
#######################################################
#                                                     #
#                        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   34 (   34),  selected   34 , name T0320TS464_1_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   34 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_1_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:    18        73 - 226         4.85    10.24
  LCS_AVERAGE:      7.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       145 - 157         1.68    12.92
  LCS_AVERAGE:      4.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        63 - 73          0.58    15.94
  LCS_AVERAGE:      3.67

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:  214
LCS_GDT     F      58     F      58      4    5   16     3    4    5   11   13   16   16   17   17   17   18   18   18   20   20   20   20   21   24   25 
LCS_GDT     S      59     S      59      4    5   16     3    4    5   12   13   16   16   17   17   17   18   18   18   20   20   20   20   22   24   26 
LCS_GDT     Y      60     Y      60      4    7   16     3    4    6   10   13   16   16   17   17   17   18   18   18   20   20   20   21   24   26   28 
LCS_GDT     N      61     N      61      4    7   16     3    4    6   10   13   16   16   17   17   17   18   18   18   20   20   20   21   24   26   28 
LCS_GDT     G      62     G      62      3   12   16     3    4    5    8    9   13   15   16   16   17   18   18   18   20   20   20   22   24   26   28 
LCS_GDT     G      63     G      63     11   12   16     5   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     K      64     K      64     11   12   16     6   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   25   26 
LCS_GDT     D      65     D      65     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     C      66     C      66     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     Q      67     Q      67     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     V      68     V      68     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   23   26   28 
LCS_GDT     L      69     L      69     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     L      70     L      70     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     L      71     L      71     11   12   16     3   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   20   23   26   28 
LCS_GDT     L      72     L      72     11   12   16     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     Y      73     Y      73     11   12   18     8   10   11   12   13   14   15   16   16   16   16   16   18   20   20   20   22   24   26   28 
LCS_GDT     A     145     A     145      8   13   18     4    7    8   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     D     146     D     146      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     A     147     A     147      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     F     148     F     148      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     R     149     R     149      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     D     150     D     150      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     F     151     F     151      9   13   18     6    7   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     I     152     I     152      9   13   18     3    7   10   11   12   13   15   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     K     153     K     153      9   13   18     3    6   10   11   12   16   16   17   17   17   18   18   18   18   19   20   21   24   25   26 
LCS_GDT     I     154     I     154      9   13   18     4    6   10   11   13   16   16   17   17   17   18   18   18   18   19   20   21   22   25   26 
LCS_GDT     Y     155     Y     155      9   13   18     4    6   10   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     P     156     P     156      6   13   18     3    3    8   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     E     157     E     157      4   13   18     3    3    7   11   13   16   16   17   17   17   18   18   18   18   19   20   22   24   26   28 
LCS_GDT     S     223     S     223      3    5   18     0    3    3    3    4    4    5    6    8   12   14   16   18   20   20   20   20   23   25   28 
LCS_GDT     I     224     I     224      4    5   18     3    4    4    4    4    5    6    8    9   12   14   16   16   20   20   20   20   23   26   28 
LCS_GDT     G     225     G     225      4    5   18     3    4    4    4    6    7    9   11   12   14   14   16   18   20   20   20   20   23   26   28 
LCS_GDT     G     226     G     226      4    5   18     3    4    8    8    9   11   11   13   13   13   14   16   18   20   20   20   20   23   25   28 
LCS_GDT     I     227     I     227      4    5    8     3    4    4    4    4    4    5    5   10   11   13   13   14   14   15   16   16   18   19   20 
LCS_AVERAGE  LCS_A:   5.50  (   3.67    4.98    7.86 )

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      8     10     11     12     13     16     16     17     17     17     18     18     18     20     20     20     22     24     26     28 
GDT PERCENT_CA   3.74   4.67   5.14   5.61   6.07   7.48   7.48   7.94   7.94   7.94   8.41   8.41   8.41   9.35   9.35   9.35  10.28  11.21  12.15  13.08
GDT RMS_LOCAL    0.26   0.48   0.58   1.22   1.46   2.01   2.01   2.17   2.17   2.17   2.65   2.65   2.65   4.89   4.89   4.89   6.36   6.63   7.36   7.71
GDT RMS_ALL_CA  15.46  15.86  15.94  17.18  17.78  12.22  12.22  12.12  12.12  12.12  12.03  12.03  12.03  17.22  17.22  17.22   9.56   9.31   8.80   8.70

