
#######################################################
#                                                     #
#                        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   23 (  115),  selected   23 , name T0300TS239_2_2
# Molecule2: number of CA atoms   89 (  695),  selected   23 , name T0300
# PARAMETERS: T0300TS239_2_2.T0300  -3  -ie  -d:4  -o1  -sda  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        80 - 98          4.73     7.24
  LONGEST_CONTINUOUS_SEGMENT:    19        81 - 99          4.97     6.60
  LCS_AVERAGE:     20.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        81 - 93          1.78    11.48
  LCS_AVERAGE:     10.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        82 - 92          0.80    11.61
  LCS_AVERAGE:      7.87

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:   89
LCS_GDT     V      80     V      80      3    4   19     0    3    3    3    5    6    9   12   14   14   17   17   17   18   18   20   22   22   22   23 
LCS_GDT     T      81     T      81      3   13   19     3    3    3    4   11   12   12   13   14   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     E      82     E      82     11   13   19     3    4   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     Q      83     Q      83     11   13   19     7   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     E      84     E      84     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     L      85     L      85     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     T      86     T      86     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     S      87     S      87     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     L      88     L      88     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     L      89     L      89     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     Q      90     Q      90     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     S      91     S      91     11   13   19     7   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     L      92     L      92     11   13   19     8   10   10   11   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     T      93     T      93      3   13   19     1    3    3    9   12   12   12   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     L      94     L      94      3    3   19     3    3    3    3    7    7   10   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     R      95     R      95      3    3   19     3    3    3    3    3    3    7   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     V      96     V      96      3    3   19     3    3    3    3    3    3    7   13   15   16   17   17   17   18   19   20   22   22   22   23 
LCS_GDT     D      97     D      97      3    3   19     1    4    4    4    4    4    5    6    7    8   12   15   17   18   19   20   22   22   22   23 
LCS_GDT     V      98     V      98      3    5   19     0    4    4    4    4    5    5    6    7    8    9   13   17   17   19   20   22   22   22   23 
LCS_GDT     S      99     S      99      4    5   19     4    4    4    4    4    5    5    6    7    8    8   10   11   13   18   20   22   22   22   23 
LCS_GDT     M     100     M     100      4    5   10     4    4    4    4    4    5    5    6    7    8    8    9   10   11   15   17   22   22   22   23 
LCS_GDT     E     101     E     101      4    5   10     4    4    4    4    4    5    5    6    7    8    8    9   10   11   15   15   19   21   22   23 
