
#######################################################
#                                                     #
#                        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 (   63),  selected    8 , name T0348TS622_1_2
# Molecule2: number of CA atoms   61 (  465),  selected    8 , name T0348.pdb
# PARAMETERS: T0348TS622_1_2.T0348.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        54 - 61          2.29     2.29
  LCS_AVERAGE:     13.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        55 - 61          1.03     2.90
  LCS_AVERAGE:     10.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        55 - 60          0.93     2.98
  LCS_AVERAGE:      9.02

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:   61
LCS_GDT     A      54     A      54      3    3    8     0    3    3    3    3    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     P      55     P      55      6    7    8     4    5    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      56     E      56      6    7    8     4    5    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      57     E      57      6    7    8     4    5    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      58     E      58      6    7    8     4    5    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V      59     V      59      6    7    8     4    5    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     K      60     K      60      6    7    8     4    4    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L      61     L      61      5    7    8     4    4    7    7    7    7    7    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:  10.93  (   9.02   10.66   13.11 )

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      5      7      7      7      7      7      8      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   6.56   8.20  11.48  11.48  11.48  11.48  11.48  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11  13.11
GDT RMS_LOCAL    0.17   0.52   1.03   1.03   1.03   1.03   1.03   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29
GDT RMS_ALL_CA   3.02   3.13   2.90   2.90   2.90   2.90   2.90   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29   2.29

#      Molecule1      Molecule2       DISTANCE
LGA    A      54      A      54          3.722
LGA    P      55      P      55          2.479
LGA    E      56      E      56          0.971
LGA    E      57      E      57          2.009
LGA    E      58      E      58          1.078
LGA    V      59      V      59          2.517
LGA    K      60      K      60          3.833
LGA    L      61      L      61          2.900

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8   61    4.0      8    2.29    11.475    11.572     0.334

LGA_LOCAL      RMSD =  2.293  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.636  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.293  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.840391 * X  +  -0.224749 * Y  +  -0.493185 * Z  +  58.711826
  Y_new =   0.535838 * X  +   0.207921 * Y  +   0.818320 * Z  +  13.115973
  Z_new =  -0.081373 * X  +  -0.951975 * Y  +   0.295164 * Z  +  66.418388 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.270141    1.871452  [ DEG:   -72.7737    107.2263 ]
  Theta =   0.081464    3.060129  [ DEG:     4.6675    175.3325 ]
  Phi   =   0.567613   -2.573980  [ DEG:    32.5218   -147.4782 ]
 
