
#######################################################
#                                                     #
#                        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   85 (   85),  selected   42 , name T0335TS393_4
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS393_4.T0335.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:    42         1 - 42          3.73     3.73
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38         4 - 41          2.00     3.97
  LCS_AVERAGE:     84.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        21 - 41          0.78     4.24
  LCS_AVERAGE:     41.21

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:   42
LCS_GDT     M       1     M       1      3    4   42     3    3    3    5    5    5    8   10   17   18   19   20   20   20   20   21   22   23   25   26 
LCS_GDT     I       2     I       2      4    4   42     3    3    4    4    5    9   16   17   19   19   19   20   28   34   36   39   41   41   41   41 
LCS_GDT     S       3     S       3      4   19   42     3    3    4    4   15   18   32   38   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N       4     N       4     16   38   42     4   12   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       5     A       5     16   38   42     6   12   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K       6     K       6     16   38   42     7   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I       7     I       7     16   38   42     7   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       8     A       8     16   38   42     7   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R       9     R       9     16   38   42     7   13   20   26   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      10     I      10     16   38   42     7   13   16   26   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N      11     N      11     16   38   42     7   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      12     E      12     16   38   42     7   13   20   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      13     L      13     16   38   42     7   13   16   17   30   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      14     A      14     16   38   42     7   13   16   16   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      15     A      15     16   38   42     7   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      16     K      16     16   38   42     6   13   16   16   30   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      17     A      17     16   38   42     5   13   16   16   17   21   37   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      18     K      18     16   38   42     5   13   16   24   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      19     A      19     16   38   42     5   12   16   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      20     G      20     16   38   42     3    3    3   17   27   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     V      21     V      21     21   38   42     6   13   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      22     I      22     21   38   42     4   17   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     T      23     T      23     21   38   42     7   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      24     E      24     21   38   42     6   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      25     E      25     21   38   42     8   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      26     E      26     21   38   42     8   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      27     K      27     21   38   42     8   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      28     A      28     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      29     E      29     21   38   42     8   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      30     Q      30     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      31     Q      31     21   38   42     8   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      32     K      32     21   38   42     4   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      33     L      33     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      34     R      34     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      35     Q      35     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      36     E      36     21   38   42     9   18   22   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Y      37     Y      37     21   38   42     9   18   21   27   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      38     L      38     21   38   42     9   18   21   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      39     K      39     21   38   42     9   18   21   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      40     G      40     21   38   42     8   15   21   24   32   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     F      41     F      41     21   38   42     7   18   21   28   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      42     R      42      3   28   42     3    3    3   24   30   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  75.40  (  41.21   84.98  100.00 )

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      9     18     22     28     33     37     38     39     39     39     40     40     40     40     40     40     41     41     41     41 
GDT PERCENT_CA  21.43  42.86  52.38  66.67  78.57  88.10  90.48  92.86  92.86  92.86  95.24  95.24  95.24  95.24  95.24  95.24  97.62  97.62  97.62  97.62
GDT RMS_LOCAL    0.31   0.64   1.07   1.36   1.61   1.89   1.95   2.05   2.05   2.05   2.26   2.26   2.26   2.26   2.26   2.26   2.90   2.90   2.90   2.90
GDT RMS_ALL_CA   4.01   4.27   4.33   4.05   4.05   4.01   4.02   4.02   4.02   4.02   3.92   3.92   3.92   3.92   3.92   3.92   3.80   3.80   3.80   3.80

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         17.696
LGA    I       2      I       2         13.001
LGA    S       3      S       3          6.636
LGA    N       4      N       4          1.470
LGA    A       5      A       5          1.340
LGA    K       6      K       6          1.510
LGA    I       7      I       7          1.166
LGA    A       8      A       8          0.781
LGA    R       9      R       9          1.747
LGA    I      10      I      10          1.895
LGA    N      11      N      11          1.078
LGA    E      12      E      12          1.453
LGA    L      13      L      13          3.010
LGA    A      14      A      14          2.395
LGA    A      15      A      15          0.847
LGA    K      16      K      16          2.681
LGA    A      17      A      17          3.959
LGA    K      18      K      18          2.107
LGA    A      19      A      19          1.779
LGA    G      20      G      20          3.272
LGA    V      21      V      21          2.065
LGA    I      22      I      22          2.285
LGA    T      23      T      23          1.512
LGA    E      24      E      24          1.605
LGA    E      25      E      25          1.157
LGA    E      26      E      26          1.649
LGA    K      27      K      27          1.624
LGA    A      28      A      28          1.015
LGA    E      29      E      29          0.918
LGA    Q      30      Q      30          1.734
LGA    Q      31      Q      31          2.161
LGA    K      32      K      32          1.960
LGA    L      33      L      33          1.407
LGA    R      34      R      34          1.917
LGA    Q      35      Q      35          1.706
LGA    E      36      E      36          1.823
LGA    Y      37      Y      37          2.618
LGA    L      38      L      38          2.586
LGA    K      39      K      39          2.658
LGA    G      40      G      40          3.377
LGA    F      41      F      41          2.550
LGA    R      42      R      42          3.566

