
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0335AL381_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   15 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_5-D1.T0335_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:    12        26 - 37          4.70     6.34
  LCS_AVERAGE:     32.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        26 - 32          1.80     9.94
  LCS_AVERAGE:     14.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        27 - 32          0.97     9.06
  LCS_AVERAGE:     11.67

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:   36
LCS_GDT     E      26     E      26      3    7   12     3    3    3    4    6    6    7    7    7    8    9   10   12   12   13   15   15   15   15   15 
LCS_GDT     K      27     K      27      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     A      28     A      28      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     E      29     E      29      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     Q      30     Q      30      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     Q      31     Q      31      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     K      32     K      32      6    7   12     1    3    5    6    6    6    7    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     L      33     L      33      3    3   12     0    3    3    3    4    5    5    7    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     R      34     R      34      3    3   12     3    3    3    3    3    4    4    6    8    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     Q      35     Q      35      3    4   12     3    3    3    3    3    4    5    6    7    9   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     E      36     E      36      3    4   12     3    3    3    3    3    4    5    6    6    7   10   11   12   12   13   15   15   15   15   15 
LCS_GDT     Y      37     Y      37      3    4   12     3    3    3    3    3    4    5    6    6    7    9   11   12   12   13   15   15   15   15   15 
LCS_GDT     L      38     L      38      3    4   10     3    3    3    3    3    4    5    6    6    7    7    8    9   11   13   15   15   15   15   15 
LCS_GDT     K      39     K      39      3    3   10     3    3    3    3    3    4    4    6    6    7    7    8    9   10   13   15   15   15   15   15 
LCS_GDT     G      40     G      40      3    3   10     3    3    3    3    3    4    5    6    6    7    7    8    9   10   13   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  19.38  (  11.67   14.26   32.22 )

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      5      6      6      6      7      7      8      9     10     11     12     12     13     15     15     15     15     15 
GDT PERCENT_CA  11.11  13.89  13.89  16.67  16.67  16.67  19.44  19.44  22.22  25.00  27.78  30.56  33.33  33.33  36.11  41.67  41.67  41.67  41.67  41.67
GDT RMS_LOCAL    0.13   0.34   0.34   0.97   0.97   0.97   1.80   1.80   3.14   3.72   4.16   4.47   4.70   4.70   5.19   5.93   5.93   5.93   5.93   5.93
GDT RMS_ALL_CA   8.93   9.16   9.16   9.06   9.06   9.06   9.94   9.94   7.42   6.79   6.55   6.46   6.34   6.34   6.11   5.93   5.93   5.93   5.93   5.93

#      Molecule1      Molecule2       DISTANCE
LGA    E      26      E      26          3.233
LGA    K      27      K      27          1.401
LGA    A      28      A      28          1.317
LGA    E      29      E      29          1.035
LGA    Q      30      Q      30          0.700
LGA    Q      31      Q      31          0.757
LGA    K      32      K      32          2.538
LGA    L      33      L      33          8.797
LGA    R      34      R      34         10.544
LGA    Q      35      Q      35         10.125
LGA    E      36      E      36         11.329
LGA    Y      37      Y      37         15.595
LGA    L      38      L      38         15.048
LGA    K      39      K      39         15.752
LGA    G      40      G      40         17.989

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   36    4.0      7    1.80    22.917    19.976     0.368

LGA_LOCAL      RMSD =  1.802  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.945  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  5.933  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.865625 * X  +   0.241478 * Y  +   0.438613 * Z  + -10.796788
  Y_new =  -0.499588 * X  +   0.474715 * Y  +   0.724609 * Z  +  11.228382
  Z_new =  -0.033240 * X  +  -0.846365 * Y  +   0.531565 * Z  + -54.837624 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.010002    2.131590  [ DEG:   -57.8689    122.1311 ]
  Theta =   0.033246    3.108347  [ DEG:     1.9048    178.0952 ]
  Phi   =  -0.523442    2.618151  [ DEG:   -29.9910    150.0090 ]
 
