
#######################################################
#                                                     #
#                        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_2_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected    8 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_2_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         3.70     3.70
  LCS_AVERAGE:      4.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       130 - 134         1.61     4.98
  LCS_AVERAGE:      2.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       130 - 133         0.77     5.44
  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      4    5    8     0    4    4    4    5    5    5    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     131     A     131      4    5    8     3    4    4    4    5    5    5    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     132     V     132      4    5    8     3    4    4    4    5    5    5    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     133     A     133      4    5    8     3    4    4    4    5    5    5    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     134     A     134      3    5    8     0    3    3    4    5    5    5    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     135     E     135      3    3    8     3    3    3    3    3    4    4    6    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     136     L     136      3    3    8     3    3    3    3    3    4    4    5    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     137     C     137      3    3    8     3    3    3    3    3    4    4    4    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.82  (   1.88    2.28    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      3      4      4      4      5      5      5      6      7      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   1.61   2.15   2.15   2.15   2.69   2.69   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
GDT RMS_LOCAL    0.19   0.77   0.77   0.77   1.61   1.61   1.61   2.58   3.63   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70
GDT RMS_ALL_CA   5.26   5.44   5.44   5.44   4.98   4.98   4.98   4.63   3.77   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          2.188
LGA    A     131      A     131          3.316
LGA    V     132      V     132          1.642
LGA    A     133      A     133          1.645
LGA    A     134      A     134          2.104
LGA    E     135      E     135          3.969
LGA    L     136      L     136          7.165
LGA    C     137      C     137          8.358

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  186    4.0      6    2.58     2.957     2.936     0.224

LGA_LOCAL      RMSD =  2.578  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.508  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.703  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.131714 * X  +   0.991165 * Y  +  -0.015583 * Z  + -94.783768
  Y_new =   0.150679 * X  +  -0.004481 * Y  +   0.988573 * Z  +  39.577957
  Z_new =   0.979769 * X  +  -0.132556 * Y  +  -0.149938 * Z  + -74.835388 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.417647    0.723946  [ DEG:  -138.5210     41.4790 ]
  Theta =  -1.369304   -1.772289  [ DEG:   -78.4553   -101.5447 ]
  Phi   =   0.852458   -2.289135  [ DEG:    48.8423   -131.1577 ]
 
# 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_2_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_2_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    6   2.58   2.936     3.70
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1g2i_A
ATOM    928  N   CYS   130     -12.599  73.385  -2.292  1.00  0.00
ATOM    929  CA  CYS   130     -11.562  72.409  -2.108  1.00  0.00
ATOM    930  C   CYS   130     -11.109  72.306  -0.686  1.00  0.00
ATOM    931  O   CYS   130     -11.728  72.815   0.247  1.00  0.00
ATOM    932  CB  CYS   130     -10.335  72.765  -2.951  1.00  0.00
ATOM    933  SG  CYS   130     -10.642  72.817  -4.731  1.00  0.00
ATOM    934  N   ALA   131      -9.955  71.624  -0.523  1.00  0.00
ATOM    935  CA  ALA   131      -9.375  71.302   0.743  1.00  0.00
ATOM    936  C   ALA   131      -9.099  72.554   1.500  1.00  0.00
ATOM    937  O   ALA   131      -9.109  73.651   0.946  1.00  0.00
ATOM    938  CB  ALA   131      -8.069  70.545   0.550  1.00  0.00
ATOM    939  N   VAL   132      -8.850  72.357   2.810  1.00  0.00
ATOM    940  CA  VAL   132      -8.664  73.320   3.855  1.00  0.00
ATOM    941  C   VAL   132      -9.196  74.656   3.475  1.00  0.00
ATOM    942  O   VAL   132      -8.551  75.463   2.807  1.00  0.00
ATOM    943  CB  VAL   132      -7.173  73.503   4.195  1.00  0.00
ATOM    944  CG1 VAL   132      -6.995  74.588   5.245  1.00  0.00
ATOM    945  CG2 VAL   132      -6.587  72.208   4.738  1.00  0.00
ATOM    946  N   ALA   133     -10.451  74.882   3.896  1.00  0.00
ATOM    947  CA  ALA   133     -11.131  76.130   3.741  1.00  0.00
ATOM    948  C   ALA   133     -12.464  75.909   4.379  1.00  0.00
ATOM    949  O   ALA   133     -13.081  74.869   4.159  1.00  0.00
ATOM    950  CB  ALA   133     -11.268  76.480   2.268  1.00  0.00
ATOM    951  N   ALA   134     -12.946  76.867   5.200  1.00  0.00
ATOM    952  CA  ALA   134     -14.245  76.690   5.791  1.00  0.00
ATOM    953  C   ALA   134     -14.467  77.735   6.841  1.00  0.00
ATOM    954  O   ALA   134     -13.528  78.406   7.266  1.00  0.00
ATOM    955  CB  ALA   134     -14.354  75.315   6.432  1.00  0.00
ATOM    956  N   GLU   135     -15.745  77.905   7.258  1.00  0.00
ATOM    957  CA  GLU   135     -16.111  78.812   8.313  1.00  0.00
ATOM    958  C   GLU   135     -17.252  78.189   9.055  1.00  0.00
ATOM    959  O   GLU   135     -18.136  77.583   8.450  1.00  0.00
ATOM    960  CB  GLU   135     -16.536  80.163   7.733  1.00  0.00
ATOM    961  CG  GLU   135     -16.867  81.212   8.783  1.00  0.00
ATOM    962  CD  GLU   135     -17.236  82.550   8.173  1.00  0.00
ATOM    963  OE1 GLU   135     -17.195  82.668   6.930  1.00  0.00
ATOM    964  OE2 GLU   135     -17.565  83.481   8.938  1.00  0.00
ATOM    965  N   LEU   136     -17.254  78.308  10.397  1.00  0.00
ATOM    966  CA  LEU   136     -18.346  77.762  11.141  1.00  0.00
ATOM    967  C   LEU   136     -19.125  78.938  11.618  1.00  0.00
ATOM    968  O   LEU   136     -18.758  79.578  12.602  1.00  0.00
ATOM    969  CB  LEU   136     -17.830  76.930  12.317  1.00  0.00
ATOM    970  CG  LEU   136     -18.893  76.294  13.215  1.00  0.00
ATOM    971  CD1 LEU   136     -19.731  75.296  12.432  1.00  0.00
ATOM    972  CD2 LEU   136     -18.244  75.559  14.379  1.00  0.00
ATOM    973  N   CYS   137     -20.239  79.254  10.932  1.00  0.00
ATOM    974  CA  CYS   137     -21.033  80.371  11.339  1.00  0.00
ATOM    975  C   CYS   137     -21.983  79.872  12.421  1.00  0.00
ATOM    976  O   CYS   137     -22.204  78.635  12.481  1.00  0.00
ATOM    977  CB  CYS   137     -21.826  80.926  10.154  1.00  0.00
ATOM    978  SG  CYS   137     -22.672  82.488  10.487  1.00  0.00
TER
END
