
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0320TS464_5_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   57 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_5_2-D1.T0320_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:    21        12 - 32          4.89    27.29
  LCS_AVERAGE:      8.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         4 - 18          1.70    19.50
  LCS_AVERAGE:      5.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         4 - 17          0.35    19.75
  LCS_AVERAGE:      4.13

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:  214
LCS_GDT     S       4     S       4     14   15   18    12   14   14   14   15   15   16   17   17   18   20   20   22   22   22   22   23   23   24   25 
LCS_GDT     K       5     K       5     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   22   23   23   24   25 
LCS_GDT     A       6     A       6     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   22   23   23   24   25 
LCS_GDT     A       7     A       7     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     E       8     E       8     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     M       9     M       9     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     C      10     C      10     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     Y      11     Y      11     14   15   18    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     E      12     E      12     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     I      13     I      13     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     T      14     T      14     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     N      15     N      15     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     S      16     S      16     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   23   24   25   25   26 
LCS_GDT     Y      17     Y      17     14   15   21    13   14   14   14   15   15   16   17   17   18   20   20   22   22   22   22   24   25   25   26 
LCS_GDT     L      18     L      18      3   15   21     3    3    3    5    6   10   13   15   16   17   18   20   22   22   22   23   24   25   25   26 
LCS_GDT     H      19     H      19      3    4   21     3    3    3    5    5    5    8   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     I      20     I      20      3    4   21     3    3    3    5    5    6    8   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     D      21     D      21      3    4   21     3    3    3    5    5    6    8   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     Q      22     Q      22      3    4   21     3    4    4    4    4    6    8   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     K      23     K      23      3    6   21     3    4    4    4    4    6    6   10   10   11   11   12   13   17   20   21   22   22   22   23 
LCS_GDT     S      24     S      24      6    9   21     5    5    6    8    8    9    9   10   12   15   16   17   18   20   21   21   22   22   24   26 
LCS_GDT     Q      25     Q      25      6    9   21     5    5    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     I      26     I      26      6    9   21     5    5    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     I      27     I      27      6    9   21     5    5    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     A      28     A      28      6    9   21     5    5    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     S      29     S      29      6    9   21     3    3    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     T      30     T      30      4    9   21     3    3    6    8    8    9    9   11   13   15   16   17   18   20   21   23   24   25   25   26 
LCS_GDT     Q      31     Q      31      4    9   21     3    3    6    8    8    9    9   10   13   13   16   17   18   20   21   21   23   25   25   25 
LCS_GDT     E      32     E      32      3    9   21     0    3    3    5    7    9    9   10   13   13   16   17   18   20   21   21   22   22   23   23 
LCS_GDT     T     112     T     112      4    4   15     3    3    5    7   12   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     F     113     F     113      4    4   15     3    3    4    4    5   12   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     P     114     P     114      4   13   15     3    3    4    4    8    9   12   13   13   14   15   18   18   19   19   19   20   21   22   23 
LCS_GDT     T     115     T     115     12   13   15    11   12   12   12   12   12   12   13   13   14   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     L     116     L     116     12   13   15    11   12   12   12   12   12   12   13   13   14   15   18   18   19   19   19   20   21   22   23 
LCS_GDT     E     117     E     117     12   13   15    11   12   12   12   12   12   12   13   13   13   14   14   17   17   18   18   20   21   22   23 
LCS_GDT     N     118     N     118     12   13   15    11   12   12   12   12   12   12   13   13   13   15   16   17   17   18   19   20   21   22   23 
LCS_GDT     F     119     F     119     12   13   15    11   12   12   12   12   12   12   13   13   14   15   16   17   19   19   19   20   21   24   24 
LCS_GDT     V     120     V     120     12   13   15    11   12   12   12   12   12   12   16   16   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     L     121     L     121     12   13   15    11   12   12   12   12   12   12   13   13   14   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     E     122     E     122     12   13   15    11   12   12   12   12   12   12   13   13   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     T     123     T     123     12   13   15    11   12   12   12   12   14   15   17   17   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     S     124     S     124     12   13   15    11   12   12   12   15   15   16   17   17   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     E     125     E     125     12   13   15    11   12   12   12   12   12   16   17   17   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     R     126     R     126     12   13   15    11   12   12   12   12   12   16   17   17   18   20   20   22   22   22   22   23   23   24   24 
LCS_GDT     L     195     L     195      4   13   13     3    4    9   12   13   13   15   15   15   15   16   18   18   19   21   23   24   25   25   26 
LCS_GDT     H     196     H     196      4   13   13     3    4    5   12   13   13   15   15   15   15   16   18   18   19   21   23   24   25   25   26 
LCS_GDT     W     197     W     197      5   13   13     3    5    8   12   13   13   15   15   15   15   16   18   18   19   19   20   22   24   25   26 
LCS_GDT     D     198     D     198      5   13   13     3    5    8   11   13   13   15   15   15   15   16   18   18   19   19   19   21   22   23   24 
LCS_GDT     L     199     L     199      5   13   13     3    5    8   12   13   13   15   15   15   15   16   18   18   19   19   19   21   22   23   24 
LCS_GDT     T     200     T     200      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   19   21   22   23 
LCS_GDT     N     201     N     201      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     I     202     I     202      8   13   13     5    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   21   22   23   24 
LCS_GDT     W     203     W     203      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     S     204     S     204      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     F     205     F     205      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     L     206     L     206      8   13   13     6    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_GDT     L     207     L     207      8   13   13     4    8    9   12   13   13   15   15   15   15   16   18   18   19   19   19   20   21   22   23 
LCS_AVERAGE  LCS_A:   5.89  (   4.13    5.53    8.03 )