LCS_GDT     E     102     E     102      4    5   10     4    4    4    4    4    5    5    6    7    8   10   15   17   17   19   20   22   22   22   23 
LCS_AVERAGE  LCS_A:  12.72  (   7.87   10.26   20.03 )

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      8     10     10     11     12     12     12     13     15     16     17     17     17     18     19     20     22     22     22     23 
GDT PERCENT_CA   8.99  11.24  11.24  12.36  13.48  13.48  13.48  14.61  16.85  17.98  19.10  19.10  19.10  20.22  21.35  22.47  24.72  24.72  24.72  25.84
GDT RMS_LOCAL    0.36   0.45   0.45   0.80   1.15   1.15   1.15   1.78   2.99   3.20   3.61   3.61   3.61   4.05   5.01   5.24   5.85   5.85   5.85   6.15
GDT RMS_ALL_CA  11.61  11.42  11.42  11.61  11.45  11.45  11.45  11.48   8.37   8.42   8.57   8.57   8.57   8.04   6.50   6.42   6.20   6.20   6.20   6.15

#      Molecule1      Molecule2       DISTANCE
LGA    V      80      V      80          7.195
LGA    T      81      T      81          3.651
LGA    E      82      E      82          3.533
LGA    Q      83      Q      83          0.885
LGA    E      84      E      84          1.245
LGA    L      85      L      85          1.539
LGA    T      86      T      86          1.042
LGA    S      87      S      87          0.733
LGA    L      88      L      88          0.562
LGA    L      89      L      89          0.642
LGA    Q      90      Q      90          0.777
LGA    S      91      S      91          0.453
LGA    L      92      L      92          0.869
LGA    T      93      T      93          3.115
LGA    L      94      L      94          8.508
LGA    R      95      R      95          9.114
LGA    V      96      V      96          9.048
LGA    D      97      D      97         14.211
LGA    V      98      V      98         19.010
LGA    S      99      S      99         19.669
LGA    M     100      M     100         20.527
LGA    E     101      E     101         25.508
LGA    E     102      E     102         25.160

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   89    4.0     13    1.78    15.169    14.067     0.690

LGA_LOCAL      RMSD =  1.784  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.399  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  6.152  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.664975 * X  +   0.495705 * Y  +   0.558646 * Z  + -101.711098
  Y_new =   0.734249 * X  +  -0.296991 * Y  +  -0.610471 * Z  + -76.206879
  Z_new =  -0.136701 * X  +   0.816133 * Y  +  -0.561462 * Z  +  10.085139 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.173392   -0.968201  [ DEG:   124.5262    -55.4738 ]
  Theta =   0.137131    3.004462  [ DEG:     7.8570    172.1430 ]
  Phi   =   0.834867   -2.306726  [ DEG:    47.8343   -132.1657 ]
 
# 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: T0300TS239_2_2                                
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300TS239_2_2.T0300 -3 -ie -d:4 -o1 -sda 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   89   4.0   13   1.78  14.067     6.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0300TS239_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0300
PARENT 1avo_B
ATOM    364  N   VAL    80      30.478  -5.818  26.557  1.00  9.99
ATOM    365  CA  VAL    80      31.858  -6.079  26.992  1.00  9.99
ATOM    366  C   VAL    80      31.969  -6.661  28.402  1.00  9.99
ATOM    367  O   VAL    80      33.023  -7.182  28.807  1.00  9.99
ATOM    368  CB  VAL    80      32.529  -4.718  26.852  1.00  9.99
ATOM    369  N   THR    81      30.876  -6.611  29.142  1.00  9.99
ATOM    370  CA  THR    81      30.888  -7.170  30.474  1.00  9.99
