
#######################################################
#                                                     #
#                        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 T0335TS599_4
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS599_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          2.80     2.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35         2 - 36          1.90     3.21
  LONGEST_CONTINUOUS_SEGMENT:    35         8 - 42          2.00     3.25
  LCS_AVERAGE:     83.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25        17 - 41          0.93     5.09
  LCS_AVERAGE:     52.32

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   32   42     3    3    3    4    4    4    5    8    9   17   26   28   35   41   42   42   42   42   42   42 
LCS_GDT     I       2     I       2      3   35   42     3   11   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     S       3     S       3      3   35   42     3    3   22   26   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     N       4     N       4     21   35   42     3   14   19   26   29   32   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A       5     A       5     21   35   42     9   16   21   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K       6     K       6     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     I       7     I       7     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A       8     A       8     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     R       9     R       9     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     I      10     I      10     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     N      11     N      11     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      12     E      12     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     L      13     L      13     22   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A      14     A      14     22   35   42     8   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A      15     A      15     22   35   42     7   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K      16     K      16     24   35   42     7   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A      17     A      17     25   35   42     9   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K      18     K      18     25   35   42     7   16   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A      19     A      19     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     G      20     G      20     25   35   42     3   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     V      21     V      21     25   35   42     6   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     I      22     I      22     25   35   42     3   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     T      23     T      23     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      24     E      24     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      25     E      25     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      26     E      26     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K      27     K      27     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     A      28     A      28     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      29     E      29     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     Q      30     Q      30     25   35   42    11   20   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     Q      31     Q      31     25   35   42    11   21   23   27   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K      32     K      32     25   35   42     9   21   23   26   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     L      33     L      33     25   35   42    11   21   23   26   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     R      34     R      34     25   35   42     9   21   23   26   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     Q      35     Q      35     25   35   42     9   21   23   26   30   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     E      36     E      36     25   35   42     9   21   23   26   29   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     Y      37     Y      37     25   35   42     9   21   23   26   29   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     L      38     L      38     25   35   42     9   21   23   26   29   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     K      39     K      39     25   35   42     9   21   23   26   29   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     G      40     G      40     25   35   42     9   17   23   26   29   31   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     F      41     F      41     25   35   42     4   21   23   26   29   31   34   37   39   41   41   41   41   41   42   42   42   42   42   42 
LCS_GDT     R      42     R      42      3   35   42     3    3    3   11   24   33   35   37   40   41   41   41   41   41   42   42   42   42   42   42 
LCS_AVERAGE  LCS_A:  78.50  (  52.32   83.16  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     11     21     23     27     30     33     35     37     40     41     41     41     41     41     42     42     42     42     42     42 
GDT PERCENT_CA  26.19  50.00  54.76  64.29  71.43  78.57  83.33  88.10  95.24  97.62  97.62  97.62  97.62  97.62 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.71   0.77   1.23   1.42   1.73   1.90   2.14   2.44   2.54   2.54   2.54   2.54   2.54   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_ALL_CA   4.45   5.29   5.36   4.23   3.80   3.31   3.21   2.96   2.81   2.81   2.81   2.81   2.81   2.81   2.80   2.80   2.80   2.80   2.80   2.80

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          8.862
LGA    I       2      I       2          6.037
LGA    S       3      S       3          3.142
LGA    N       4      N       4          6.385
LGA    A       5      A       5          4.990
LGA    K       6      K       6          3.936
LGA    I       7      I       7          3.343
LGA    A       8      A       8          2.783
LGA    R       9      R       9          2.637
LGA    I      10      I      10          1.996
LGA    N      11      N      11          1.330
LGA    E      12      E      12          0.976
LGA    L      13      L      13          1.376
LGA    A      14      A      14          1.103
LGA    A      15      A      15          1.661
LGA    K      16      K      16          1.787
LGA    A      17      A      17          0.837
LGA    K      18      K      18          2.075
LGA    A      19      A      19          4.053
LGA    G      20      G      20          3.513
LGA    V      21      V      21          1.104
LGA    I      22      I      22          1.368
LGA    T      23      T      23          0.982
LGA    E      24      E      24          1.837
LGA    E      25      E      25          2.482
LGA    E      26      E      26          1.593
LGA    K      27      K      27          1.048
LGA    A      28      A      28          2.092
LGA    E      29      E      29          1.930
LGA    Q      30      Q      30          0.988
LGA    Q      31      Q      31          1.425
LGA    K      32      K      32          1.610
LGA    L      33      L      33          1.294
LGA    R      34      R      34          0.769
LGA    Q      35      Q      35          0.835
LGA    E      36      E      36          0.899
LGA    Y      37      Y      37          2.285
LGA    L      38      L      38          2.680
LGA    K      39      K      39          2.244
LGA    G      40      G      40          3.377
LGA    F      41      F      41          3.793
LGA    R      42      R      42          2.947

