
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0350AL381_2
# Molecule2: number of CA atoms  109 ( 1798),  selected   19 , name T0350.pdb
# PARAMETERS: T0350AL381_2.T0350.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:    19        56 - 74          2.52     2.52
  LCS_AVERAGE:     17.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        58 - 74          1.65     2.96
  LCS_AVERAGE:     14.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        60 - 73          0.94     3.94
  LCS_AVERAGE:     11.06

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:  109
LCS_GDT     V      56     V      56      5    8   19     3    5    8    8   10   11   15   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H      57     H      57      5   10   19     4    5    8    8   10   11   15   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      58     L      58      5   17   19     4    5    8   10   15   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K      59     K      59      5   17   19     4    5   13   14   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     F      60     F      60     14   17   19     7   10   13   15   16   17   17   17   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      61     E      61     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      62     L      62     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H      63     H      63     14   17   19     4   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      64     D      64     14   17   19     6   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K      65     K      65     14   17   19     5   10   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      66     L      66     14   17   19     4    9   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     N      67     N      67     14   17   19     6   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      68     E      68     14   17   19     6   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Y      69     Y      69     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Y      70     Y      70     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      71     V      71     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K      72     K      72     14   17   19     7   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      73     V      73     14   17   19     6   11   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I      74     I      74     13   17   19     3   10   13   15   16   17   17   18   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  14.44  (  11.06   14.82   17.43 )

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      7     11     13     15     16     17     17     18     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   6.42  10.09  11.93  13.76  14.68  15.60  15.60  16.51  17.43  17.43  17.43  17.43  17.43  17.43  17.43  17.43  17.43  17.43  17.43  17.43
GDT RMS_LOCAL    0.24   0.57   0.78   1.07   1.25   1.65   1.65   2.39   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52
GDT RMS_ALL_CA   4.57   3.65   3.60   3.63   3.35   2.96   2.96   2.54   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52   2.52

#      Molecule1      Molecule2       DISTANCE
LGA    V      56      V      56          3.843
LGA    H      57      H      57          3.865
LGA    L      58      L      58          1.556
LGA    K      59      K      59          0.713
LGA    F      60      F      60          4.222
LGA    E      61      E      61          2.587
LGA    L      62      L      62          1.091
LGA    H      63      H      63          0.594
LGA    D      64      D      64          1.021
LGA    K      65      K      65          2.118
LGA    L      66      L      66          3.299
LGA    N      67      N      67          2.267
LGA    E      68      E      68          1.870
LGA    Y      69      Y      69          1.918
LGA    Y      70      Y      70          2.116
LGA    V      71      V      71          2.673
LGA    K      72      K      72          3.488
LGA    V      73      V      73          3.460
LGA    I      74      I      74          3.248

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  109    4.0     18    2.39    14.450    15.085     0.723

LGA_LOCAL      RMSD =  2.391  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.653  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  2.516  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.606358 * X  +  -0.755654 * Y  +  -0.247624 * Z  +  55.010429
  Y_new =  -0.687643 * X  +   0.654663 * Y  +  -0.313948 * Z  +  26.040224
  Z_new =   0.399347 * X  +  -0.020088 * Y  +  -0.916580 * Z  + -37.779385 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.119680    0.021913  [ DEG:  -178.7445      1.2555 ]
  Theta =  -0.410804   -2.730789  [ DEG:   -23.5373   -156.4627 ]
  Phi   =  -2.293460    0.848133  [ DEG:  -131.4056     48.5944 ]
 
