
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0343AL242_1
# Molecule2: number of CA atoms   94 (  282),  selected   20 , name T0343.pdb
# PARAMETERS: T0343AL242_1.T0343.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:    13        83 - 95          4.89    14.98
  LONGEST_CONTINUOUS_SEGMENT:    13        84 - 96          4.80    16.56
  LONGEST_CONTINUOUS_SEGMENT:    13        85 - 97          4.59    17.19
  LCS_AVERAGE:     13.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        78 - 85          1.40    24.89
  LCS_AVERAGE:      6.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.95    25.41
  LONGEST_CONTINUOUS_SEGMENT:     4        85 - 88          0.94    17.04
  LONGEST_CONTINUOUS_SEGMENT:     4        87 - 90          0.97    13.58
  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:   94
LCS_GDT     V      78     V      78      3    8   10     4    4    6    7    8    8    8    8    9    9    9    9    9   10   10   10   10   10   11   11 
LCS_GDT     K      79     K      79      3    8   10     3    4    6    7    8    8    8    8    9    9    9    9    9   10   10   10   11   12   12   12 
LCS_GDT     L      80     L      80      3    8   10     4    4    6    7    8    8    8    8    9    9    9    9   10   11   11   11   11   12   12   13 
LCS_GDT     V      81     V      81      3    8   10     3    3    4    6    8    8    8    8    9    9    9    9   10   11   11   11   11   14   14   14 
LCS_GDT     S      82     S      82      4    8   12     4    4    6    7    8    8    8    8    9    9    9    9   10   11   11   12   12   14   14   14 
LCS_GDT     L      83     L      83      4    8   13     4    4    6    7    8    8    8    8    9   10   11   12   12   12   12   12   12   14   14   15 
LCS_GDT     D      84     D      84      4    8   13     0    3    6    7    8    8    8   10   10   11   11   12   12   12   12   12   14   14   14   15 
LCS_GDT     G      85     G      85      4    8   13     3    4    6    7    8    8    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     P      86     P      86      4    7   13     3    3    4    5    5    7    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     A      87     A      87      4    7   13     3    3    4    4    6    7    7   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     P      88     P      88      4    7   13     2    3    4    5    6    7    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     P      89     P      89      4    7   13     0    3    4    4    6    7    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     K      90     K      90      4    7   13     3    3    4    5    6    7    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     V      91     V      91      3    7   13     3    3    4    5    6    7    7   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     M      92     M      92      3    4   13     3    3    4    5    5    6    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     K      93     K      93      3    4   13     3    3    4    5    5    6    8   10   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     R      94     R      94      3    4   13     3    3    3    5    5    6    6    7   10   11   11   12   13   13   13   13   14   14   14   15 
LCS_GDT     L      95     L      95      3    3   13     3    3    3    3    4    4    4    5    6    8   10   11   13   13   13   13   14   14   14   15 
LCS_GDT     S      96     S      96      3    3   13     3    3    3    3    4    4    4    4    6    8    8   11   13   13   13   13   14   14   14   15 
LCS_GDT     L      97     L      97      3    3   13     0    3    3    3    4    4    4    4    6    8    8   11   13   13   13   13   14   14   14   15 
LCS_AVERAGE  LCS_A:   7.85  (   3.67    6.76   13.14 )

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      4      4      6      7      8      8      8     10     10     11     11     12     13     13     13     13     14     14     14     15 
GDT PERCENT_CA   4.26   4.26   6.38   7.45   8.51   8.51   8.51  10.64  10.64  11.70  11.70  12.77  13.83  13.83  13.83  13.83  14.89  14.89  14.89  15.96
GDT RMS_LOCAL    0.37   0.37   0.99   1.19   1.40   1.40   1.40   2.92   2.92   3.32   3.32   4.02   4.59   4.59   4.59   4.59   5.07   5.07   5.07   5.81
GDT RMS_ALL_CA  23.76  23.76  24.58  24.83  24.89  24.89  24.89  15.58  15.58  15.62  15.62  14.47  17.19  17.19  17.19  17.19  16.71  16.71  16.71  15.90