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     37    2.14    75.595    80.544     1.653

LGA_LOCAL      RMSD =  2.138  Number of atoms =   37  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.960  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  2.801  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.220196 * X  +  -0.975275 * Y  +  -0.018782 * Z  +   4.541501
  Y_new =   0.752902 * X  +   0.182169 * Y  +  -0.632418 * Z  +  -2.866663
  Z_new =   0.620203 * X  +   0.125115 * Y  +   0.774399 * Z  + -18.897079 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.160180   -2.981413  [ DEG:     9.1776   -170.8224 ]
  Theta =  -0.669001   -2.472591  [ DEG:   -38.3310   -141.6690 ]
  Phi   =   1.286268   -1.855325  [ DEG:    73.6977   -106.3023 ]
 
# 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: T0335TS599_4                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS599_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   37   2.14  80.544     2.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS599_4
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -1.270   0.498 -10.275  1.00  0.00              
ATOM      2  CA  ILE     2       0.342  -0.693 -13.262  1.00  0.00              
ATOM      3  CA  SER     3       0.204  -4.892 -13.257  1.00  0.00              
ATOM      4  CA  ASN     4      -3.224  -5.908 -12.389  1.00  0.00              
ATOM      5  CA  ALA     5      -2.197  -8.168  -9.485  1.00  0.00              
ATOM      6  CA  LYS     6      -0.315  -5.258  -7.943  1.00  0.00              
ATOM      7  CA  ILE     7      -3.305  -2.987  -8.387  1.00  0.00              
ATOM      8  CA  ALA     8      -5.602  -5.537  -6.727  1.00  0.00              
ATOM      9  CA  ARG     9      -3.200  -5.996  -3.827  1.00  0.00              
ATOM     10  CA  ILE    10      -2.877  -2.292  -3.215  1.00  0.00              
ATOM     11  CA  ASN    11      -6.608  -1.924  -3.204  1.00  0.00              
ATOM     12  CA  GLU    12      -7.032  -4.699  -0.711  1.00  0.00              
ATOM     13  CA  LEU    13      -4.424  -3.174   1.623  1.00  0.00              
ATOM     14  CA  ALA    14      -6.085   0.241   1.384  1.00  0.00              
ATOM     15  CA  ALA    15      -9.409  -1.322   2.380  1.00  0.00              
ATOM     16  CA  LYS    16      -7.729  -3.161   5.308  1.00  0.00              
ATOM     17  CA  ALA    17      -6.135   0.092   6.418  1.00  0.00              
ATOM     18  CA  LYS    18      -9.435   1.951   6.236  1.00  0.00              
ATOM     19  CA  ALA    19     -11.130  -0.656   8.391  1.00  0.00              
ATOM     20  CA  GLY    20      -8.391  -0.531  10.984  1.00  0.00              
ATOM     21  CA  VAL    21      -7.918   3.238  10.969  1.00  0.00              
ATOM     22  CA  ILE    22      -4.429   3.307   9.647  1.00  0.00              
ATOM     23  CA  THR    23      -1.901   5.377  11.486  1.00  0.00              
ATOM     24  CA  GLU    24       0.314   7.915   9.838  1.00  0.00              
ATOM     25  CA  GLU    25       3.217   5.392   9.938  1.00  0.00              
ATOM     26  CA  GLU    26       1.099   2.763   8.213  1.00  0.00              
ATOM     27  CA  LYS    27       0.133   5.313   5.507  1.00  0.00              
ATOM     28  CA  ALA    28       3.784   6.253   4.905  1.00  0.00              
ATOM     29  CA  GLU    29       4.764   2.569   4.599  1.00  0.00              
ATOM     30  CA  GLN    30       1.929   1.970   2.114  1.00  0.00              
ATOM     31  CA  GLN    31       3.002   4.900   0.007  1.00  0.00              
ATOM     32  CA  LYS    32       6.634   3.659  -0.055  1.00  0.00              
ATOM     33  CA  LEU    33       5.542   0.152  -1.022  1.00  0.00              
ATOM     34  CA  ARG    34       3.371   1.452  -3.827  1.00  0.00              
ATOM     35  CA  GLN    35       6.185   3.566  -5.202  1.00  0.00              
ATOM     36  CA  GLU    36       8.628   0.625  -5.147  1.00  0.00              