# 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: T0350AL381_2                                  
REMARK     2: T0350.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_2.T0350.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  109   4.0   18   2.39  15.085     2.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_2
REMARK Aligment from pdb entry: 1nnxA
ATOM      1  N   VAL    56       8.416   2.168 -11.659  1.00  0.00              
ATOM      2  CA  VAL    56       9.757   2.666 -12.015  1.00  0.00              
ATOM      3  C   VAL    56       9.699   3.903 -12.866  1.00  0.00              
ATOM      4  O   VAL    56       8.655   4.192 -13.554  1.00  0.00              
ATOM      5  N   HIS    57      10.736   4.700 -12.757  1.00  0.00              
ATOM      6  CA  HIS    57      10.847   5.848 -13.597  1.00  0.00              
ATOM      7  C   HIS    57      11.984   5.549 -14.624  1.00  0.00              
ATOM      8  O   HIS    57      13.102   5.149 -14.229  1.00  0.00              
ATOM      9  N   LEU    58      11.747   5.746 -15.907  1.00  0.00              
ATOM     10  CA  LEU    58      12.771   5.569 -16.923  1.00  0.00              
ATOM     11  C   LEU    58      12.996   6.865 -17.654  1.00  0.00              
ATOM     12  O   LEU    58      12.069   7.675 -17.803  1.00  0.00              
ATOM     13  N   LYS    59      14.232   7.115 -18.047  1.00  0.00              
ATOM     14  CA  LYS    59      14.609   8.279 -18.825  1.00  0.00              
ATOM     15  C   LYS    59      15.418   7.775 -20.003  1.00  0.00              
ATOM     16  O   LYS    59      16.272   6.882 -19.834  1.00  0.00              
ATOM     17  N   PHE    60      15.186   8.333 -21.176  1.00  0.00              
ATOM     18  CA  PHE    60      15.927   7.930 -22.364  1.00  0.00              
ATOM     19  C   PHE    60      15.370   8.614 -23.572  1.00  0.00              
ATOM     20  O   PHE    60      14.609   9.583 -23.439  1.00  0.00              
ATOM     21  N   GLU    61      15.725   8.107 -24.729  1.00  0.00              
ATOM     22  CA  GLU    61      15.287   8.724 -25.998  1.00  0.00              
ATOM     23  C   GLU    61      14.285   7.935 -26.744  1.00  0.00              
ATOM     24  O   GLU    61      14.378   6.713 -26.827  1.00  0.00              
ATOM     25  N   LEU    62      13.308   8.650 -27.298  1.00  0.00              
ATOM     26  CA  LEU    62      12.332   8.003 -28.183  1.00  0.00              
ATOM     27  C   LEU    62      13.144   7.635 -29.445  1.00  0.00              
ATOM     28  O   LEU    62      13.858   8.474 -29.990  1.00  0.00              
ATOM     29  N   HIS    63      13.101   6.366 -29.855  1.00  0.00              
ATOM     30  CA  HIS    63      13.806   5.855 -31.053  1.00  0.00              
ATOM     31  C   HIS    63      12.671   5.413 -31.953  1.00  0.00              
ATOM     32  O   HIS    63      12.057   4.366 -31.740  1.00  0.00              
ATOM     33  N   ASP    64      12.432   6.182 -33.003  1.00  0.00              
ATOM     34  CA  ASP    64      11.307   5.908 -33.877  1.00  0.00              
ATOM     35  C   ASP    64      11.794   5.746 -35.259  1.00  0.00              
ATOM     36  O   ASP    64      12.518   6.584 -35.775  1.00  0.00              
ATOM     37  N   LYS    65      11.372   4.636 -35.852  1.00  0.00              
ATOM     38  CA  LYS    65      11.712   4.284 -37.236  1.00  0.00              
ATOM     39  C   LYS    65      10.428   4.033 -37.988  1.00  0.00              
ATOM     40  O   LYS    65       9.387   4.074 -37.431  1.00  0.00              
ATOM     41  N   LEU    66      10.533   3.688 -39.275  1.00  0.00              
ATOM     42  CA  LEU    66       9.332   3.425 -40.057  1.00  0.00              
ATOM     43  C   LEU    66       8.483   2.293 -39.499  1.00  0.00              
ATOM     44  O   LEU    66       7.259   2.321 -39.596  1.00  0.00              
ATOM     45  N   ASN    67       9.116   1.345 -38.811  1.00  0.00              
ATOM     46  CA  ASN    67       8.390   0.224 -38.325  1.00  0.00              
ATOM     47  C   ASN    67       8.332   0.080 -36.830  1.00  0.00              
ATOM     48  O   ASN    67       7.819  -0.913 -36.357  1.00  0.00              
ATOM     49  N   GLU    68       8.824   1.053 -36.102  1.00  0.00              
ATOM     50  CA  GLU    68       8.784   0.773 -34.668  1.00  0.00              
ATOM     51  C   GLU    68       9.007   2.026 -33.848  1.00  0.00              
ATOM     52  O   GLU    68       9.515   3.029 -34.335  1.00  0.00              
ATOM     53  N   TYR    69       8.594   1.963 -32.577  1.00  0.00              
ATOM     54  CA  TYR    69       8.928   3.069 -31.688  1.00  0.00              
ATOM     55  C   TYR    69       9.364   2.341 -30.424  1.00  0.00              
ATOM     56  O   TYR    69       8.845   1.231 -30.071  1.00  0.00              
ATOM     57  N   TYR    70      10.415   2.832 -29.785  1.00  0.00              
ATOM     58  CA  TYR    70      10.876   2.185 -28.562  1.00  0.00              
ATOM     59  C   TYR    70      11.552   3.331 -27.785  1.00  0.00              
ATOM     60  O   TYR    70      11.786   4.433 -28.278  1.00  0.00              
ATOM     61  N   VAL    71      11.797   3.087 -26.531  1.00  0.00              
ATOM     62  CA  VAL    71      12.576   4.028 -25.732  1.00  0.00              
ATOM     63  C   VAL    71      13.960   3.415 -25.479  1.00  0.00              
ATOM     64  O   VAL    71      14.034   2.255 -25.021  1.00  0.00              
ATOM     65  N   LYS    72      15.033   4.148 -25.771  1.00  0.00              
ATOM     66  CA  LYS    72      16.409   3.619 -25.462  1.00  0.00              
ATOM     67  C   LYS    72      16.664   4.158 -24.082  1.00  0.00              
ATOM     68  O   LYS    72      16.877   5.355 -23.930  1.00  0.00              
ATOM     69  N   VAL    73      16.664   3.279 -23.091  1.00  0.00              
ATOM     70  CA  VAL    73      16.746   3.730 -21.710  1.00  0.00              
ATOM     71  C   VAL    73      18.136   4.057 -21.200  1.00  0.00              
ATOM     72  O   VAL    73      19.055   3.193 -21.260  1.00  0.00              
ATOM     73  N   ILE    74      18.302   5.268 -20.670  1.00  0.00              
ATOM     74  CA  ILE    74      19.613   5.635 -20.066  1.00  0.00              
ATOM     75  C   ILE    74      19.631   5.403 -18.571  1.00  0.00              
ATOM     76  O   ILE    74      20.689   5.212 -17.979  1.00  0.00              
END
