
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected    8 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_1_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         3.75     3.75
  LCS_AVERAGE:      4.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       130 - 134         1.94     5.37
  LONGEST_CONTINUOUS_SEGMENT:     5       133 - 137         1.35     5.45
  LCS_AVERAGE:      2.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       130 - 133         0.34     4.36
  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     4    4    5    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     131     A     131      4    5    8     4    4    5    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     132     V     132      4    5    8     4    4    5    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     133     A     133      4    5    8     4    4    5    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     134     A     134      3    5    8     3    3    4    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     135     E     135      3    5    8     3    4    4    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     136     L     136      3    5    8     3    4    4    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     137     C     137      3    5    8     3    4    5    5    5    5    5    6    6    7    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.96  (   1.88    2.69    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      5      5      5      5      6      6      7      7      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.15   2.15   2.69   2.69   2.69   2.69   3.23   3.23   3.76   3.76   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30
GDT RMS_LOCAL    0.34   0.34   0.78   0.78   0.78   0.78   2.50   2.22   3.18   3.18   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75
GDT RMS_ALL_CA   4.36   4.36   4.75   4.75   4.75   4.75   4.90   4.45   4.10   4.10   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          2.721
LGA    A     131      A     131          8.173
LGA    V     132      V     132          7.866
LGA    A     133      A     133          3.577
LGA    A     134      A     134          2.127
LGA    E     135      E     135          0.640
LGA    L     136      L     136          0.891
LGA    C     137      C     137          1.905

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  186    4.0      6    2.22     3.091     3.122     0.259

LGA_LOCAL      RMSD =  2.220  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.447  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.747  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.970232 * X  +  -0.064602 * Y  +   0.233401 * Z  +  22.920626
  Y_new =   0.001227 * X  +  -0.965063 * Y  +  -0.262013 * Z  + 102.738113
  Z_new =   0.242174 * X  +  -0.253928 * Y  +   0.936415 * Z  + -14.811433 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.264802    2.876791  [ DEG:   -15.1720    164.8280 ]
  Theta =  -0.244606   -2.896987  [ DEG:   -14.0149   -165.9851 ]
  Phi   =   3.140328   -0.001264  [ DEG:   179.9276     -0.0724 ]
 
# 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_1_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_1_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   2.22   3.122     3.75
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1oi4_B
ATOM    928  N   CYS   130      -8.520  74.542   0.590  1.00  0.00
ATOM    929  CA  CYS   130      -8.430  75.081  -0.742  1.00  0.00
ATOM    930  C   CYS   130      -8.984  76.470  -0.788  1.00  0.00
ATOM    931  O   CYS   130      -9.157  77.138   0.229  1.00  0.00
ATOM    932  CB  CYS   130      -9.221  74.214  -1.725  1.00  0.00
ATOM    933  SG  CYS   130     -11.003  74.176  -1.420  1.00  0.00
ATOM    934  N   ALA   131      -9.252  76.941  -2.026  1.00  0.00
ATOM    935  CA  ALA   131      -9.785  78.251  -2.253  1.00  0.00
ATOM    936  C   ALA   131     -11.128  78.316  -1.609  1.00  0.00
ATOM    937  O   ALA   131     -11.456  79.290  -0.933  1.00  0.00
ATOM    938  CB  ALA   131      -9.915  78.518  -3.745  1.00  0.00
ATOM    939  N   VAL   132     -11.956  77.272  -1.800  1.00  0.00
ATOM    940  CA  VAL   132     -13.226  77.290  -1.144  1.00  0.00
ATOM    941  C   VAL   132     -13.239  76.176  -0.149  1.00  0.00
ATOM    942  O   VAL   132     -13.595  75.036  -0.449  1.00  0.00
ATOM    943  CB  VAL   132     -14.381  77.095  -2.143  1.00  0.00
ATOM    944  CG1 VAL   132     -15.720  77.138  -1.424  1.00  0.00
ATOM    945  CG2 VAL   132     -14.365  78.193  -3.195  1.00  0.00
ATOM    946  N   ALA   133     -12.858  76.485   1.098  1.00  0.00
ATOM    947  CA  ALA   133     -12.887  75.445   2.075  1.00  0.00
ATOM    948  C   ALA   133     -13.848  75.889   3.118  1.00  0.00
ATOM    949  O   ALA   133     -13.751  77.007   3.620  1.00  0.00
ATOM    950  CB  ALA   133     -11.503  75.237   2.670  1.00  0.00
ATOM    951  N   ALA   134     -14.813  75.024   3.473  1.00  0.00
ATOM    952  CA  ALA   134     -15.715  75.441   4.497  1.00  0.00
ATOM    953  C   ALA   134     -14.961  75.236   5.758  1.00  0.00
ATOM    954  O   ALA   134     -14.881  74.126   6.277  1.00  0.00
ATOM    955  CB  ALA   134     -16.982  74.600   4.461  1.00  0.00
ATOM    956  N   GLU   135     -14.392  76.331   6.285  1.00  0.00
ATOM    957  CA  GLU   135     -13.591  76.260   7.466  1.00  0.00
ATOM    958  C   GLU   135     -13.338  77.652   7.911  1.00  0.00
ATOM    959  O   GLU   135     -14.169  78.536   7.713  1.00  0.00
ATOM    960  CB  GLU   135     -12.266  75.553   7.173  1.00  0.00
ATOM    961  CG  GLU   135     -12.409  74.076   6.846  1.00  0.00
ATOM    962  CD  GLU   135     -11.084  73.422   6.510  1.00  0.00
ATOM    963  OE1 GLU   135     -10.058  74.134   6.493  1.00  0.00
ATOM    964  OE2 GLU   135     -11.071  72.197   6.264  1.00  0.00
ATOM    965  N   LEU   136     -12.185  77.895   8.555  1.00  0.00
ATOM    966  CA  LEU   136     -12.030  79.216   9.061  1.00  0.00
ATOM    967  C   LEU   136     -11.749  80.117   7.910  1.00  0.00
ATOM    968  O   LEU   136     -10.688  80.047   7.292  1.00  0.00
ATOM    969  CB  LEU   136     -10.873  79.275  10.060  1.00  0.00
ATOM    970  CG  LEU   136     -10.643  80.620  10.752  1.00  0.00
ATOM    971  CD1 LEU   136     -11.832  80.986  11.625  1.00  0.00
ATOM    972  CD2 LEU   136      -9.404  80.565  11.634  1.00  0.00
ATOM    973  N   CYS   137     -12.712  81.003   7.600  1.00  0.00
ATOM    974  CA  CYS   137     -12.549  81.913   6.510  1.00  0.00
ATOM    975  C   CYS   137     -13.058  83.259   7.001  1.00  0.00
ATOM    976  O   CYS   137     -13.609  83.295   8.134  1.00  0.00
ATOM    977  CB  CYS   137     -13.353  81.444   5.296  1.00  0.00
ATOM    978  SG  CYS   137     -12.865  79.825   4.657  1.00  0.00
TER
END