ATOM     37  CA  TYR    37       6.175  -1.709  -6.887  1.00  0.00              
ATOM     38  CA  LEU    38       5.437   0.870  -9.519  1.00  0.00              
ATOM     39  CA  LYS    39       9.180   1.446 -10.172  1.00  0.00              
ATOM     40  CA  GLY    40       9.756  -2.310 -10.404  1.00  0.00              
ATOM     41  CA  PHE    41       6.847  -2.650 -12.906  1.00  0.00              
ATOM     42  CA  ARG    42       8.198   0.237 -14.981  1.00  0.00              
ATOM     43  CA  SER    43      11.612  -1.453 -15.089  1.00  0.00              
ATOM     44  CA  SER    44      10.017  -4.792 -16.137  1.00  0.00              
ATOM     45  CA  MET    45       8.011  -3.005 -18.853  1.00  0.00              
ATOM     46  CA  LYS    46      11.156  -1.213 -20.114  1.00  0.00              
ATOM     47  CA  ASN    47      12.994  -4.543 -20.324  1.00  0.00              
ATOM     48  CA  THR    48      10.102  -6.071 -22.281  1.00  0.00              
ATOM     49  CA  LEU    49      10.009  -3.101 -24.656  1.00  0.00              
ATOM     50  CA  LYS    50      13.755  -3.278 -25.367  1.00  0.00              
ATOM     51  CA  SER    51      13.539  -7.047 -26.041  1.00  0.00              
ATOM     52  CA  VAL    52      10.522  -7.076 -28.266  1.00  0.00              
ATOM     53  CA  LYS    53      10.535  -9.386 -31.307  1.00  0.00              
ATOM     54  CA  ILE    54       8.168  -8.995 -34.167  1.00  0.00              
ATOM     55  CA  ILE    55       6.603 -12.003 -35.769  1.00  0.00              
ATOM     56  CA  ASP    56       5.033 -11.326 -39.111  1.00  0.00              
ATOM     57  CA  PRO    57       1.751 -12.510 -40.519  1.00  0.00              
ATOM     58  CA  GLU    58       3.317 -15.800 -41.719  1.00  0.00              
ATOM     59  CA  GLY    59       4.831 -16.597 -38.348  1.00  0.00              
ATOM     60  CA  ASN    60       8.434 -15.786 -39.002  1.00  0.00              
ATOM     61  CA  ASP    61      10.248 -14.092 -36.184  1.00  0.00              
ATOM     62  CA  VAL    62      11.397 -10.657 -37.089  1.00  0.00              
ATOM     63  CA  THR    63      14.205  -9.282 -34.978  1.00  0.00              
ATOM     64  CA  PRO    64      14.121  -5.522 -34.249  1.00  0.00              
ATOM     65  CA  GLU    65      17.195  -4.959 -36.335  1.00  0.00              
ATOM     66  CA  LYS    66      15.901  -6.825 -39.336  1.00  0.00              
ATOM     67  CA  LEU    67      12.591  -5.050 -39.329  1.00  0.00              
ATOM     68  CA  LYS    68      14.064  -1.613 -39.143  1.00  0.00              
ATOM     69  CA  ARG    69      16.510  -2.297 -41.933  1.00  0.00              
ATOM     70  CA  GLU    70      13.909  -3.748 -44.229  1.00  0.00              
ATOM     71  CA  GLN    71      11.523  -0.834 -43.648  1.00  0.00              
ATOM     72  CA  ARG    72      14.196   1.713 -44.325  1.00  0.00              
ATOM     73  CA  ASN    73      15.299   0.091 -47.553  1.00  0.00              
ATOM     74  CA  ASN    74      11.874  -0.261 -49.063  1.00  0.00              
ATOM     75  CA  LYS    75      10.054   2.675 -47.324  1.00  0.00              
ATOM     76  CA  LEU    76       7.651   0.419 -45.512  1.00  0.00              
ATOM     77  CA  HIS    77       6.457   0.771 -41.962  1.00  0.00              
ATOM     78  CA  LEU    78       6.195  -2.755 -40.690  1.00  0.00              
ATOM     79  CA  GLU    79       3.533  -3.406 -37.981  1.00  0.00              
ATOM     80  CA  HIS    80       2.324  -6.989 -38.479  1.00  0.00              
ATOM     81  CA  HIS    81      -1.336  -6.104 -39.275  1.00  0.00              
ATOM     82  CA  HIS    82      -0.192  -3.863 -42.155  1.00  0.00              
ATOM     83  CA  HIS    83       3.133  -6.325 -42.906  1.00  0.00              
ATOM     84  CA  HIS    84       6.195  -6.868 -44.884  1.00  0.00              
ATOM     85  CA  HIS    85       6.468  -3.816 -47.764  1.00  0.00              
TER                                                                             
END
