
#######################################################
#                                                     #
#                        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   49 (   49),  selected   49 , name T0372TS464_4_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   49 , name T0372_D1.pdb
# PARAMETERS: T0372TS464_4_1-D1.T0372_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:    31        63 - 93          4.81    12.43
  LCS_AVERAGE:     20.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        72 - 93          1.83    11.66
  LCS_AVERAGE:     13.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        43 - 55          0.99    20.42
  LCS_AVERAGE:      7.13

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:  126
LCS_GDT     D      42     D      42      3   16   17     0    3    3    3    5    5   10   15   16   16   17   17   18   18   22   24   24   24   25   26 
LCS_GDT     T      43     T      43     13   16   17     6   10   12   13   14   15   15   15   16   16   17   17   18   20   22   24   29   32   33   35 
LCS_GDT     Q      44     Q      44     13   16   17     6   10   12   13   14   15   15   15   19   20   27   28   29   30   31   32   33   33   33   35 
LCS_GDT     F      45     F      45     13   16   17     6   10   12   13   14   18   21   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     A      46     A      46     13   16   17     5   10   12   13   14   18   19   19   22   24   26   29   30   30   31   32   33   33   33   34 
LCS_GDT     V      47     V      47     13   16   17     5   10   12   13   14   15   15   15   16   16   17   21   21   24   27   29   30   32   33   34 
LCS_GDT     I      48     I      48     13   16   17     6   10   12   13   14   15   15   15   16   16   17   17   18   20   22   24   24   24   26   27 
LCS_GDT     D      49     D      49     13   16   17     4    8   12   13   14   15   15   15   16   16   17   17   18   20   22   24   24   24   26   26 
LCS_GDT     D      50     D      50     13   16   17     3    8   12   13   14   15   15   15   16   16   17   17   18   20   22   24   24   24   26   26 
LCS_GDT     F      51     F      51     13   16   17     6   10   12   13   14   15   15   15   16   16   17   17   18   20   22   24   24   24   26   26 
LCS_GDT     L      52     L      52     13   16   17     5   10   12   13   14   15   15   15   16   16   17   21   21   24   27   29   30   31   32   32 
LCS_GDT     V      53     V      53     13   16   17     6   10   12   13   14   18   19   19   22   24   26   29   30   30   31   32   33   33   33   34 
LCS_GDT     F      54     F      54     13   16   17     5   10   12   13   14   18   21   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K      55     K      55     13   16   17     5    8   12   13   14   15   15   15   17   19   23   24   27   30   31   32   33   33   33   35 
LCS_GDT     F      56     F      56      7   16   17     4    7   10   13   14   15   15   15   16   16   17   17   18   20   22   25   27   30   33   34 
LCS_GDT     W      57     W      57      7   16   17     4    7   10   11   14   15   15   15   16   16   17   17   18   20   22   24   24   24   26   27 
LCS_GDT     A      63     A      63      4    7   31     3    4    4    6    6    7    7   11   16   17   21   23   24   29   29   31   31   31   31   32 
LCS_GDT     Y      64     Y      64      4    7   31     3    4    4    6    6    7   10   13   16   18   21   23   27   29   30   31   31   31   31   35 
LCS_GDT     M      65     M      65      4    7   31     3    4    4    6    6    7   10   13   16   18   22   26   27   29   30   31   31   31   33   35 
LCS_GDT     M      66     M      66      5    7   31     4    4    5    6    6    7    9   11   16   17   20   23   24   29   30   31   31   31   33   35 
LCS_GDT     P      67     P      67      5    7   31     4    4    5    6    6    7   10   13   16   18   24   26   27   30   31   31   33   33   33   35 
LCS_GDT     V      68     V      68      5    7   31     4    4    5    9   14   17   19   23   26   28   28   28   30   30   31   32   33   33   33   35 
LCS_GDT     G      69     G      69      5    7   31     4    4    5    6   13   17   21   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     N      70     N      70      5    6   31     3    4    5   13   13   17   21   22   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     G      71     G      71      4   21   31     3    3   11   14   15   18   21   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     D      72     D      72     10   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     L      73     L      73     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K      74     K      74     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     A      75     A      75     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     V      76     V      76     11   22   31     6    9   13   16   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     L      77     L      77     11   22   31     6    9   13   16   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     R      78     R      78     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K      79     K      79     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     L      80     L      80     11   22   31     5    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     I      81     I      81     11   22   31     5    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     E      82     E      82     11   22   31     5    9   13   16   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     D      83     D      83     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     A      84     A      84     11   22   31     6    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     D      85     D      85      9   22   31     3    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K      86     K      86      9   22   31     6    9   12   17   21   21   22   23   25   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     E      87     E      87      9   22   31     3    8   13   17   21   21   22   23   25   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K      88     K      88      9   22   31     4    7   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     H      89     H      89      9   22   31     4    7   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     N      90     N      90      9   22   31     4    8   12   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     F      91     F      91      9   22   31     4    9   13   17   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     C      92     C      92      4   22   31     3    5   10   15   21   21   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     M      93     M      93      4   22   31     3    5    5   14   15   20   22   23   26   28   28   29   30   30   31   32   33   33   33   35 
LCS_GDT     K     290     K     290      0    0   30     1    1    1    1    3    4    5    6    7    9   10   19   19   19   21   23   26   27   29   32 
LCS_GDT     Y     291     Y     291      0    0   25     0    0    0    0    1    4    5    6    7    7   10   12   14   17   18   23   23   24   27   29 
LCS_AVERAGE  LCS_A:  13.74  (   7.13   13.22   20.86 )