#      Molecule1      Molecule2       DISTANCE
LGA    F      58      F      58          2.937
LGA    S      59      S      59          3.142
LGA    Y      60      Y      60          1.450
LGA    N      61      N      61          1.404
LGA    G      62      G      62          7.333
LGA    G      63      G      63         11.928
LGA    K      64      K      64         17.512
LGA    D      65      D      65         15.726
LGA    C      66      C      66         11.825
LGA    Q      67      Q      67         17.278
LGA    V      68      V      68         20.774
LGA    L      69      L      69         16.500
LGA    L      70      L      70         15.974
LGA    L      71      L      71         22.512
LGA    L      72      L      72         21.540
LGA    Y      73      Y      73         16.199
LGA    A     145      A     145          1.992
LGA    D     146      D     146          2.218
LGA    A     147      A     147          2.528
LGA    F     148      F     148          2.073
LGA    R     149      R     149          1.215
LGA    D     150      D     150          0.164
LGA    F     151      F     151          2.193
LGA    I     152      I     152          3.777
LGA    K     153      K     153          2.773
LGA    I     154      I     154          0.741
LGA    Y     155      Y     155          1.518
LGA    P     156      P     156          1.846
LGA    E     157      E     157          1.784
LGA    S     223      S     223         22.045
LGA    I     224      I     224         17.782
LGA    G     225      G     225         14.981
LGA    G     226      G     226         13.747
LGA    I     227      I     227         17.852

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  214    4.0     17    2.17     6.893     6.611     0.750

LGA_LOCAL      RMSD =  2.167  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.120  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  8.625  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.750325 * X  +   0.533519 * Y  +  -0.390346 * Z  +   5.119714
  Y_new =   0.549620 * X  +   0.175360 * Y  +  -0.816803 * Z  + -44.316586
  Z_new =  -0.367329 * X  +  -0.827410 * Y  +  -0.424809 * Z  + 124.744095 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.045123    1.096470  [ DEG:  -117.1769     62.8231 ]
  Theta =   0.376135    2.765457  [ DEG:    21.5510    158.4490 ]
  Phi   =   2.509380   -0.632212  [ DEG:   143.7769    -36.2231 ]
 
# 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_1_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_1_2-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  214   4.0   17   2.17   6.611     8.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  PHE    58      16.694  28.924  26.146  1.00  0.00
ATOM      2  CA  SER    59      18.715  26.745  23.830  1.00  0.00
ATOM      3  CA  TYR    60      20.203  28.798  21.013  1.00  0.00
ATOM      4  CA  ASN    61      21.159  27.132  17.736  1.00  0.00
ATOM      5  CA  GLY    62      24.545  28.789  18.239  1.00  0.00
ATOM      6  CA  GLY    63      26.859  28.981  21.227  1.00  0.00
ATOM      7  CA  LYS    64      27.975  32.327  19.841  1.00  0.00
ATOM      8  CA  ASP    65      24.379  33.471  20.282  1.00  0.00
ATOM      9  CA  CYS    66      24.379  32.051  23.807  1.00  0.00
ATOM     10  CA  GLN    67      27.617  33.886  24.606  1.00  0.00
ATOM     11  CA  VAL    68      25.995  37.143  23.564  1.00  0.00
ATOM     12  CA  LEU    69      22.807  36.414  25.530  1.00  0.00
ATOM     13  CA  LEU    70      24.930  36.049  28.647  1.00  0.00
ATOM     14  CA  LEU    71      26.683  39.328  29.438  1.00  0.00
ATOM     15  CA  LEU    72      23.230  40.294  27.874  1.00  0.00
ATOM     16  CA  TYR    73      21.896  38.316  30.829  1.00  0.00
ATOM     17  CA  ALA   145      31.110  23.483  26.109  1.00  0.00
ATOM     18  CA  ASP   146      33.438  26.260  25.093  1.00  0.00
ATOM     19  CA  ALA   147      30.898  28.846  26.249  1.00  0.00
ATOM     20  CA  PHE   148      31.207  27.392  29.765  1.00  0.00
ATOM     21  CA  ARG   149      34.948  28.152  29.563  1.00  0.00
ATOM     22  CA  ASP   150      34.344  31.726  28.386  1.00  0.00
ATOM     23  CA  PHE   151      31.642  32.322  30.994  1.00  0.00
ATOM     24  CA  ILE   152      34.233  32.570  33.763  1.00  0.00
ATOM     25  CA  LYS   153      34.993  35.945  32.190  1.00  0.00
ATOM     26  CA  ILE   154      31.356  36.854  31.649  1.00  0.00
ATOM     27  CA  TYR   155      29.721  36.185  34.976  1.00  0.00
ATOM     28  CA  PRO   156      30.521  34.905  38.502  1.00  0.00
ATOM     29  CA  GLU   157      27.284  32.928  38.566  1.00  0.00
ATOM     30  CA  SER   223      17.065  38.972  19.409  1.00  0.00
ATOM     31  CA  ILE   224      20.401  37.226  19.977  1.00  0.00
ATOM     32  CA  GLY   225      19.716  34.595  17.326  1.00  0.00
ATOM     33  CA  GLY   226      17.725  31.466  16.531  1.00  0.00
ATOM     34  CA  ILE   227      16.590  29.674  19.656  1.00  0.00
TER
END
