
#######################################################
#                                                     #
#                        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_4_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected    8 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_4_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         4.01     4.01
  LCS_AVERAGE:      4.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       130 - 133         1.56     6.54
  LCS_AVERAGE:      1.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       130 - 132         0.42    11.65
  LONGEST_CONTINUOUS_SEGMENT:     3       131 - 133         0.07     7.53
  LONGEST_CONTINUOUS_SEGMENT:     3       132 - 134         0.75     8.31
  LONGEST_CONTINUOUS_SEGMENT:     3       133 - 135         0.42     7.10
  LONGEST_CONTINUOUS_SEGMENT:     3       134 - 136         0.45     7.64
  LONGEST_CONTINUOUS_SEGMENT:     3       135 - 137         0.50     8.55
  LCS_AVERAGE:      1.61

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     3    3    3    4    4    5    5    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     131     A     131      3    4    8     3    3    3    4    4    4    4    5    7    7    7    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    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     133     A     133      3    4    8     3    3    3    4    4    5    5    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     134     A     134      3    3    8     3    3    3    3    4    5    5    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     135     E     135      3    3    8     3    3    3    3    4    5    5    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     136     L     136      3    3    8     3    3    3    3    3    3    4    5    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     C     137     C     137      3    3    8     0    3    3    3    3    3    4    5    6    7    7    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.60  (   1.61    1.88    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      3      3      4      4      5      5      5      7      7      7      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   1.61   1.61   1.61   2.15   2.15   2.69   2.69   2.69   3.76   3.76   3.76   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30   4.30
GDT RMS_LOCAL    0.07   0.07   0.07   1.56   1.56   2.46   2.46   2.46   3.49   3.49   3.49   4.01   4.01   4.01   4.01   4.01   4.01   4.01   4.01   4.01
GDT RMS_ALL_CA   7.53   7.53   7.53   6.54   6.54   5.07   5.07   5.07   4.30   4.30   4.30   4.01   4.01   4.01   4.01   4.01   4.01   4.01   4.01   4.01

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          2.662
LGA    A     131      A     131          4.208
LGA    V     132      V     132          1.155
LGA    A     133      A     133          3.014
LGA    A     134      A     134          3.127
LGA    E     135      E     135          3.207
LGA    L     136      L     136          6.715
LGA    C     137      C     137          8.974

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  186    4.0      5    2.46     2.688     2.645     0.195

LGA_LOCAL      RMSD =  2.463  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.755  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.009  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.243817 * X  +  -0.955772 * Y  +  -0.164476 * Z  + -12.166058
  Y_new =  -0.538336 * X  +   0.007687 * Y  +  -0.842695 * Z  +  78.764153
  Z_new =   0.806689 * X  +   0.294007 * Y  +  -0.512652 * Z  +  -9.690773 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.620885   -0.520708  [ DEG:   150.1656    -29.8343 ]
  Theta =  -0.938528   -2.203064  [ DEG:   -53.7737   -126.2263 ]
  Phi   =  -1.145525    1.996067  [ DEG:   -65.6338    114.3662 ]
 