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      6     10     13     17     21     21     22     23     26     28     28     29     30     30     31     32     33     33     33     35 
GDT PERCENT_CA   4.76   7.94  10.32  13.49  16.67  16.67  17.46  18.25  20.63  22.22  22.22  23.02  23.81  23.81  24.60  25.40  26.19  26.19  26.19  27.78
GDT RMS_LOCAL    0.15   0.58   1.02   1.31   1.64   1.64   1.83   2.13   2.82   3.04   3.04   3.42   3.55   3.55   3.77   4.01   4.32   4.32   4.32   5.61
GDT RMS_ALL_CA  12.79  20.56  11.73  12.19  11.86  11.86  11.66  11.55  11.11  11.14  11.14  11.35  11.24  11.24  11.22  11.19  11.09  11.09  11.09  11.08

#      Molecule1      Molecule2       DISTANCE
LGA    D      42      D      42         19.356
LGA    T      43      T      43         15.629
LGA    Q      44      Q      44         11.584
LGA    F      45      F      45          7.354
LGA    A      46      A      46         11.658
LGA    V      47      V      47         14.665
LGA    I      48      I      48         19.716
LGA    D      49      D      49         25.013
LGA    D      50      D      50         25.290
LGA    F      51      F      51         18.728
LGA    L      52      L      52         13.053
LGA    V      53      V      53          9.508
LGA    F      54      F      54          7.231
LGA    K      55      K      55         12.266
LGA    F      56      F      56         16.220
LGA    W      57      W      57         22.970
LGA    A      63      A      63         15.589
LGA    Y      64      Y      64         13.440
LGA    M      65      M      65         12.842
LGA    M      66      M      66         13.807
LGA    P      67      P      67          9.687
LGA    V      68      V      68          5.878
LGA    G      69      G      69          6.751
LGA    N      70      N      70          6.749
LGA    G      71      G      71          3.836
LGA    D      72      D      72          3.149
LGA    L      73      L      73          1.875
LGA    K      74      K      74          1.809
LGA    A      75      A      75          2.781
LGA    V      76      V      76          2.326
LGA    L      77      L      77          1.247
LGA    R      78      R      78          1.377
LGA    K      79      K      79          1.000
LGA    L      80      L      80          1.169
LGA    I      81      I      81          1.630
LGA    E      82      E      82          2.610
LGA    D      83      D      83          1.424
LGA    A      84      A      84          0.732
LGA    D      85      D      85          0.594
LGA    K      86      K      86          2.953
LGA    E      87      E      87          2.981
LGA    K      88      K      88          2.392
LGA    H      89      H      89          1.133
LGA    N      90      N      90          1.898
LGA    F      91      F      91          1.813
LGA    C      92      C      92          2.349
LGA    M      93      M      93          3.616
LGA    K     290      K     290         21.460
LGA    Y     291      Y     291         21.553

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   49  126    4.0     23    2.13    16.270    16.410     1.033

LGA_LOCAL      RMSD =  2.127  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.476  Number of atoms =   49 
Std_ALL_ATOMS  RMSD = 10.365  (standard rmsd on all 49 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.081067 * X  +  -0.006206 * Y  +   0.996689 * Z  +  -1.945827
  Y_new =  -0.188836 * X  +  -0.981965 * Y  +   0.009245 * Z  + 115.472244
  Z_new =   0.978657 * X  +  -0.188960 * Y  +  -0.080777 * Z  + -102.723328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.974766    1.166826  [ DEG:  -113.1458     66.8542 ]
  Theta =  -1.363820   -1.777773  [ DEG:   -78.1411   -101.8589 ]
  Phi   =  -1.165290    1.976302  [ DEG:   -66.7662    113.2338 ]
 