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     13     14     14     14     15     15     16     17     17     18     20     20     22     22     22     23     24     25     25     26 
GDT PERCENT_CA   6.07   6.54   6.54   6.54   7.01   7.01   7.48   7.94   7.94   8.41   9.35   9.35  10.28  10.28  10.28  10.75  11.21  11.68  11.68  12.15
GDT RMS_LOCAL    0.30   0.35   0.35   0.35   0.92   0.92   1.27   1.55   1.55   2.04   2.66   2.66   3.29   3.29   3.29   6.13   6.22   6.39   6.39   6.67
GDT RMS_ALL_CA  19.71  19.75  19.75  19.75  19.27  19.27  19.56  19.41  19.41  18.97  19.00  19.00  18.63  18.63  18.63  20.02  20.08  20.37  20.37  19.46

#      Molecule1      Molecule2       DISTANCE
LGA    S       4      S       4          0.370
LGA    K       5      K       5          0.807
LGA    A       6      A       6          0.985
LGA    A       7      A       7          0.338
LGA    E       8      E       8          0.962
LGA    M       9      M       9          1.125
LGA    C      10      C      10          0.531
LGA    Y      11      Y      11          0.590
LGA    E      12      E      12          0.988
LGA    I      13      I      13          1.029
LGA    T      14      T      14          0.518
LGA    N      15      N      15          0.646
LGA    S      16      S      16          1.143
LGA    Y      17      Y      17          0.609
LGA    L      18      L      18          7.246
LGA    H      19      H      19         11.463
LGA    I      20      I      20         14.196
LGA    D      21      D      21         19.121
LGA    Q      22      Q      22         16.632
LGA    K      23      K      23         20.710
LGA    S      24      S      24         22.204
LGA    Q      25      Q      25         23.236
LGA    I      26      I      26         20.692
LGA    I      27      I      27         20.798
LGA    A      28      A      28         25.508
LGA    S      29      S      29         25.744
LGA    T      30      T      30         21.021
LGA    Q      31      Q      31         22.692
LGA    E      32      E      32         28.706
LGA    T     112      T     112         26.350
LGA    F     113      F     113         27.060
LGA    P     114      P     114         24.829
LGA    T     115      T     115         23.616
LGA    L     116      L     116         20.260
LGA    E     117      E     117         16.473
LGA    N     118      N     118         15.627
LGA    F     119      F     119         14.018
LGA    V     120      V     120          9.863
LGA    L     121      L     121          7.171
LGA    E     122      E     122          7.012
LGA    T     123      T     123          6.424
LGA    S     124      S     124          2.727
LGA    E     125      E     125          3.213
LGA    R     126      R     126          3.756
LGA    L     195      L     195         30.087
LGA    H     196      H     196         32.113
LGA    W     197      W     197         29.713
LGA    D     198      D     198         29.785
LGA    L     199      L     199         25.116
LGA    T     200      T     200         28.523
LGA    N     201      N     201         29.756
LGA    I     202      I     202         25.545
LGA    W     203      W     203         26.449
LGA    S     204      S     204         31.829
LGA    F     205      F     205         30.066
LGA    L     206      L     206         26.906
LGA    L     207      L     207         31.628

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57  214    4.0     17    1.55     7.944     7.331     1.029

LGA_LOCAL      RMSD =  1.552  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 19.411  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 14.484  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.458128 * X  +   0.888547 * Y  +   0.024548 * Z  + -89.212067
  Y_new =   0.703200 * X  +  -0.379181 * Y  +   0.601441 * Z  +  38.681419
  Z_new =   0.543717 * X  +  -0.258275 * Y  +  -0.798540 * Z  +  -8.651453 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.828778    0.312815  [ DEG:  -162.0770     17.9230 ]
  Theta =  -0.574860   -2.566733  [ DEG:   -32.9370   -147.0630 ]
  Phi   =   0.993374   -2.148218  [ DEG:    56.9162   -123.0838 ]
 