ATOM    371  C   THR    81      30.648  -8.681  30.441  1.00  9.99
ATOM    372  O   THR    81      30.924  -9.382  31.425  1.00  9.99
ATOM    373  CB  THR    81      29.817  -6.483  31.349  1.00  9.99
ATOM    374  N   GLU    82      30.080  -9.168  29.334  1.00  9.99
ATOM    375  CA  GLU    82      29.756 -10.576  29.207  1.00  9.99
ATOM    376  C   GLU    82      30.936 -11.244  28.576  1.00  9.99
ATOM    377  O   GLU    82      31.232 -11.003  27.411  1.00  9.99
ATOM    378  CB  GLU    82      28.530 -10.790  28.383  1.00  9.99
ATOM    379  N   GLN    83      31.639 -12.033  29.387  1.00  9.99
ATOM    380  CA  GLN    83      32.827 -12.693  28.934  1.00  9.99
ATOM    381  C   GLN    83      32.585 -13.903  28.085  1.00  9.99
ATOM    382  O   GLN    83      33.497 -14.359  27.383  1.00  9.99
ATOM    383  CB  GLN    83      33.670 -13.062  30.165  1.00  9.99
ATOM    384  N   GLU    84      31.372 -14.445  28.155  1.00  9.99
ATOM    385  CA  GLU    84      31.026 -15.631  27.378  1.00  9.99
ATOM    386  C   GLU    84      31.027 -15.342  25.894  1.00  9.99
ATOM    387  O   GLU    84      31.305 -16.231  25.089  1.00  9.99
ATOM    388  CB  GLU    84      29.704 -16.203  27.835  1.00  9.99
ATOM    389  N   LEU    85      30.799 -14.082  25.532  1.00  9.99
ATOM    390  CA  LEU    85      30.804 -13.709  24.135  1.00  9.99
ATOM    391  C   LEU    85      32.227 -13.675  23.591  1.00  9.99
ATOM    392  O   LEU    85      32.460 -13.973  22.416  1.00  9.99
ATOM    393  CB  LEU    85      30.118 -12.366  23.929  1.00  9.99
ATOM    394  N   THR    86      33.201 -13.350  24.424  1.00  9.99
ATOM    395  CA  THR    86      34.549 -13.341  23.901  1.00  9.99
ATOM    396  C   THR    86      34.982 -14.766  23.783  1.00  9.99
ATOM    397  O   THR    86      35.671 -15.122  22.823  1.00  9.99
ATOM    398  CB  THR    86      35.511 -12.591  24.782  1.00  9.99
ATOM    399  N   SER    87      34.549 -15.592  24.736  1.00  9.99
ATOM    400  CA  SER    87      34.925 -16.991  24.671  1.00  9.99
ATOM    401  C   SER    87      34.261 -17.660  23.468  1.00  9.99
ATOM    402  O   SER    87      34.869 -18.477  22.785  1.00  9.99
ATOM    403  CB  SER    87      34.558 -17.721  25.939  1.00  9.99
ATOM    404  N   LEU    88      33.013 -17.291  23.202  1.00  9.99
ATOM    405  CA  LEU    88      32.274 -17.852  22.087  1.00  9.99
ATOM    406  C   LEU    88      33.061 -17.571  20.838  1.00  9.99
ATOM    407  O   LEU    88      33.341 -18.481  20.074  1.00  9.99
ATOM    408  CB  LEU    88      30.919 -17.202  21.958  1.00  9.99
ATOM    409  N   LEU    89      33.466 -16.329  20.634  1.00  9.99
ATOM    410  CA  LEU    89      34.245 -16.058  19.426  1.00  9.99
ATOM    411  C   LEU    89      35.441 -16.995  19.257  1.00  9.99
ATOM    412  O   LEU    89      35.733 -17.452  18.167  1.00  9.99
ATOM    413  CB  LEU    89      34.780 -14.647  19.389  1.00  9.99
ATOM    414  N   GLN    90      36.114 -17.328  20.340  1.00  9.99
ATOM    415  CA  GLN    90      37.265 -18.210  20.210  1.00  9.99
ATOM    416  C   GLN    90      36.879 -19.643  20.054  1.00  9.99
ATOM    417  O   GLN    90      37.604 -20.432  19.489  1.00  9.99
ATOM    418  CB  GLN    90      38.254 -18.006  21.352  1.00  9.99
ATOM    419  N   SER    91      35.684 -19.963  20.490  1.00  9.99
ATOM    420  CA  SER    91      35.218 -21.311  20.361  1.00  9.99
ATOM    421  C   SER    91      34.819 -21.565  18.913  1.00  9.99
ATOM    422  O   SER    91      35.064 -22.652  18.391  1.00  9.99
ATOM    423  CB  SER    91      34.077 -21.548  21.327  1.00  9.99
ATOM    424  N   LEU    92      34.285 -20.544  18.241  1.00  9.99
