
#######################################################
#                                                     #
#                        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   13 (   63),  selected   13 , name T0322TS239_5_1-D1
# Molecule2: number of CA atoms  128 (  980),  selected   13 , name T0322_D1.pdb
# PARAMETERS: T0322TS239_5_1-D1.T0322_D1.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:    10        19 - 37          3.86     9.59
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        30 - 37          1.64    10.36
  LCS_AVERAGE:      5.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          0.78     9.79
  LCS_AVERAGE:      3.43

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:  128
LCS_GDT     G      16     G      16      3    4    4     3    3    3    4    5    5    5    6    6    6    7    7    7    9    9    9    9    9    9   10 
LCS_GDT     F      17     F      17      3    4    4     3    3    3    4    5    5    5    6    6    6    7    7    7    9    9    9    9    9   10   11 
LCS_GDT     S      18     S      18      3    4    6     3    3    3    4    5    5    5    6    6    6    7    7    7    9    9   10   10   10   10   11 
LCS_GDT     Q      19     Q      19      3    4   10     0    3    3    4    5    5    6    7    8    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     Q      29     Q      29      3    4   10     3    3    3    3    4    5    5    5    9    9    9    9    9    9    9   10   10   10   10   10 
LCS_GDT     I      30     I      30      3    8   10     4    4    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     G      31     G      31      6    8   10     3    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     P      32     P      32      6    8   10     3    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     L      33     L      33      6    8   10     4    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     F      34     F      34      6    8   10     3    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     E      35     E      35      6    8   10     4    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     H      36     H      36      6    8   10     3    6    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_GDT     R      37     R      37      3    8   10     4    4    6    7    7    8    8    8    9    9    9    9    9    9    9   10   10   10   10   11 
LCS_AVERAGE  LCS_A:   5.11  (   3.43    5.05    6.85 )

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      6      6      7      7      8      8      8      9      9      9      9      9      9      9     10     10     10     10     11 
GDT PERCENT_CA   3.12   4.69   4.69   5.47   5.47   6.25   6.25   6.25   7.03   7.03   7.03   7.03   7.03   7.03   7.03   7.81   7.81   7.81   7.81   8.59
GDT RMS_LOCAL    0.32   0.78   0.78   1.30   1.30   1.64   1.64   1.64   2.32   2.32   2.32   2.32   2.32   2.32   2.32   3.86   3.86   3.86   3.86   5.77
GDT RMS_ALL_CA  10.28   9.79   9.79   9.72   9.72  10.36  10.36  10.36  10.59  10.59  10.59  10.59  10.59  10.59  10.59   9.59   9.59   9.59   9.59   7.54

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16         23.886
LGA    F      17      F      17         19.214
LGA    S      18      S      18         16.856
LGA    Q      19      Q      19         10.815
LGA    Q      29      Q      29          5.642
LGA    I      30      I      30          1.550
LGA    G      31      G      31          2.188
LGA    P      32      P      32          1.148
LGA    L      33      L      33          1.012
LGA    F      34      F      34          1.376
LGA    E      35      E      35          0.330
LGA    H      36      H      36          2.581
LGA    R      37      R      37          1.810

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  128    4.0      8    1.64     6.055     5.864     0.460

LGA_LOCAL      RMSD =  1.638  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.356  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  7.432  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.300692 * X  +   0.652636 * Y  +   0.695450 * Z  +  -0.476145
  Y_new =  -0.001691 * X  +   0.729560 * Y  +  -0.683915 * Z  + -22.702751
  Z_new =  -0.953720 * X  +   0.204472 * Y  +   0.220476 * Z  + -25.532404 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.747754   -2.393839  [ DEG:    42.8431   -137.1569 ]
  Theta =   1.265373    1.876220  [ DEG:    72.5005    107.4995 ]
  Phi   =  -0.005623    3.135970  [ DEG:    -0.3222    179.6778 ]
 