# 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_4_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_4_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    5   2.46   2.645     4.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1hdo_A
ATOM    928  N   CYS   130     -10.526  69.936  -1.820  1.00  0.00
ATOM    929  CA  CYS   130     -10.418  71.369  -1.835  1.00  0.00
ATOM    930  C   CYS   130      -9.551  71.749  -0.680  1.00  0.00
ATOM    931  O   CYS   130      -9.058  70.897   0.059  1.00  0.00
ATOM    932  CB  CYS   130     -11.799  72.012  -1.696  1.00  0.00
ATOM    933  SG  CYS   130     -12.630  71.669  -0.128  1.00  0.00
ATOM    934  N   ALA   131      -9.331  73.064  -0.505  1.00  0.00
ATOM    935  CA  ALA   131      -8.507  73.536   0.569  1.00  0.00
ATOM    936  C   ALA   131      -9.290  73.392   1.829  1.00  0.00
ATOM    937  O   ALA   131     -10.501  73.175   1.792  1.00  0.00
ATOM    938  CB  ALA   131      -8.135  74.995   0.350  1.00  0.00
ATOM    939  N   VAL   132      -8.612  73.455   2.991  1.00  0.00
ATOM    940  CA  VAL   132      -9.401  73.424   4.182  1.00  0.00
ATOM    941  C   VAL   132     -10.252  74.645   4.085  1.00  0.00
ATOM    942  O   VAL   132      -9.756  75.746   3.847  1.00  0.00
ATOM    943  CB  VAL   132      -8.520  73.459   5.445  1.00  0.00
ATOM    944  CG1 VAL   132      -9.381  73.563   6.694  1.00  0.00
ATOM    945  CG2 VAL   132      -7.682  72.192   5.544  1.00  0.00
ATOM    946  N   ALA   133     -11.575  74.456   4.231  1.00  0.00
ATOM    947  CA  ALA   133     -12.522  75.508   4.033  1.00  0.00
ATOM    948  C   ALA   133     -12.602  76.377   5.237  1.00  0.00
ATOM    949  O   ALA   133     -12.058  76.073   6.298  1.00  0.00
ATOM    950  CB  ALA   133     -13.905  74.933   3.764  1.00  0.00
ATOM    951  N   ALA   134     -13.240  77.545   5.046  1.00  0.00
ATOM    952  CA  ALA   134     -13.488  78.439   6.125  1.00  0.00
ATOM    953  C   ALA   134     -14.720  77.938   6.808  1.00  0.00
ATOM    954  O   ALA   134     -15.658  77.482   6.157  1.00  0.00
ATOM    955  CB  ALA   134     -13.701  79.852   5.605  1.00  0.00
ATOM    956  N   GLU   135     -14.733  77.988   8.150  1.00  0.00
ATOM    957  CA  GLU   135     -15.928  77.635   8.857  1.00  0.00
ATOM    958  C   GLU   135     -16.359  78.891   9.527  1.00  0.00
ATOM    959  O   GLU   135     -15.525  79.651  10.014  1.00  0.00
ATOM    960  CB  GLU   135     -15.641  76.531   9.877  1.00  0.00
ATOM    961  CG  GLU   135     -15.243  75.202   9.258  1.00  0.00
ATOM    962  CD  GLU   135     -15.023  74.118  10.295  1.00  0.00
ATOM    963  OE1 GLU   135     -15.165  74.412  11.500  1.00  0.00
ATOM    964  OE2 GLU   135     -14.709  72.975   9.902  1.00  0.00
ATOM    965  N   LEU   136     -17.675  79.169   9.535  1.00  0.00
ATOM    966  CA  LEU   136     -18.093  80.399  10.134  1.00  0.00
ATOM    967  C   LEU   136     -19.151  80.058  11.137  1.00  0.00
ATOM    968  O   LEU   136     -20.252  79.641  10.781  1.00  0.00
ATOM    969  CB  LEU   136     -18.655  81.347   9.073  1.00  0.00
ATOM    970  CG  LEU   136     -19.161  82.702   9.575  1.00  0.00
ATOM    971  CD1 LEU   136     -18.027  83.503  10.195  1.00  0.00
ATOM    972  CD2 LEU   136     -19.745  83.515   8.429  1.00  0.00
ATOM    973  N   CYS   137     -18.839  80.230  12.436  1.00  0.00
ATOM    974  CA  CYS   137     -19.788  79.897  13.458  1.00  0.00
ATOM    975  C   CYS   137     -20.659  81.112  13.757  1.00  0.00
ATOM    976  O   CYS   137     -21.669  80.938  14.493  1.00  0.00
ATOM    977  CB  CYS   137     -19.067  79.474  14.739  1.00  0.00
ATOM    978  SG  CYS   137     -18.133  77.932  14.598  1.00  0.00
TER
END