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     39    2.05    74.405    81.249     1.817

LGA_LOCAL      RMSD =  2.046  Number of atoms =   39  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.078  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  3.727  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.141192 * X  +   0.599617 * Y  +   0.787734 * Z  +   4.217349
  Y_new =   0.465357 * X  +  -0.742513 * Y  +   0.481786 * Z  +   1.746468
  Z_new =   0.873789 * X  +   0.298553 * Y  +  -0.383872 * Z  +  -6.652188 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.480573   -0.661020  [ DEG:   142.1264    -37.8736 ]
  Theta =  -1.062941   -2.078652  [ DEG:   -60.9020   -119.0980 ]
  Phi   =   1.276219   -1.865374  [ DEG:    73.1219   -106.8781 ]
 
# 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: T0335TS393_4                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_4.T0335.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   85   42   4.0   39   2.05  81.249     3.73
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_4
PFRMAT TS
TARGET T0335
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      -3.566 -18.464  -7.349  1.00 25.00           C
ATOM      2  CA  ILE     2      -5.288 -15.575  -9.049  1.00 25.00           C
ATOM      3  CA  SER     3      -2.516 -13.506 -10.590  1.00 25.00           C
ATOM      4  CA  ASN     4      -1.188 -10.050  -9.852  1.00 25.00           C
ATOM      5  CA  ALA     5       0.132 -10.501  -6.285  1.00 25.00           C
ATOM      6  CA  LYS     6       1.488  -6.920  -6.307  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.900  -5.618  -7.530  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.677  -7.558  -4.746  1.00 25.00           C
ATOM      9  CA  ARG     9      -1.269  -6.092  -2.154  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.925  -2.568  -3.501  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.702  -3.163  -3.288  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.331  -4.387   0.322  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.280  -1.271   1.192  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.961   0.964  -0.384  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.678  -0.834   1.631  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.650  -0.351   4.843  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.236   3.373   4.051  1.00 25.00           C
ATOM     18  CA  LYS    18     -10.003   3.691   3.450  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.708   1.951   6.788  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.699   4.540   9.622  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.406   2.209  11.671  1.00 25.00           C
ATOM     22  CA  ILE    22      -5.006   2.047   9.886  1.00 25.00           C
ATOM     23  CA  THR    23      -2.108   3.547  11.898  1.00 25.00           C
ATOM     24  CA  GLU    24       0.894   5.818  11.529  1.00 25.00           C
ATOM     25  CA  GLU    25       3.856   3.489  10.844  1.00 25.00           C
ATOM     26  CA  GLU    26       1.507   0.944   9.208  1.00 25.00           C
ATOM     27  CA  LYS    27      -0.005   3.705   7.027  1.00 25.00           C
ATOM     28  CA  ALA    28       3.503   4.838   5.987  1.00 25.00           C
ATOM     29  CA  GLU    29       4.431   1.231   5.095  1.00 25.00           C
ATOM     30  CA  GLN    30       1.235   0.898   3.012  1.00 25.00           C
ATOM     31  CA  GLN    31       2.051   4.168   1.193  1.00 25.00           C
ATOM     32  CA  LYS    32       5.598   2.912   0.475  1.00 25.00           C
ATOM     33  CA  LEU    33       4.184  -0.375  -0.891  1.00 25.00           C
ATOM     34  CA  ARG    34       1.763   1.570  -3.132  1.00 25.00           C
ATOM     35  CA  GLN    35       4.651   3.729  -4.422  1.00 25.00           C
ATOM     36  CA  GLU    36       6.704   0.582  -5.166  1.00 25.00           C