# 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: T0348TS622_1_2                                
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS622_1_2.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8   61   4.0    8   2.29  11.572     2.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS622_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0348
PARENT N/A
ATOM      1  N   ALA   54       10.846  10.886  58.155 1.00  0.00
ATOM      2  CA  ALA   54       12.292  11.152  58.108 1.00  0.00
ATOM      3  C   ALA   54       12.679  11.617  56.703 1.00  0.00
ATOM      4  O   ALA   54       12.191  11.130  55.672 1.00  0.00
ATOM      5  CB  ALA   54       13.074   9.893  58.446 1.00  0.00
ATOM      6  N   PRO   55       13.577  12.580  56.616 1.00  0.00
ATOM      7  CA  PRO   55       13.999  13.076  55.298 1.00  0.00
ATOM      8  C   PRO   55       15.515  12.927  55.158 1.00  0.00
ATOM      9  O   PRO   55       16.423  13.105  55.985 1.00  0.00
ATOM     10  CB  PRO   55       13.561  14.542  55.297 1.00  0.00
ATOM     11  CG  PRO   55       13.598  14.944  56.734 1.00  0.00
ATOM     12  CD  PRO   55       13.217  13.719  57.518 1.00  0.00
ATOM     13  N   GLU   56       15.973  12.547  53.980 1.00  0.00
ATOM     14  CA  GLU   56       17.420  12.382  53.772 1.00  0.00
ATOM     15  C   GLU   56       18.130  13.706  54.058 1.00  0.00
ATOM     16  O   GLU   56       19.106  13.800  54.817 1.00  0.00
ATOM     17  CB  GLU   56       17.709  11.964  52.329 1.00  0.00
ATOM     18  CG  GLU   56       19.181  11.726  52.034 1.00  0.00
ATOM     19  CD  GLU   56       19.425  11.282  50.605 1.00  0.00
ATOM     20  OE1 GLU   56       18.440  11.148  49.848 1.00  0.00
ATOM     21  OE2 GLU   56       20.601  11.068  50.243 1.00  0.00
ATOM     22  N   GLU   57       17.659  14.781  53.455 1.00  0.00
ATOM     23  CA  GLU   57       18.291  16.088  53.682 1.00  0.00
ATOM     24  C   GLU   57       18.242  16.426  55.173 1.00  0.00
ATOM     25  O   GLU   57       19.140  16.788  55.948 1.00  0.00
ATOM     26  CB  GLU   57       17.559  17.182  52.901 1.00  0.00
ATOM     27  CG  GLU   57       18.175  18.564  53.041 1.00  0.00
ATOM     28  CD  GLU   57       17.444  19.613  52.228 1.00  0.00
ATOM     29  OE1 GLU   57       16.463  19.256  51.542 1.00  0.00
ATOM     30  OE2 GLU   57       17.852  20.793  52.275 1.00  0.00
ATOM     31  N   GLU   58       17.069  16.329  55.771 1.00  0.00
ATOM     32  CA  GLU   58       16.946  16.637  57.204 1.00  0.00
ATOM     33  C   GLU   58       17.869  15.717  58.004 1.00  0.00
ATOM     34  O   GLU   58       18.675  16.138  58.848 1.00  0.00
ATOM     35  CB  GLU   58       15.506  16.428  57.675 1.00  0.00
ATOM     36  CG  GLU   58       15.276  16.768  59.138 1.00  0.00
ATOM     37  CD  GLU   58       13.831  16.580  59.560 1.00  0.00
ATOM     38  OE1 GLU   58       13.007  16.197  58.704 1.00  0.00
ATOM     39  OE2 GLU   58       13.523  16.817  60.747 1.00  0.00
ATOM     40  N   VAL   59       17.782  14.423  57.764 1.00  0.00
ATOM     41  CA  VAL   59       18.638  13.478  58.497 1.00  0.00
ATOM     42  C   VAL   59       20.108  13.822  58.244 1.00  0.00
ATOM     43  O   VAL   59       21.042  13.998  59.040 1.00  0.00
ATOM     44  CB  VAL   59       18.392  12.026  58.046 1.00  0.00
ATOM     45  CG1 VAL   59       19.420  11.094  58.666 1.00  0.00
ATOM     46  CG2 VAL   59       17.006  11.564  58.469 1.00  0.00
ATOM     47  N   LYS   60       20.482  13.962  56.987 1.00  0.00
ATOM     48  CA  LYS   60       21.879  14.292  56.668 1.00  0.00
ATOM     49  C   LYS   60       22.255  15.616  57.337 1.00  0.00
ATOM     50  O   LYS   60       23.270  15.754  58.037 1.00  0.00
ATOM     51  CB  LYS   60       22.066  14.429  55.156 1.00  0.00
ATOM     52  CG  LYS   60       23.494  14.730  54.731 1.00  0.00
ATOM     53  CD  LYS   60       23.621  14.782  53.217 1.00  0.00
ATOM     54  CE  LYS   60       25.038  15.132  52.793 1.00  0.00
ATOM     55  NZ  LYS   60       25.172  15.210  51.312 1.00  0.00
ATOM     56  N   LEU   61       21.444  16.638  57.141 1.00  0.00
ATOM     57  CA  LEU   61       21.742  17.941  57.753 1.00  0.00
ATOM     58  C   LEU   61       21.815  17.786  59.274 1.00  0.00
ATOM     59  O   LEU   61       22.687  18.142  60.080 1.00  0.00
ATOM     60  CB  LEU   61       20.652  18.958  57.409 1.00  0.00
ATOM     61  CG  LEU   61       20.421  19.226  55.921 1.00  0.00
ATOM     62  CD1 LEU   61       19.235  20.156  55.720 1.00  0.00
ATOM     63  CD2 LEU   61       21.646  19.877  55.296 1.00  0.00
TER
END
