
#######################################################
#                                                     #
#                        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   24 (   96),  selected   19 , name T0326AL044_1
# Molecule2: number of CA atoms  289 ( 2373),  selected   19 , name T0326.pdb
# PARAMETERS: T0326AL044_1.T0326.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        21 - 36          4.82    14.50
  LCS_AVERAGE:      2.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4         3 - 7           1.83    32.39
  LONGEST_CONTINUOUS_SEGMENT:     4         5 - 8           1.03    34.54
  LONGEST_CONTINUOUS_SEGMENT:     4         6 - 9           1.99    29.85
  LONGEST_CONTINUOUS_SEGMENT:     4        18 - 21          0.28    20.22
  LONGEST_CONTINUOUS_SEGMENT:     4        33 - 36          0.76    33.29
  LCS_AVERAGE:      1.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        18 - 21          0.28    20.22
  LONGEST_CONTINUOUS_SEGMENT:     4        33 - 36          0.76    33.29
  LCS_AVERAGE:      0.91

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:  289
LCS_GDT     I       3     I       3      0    4    6     0    0    0    0    3    5    5    6    6    6    6    6    6    6    7    8    8    9   10   10 
LCS_GDT     V       5     V       5      3    4    6     3    3    4    4    4    5    5    6    6    6    6    6    7    7    9    9   10   10   10   10 
LCS_GDT     P       6     P       6      3    4    7     3    3    4    4    4    5    5    6    6    6    6    6    7    8    9    9   10   10   10   10 
LCS_GDT     S       7     S       7      3    4    7     3    3    4    4    4    5    5    6    6    6    6    6    7    8    9    9   10   10   10   10 
LCS_GDT     G       8     G       8      3    4    7     3    3    4    4    4    5    5    6    6    6    7    7    7    8    9    9   10   10   11   12 
LCS_GDT     L       9     L       9      3    4    7     3    3    3    3    4    4    5    6    6    6    7    7    7    8    9    9   10   10   11   12 
LCS_GDT     E      18     E      18      4    4    7     4    4    5    5    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     G      19     G      19      4    4    7     4    4    5    5    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     I      20     I      20      4    4    7     4    4    5    5    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     F      21     F      21      4    4    8     4    4    5    5    5    5    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     V      22     V      22      3    3    8     3    3    4    4    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     T      24     T      24      0    0    8     1    1    1    2    3    3    5    5    5    6    7    8    9    9   10   11   11   11   12   12 
LCS_GDT     K      26     K      26      0    0    8     0    1    1    2    3    3    3    4    4    6    7    7    8    8    8    9   10   10   11   12 
LCS_GDT     I      33     I      33      4    4    8     3    4    4    4    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     R      34     R      34      4    4    8     3    4    5    5    5    6    7    7    7    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     P      35     P      35      4    4    8     3    4    4    4    4    4    4    5    6    8    8    9    9   10   10   11   11   11   12   12 
LCS_GDT     L      36     L      36      4    4    8     3    4    4    4    4    4    4    5    6    6    7    9    9   10   10   11   11   11   12   12 
LCS_GDT     L      39     L      39      0    0    7     0    0    0    1    2    3    4    5    6    6    6    8    9   10   10   11   11   11   12   12 
LCS_GDT     I      40     I      40      0    0    7     0    0    0    0    2    3    4    5    6    6    6    7    7    7   10   11   11   11   12   12 
LCS_AVERAGE  LCS_A:   1.51  (   0.91    1.07    2.53 )

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      4      5      5      5      6      7      7      7      8      8      9      9     10     10     11     11     11     12     12 
GDT PERCENT_CA   1.38   1.38   1.73   1.73   1.73   2.08   2.42   2.42   2.42   2.77   2.77   3.11   3.11   3.46   3.46   3.81   3.81   3.81   4.15   4.15
GDT RMS_LOCAL    0.28   0.28   0.99   0.99   0.99   1.97   2.38   2.38   2.38   3.19   3.19   3.92   3.92   4.85   4.69   5.44   5.44   5.44   5.96   5.96
GDT RMS_ALL_CA  20.22  20.22  19.15  19.15  19.15  16.19  16.77  16.77  16.77  16.27  16.27  15.88  15.88  16.32  15.05  16.96  16.96  16.96  16.25  16.25

#      Molecule1      Molecule2       DISTANCE
LGA    I       3      I       3         29.519
LGA    V       5      V       5         29.881
LGA    P       6      P       6         28.578
LGA    S       7      S       7         24.296
LGA    G       8      G       8         22.083
LGA    L       9      L       9         16.986
LGA    E      18      E      18          1.048
LGA    G      19      G      19          2.406
LGA    I      20      I      20          1.319
LGA    F      21      F      21          3.487
LGA    V      22      V      22          2.877
LGA    T      24      T      24         11.710
LGA    K      26      K      26         14.309
LGA    I      33      I      33          2.725
LGA    R      34      R      34          1.745
LGA    P      35      P      35          7.397
LGA    L      36      L      36         11.523
LGA    L      39      L      39         19.062
LGA    I      40      I      40         21.599

