16.397   6.809  1.00  2.67              
ATOM   2152  CG  LEU   231      18.253  18.368   4.197  1.00  1.13              
ATOM   2153  CD1 LEU   231      18.485  19.771   3.651  1.00  1.70              
ATOM   2154  CD2 LEU   231      17.088  17.708   3.480  1.00  1.00              
ATOM   2155  N   PRO   232      20.024  18.542   7.255  1.00  3.15              
ATOM   2156  CA  PRO   232      19.725  18.267   8.661  1.00  2.81              
ATOM   2157  CB  PRO   232      19.654  19.651   9.304  1.00  1.00              
ATOM   2158  C   PRO   232      18.451  17.465   8.874  1.00  2.52              
ATOM   2159  O   PRO   232      18.167  17.044   9.999  1.00  1.45              
ATOM   2160  CG  PRO   232      19.200  20.532   8.181  1.00  1.00              
ATOM   2161  CD  PRO   232      19.928  19.988   6.972  1.00  1.00              
ATOM   2162  H   ASN   233      17.864  17.640   6.989  1.00  1.00              
ATOM   2163  N   ASN   233      17.675  17.242   7.820  1.00  4.83              
ATOM   2164  CA  ASN   233      16.535  16.348   7.960  1.00  2.37              
ATOM   2165  CB  ASN   233      15.541  16.479   6.801  1.00  1.00              
ATOM   2166  C   ASN   233      17.163  14.964   8.016  1.00  3.33              
ATOM   2167  O   ASN   233      18.207  14.760   7.400  1.00  2.55              
ATOM   2168  CG  ASN   233      14.821  17.814   6.790  1.00  1.00              
ATOM   2169  ND2 ASN   233      14.350  18.227   5.619  1.00  1.43              
ATOM   2170 HD21 ASN   233      14.483  17.682   4.862  1.00  1.00              
ATOM   2171 HD22 ASN   233      13.896  19.052   5.566  1.00  1.00              
ATOM   2172  OD1 ASN   233      14.660  18.455   7.832  1.00  1.49              
ATOM   2173  N   PRO   234      16.582  13.962   8.660  1.00  4.46              
ATOM   2174  CA  PRO   234      17.262  12.673   8.684  1.00  4.01              
ATOM   2175  CB  PRO   234      16.380  11.832   9.614  1.00  1.00              
ATOM   2176  C   PRO   234      17.347  12.011   7.312  1.00  3.05              
ATOM   2177  O   PRO   234      18.333  11.327   7.028  1.00  1.49              
ATOM   2178  CG  PRO   234      15.608  12.833  10.423  1.00  1.06              
ATOM   2179  CD  PRO   234      15.346  13.967   9.457  1.00  1.00              
ATOM   2180  H   HIS   235      15.589  12.694   6.695  1.00  1.00              
ATOM   2181  N   HIS   235      16.347  12.184   6.452  1.00  4.47              
ATOM   2182  CA  HIS   235      16.428  11.559   5.138  1.00  1.73              
ATOM   2183  CB  HIS   235      15.861  10.135   5.189  1.00  1.00              
ATOM   2184  C   HIS   235      15.790  12.323   3.975  1.00  2.29              
ATOM   2185  O   HIS   235      14.670  12.824   4.096  1.00  2.14              
ATOM   2186  CG  HIS   235      15.977   9.398   3.888  1.00  1.15              
ATOM   2187  ND1 HIS   235      17.184   8.978   3.371  1.00  1.33              
ATOM   2188  HD1 HIS   235      18.040   9.131   3.756  1.00  1.00              
ATOM   2189  CE1 HIS   235      16.974   8.384   2.208  1.00  1.00              
ATOM   2190  NE2 HIS   235      15.672   8.359   1.981  1.00  1.16              
ATOM   2191  HE2 HIS   235      15.265   8.003   1.198  1.00  1.00              
ATOM   2192  CD2 HIS   235      15.027   9.013   3.000  1.00  1.00              
ATOM   2193  H   LEU   236      17.398  12.101   2.849  1.00  1.00              
ATOM   2194  N   LEU   236      16.509  12.423   2.854  1.00  6.39              
ATOM   2195  CA  LEU   236      15.972  13.014   1.625  1.00  5.20              
ATOM   2196  CB  LEU   236      16.176  14.528   1.539  1.00  2.83              
ATOM   2197  C   LEU   236      16.480  12.316   0.364  1.00  2.43              
ATOM   2198  O   LEU   236      17.659  11.966   0.279  1.00  2.35              
ATOM   2199  CG  LEU   236      14.908  15.367   1.722  1.00  3.73              
ATOM   2200  CD1 LEU   236      14.919  16.548   0.762  1.00  1.92              
ATOM   2201  CD2 LEU   236      13.677  14.503   1.485  1.00  1.05              
ATOM   2202  H   ARG   237      14.680  12.313  -0.452  1.00  1.00              
ATOM   2203  N   ARG   237      15.595  12.096  -0.603  1.00  4.76              
ATOM   2204  CA  ARG   237      15.986  11.529  -1.892  1.00  1.38              
ATOM   2205  CB  ARG   237      15.046  10.383  -2.276  1.00  1.00              
ATOM   2206  C   ARG   237      15.908  12.629  -2.941  1.00  1.00              
ATOM   2207  O   ARG   237      16.468  12.511  -4.033  1.00  1.00              
ATOM   2208  CG  ARG   237      15.081   9.204  -1.312  1.00  1.00              
ATOM   2209  CD  ARG   237      14.123   8.098  -1.736  1.00  1.00              
ATOM   2210  NE  ARG   237      14.168   6.959  -0.821  1.00  1.00              
ATOM   2211  HE  ARG   237      14.774   7.009  -0.090  1.00  1.00              
ATOM   2212  CZ  ARG   237      13.432   5.854  -0.933  1.00  1.00              
ATOM   2213  NH1 ARG   237      12.548   5.730  -1.917  1.00  1.00              
ATOM   2214  NH2 ARG   237      13.598   4.853  -0.075  1.00  1.00              
ATOM   2215  H   LYS   238      14.738  13.702  -1.765  1.00  1.00              
ATOM   2216  N   LYS   238      15.190  13.694  -2.599  1.00  2.49              
ATOM   2217  CA  LYS   238      15.069  14.855  -3.471  1.00  1.00              
ATOM   2218  CB  LYS   238      13.821  15.661  -3.105  1.00  1.00              
ATOM   2219  C   LYS   238      16.304  15.747  -3.385  1.00  1.00              
ATOM   2220  O   LYS   238      17.325  15.409  -4.020  1.00  1.00              
ATOM   2221  OXT LYS   238      16.195  16.858  -2.826  1.00  1.00              
ATOM   2222  CG  LYS   238      12.517  14.912  -3.335  1.00  1.00              
ATOM   2223  CD  LYS   238      11.314  15.758  -2.940  1.00  1.00              
ATOM   2224  CE  LYS   238      10.004  15.016  -3.176  1.00  1.00              
ATOM   2225  NZ  LYS   238       8.823  15.839  -2.785  1.00  1.00              
TER
END
