
#######################################################
#                                                     #
#                        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 (   44),  selected   11 , name T0316AL380_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   11 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_5-D2.T0316_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:     9       220 - 228         4.02     7.80
  LCS_AVERAGE:     14.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       221 - 226         1.94     9.68
  LCS_AVERAGE:      8.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       222 - 225         0.43    11.65
  LONGEST_CONTINUOUS_SEGMENT:     4       227 - 230         0.66    14.70
  LCS_AVERAGE:      6.21

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:   60
LCS_GDT     G     220     G     220      3    3    9     0    3    3    3    3    4    4    5    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     R     221     R     221      3    6    9     3    3    3    4    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     M     222     M     222      4    6    9     4    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     M     223     M     223      4    6    9     4    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     T     224     T     224      4    6    9     4    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     V     225     V     225      4    6    9     4    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     D     226     D     226      3    6    9     0    3    4    5    5    6    6    7    7    7    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     G     227     G     227      4    5    9     3    4    4    4    5    5    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     R     228     R     228      4    5    9     3    4    4    4    5    5    6    6    6    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     D     229     D     229      4    5    7     3    4    4    4    5    5    6    6    6    6    6    6    6    7    7    7    7   10   10   10 
LCS_GDT     M     230     M     230      4    5    7     3    4    4    4    4    5    6    6    6    6    6    6    6    6    7    7    7    7    8    8 
LCS_AVERAGE  LCS_A:   9.85  (   6.21    8.94   14.39 )

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      4      5      5      6      6      7      7      8      9      9      9      9      9      9      9     10     10     10 
GDT PERCENT_CA   6.67   6.67   6.67   8.33   8.33  10.00  10.00  11.67  11.67  13.33  15.00  15.00  15.00  15.00  15.00  15.00  15.00  16.67  16.67  16.67
GDT RMS_LOCAL    0.43   0.43   0.43   1.43   1.43   1.94   1.94   2.53   2.53   3.92   4.02   4.02   4.02   4.02   4.02   4.02   4.02   5.37   5.37   5.37
GDT RMS_ALL_CA  11.65  11.65  11.65   9.98   9.98   9.68   9.68   9.11   9.11   7.59   7.80   7.80   7.80   7.80   7.80   7.80   7.80   7.13   7.13   7.13

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220          6.043
LGA    R     221      R     221          2.757
LGA    M     222      M     222          1.709
LGA    M     223      M     223          1.935
LGA    T     224      T     224          2.923
LGA    V     225      V     225          2.163
LGA    D     226      D     226          3.789
LGA    G     227      G     227          3.442
LGA    R     228      R     228          8.731
LGA    D     229      D     229         14.852
LGA    M     230      M     230         21.126

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   60    4.0      7    2.53    10.417    10.320     0.266

LGA_LOCAL      RMSD =  2.528  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.704  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  6.761  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.668385 * X  +   0.729719 * Y  +   0.144121 * Z  +  66.934128
  Y_new =   0.092364 * X  +   0.273684 * Y  +  -0.957375 * Z  +  51.383663
  Z_new =  -0.738058 * X  +  -0.626584 * Y  +  -0.250326 * Z  +  94.383400 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.950879    1.190714  [ DEG:  -111.7771     68.2229 ]
  Theta =   0.830188    2.311404  [ DEG:    47.5663    132.4337 ]
  Phi   =   3.004273   -0.137320  [ DEG:   172.1322     -7.8678 ]
 
# 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: T0316AL380_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_5-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   60   4.0    7   2.53  10.320     6.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_5-D2
REMARK Aligment from pdb entry: 1gpmC
ATOM    693  N   GLY   220      42.691  18.737 -25.185  1.00  0.00              
ATOM    694  CA  GLY   220      41.843  17.770 -24.484  1.00  0.00              
ATOM    695  C   GLY   220      40.882  18.407 -23.471  1.00  0.00              
ATOM    696  O   GLY   220      39.708  18.045 -23.404  1.00  0.00              
ATOM    697  N   ARG   221      41.398  19.341 -22.678  1.00  0.00              
ATOM    698  CA  ARG   221      40.605  20.034 -21.664  1.00  0.00              
ATOM    699  C   ARG   221      39.604  21.003 -22.287  1.00  0.00              
ATOM    700  O   ARG   221      38.662  21.437 -21.630  1.00  0.00              
ATOM    701  N   MET   222      39.803  21.341 -23.557  1.00  0.00              
ATOM    702  CA  MET   222      38.912  22.271 -24.247  1.00  0.00              
ATOM    703  C   MET   222      37.688  21.639 -24.917  1.00  0.00              
ATOM    704  O   MET   222      36.841  22.350 -25.453  1.00  0.00              
ATOM    705  N   MET   223      37.586  20.311 -24.863  1.00  0.00              
ATOM    706  CA  MET   223      36.443  19.596 -25.442  1.00  0.00              
ATOM    707  C   MET   223      35.720  18.816 -24.341  1.00  0.00              
ATOM    708  O   MET   223      36.336  18.438 -23.336  1.00  0.00              
ATOM    709  N   THR   224      34.429  18.563 -24.536  1.00  0.00              
ATOM    710  CA  THR   224      33.639  17.790 -23.581  1.00  0.00              
ATOM    711  C   THR   224      33.862  16.300 -23.807  1.00  0.00              
ATOM    712  O   THR   224      33.923  15.511 -22.857  1.00  0.00              
ATOM    713  N   VAL   225      33.912  15.902 -25.074  1.00  0.00              
ATOM    714  CA  VAL   225      34.127  14.504 -25.425  1.00  0.00              
ATOM    715  C   VAL   225      34.945  14.496 -26.702  1.00  0.00              
ATOM    716  O   VAL   225      34.892  15.442 -27.486  1.00  0.00              
ATOM    717  N   ASP   226      35.732  13.448 -26.889  1.00  0.00              
ATOM    718  CA  ASP   226      36.558  13.324 -28.076  1.00  0.00              
ATOM    719  C   ASP   226      36.935  11.849 -28.237  1.00  0.00              
ATOM    720  O   ASP   226      37.539  11.237 -27.344  1.00  0.00              
ATOM    721  N   GLY   227      36.541  11.275 -29.369  1.00  0.00              
ATOM    722  CA  GLY   227      36.786   9.873 -29.644  1.00  0.00              
ATOM    723  C   GLY   227      36.734   9.620 -31.132  1.00  0.00              
ATOM    724  O   GLY   227      36.286  10.473 -31.898  1.00  0.00              
ATOM    725  N   ARG   228      37.123   8.410 -31.513  1.00  0.00              
ATOM    726  CA  ARG   228      37.141   7.971 -32.897  1.00  0.00              
ATOM    727  C   ARG   228      36.058   6.898 -33.127  1.00  0.00              
ATOM    728  O   ARG   228      35.738   6.123 -32.218  1.00  0.00              
ATOM    729  N   ASP   229      35.454   6.905 -34.314  1.00  0.00              
ATOM    730  CA  ASP   229      34.429   5.935 -34.678  1.00  0.00              
ATOM    731  C   ASP   229      34.960   5.114 -35.857  1.00  0.00              
ATOM    732  O   ASP   229      35.639   5.643 -36.731  1.00  0.00              
ATOM    733  N   MET   230      34.688   3.817 -35.867  1.00  0.00              
ATOM    734  CA  MET   230      35.148   2.957 -36.950  1.00  0.00              
ATOM    735  C   MET   230      34.043   2.785 -37.992  1.00  0.00              
ATOM    736  O   MET   230      32.944   2.306 -37.684  1.00  0.00              
END