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  289    4.0      7    2.38     2.336     2.023     0.283

LGA_LOCAL      RMSD =  2.376  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.774  Number of atoms =   19 
Std_ALL_ATOMS  RMSD = 12.893  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.342401 * X  +  -0.037782 * Y  +  -0.938794 * Z  +  53.768616
  Y_new =  -0.842210 * X  +   0.430558 * Y  +  -0.324502 * Z  +   9.965164
  Z_new =   0.416466 * X  +   0.901772 * Y  +   0.115603 * Z  + -39.739517 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.443297   -1.698296  [ DEG:    82.6948    -97.3052 ]
  Theta =  -0.429554   -2.712038  [ DEG:   -24.6117   -155.3884 ]
  Phi   =  -1.184656    1.956937  [ DEG:   -67.8758    112.1242 ]
 
# 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: T0326AL044_1                                  
REMARK     2: T0326.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0326AL044_1.T0326.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  289   4.0    7   2.38   2.023    12.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0326AL044_1
REMARK Aligment from pdb entry: 1vcm_A
ATOM      1  N   ILE     3       5.314 -33.841 -10.537  1.00  0.00              
ATOM      2  CA  ILE     3       6.406 -33.881  -9.576  1.00  0.00              
ATOM      3  C   ILE     3       5.820 -34.416  -8.278  1.00  0.00              
ATOM      4  O   ILE     3       4.721 -34.019  -7.894  1.00  0.00              
ATOM      5  N   VAL     5       6.538 -35.326  -7.621  1.00  0.00              
ATOM      6  CA  VAL     5       6.078 -35.908  -6.356  1.00  0.00              
ATOM      7  C   VAL     5       6.020 -34.841  -5.264  1.00  0.00              
ATOM      8  O   VAL     5       6.959 -34.063  -5.089  1.00  0.00              
ATOM      9  N   PRO     6       4.914 -34.821  -4.530  1.00  0.00              
ATOM     10  CA  PRO     6       4.694 -33.852  -3.468  1.00  0.00              
ATOM     11  C   PRO     6       5.860 -33.634  -2.501  1.00  0.00              
ATOM     12  O   PRO     6       6.406 -34.585  -1.926  1.00  0.00              
ATOM     13  N   SER     7       6.229 -32.368  -2.328  1.00  0.00              
ATOM     14  CA  SER     7       7.290 -31.975  -1.413  1.00  0.00              
ATOM     15  C   SER     7       6.670 -30.981  -0.437  1.00  0.00              
ATOM     16  O   SER     7       6.023 -30.021  -0.856  1.00  0.00              
ATOM     17  N   GLY     8       6.839 -31.213   0.861  1.00  0.00              
ATOM     18  CA  GLY     8       6.278 -30.301   1.848  1.00  0.00              
ATOM     19  C   GLY     8       7.185 -29.082   1.945  1.00  0.00              
ATOM     20  O   GLY     8       8.337 -29.182   2.355  1.00  0.00              
ATOM     21  N   LEU     9       6.672 -27.910   1.553  1.00  0.00              
ATOM     22  CA  LEU     9       7.436 -26.661   1.589  1.00  0.00              
ATOM     23  C   LEU     9       7.721 -26.153   2.999  1.00  0.00              
ATOM     24  O   LEU     9       6.932 -26.346   3.919  1.00  0.00              
ATOM     25  N   GLU    18       8.866 -25.503   3.154  1.00  0.00              
ATOM     26  CA  GLU    18       9.245 -24.931   4.435  1.00  0.00              
ATOM     27  C   GLU    18       9.034 -23.445   4.245  1.00  0.00              
ATOM     28  O   GLU    18       9.829 -22.773   3.586  1.00  0.00              
ATOM     29  N   GLY    19       7.947 -22.935   4.803  1.00  0.00              
ATOM     30  CA  GLY    19       7.631 -21.526   4.669  1.00  0.00              
ATOM     31  C   GLY    19       7.838 -20.771   5.987  1.00  0.00              
ATOM     32  O   GLY    19       7.323 -19.662   6.165  1.00  0.00              
ATOM     33  N   ILE    20       8.601 -21.375   6.899  1.00  0.00              
ATOM     34  CA  ILE    20       8.874 -20.789   8.214  1.00  0.00              
ATOM     35  C   ILE    20       9.315 -19.330   8.138  1.00  0.00              
ATOM     36  O   ILE    20       8.880 -18.498   8.941  1.00  0.00              
ATOM     37  N   PHE    21      10.178 -19.013   7.179  1.00  0.00              
ATOM     38  CA  PHE    21      10.633 -17.638   7.046  1.00  0.00              
ATOM     39  C   PHE    21       9.483 -16.667   6.784  1.00  0.00              
ATOM     40  O   PHE    21       9.324 -15.677   7.498  1.00  0.00              
ATOM     41  N   VAL    22       8.695 -16.942   5.744  1.00  0.00              