# 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: T0322TS239_5_1-D1                             
REMARK     2: T0322_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_5_1-D1.T0322_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  128   4.0    8   1.64   5.864     7.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM     76  N   GLY    16       8.108   0.552  -7.472  1.00  9.99
ATOM     77  CA  GLY    16       7.264   1.703  -7.686  1.00  9.99
ATOM     78  C   GLY    16       6.274   1.547  -8.836  1.00  9.99
ATOM     79  O   GLY    16       5.658   2.530  -9.250  1.00  9.99
ATOM     80  N   PHE    17       6.118   0.320  -9.341  1.00  9.99
ATOM     81  CA  PHE    17       5.120   0.047 -10.399  1.00  9.99
ATOM     82  C   PHE    17       4.373  -1.231 -10.071  1.00  9.99
ATOM     83  O   PHE    17       4.547  -1.799  -9.004  1.00  9.99
ATOM     84  CB  PHE    17       5.734   0.095 -11.820  1.00  9.99
ATOM     85  N   SER    18       3.552  -1.711 -11.002  1.00  9.99
ATOM     86  CA  SER    18       2.636  -2.794 -10.667  1.00  9.99
ATOM     87  C   SER    18       3.370  -4.076 -10.251  1.00  9.99
ATOM     88  O   SER    18       2.908  -4.796  -9.370  1.00  9.99
ATOM     89  CB  SER    18       1.685  -3.082 -11.836  1.00  9.99
ATOM     90  N   GLN    19       4.474  -4.377 -10.922  1.00  9.99
ATOM     91  CA  GLN    19       5.218  -5.589 -10.609  1.00  9.99
ATOM     92  C   GLN    19       5.639  -5.559  -9.112  1.00  9.99
ATOM     93  O   GLN    19       5.458  -6.538  -8.395  1.00  9.99
ATOM     94  CB  GLN    19       6.438  -5.788 -11.550  1.00  9.99
ATOM     95  N   GLN    29       6.158  -4.417  -8.669  1.00  9.99
ATOM     96  CA  GLN    29       6.550  -4.231  -7.279  1.00  9.99
ATOM     97  C   GLN    29       5.356  -4.282  -6.347  1.00  9.99
ATOM     98  O   GLN    29       5.398  -4.954  -5.310  1.00  9.99
ATOM     99  CB  GLN    29       7.300  -2.895  -7.141  1.00  9.99
ATOM    100  N   ILE    30       4.293  -3.589  -6.722  1.00  9.99
ATOM    101  CA  ILE    30       3.058  -3.548  -5.922  1.00  9.99
ATOM    102  C   ILE    30       2.511  -4.939  -5.642  1.00  9.99
ATOM    103  O   ILE    30       2.048  -5.209  -4.543  1.00  9.99
ATOM    104  CB  ILE    30       2.008  -2.682  -6.629  1.00  9.99
ATOM    105  N   GLY    31       2.546  -5.818  -6.648  1.00  9.99
ATOM    106  CA  GLY    31       2.005  -7.155  -6.479  1.00  9.99
ATOM    107  C   GLY    31       3.014  -8.191  -5.968  1.00  9.99
ATOM    108  O   GLY    31       2.674  -9.382  -5.845  1.00  9.99
ATOM    109  N   PRO    32       4.257  -7.756  -5.729  1.00  9.99
ATOM    110  CA  PRO    32       5.331  -8.667  -5.285  1.00  9.99
ATOM    111  C   PRO    32       5.604  -9.775  -6.281  1.00  9.99
ATOM    112  O   PRO    32       5.849 -10.909  -5.898  1.00  9.99
ATOM    113  CB  PRO    32       5.003  -9.267  -3.897  1.00  9.99
ATOM    114  N   LEU    33       5.541  -9.432  -7.560  1.00  9.99
ATOM    115  CA  LEU    33       6.038 -10.353  -8.566  1.00  9.99
ATOM    116  C   LEU    33       7.575 -10.389  -8.472  1.00  9.99
ATOM    117  O   LEU    33       8.217  -9.319  -8.467  1.00  9.99
ATOM    118  CB  LEU    33       5.514  -9.916  -9.953  1.00  9.99
ATOM    119  N   PHE    34       8.142 -11.599  -8.406  1.00  9.99
ATOM    120  CA  PHE    34       9.577 -11.775  -8.210  1.00  9.99
ATOM    121  C   PHE    34      10.091 -12.693  -9.314  1.00  9.99
ATOM    122  O   PHE    34       9.679 -13.853  -9.413  1.00  9.99
ATOM    123  CB  PHE    34       9.863 -12.464  -6.863  1.00  9.99
ATOM    124  N   GLU    35      11.042 -12.200 -10.104  1.00  9.99
ATOM    125  CA  GLU    35      11.768 -13.095 -11.023  1.00  9.99
ATOM    126  C   GLU    35      12.679 -14.050 -10.236  1.00  9.99
ATOM    127  O   GLU    35      13.385 -13.622  -9.325  1.00  9.99
ATOM    128  CB  GLU    35      12.555 -12.270 -12.064  1.00  9.99
ATOM    129  N   HIS    36      12.619 -15.324 -10.575  1.00  9.99
ATOM    130  CA  HIS    36      13.284 -16.388  -9.821  1.00  9.99
ATOM    131  C   HIS    36      14.333 -17.132 -10.616  1.00  9.99
ATOM    132  O   HIS    36      15.218 -17.774 -10.025  1.00  9.99
ATOM    133  CB  HIS    36      12.268 -17.438  -9.408  1.00  9.99
ATOM    134  N   ARG    37      14.207 -17.188 -11.942  1.00  9.99
ATOM    135  CA  ARG    37      15.105 -18.018 -12.721  1.00  9.99
ATOM    136  C   ARG    37      15.209 -17.507 -14.142  1.00  9.99
ATOM    137  O   ARG    37      14.177 -17.245 -14.782  1.00  9.99
ATOM    138  CB  ARG    37      14.617 -19.474 -12.692  1.00  9.99
TER
END