#      Molecule1      Molecule2       DISTANCE
LGA    V      78      V      78         38.686
LGA    K      79      K      79         33.803
LGA    L      80      L      80         28.196
LGA    V      81      V      81         21.253
LGA    S      82      S      82         15.359
LGA    L      83      L      83          9.771
LGA    D      84      D      84          3.339
LGA    G      85      G      85          2.248
LGA    P      86      P      86          2.360
LGA    A      87      A      87          3.959
LGA    P      88      P      88          1.744
LGA    P      89      P      89          3.199
LGA    K      90      K      90          1.545
LGA    V      91      V      91          3.818
LGA    M      92      M      92          2.973
LGA    K      93      K      93          2.931
LGA    R      94      R      94          6.802
LGA    L      95      L      95         12.053
LGA    S      96      S      96         12.957
LGA    L      97      L      97         13.857

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   94    4.0     10    2.92     9.043     8.814     0.331

LGA_LOCAL      RMSD =  2.918  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.579  Number of atoms =   20 
Std_ALL_ATOMS  RMSD = 11.697  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.481606 * X  +  -0.640543 * Y  +   0.598131 * Z  +  13.634641
  Y_new =   0.755854 * X  +  -0.041833 * Y  +  -0.653402 * Z  +  15.496768
  Z_new =   0.443553 * X  +   0.766782 * Y  +   0.464010 * Z  + -90.013199 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.026607   -2.114986  [ DEG:    58.8202   -121.1798 ]
  Theta =  -0.459559   -2.682033  [ DEG:   -26.3308   -153.6692 ]
  Phi   =   1.003495   -2.138098  [ DEG:    57.4960   -122.5040 ]
 
