
#######################################################
#                                                     #
#                        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    8 (   51),  selected    8 , name T0298TS268_5_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected    8 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_5_1-D2.T0298_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:     8       130 - 137         3.21     3.21
  LCS_AVERAGE:      4.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       130 - 133         1.67     6.14
  LONGEST_CONTINUOUS_SEGMENT:     4       131 - 134         1.83     5.57
  LONGEST_CONTINUOUS_SEGMENT:     4       132 - 135         1.77     6.33
  LONGEST_CONTINUOUS_SEGMENT:     4       133 - 136         1.99     4.77
  LONGEST_CONTINUOUS_SEGMENT:     4       134 - 137         0.14     6.64
  LCS_AVERAGE:      2.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       134 - 137         0.14     6.64
  LCS_AVERAGE:      1.88

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:  186
LCS_GDT     C     130     C     130      3    4    8     0    3    3    4    4    4    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     131     A     131      3    4    8     3    3    3    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     132     V     132      3    4    8     3    3    3    4    4    5    5    6    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     133     A     133      3    4    8     3    3    3    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     134     A     134      4    4    8     4    4    4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     135     E     135      4    4    8     4    4    4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     136     L     136      4    4    8     4    4    4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     137     C     137      4    4    8     4    4    4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.78  (   1.88    2.15    4.30 )

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      4      4      5      6      7      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.15   2.15   2.15   2.15   2.15   2.69   3.23   3.76   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30
GDT RMS_LOCAL    0.14   0.14   0.14   0.14   0.14   2.04   2.51   2.76   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21
GDT RMS_ALL_CA   6.64   6.64   6.64   6.64   6.64   4.12   3.42   3.37   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          3.597
LGA    A     131      A     131          2.920
LGA    V     132      V     132          6.116
LGA    A     133      A     133          2.573
LGA    A     134      A     134          3.562
LGA    E     135      E     135          1.990
LGA    L     136      L     136          2.787
LGA    C     137      C     137          0.910

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  186    4.0      7    2.76     3.091     2.952     0.245

LGA_LOCAL      RMSD =  2.760  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.368  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.211  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.546964 * X  +  -0.721419 * Y  +   0.424718 * Z  +  22.562418
  Y_new =   0.231811 * X  +   0.356979 * Y  +   0.904892 * Z  +  56.067093
  Z_new =  -0.804421 * X  +   0.593398 * Y  +  -0.028022 * Z  +  -8.203324 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.617984   -1.523609  [ DEG:    92.7037    -87.2963 ]
  Theta =   0.934701    2.206892  [ DEG:    53.5544    126.4456 ]
  Phi   =   2.740727   -0.400866  [ DEG:   157.0321    -22.9679 ]
 
# 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: T0298TS268_5_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_5_1-D2.T0298_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  186   4.0    7   2.76   2.952     3.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1byi
ATOM    928  N   CYS   130      -8.236  70.604  -3.152  1.00  0.00
ATOM    929  CA  CYS   130      -9.354  71.484  -3.023  1.00  0.00
ATOM    930  C   CYS   130     -10.192  71.003  -1.892  1.00  0.00
ATOM    931  O   CYS   130     -10.366  69.802  -1.689  1.00  0.00
ATOM    932  CB  CYS   130     -10.182  71.492  -4.310  1.00  0.00
ATOM    933  SG  CYS   130      -9.326  72.185  -5.744  1.00  0.00
ATOM    934  N   ALA   131     -10.715  71.956  -1.099  1.00  0.00
ATOM    935  CA  ALA   131     -11.560  71.611  -0.001  1.00  0.00
ATOM    936  C   ALA   131     -12.371  72.823   0.293  1.00  0.00
ATOM    937  O   ALA   131     -12.034  73.926  -0.134  1.00  0.00
ATOM    938  CB  ALA   131     -10.726  71.217   1.207  1.00  0.00
ATOM    939  N   VAL   132     -13.482  72.645   1.030  1.00  0.00
ATOM    940  CA  VAL   132     -14.271  73.793   1.343  1.00  0.00
ATOM    941  C   VAL   132     -13.376  74.684   2.131  1.00  0.00
ATOM    942  O   VAL   132     -12.447  74.220   2.791  1.00  0.00
ATOM    943  CB  VAL   132     -15.518  73.415   2.163  1.00  0.00
ATOM    944  CG1 VAL   132     -16.399  72.453   1.381  1.00  0.00
ATOM    945  CG2 VAL   132     -15.114  72.744   3.468  1.00  0.00
ATOM    946  N   ALA   133     -13.624  76.003   2.061  1.00  0.00
ATOM    947  CA  ALA   133     -12.773  76.922   2.750  1.00  0.00
ATOM    948  C   ALA   133     -12.804  76.556   4.193  1.00  0.00
ATOM    949  O   ALA   133     -13.704  75.855   4.653  1.00  0.00
ATOM    950  CB  ALA   133     -13.269  78.347   2.560  1.00  0.00
ATOM    951  N   ALA   134     -11.784  77.007   4.942  1.00  0.00
ATOM    952  CA  ALA   134     -11.704  76.678   6.331  1.00  0.00
ATOM    953  C   ALA   134     -12.962  77.151   6.973  1.00  0.00
ATOM    954  O   ALA   134     -13.673  77.993   6.433  1.00  0.00
ATOM    955  CB  ALA   134     -10.504  77.360   6.968  1.00  0.00
ATOM    956  N   GLU   135     -13.279  76.575   8.144  1.00  0.00
ATOM    957  CA  GLU   135     -14.492  76.861   8.852  1.00  0.00
ATOM    958  C   GLU   135     -14.532  78.308   9.219  1.00  0.00
ATOM    959  O   GLU   135     -15.574  78.953   9.109  1.00  0.00
ATOM    960  CB  GLU   135     -14.576  76.025  10.130  1.00  0.00
ATOM    961  CG  GLU   135     -14.814  74.544   9.888  1.00  0.00
ATOM    962  CD  GLU   135     -14.768  73.730  11.167  1.00  0.00
ATOM    963  OE1 GLU   135     -14.477  74.313  12.232  1.00  0.00
ATOM    964  OE2 GLU   135     -15.022  72.509  11.103  1.00  0.00
ATOM    965  N   LEU   136     -13.389  78.867   9.651  1.00  0.00
ATOM    966  CA  LEU   136     -13.399  80.224  10.106  1.00  0.00
ATOM    967  C   LEU   136     -13.862  81.103   8.992  1.00  0.00
ATOM    968  O   LEU   136     -14.746  81.939   9.177  1.00  0.00
ATOM    969  CB  LEU   136     -11.997  80.655  10.540  1.00  0.00
ATOM    970  CG  LEU   136     -11.853  82.094  11.037  1.00  0.00
ATOM    971  CD1 LEU   136     -12.706  82.324  12.275  1.00  0.00
ATOM    972  CD2 LEU   136     -10.406  82.398  11.393  1.00  0.00
ATOM    973  N   CYS   137     -13.291  80.923   7.790  1.00  0.00
ATOM    974  CA  CYS   137     -13.693  81.762   6.706  1.00  0.00
ATOM    975  C   CYS   137     -13.469  80.982   5.421  1.00  0.00
ATOM    976  O   CYS   137     -14.286  80.070   5.127  1.00  0.00
ATOM    977  CB  CYS   137     -12.865  83.048   6.689  1.00  0.00
ATOM    978  SG  CYS   137     -13.460  84.304   5.533  1.00  0.00
TER
END