ATOM     37  CA  TYR    37       3.736  -0.938  -7.052  1.00 25.00           C
ATOM     38  CA  LEU    38       3.348   2.284  -9.086  1.00 25.00           C
ATOM     39  CA  LYS    39       7.085   2.232  -9.927  1.00 25.00           C
ATOM     40  CA  GLY    40       6.809  -1.424 -11.035  1.00 25.00           C
ATOM     41  CA  PHE    41       3.803  -0.554 -13.243  1.00 25.00           C
ATOM     42  CA  ARG    42       5.757   2.347 -14.803  1.00 25.00           C
ATOM     43  CA  SER    43       8.718   0.016 -15.486  1.00 25.00           C
ATOM     44  CA  SER    44       6.369  -2.528 -17.122  1.00 25.00           C
ATOM     45  CA  MET    45       4.858   0.233 -19.304  1.00 25.00           C
ATOM     46  CA  LYS    46       8.365   1.366 -20.344  1.00 25.00           C
ATOM     47  CA  ASN    47       9.293  -2.241 -21.235  1.00 25.00           C
ATOM     48  CA  THR    48       6.098  -2.574 -23.320  1.00 25.00           C
ATOM     49  CA  LEU    49       6.915   0.697 -25.138  1.00 25.00           C
ATOM     50  CA  LYS    50       3.961   2.877 -24.120  1.00 25.00           C
ATOM     51  CA  SER    51       0.719   2.507 -22.116  1.00 25.00           C
ATOM     52  CA  VAL    52      -0.206   2.269 -18.439  1.00 25.00           C
ATOM     53  CA  LYS    53       0.169   2.956 -14.679  1.00 25.00           C
ATOM     54  CA  ILE    54      -2.153   5.985 -14.575  1.00 25.00           C
ATOM     55  CA  ILE    55      -4.020   8.820 -12.864  1.00 25.00           C
ATOM     56  CA  ASP    56      -3.701  10.901 -15.976  1.00 25.00           C
ATOM     57  CA  PRO    57      -5.052  13.850 -14.062  1.00 25.00           C
ATOM     58  CA  GLU    58      -5.228  16.777 -16.488  1.00 25.00           C
ATOM     59  CA  GLY    59      -2.133  18.952 -16.912  1.00 25.00           C
ATOM     60  CA  ASN    60       0.251  17.570 -14.361  1.00 25.00           C
ATOM     61  CA  ASP    61       0.127  14.280 -12.372  1.00 25.00           C
ATOM     62  CA  VAL    62       1.496  10.861 -13.423  1.00 25.00           C
ATOM     63  CA  THR    63       3.142   9.869 -16.757  1.00 25.00           C
ATOM     64  CA  PRO    64       6.763  10.852 -17.168  1.00 25.00           C
ATOM     65  CA  GLU    65       9.678  13.245 -16.505  1.00 25.00           C
ATOM     66  CA  LYS    66       9.560  12.393 -12.773  1.00 25.00           C
ATOM     67  CA  LEU    67       9.589   8.654 -13.601  1.00 25.00           C
ATOM     68  CA  LYS    68      12.599   9.164 -15.913  1.00 25.00           C
ATOM     69  CA  ARG    69      14.427  11.085 -13.150  1.00 25.00           C
ATOM     70  CA  GLU    70      13.684   8.266 -10.665  1.00 25.00           C
ATOM     71  CA  GLN    71      15.016   5.683 -13.159  1.00 25.00           C
ATOM     72  CA  ARG    72      18.198   7.758 -13.645  1.00 25.00           C
ATOM     73  CA  ASN    73      18.663   7.979  -9.851  1.00 25.00           C
ATOM     74  CA  ASN    74      18.222   4.187  -9.550  1.00 25.00           C
ATOM     75  CA  LYS    75      21.150   2.350 -11.267  1.00 25.00           C
ATOM     76  CA  LEU    76      23.285   3.004  -8.149  1.00 25.00           C
ATOM     77  CA  HIS    77      23.677   0.738  -5.190  1.00 25.00           C
ATOM     78  CA  LEU    78      21.944  -2.104  -7.118  1.00 25.00           C
ATOM     79  CA  GLU    79      19.846  -5.157  -6.261  1.00 25.00           C
ATOM     80  CA  HIS    80      19.599  -5.371  -2.470  1.00 25.00           C
ATOM     81  CA  HIS    81      16.255  -6.797  -1.564  1.00 25.00           C
ATOM     82  CA  HIS    82      15.051  -7.890   1.855  1.00 25.00           C
ATOM     83  CA  HIS    83      16.619  -5.402   4.311  1.00 25.00           C
ATOM     84  CA  HIS    84      14.308  -3.112   6.316  1.00 25.00           C
ATOM     85  CA  HIS    85      15.162  -2.989  10.012  1.00 25.00           C
TER
END