ATOM    425  CA  LEU    92      33.893 -20.674  16.839  1.00  9.99
ATOM    426  C   LEU    92      35.118 -20.914  15.960  1.00  9.99
ATOM    427  O   LEU    92      35.070 -21.719  15.034  1.00  9.99
ATOM    428  CB  LEU    92      33.143 -19.424  16.343  1.00  9.99
ATOM    429  N   THR    93      36.205 -20.203  16.236  1.00  9.99
ATOM    430  CA  THR    93      37.405 -20.359  15.439  1.00  9.99
ATOM    431  C   THR    93      37.973 -21.743  15.627  1.00  9.99
ATOM    432  O   THR    93      38.327 -22.413  14.675  1.00  9.99
ATOM    433  CB  THR    93      38.449 -19.313  15.817  1.00  9.99
ATOM    434  N   LEU    94      38.022 -22.205  16.865  1.00  9.99
ATOM    435  CA  LEU    94      38.567 -23.526  17.118  1.00  9.99
ATOM    436  C   LEU    94      37.751 -24.543  16.416  1.00  9.99
ATOM    437  O   LEU    94      38.282 -25.435  15.789  1.00  9.99
ATOM    438  CB  LEU    94      38.571 -23.845  18.591  1.00  9.99
ATOM    439  N   ARG    95      36.439 -24.380  16.476  1.00  9.99
ATOM    440  CA  ARG    95      35.567 -25.330  15.818  1.00  9.99
ATOM    441  C   ARG    95      35.715 -25.246  14.342  1.00  9.99
ATOM    442  O   ARG    95      35.803 -26.255  13.709  1.00  9.99
ATOM    443  CB  ARG    95      34.173 -25.110  16.176  1.00  9.99
ATOM    444  N   VAL    96      35.802 -24.052  13.770  1.00  9.99
ATOM    445  CA  VAL    96      35.915 -23.985  12.317  1.00  9.99
ATOM    446  C   VAL    96      37.211 -24.661  11.925  1.00  9.99
ATOM    447  O   VAL    96      37.293 -25.347  10.921  1.00  9.99
ATOM    448  CB  VAL    96      35.825 -22.564  11.794  1.00  9.99
ATOM    449  N   ASP    97      38.196 -24.577  12.796  1.00  9.99
ATOM    450  CA  ASP    97      39.446 -25.199  12.466  1.00  9.99
ATOM    451  C   ASP    97      39.283 -26.712  12.514  1.00  9.99
ATOM    452  O   ASP    97      39.737 -27.413  11.630  1.00  9.99
ATOM    453  CB  ASP    97      40.541 -24.717  13.394  1.00  9.99
ATOM    454  N   VAL    98      38.582 -27.212  13.523  1.00  9.99
ATOM    455  CA  VAL    98      38.380 -28.646  13.639  1.00  9.99
ATOM    456  C   VAL    98      37.572 -29.220  12.515  1.00  9.99
ATOM    457  O   VAL    98      37.762 -30.369  12.162  1.00  9.99
ATOM    458  CB  VAL    98      37.761 -28.998  14.961  1.00  9.99
ATOM    459  N   SER    99      36.716 -28.390  11.925  1.00  9.99
ATOM    460  CA  SER    99      35.842 -28.781  10.805  1.00  9.99
ATOM    461  C   SER    99      36.574 -28.844   9.499  1.00  9.99
ATOM    462  O   SER    99      36.365 -29.768   8.719  1.00  9.99
ATOM    463  CB  SER    99      34.724 -27.794  10.605  1.00  9.99
ATOM    464  N   MET   100      37.372 -27.823   9.214  1.00  9.99
ATOM    465  CA  MET   100      38.146 -27.819   7.998  1.00  9.99
ATOM    466  C   MET   100      38.935 -29.123   7.886  1.00  9.99
ATOM    467  O   MET   100      38.966 -29.756   6.841  1.00  9.99
ATOM    468  CB  MET   100      39.128 -26.698   7.988  1.00  9.99
ATOM    469  N   GLU   101      39.557 -29.542   8.983  1.00  9.99
ATOM    470  CA  GLU   101      40.326 -30.770   8.961  1.00  9.99
ATOM    471  C   GLU   101      39.386 -31.913   8.629  1.00  9.99
ATOM    472  O   GLU   101      39.667 -32.708   7.763  1.00  9.99
ATOM    473  CB  GLU   101      41.023 -30.985  10.287  1.00  9.99
ATOM    474  N   GLU   102      38.237 -31.947   9.276  1.00  9.99
ATOM    475  CA  GLU   102      37.259 -32.969   9.005  1.00  9.99
ATOM    476  C   GLU   102      36.702 -32.905   7.609  1.00  9.99
ATOM    477  O   GLU   102      36.394 -33.948   7.054  1.00  9.99
ATOM    478  CB  GLU   102      36.115 -32.841   9.945  1.00  9.99
TER
END