# 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: T0320TS464_5_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_2-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   57  214   4.0   17   1.55   7.331    14.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  SER     4       5.080  39.629  28.913  1.00  0.00
ATOM      2  CA  LYS     5       2.722  39.418  25.964  1.00  0.00
ATOM      3  CA  ALA     6       4.818  36.558  24.562  1.00  0.00
ATOM      4  CA  ALA     7       4.870  34.513  27.775  1.00  0.00
ATOM      5  CA  GLU     8       1.128  34.359  28.238  1.00  0.00
ATOM      6  CA  MET     9       0.387  33.946  24.517  1.00  0.00
ATOM      7  CA  CYS    10       2.790  30.976  24.438  1.00  0.00
ATOM      8  CA  TYR    11       1.183  29.563  27.542  1.00  0.00
ATOM      9  CA  GLU    12      -2.309  30.040  26.023  1.00  0.00
ATOM     10  CA  ILE    13      -1.268  28.447  22.750  1.00  0.00
ATOM     11  CA  THR    14       0.270  25.468  24.575  1.00  0.00
ATOM     12  CA  ASN    15      -2.714  25.059  26.893  1.00  0.00
ATOM     13  CA  SER    16      -5.008  24.611  23.902  1.00  0.00
ATOM     14  CA  TYR    17      -2.833  22.192  22.026  1.00  0.00
ATOM     15  CA  LEU    18      -0.085  23.844  20.055  1.00  0.00
ATOM     16  CA  HIS    19       3.390  22.477  20.225  1.00  0.00
ATOM     17  CA  ILE    20       6.306  24.806  20.818  1.00  0.00
ATOM     18  CA  ASP    21       6.911  25.464  17.132  1.00  0.00
ATOM     19  CA  GLN    22       3.303  26.105  16.216  1.00  0.00
ATOM     20  CA  LYS    23       2.956  28.272  19.331  1.00  0.00
ATOM     21  CA  SER    24       6.022  30.298  18.344  1.00  0.00
ATOM     22  CA  GLN    25       4.847  30.597  14.760  1.00  0.00
ATOM     23  CA  ILE    26       1.572  32.166  15.982  1.00  0.00
ATOM     24  CA  ILE    27       3.414  34.569  18.282  1.00  0.00
ATOM     25  CA  ALA    28       5.594  35.559  15.354  1.00  0.00
ATOM     26  CA  SER    29       1.951  35.911  15.037  1.00  0.00
ATOM     27  CA  THR    30      -0.226  35.524  18.147  1.00  0.00
ATOM     28  CA  GLN    31       1.321  38.408  20.043  1.00  0.00
ATOM     29  CA  GLU    32      -0.595  41.691  20.501  1.00  0.00
ATOM     30  CA  THR   112       5.500  24.473  25.867  1.00  0.00
ATOM     31  CA  PHE   113       5.657  27.705  27.864  1.00  0.00
ATOM     32  CA  PRO   114       8.926  29.618  27.559  1.00  0.00
ATOM     33  CA  THR   115      12.063  28.984  29.619  1.00  0.00
ATOM     34  CA  LEU   116      14.276  31.960  30.395  1.00  0.00
ATOM     35  CA  GLU   117      16.646  30.619  27.744  1.00  0.00
ATOM     36  CA  ASN   118      14.182  30.744  24.856  1.00  0.00
ATOM     37  CA  PHE   119      12.749  34.109  25.904  1.00  0.00
ATOM     38  CA  VAL   120      16.233  35.578  25.324  1.00  0.00
ATOM     39  CA  LEU   121      16.601  34.144  21.841  1.00  0.00
ATOM     40  CA  GLU   122      13.235  35.568  20.963  1.00  0.00
ATOM     41  CA  THR   123      14.310  39.012  22.176  1.00  0.00
ATOM     42  CA  SER   124      17.509  38.801  20.122  1.00  0.00
ATOM     43  CA  GLU   125      15.448  38.110  17.075  1.00  0.00
ATOM     44  CA  ARG   126      12.742  40.683  17.762  1.00  0.00
ATOM     45  CA  LEU   195      15.257  43.515  18.031  1.00  0.00
ATOM     46  CA  HIS   196      17.820  42.093  15.614  1.00  0.00
ATOM     47  CA  TRP   197      20.694  41.652  18.038  1.00  0.00
ATOM     48  CA  ASP   198      23.401  39.021  17.488  1.00  0.00
ATOM     49  CA  LEU   199      22.441  35.649  18.985  1.00  0.00
ATOM     50  CA  THR   200      23.274  35.731  22.678  1.00  0.00
ATOM     51  CA  ASN   201      23.208  39.487  23.247  1.00  0.00
ATOM     52  CA  ILE   202      20.333  39.513  25.737  1.00  0.00
ATOM     53  CA  TRP   203      21.642  36.454  27.597  1.00  0.00
ATOM     54  CA  SER   204      24.943  38.314  27.964  1.00  0.00
ATOM     55  CA  PHE   205      23.165  41.367  29.307  1.00  0.00
ATOM     56  CA  LEU   206      21.140  39.397  31.828  1.00  0.00
ATOM     57  CA  LEU   207      24.238  37.406  32.780  1.00  0.00
TER
END