# 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: T0343AL242_1                                  
REMARK     2: T0343.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0343AL242_1.T0343.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   94   4.0   10   2.92   8.814    11.70
REMARK  ---------------------------------------------------------- 
MOLECULE T0343AL242_1
REMARK Aligment from pdb entry: 1pjm_A
ATOM      1  N   VAL    78      25.277  23.807 -15.997  1.00  0.00              
ATOM      2  CA  VAL    78      24.286  23.099 -15.132  1.00  0.00              
ATOM      3  C   VAL    78      24.674  21.626 -14.951  1.00  0.00              
ATOM      4  O   VAL    78      25.361  21.038 -15.797  1.00  0.00              
ATOM      5  N   LYS    79      24.238  21.031 -13.845  1.00  0.00              
ATOM      6  CA  LYS    79      24.574  19.643 -13.613  1.00  0.00              
ATOM      7  C   LYS    79      23.907  18.954 -12.440  1.00  0.00              
ATOM      8  O   LYS    79      22.683  18.961 -12.289  1.00  0.00              
ATOM      9  N   LEU    80      24.753  18.345 -11.618  1.00  0.00              
ATOM     10  CA  LEU    80      24.344  17.584 -10.450  1.00  0.00              
ATOM     11  C   LEU    80      23.412  18.309  -9.496  1.00  0.00              
ATOM     12  O   LEU    80      23.678  19.437  -9.087  1.00  0.00              
ATOM     13  N   VAL    81      22.319  17.645  -9.139  1.00  0.00              
ATOM     14  CA  VAL    81      21.351  18.189  -8.202  1.00  0.00              
ATOM     15  C   VAL    81      21.352  17.247  -7.012  1.00  0.00              
ATOM     16  O   VAL    81      21.128  16.044  -7.158  1.00  0.00              
ATOM     17  N   SER    82      21.623  17.797  -5.834  1.00  0.00              
ATOM     18  CA  SER    82      21.697  16.996  -4.615  1.00  0.00              
ATOM     19  C   SER    82      20.428  16.285  -4.195  1.00  0.00              
ATOM     20  O   SER    82      19.316  16.685  -4.561  1.00  0.00              
ATOM     21  N   LEU    83      20.624  15.208  -3.435  1.00  0.00              
ATOM     22  CA  LEU    83      19.538  14.408  -2.892  1.00  0.00              
ATOM     23  C   LEU    83      18.951  15.276  -1.806  1.00  0.00              
ATOM     24  O   LEU    83      19.565  15.466  -0.745  1.00  0.00              
ATOM     25  N   ASP    84      17.789  15.844  -2.077  1.00  0.00              
ATOM     26  CA  ASP    84      17.164  16.697  -1.090  1.00  0.00              
ATOM     27  C   ASP    84      15.673  16.483  -0.958  1.00  0.00              
ATOM     28  O   ASP    84      14.946  16.353  -1.946  1.00  0.00              
ATOM     29  N   GLY    85      15.241  16.435   0.298  1.00  0.00              
ATOM     30  CA  GLY    85      13.851  16.190   0.622  1.00  0.00              
ATOM     31  C   GLY    85      13.839  14.876   1.381  1.00  0.00              
ATOM     32  O   GLY    85      14.867  14.192   1.452  1.00  0.00              
ATOM     33  N   PRO    86      12.689  14.519   1.941  1.00  0.00              
ATOM     34  CA  PRO    86      12.541  13.281   2.705  1.00  0.00              
ATOM     35  C   PRO    86      12.965  12.007   1.957  1.00  0.00              
ATOM     36  O   PRO    86      13.871  12.026   1.120  1.00  0.00              
ATOM     37  N   ALA    87      12.314  10.895   2.289  1.00  0.00              
ATOM     38  CA  ALA    87      12.583   9.608   1.650  1.00  0.00              
ATOM     39  C   ALA    87      11.324   8.748   1.841  1.00  0.00              
ATOM     40  O   ALA    87      10.720   8.301   0.863  1.00  0.00              
ATOM     41  N   PRO    88      10.908   8.506   3.106  1.00  0.00              
ATOM     42  CA  PRO    88      11.514   8.964   4.366  1.00  0.00              
ATOM     43  C   PRO    88      12.502   7.907   4.880  1.00  0.00              
ATOM     44  O   PRO    88      12.204   6.711   4.859  1.00  0.00              
ATOM     45  N   PRO    89      13.688   8.334   5.347  1.00  0.00              
ATOM     46  CA  PRO    89      14.681   7.378   5.852  1.00  0.00              
ATOM     47  C   PRO    89      14.251   6.638   7.128  1.00  0.00              
ATOM     48  O   PRO    89      13.175   6.896   7.682  1.00  0.00              
ATOM     49  N   LYS    90      15.096   5.710   7.574  1.00  0.00              
ATOM     50  CA  LYS    90      14.834   4.935   8.788  1.00  0.00              
ATOM     51  C   LYS    90      14.385   5.822   9.954  1.00  0.00              
ATOM     52  O   LYS    90      14.605   7.033   9.946  1.00  0.00              
ATOM     53  N   VAL    91      13.720   5.229  10.961  1.00  0.00              
ATOM     54  CA  VAL    91      13.310   6.066  12.093  1.00  0.00              
ATOM     55  C   VAL    91      14.602   6.393  12.849  1.00  0.00              
ATOM     56  O   VAL    91      15.523   5.578  12.896  1.00  0.00              
ATOM     57  N   MET    92      14.684   7.585  13.418  1.00  0.00              
ATOM     58  CA  MET    92      15.875   7.976  14.154  1.00  0.00              
ATOM     59  C   MET    92      16.092   7.084  15.387  1.00  0.00              
ATOM     60  O   MET    92      17.225   6.716  15.708  1.00  0.00              
ATOM     61  N   LYS    93      15.003   6.725  16.062  1.00  0.00              
ATOM     62  CA  LYS    93      15.095   5.926  17.274  1.00  0.00              
ATOM     63  C   LYS    93      14.228   4.665  17.255  1.00  0.00              
ATOM     64  O   LYS    93      13.378   4.502  16.376  1.00  0.00              
ATOM     65  N   ARG    94      14.465   3.779  18.227  1.00  0.00              
ATOM     66  CA  ARG    94      13.738   2.510  18.354  1.00  0.00              
ATOM     67  C   ARG    94      13.372   2.190  19.795  1.00  0.00              
ATOM     68  O   ARG    94      14.241   2.090  20.668  1.00  0.00              
ATOM     69  N   LEU    95      12.084   2.001  20.040  1.00  0.00              
ATOM     70  CA  LEU    95      11.596   1.656  21.372  1.00  0.00              
ATOM     71  C   LEU    95      11.648   0.130  21.448  1.00  0.00              
ATOM     72  O   LEU    95      11.295  -0.553  20.488  1.00  0.00              
ATOM     73  N   SER    96      12.104  -0.405  22.573  1.00  0.00              
ATOM     74  CA  SER    96      12.154  -1.850  22.702  1.00  0.00              
ATOM     75  C   SER    96      10.867  -2.390  23.334  1.00  0.00              
ATOM     76  O   SER    96      10.561  -2.100  24.486  1.00  0.00              
ATOM     77  N   LEU    97      10.098  -3.152  22.562  1.00  0.00              
ATOM     78  CA  LEU    97       8.859  -3.719  23.066  1.00  0.00              
ATOM     79  C   LEU    97       9.142  -5.006  23.813  1.00  0.00              
ATOM     80  O   LEU    97       8.417  -5.331  24.784  1.00  0.00              
END