ATOM     42  CA  VAL    22       7.573 -16.084   5.403  1.00  0.00              
ATOM     43  C   VAL    22       6.608 -15.970   6.574  1.00  0.00              
ATOM     44  O   VAL    22       6.108 -14.884   6.869  1.00  0.00              
ATOM     45  N   THR    24       6.357 -17.087   7.252  1.00  0.00              
ATOM     46  CA  THR    24       5.445 -17.079   8.394  1.00  0.00              
ATOM     47  C   THR    24       5.925 -16.140   9.500  1.00  0.00              
ATOM     48  O   THR    24       5.134 -15.389  10.067  1.00  0.00              
ATOM     49  N   LYS    26       7.220 -16.190   9.804  1.00  0.00              
ATOM     50  CA  LYS    26       7.795 -15.351  10.848  1.00  0.00              
ATOM     51  C   LYS    26       7.811 -13.888  10.426  1.00  0.00              
ATOM     52  O   LYS    26       7.498 -12.999  11.221  1.00  0.00              
ATOM     53  N   ARG    27       8.167 -13.639   9.173  1.00  0.00              
ATOM     54  CA  ARG    27       8.219 -12.276   8.662  1.00  0.00              
ATOM     55  C   ARG    27       6.850 -11.602   8.737  1.00  0.00              
ATOM     56  O   ARG    27       6.751 -10.406   9.031  1.00  0.00              
ATOM     57  N   ALA    28       5.794 -12.361   8.464  1.00  0.00              
ATOM     58  CA  ALA    28       4.448 -11.807   8.504  1.00  0.00              
ATOM     59  C   ALA    28       4.014 -11.629   9.949  1.00  0.00              
ATOM     60  O   ALA    28       3.221 -10.739  10.258  1.00  0.00              
ATOM     61  N   HIS    30       4.535 -12.471  10.835  1.00  0.00              
ATOM     62  CA  HIS    30       4.194 -12.368  12.247  1.00  0.00              
ATOM     63  C   HIS    30       4.796 -11.065  12.775  1.00  0.00              
ATOM     64  O   HIS    30       4.118 -10.268  13.438  1.00  0.00              
ATOM     65  N   GLN    31       2.673  -7.879  14.089  1.00  0.00              
ATOM     66  CA  GLN    31       2.864  -7.585  15.506  1.00  0.00              
ATOM     67  C   GLN    31       4.258  -7.039  15.792  1.00  0.00              
ATOM     68  O   GLN    31       5.100  -7.725  16.371  1.00  0.00              
ATOM     69  N   ASP    32       4.522  -5.793  15.380  1.00  0.00              
ATOM     70  CA  ASP    32       5.836  -5.201  15.621  1.00  0.00              
ATOM     71  C   ASP    32       6.115  -5.080  17.114  1.00  0.00              
ATOM     72  O   ASP    32       5.198  -4.888  17.919  1.00  0.00              
ATOM     73  N   ILE    33       7.385  -5.206  17.472  1.00  0.00              
ATOM     74  CA  ILE    33       7.818  -5.113  18.854  1.00  0.00              
ATOM     75  C   ILE    33       7.879  -3.635  19.233  1.00  0.00              
ATOM     76  O   ILE    33       7.485  -3.243  20.331  1.00  0.00              
ATOM     77  N   ARG    34       8.370  -2.822  18.302  1.00  0.00              
ATOM     78  CA  ARG    34       8.509  -1.383  18.505  1.00  0.00              
ATOM     79  C   ARG    34       8.080  -0.641  17.240  1.00  0.00              
ATOM     80  O   ARG    34       7.549  -1.244  16.312  1.00  0.00              
ATOM     81  N   PRO    35       8.311   0.667  17.201  1.00  0.00              
ATOM     82  CA  PRO    35       7.943   1.470  16.039  1.00  0.00              
ATOM     83  C   PRO    35       8.742   2.770  16.014  1.00  0.00              
ATOM     84  O   PRO    35       8.785   3.498  17.005  1.00  0.00              
ATOM     85  N   LEU    36       9.380   3.049  14.881  1.00  0.00              
ATOM     86  CA  LEU    36      10.171   4.265  14.715  1.00  0.00              
ATOM     87  C   LEU    36       9.905   4.850  13.348  1.00  0.00              
ATOM     88  O   LEU    36       9.748   4.114  12.377  1.00  0.00              
ATOM     89  N   LEU    39       9.855   6.174  13.269  1.00  0.00              
ATOM     90  CA  LEU    39       9.617   6.838  11.998  1.00  0.00              
ATOM     91  C   LEU    39      10.907   7.480  11.524  1.00  0.00              
ATOM     92  O   LEU    39      11.675   8.017  12.325  1.00  0.00              
ATOM     93  N   ILE    40      11.163   7.391  10.225  1.00  0.00              
ATOM     94  CA  ILE    40      12.346   8.012   9.662  1.00  0.00              
ATOM     95  C   ILE    40      11.872   8.824   8.475  1.00  0.00              
ATOM     96  O   ILE    40      10.805   8.560   7.921  1.00  0.00              
END