# 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: T0372TS464_4_1-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_1-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   49  126   4.0   23   2.13  16.410    10.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  ASP    42      34.285  58.332   3.420  1.00  0.00
ATOM      2  CA  THR    43      34.770  57.781   7.036  1.00  0.00
ATOM      3  CA  GLN    44      36.199  54.184   6.781  1.00  0.00
ATOM      4  CA  PHE    45      37.261  51.851   4.032  1.00  0.00
ATOM      5  CA  ALA    46      37.659  47.967   4.386  1.00  0.00
ATOM      6  CA  VAL    47      39.417  46.009   1.743  1.00  0.00
ATOM      7  CA  ILE    48      37.813  42.562   2.073  1.00  0.00
ATOM      8  CA  ASP    49      38.533  39.697  -0.291  1.00  0.00
ATOM      9  CA  ASP    50      36.525  40.515  -3.377  1.00  0.00
ATOM     10  CA  PHE    51      34.694  43.680  -2.154  1.00  0.00
ATOM     11  CA  LEU    52      35.591  47.000  -0.708  1.00  0.00
ATOM     12  CA  VAL    53      33.140  48.188   1.857  1.00  0.00
ATOM     13  CA  PHE    54      32.943  51.929   2.730  1.00  0.00
ATOM     14  CA  LYS    55      31.103  53.788   5.423  1.00  0.00
ATOM     15  CA  PHE    56      29.901  57.112   3.786  1.00  0.00
ATOM     16  CA  TRP    57      28.445  60.041   5.617  1.00  0.00
ATOM     17  CA  ALA    63      43.994  59.221  -1.421  1.00  0.00
ATOM     18  CA  TYR    64      43.009  60.670   1.939  1.00  0.00
ATOM     19  CA  MET    65      39.826  62.759   2.049  1.00  0.00
ATOM     20  CA  MET    66      39.331  65.341   4.792  1.00  0.00
ATOM     21  CA  PRO    67      35.609  66.097   5.053  1.00  0.00
ATOM     22  CA  VAL    68      32.695  63.753   4.438  1.00  0.00
ATOM     23  CA  GLY    69      30.176  66.030   2.745  1.00  0.00
ATOM     24  CA  ASN    70      28.692  65.454  -0.702  1.00  0.00
ATOM     25  CA  GLY    71      31.735  66.780  -2.589  1.00  0.00
ATOM     26  CA  ASP    72      33.953  64.656  -0.363  1.00  0.00
ATOM     27  CA  LEU    73      31.836  61.494  -0.712  1.00  0.00
ATOM     28  CA  LYS    74      31.208  61.757  -4.549  1.00  0.00
ATOM     29  CA  ALA    75      34.888  62.227  -4.816  1.00  0.00
ATOM     30  CA  VAL    76      34.613  58.556  -3.896  1.00  0.00
ATOM     31  CA  LEU    77      32.172  57.911  -6.779  1.00  0.00
ATOM     32  CA  ARG    78      34.562  59.603  -9.237  1.00  0.00
ATOM     33  CA  LYS    79      37.427  57.309  -8.228  1.00  0.00
ATOM     34  CA  LEU    80      36.287  53.814  -6.678  1.00  0.00
ATOM     35  CA  ILE    81      35.940  54.182 -10.482  1.00  0.00
ATOM     36  CA  GLU    82      39.669  54.989 -10.826  1.00  0.00
ATOM     37  CA  ASP    83      40.688  51.825  -8.962  1.00  0.00
ATOM     38  CA  ALA    84      38.237  49.171 -10.039  1.00  0.00
ATOM     39  CA  ASP    85      37.105  50.179 -13.494  1.00  0.00
ATOM     40  CA  LYS    86      39.607  50.630 -16.084  1.00  0.00
ATOM     41  CA  GLU    87      39.959  47.273 -14.344  1.00  0.00
ATOM     42  CA  LYS    88      36.462  45.866 -14.915  1.00  0.00
ATOM     43  CA  HIS    89      36.386  45.606 -11.158  1.00  0.00
ATOM     44  CA  ASN    90      33.264  46.007  -8.949  1.00  0.00
ATOM     45  CA  PHE    91      33.254  48.785  -6.364  1.00  0.00
ATOM     46  CA  CYS    92      31.123  49.206  -3.263  1.00  0.00
ATOM     47  CA  MET    93      30.320  52.535  -1.621  1.00  0.00
ATOM    112  CA  LYS   290      35.357  65.230  12.463  1.00  0.00
ATOM    113  CA  TYR   291      31.684  64.855  13.309  1.00  0.00
TER
END