# 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: T0335AL381_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_5-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   36   4.0    7   1.80  19.976     5.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_5-D1
REMARK Aligment from pdb entry: 1qw7A
ATOM      1  N   GLU    26      -1.166   5.266   8.992  1.00  0.00              
ATOM      2  CA  GLU    26      -0.836   3.877   9.241  1.00  0.00              
ATOM      3  C   GLU    26      -0.471   3.056   8.036  1.00  0.00              
ATOM      4  O   GLU    26      -0.595   1.843   8.080  1.00  0.00              
ATOM      5  N   LYS    27       0.018   3.684   6.970  1.00  0.00              
ATOM      6  CA  LYS    27       0.373   2.927   5.776  1.00  0.00              
ATOM      7  C   LYS    27       1.830   2.976   5.397  1.00  0.00              
ATOM      8  O   LYS    27       2.158   2.951   4.228  1.00  0.00              
ATOM      9  N   ALA    28       2.720   3.037   6.379  1.00  0.00              
ATOM     10  CA  ALA    28       4.143   3.108   6.057  1.00  0.00              
ATOM     11  C   ALA    28       4.577   2.003   5.113  1.00  0.00              
ATOM     12  O   ALA    28       5.393   2.233   4.250  1.00  0.00              
ATOM     13  N   GLU    29       4.007   0.808   5.255  1.00  0.00              
ATOM     14  CA  GLU    29       4.380  -0.328   4.405  1.00  0.00              
ATOM     15  C   GLU    29       3.962  -0.219   2.945  1.00  0.00              
ATOM     16  O   GLU    29       4.456  -0.977   2.107  1.00  0.00              
ATOM     17  N   GLN    30       3.085   0.741   2.647  1.00  0.00              
ATOM     18  CA  GLN    30       2.522   0.922   1.305  1.00  0.00              
ATOM     19  C   GLN    30       3.182   2.022   0.505  1.00  0.00              
ATOM     20  O   GLN    30       2.808   2.251  -0.634  1.00  0.00              
ATOM     21  N   GLN    31       4.120   2.716   1.116  1.00  0.00              
ATOM     22  CA  GLN    31       4.774   3.849   0.456  1.00  0.00              
ATOM     23  C   GLN    31       6.068   3.510  -0.261  1.00  0.00              
ATOM     24  O   GLN    31       6.885   2.757   0.260  1.00  0.00              
ATOM     25  N   LYS    32       6.243   4.075  -1.460  1.00  0.00              
ATOM     26  CA  LYS    32       7.477   3.913  -2.231  1.00  0.00              
ATOM     27  C   LYS    32       7.832   5.358  -2.625  1.00  0.00              
ATOM     28  O   LYS    32       6.978   6.136  -3.044  1.00  0.00              
ATOM     29  N   LEU    33       9.093   5.719  -2.469  1.00  0.00              
ATOM     30  CA  LEU    33       9.497   7.085  -2.731  1.00  0.00              
ATOM     31  C   LEU    33      10.527   7.169  -3.833  1.00  0.00              
ATOM     32  O   LEU    33      11.383   6.284  -3.959  1.00  0.00              
ATOM     33  N   ARG    34      10.467   8.235  -4.629  1.00  0.00              
ATOM     34  CA  ARG    34      11.455   8.409  -5.689  1.00  0.00              
ATOM     35  C   ARG    34      11.540   9.868  -6.158  1.00  0.00              
ATOM     36  O   ARG    34      10.851  10.723  -5.603  1.00  0.00              
ATOM     37  N   GLN    35      12.396  10.142  -7.145  1.00  0.00              
ATOM     38  CA  GLN    35      12.639  11.506  -7.650  1.00  0.00              
ATOM     39  C   GLN    35      12.085  11.672  -9.050  1.00  0.00              
ATOM     40  O   GLN    35      11.865  12.789  -9.496  1.00  0.00              
ATOM     41  N   GLU    36      11.880  10.567  -9.766  1.00  0.00              
ATOM     42  CA  GLU    36      11.423  10.666 -11.154  1.00  0.00              
ATOM     43  C   GLU    36      12.386  11.621 -11.876  1.00  0.00              
ATOM     44  O   GLU    36      11.973  12.559 -12.556  1.00  0.00              
ATOM     45  N   TYR    37      13.680  11.373 -11.691  1.00  0.00              
ATOM     46  CA  TYR    37      14.728  12.161 -12.314  1.00  0.00              
ATOM     47  C   TYR    37      15.234  11.507 -13.614  1.00  0.00              
ATOM     48  O   TYR    37      14.786  10.439 -14.008  1.00  0.00              
ATOM     49  N   LEU    38      16.172  12.172 -14.274  1.00  0.00              
ATOM     50  CA  LEU    38      16.774  11.680 -15.509  1.00  0.00              
ATOM     51  C   LEU    38      18.032  12.506 -15.778  1.00  0.00              
ATOM     52  O   LEU    38      18.303  13.479 -15.063  1.00  0.00              
ATOM     53  N   LYS    39      18.795  12.115 -16.789  1.00  0.00              
ATOM     54  CA  LYS    39      20.045  12.787 -17.086  1.00  0.00              
ATOM     55  C   LYS    39      20.020  13.302 -18.504  1.00  0.00              
ATOM     56  O   LYS    39      20.884  14.070 -18.912  1.00  0.00              
ATOM     57  N   GLY    40      18.983  12.885 -19.229  1.00  0.00              
ATOM     58  CA  GLY    40      18.748  13.322 -20.602  1.00  0.00              
ATOM     59  C   GLY    40      17.227  13.366 -20.744  1.00  0.00              
ATOM     60  O   GLY    40      16.557  12.482 -20.212  1.00  0.00              
END
