
#######################################################
#                                                     #
#                        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   18 (   89),  selected   18 , name T0386TS261_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   18 , name T0386_D2.pdb
# PARAMETERS: T0386TS261_1-D2.T0386_D2.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:    11       228 - 238         4.88    12.78
  LONGEST_CONTINUOUS_SEGMENT:    11       229 - 239         3.04    16.62
  LCS_AVERAGE:     12.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       229 - 237         1.38    16.20
  LCS_AVERAGE:      9.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       222 - 228         0.29    15.11
  LCS_AVERAGE:      7.00

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:   81
LCS_GDT     K     222     K     222      7    7    8     7    7    7    7    7    7    7    7    9   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     I     223     I     223      7    7    8     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     R     224     R     224      7    7    8     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     L     225     L     225      7    7    8     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     L     226     L     226      7    7    8     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     K     227     K     227      7    7    8     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     E     228     E     228      7    7   11     7    7    7    7    7    7    8    9   10   10   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     F     229     F     229      6    9   11     4    6    7    9    9    9    9    9   10   11   11   11   11   11   11   11   13   14   15   16 
LCS_GDT     M     230     M     230      6    9   11     4    6    7    9    9    9    9   10   10   11   11   11   11   11   11   11   13   14   15   16 
LCS_GDT     H     231     H     231      6    9   11     4    6    7    9    9    9    9   10   10   11   11   11   11   15   16   16   16   16   16   16 
LCS_GDT     T     232     T     232      6    9   11     4    6    7    9    9    9    9   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     M     233     M     233      6    9   11     4    6    7    9    9    9    9   10   10   11   11   14   14   15   16   16   16   16   16   16 
LCS_GDT     K     234     K     234      6    9   11     4    6    7    9    9    9    9   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     N     235     N     235      4    9   11     3    4    4    9    9    9    9   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     T     236     T     236      4    9   11     3    5    7    9    9    9    9   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     G     237     G     237      3    9   11     3    3    4    9    9    9    9   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     R     238     R     238      3    4   11     3    3    3    4    5    6    8   10   10   11   13   14   14   15   16   16   16   16   16   16 
LCS_GDT     N     239     N     239      3    4   11     0    0    3    3    5    5    8   10   10   11   11   11   12   15   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   9.60  (   7.00    9.47   12.35 )

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      7      7      7      9      9      9      9     10     10     11     13     14     14     15     16     16     16     16     16     16 
GDT PERCENT_CA   8.64   8.64   8.64  11.11  11.11  11.11  11.11  12.35  12.35  13.58  16.05  17.28  17.28  18.52  19.75  19.75  19.75  19.75  19.75  19.75
GDT RMS_LOCAL    0.29   0.29   0.29   1.38   1.38   1.38   1.38   2.91   2.43   3.04   4.11   4.28   4.28   4.72   5.06   5.06   5.06   5.06   5.06   5.06
GDT RMS_ALL_CA  15.11  15.11  15.11  16.20  16.20  16.20  16.20  17.51  16.27  16.62   6.96   6.84   6.84   6.58   6.47   6.47   6.47   6.47   6.47   6.47

#      Molecule1      Molecule2       DISTANCE
LGA    K     222      K     222         34.372
LGA    I     223      I     223         32.590
LGA    R     224      R     224         29.913
LGA    L     225      L     225         27.420
LGA    L     226      L     226         24.126
LGA    K     227      K     227         22.864
LGA    E     228      E     228         20.292
LGA    F     229      F     229          5.048
LGA    M     230      M     230          2.587
LGA    H     231      H     231          1.973
LGA    T     232      T     232          3.093
LGA    M     233      M     233          2.450
LGA    K     234      K     234          3.866
LGA    N     235      N     235          2.527
LGA    T     236      T     236          0.980
LGA    G     237      G     237          3.608
LGA    R     238      R     238          3.081
LGA    N     239      N     239          3.742

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   81    4.0     10    2.91    12.963    11.918     0.332

LGA_LOCAL      RMSD =  2.915  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.507  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  6.293  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.480612 * X  +   0.381427 * Y  +   0.789636 * Z  +   2.511187
  Y_new =  -0.703774 * X  +  -0.369441 * Y  +   0.606808 * Z  +  82.262146
  Z_new =   0.523177 * X  +  -0.847364 * Y  +   0.090881 * Z  + 132.738327 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.463954    1.677639  [ DEG:   -83.8784     96.1216 ]
  Theta =  -0.550575   -2.591018  [ DEG:   -31.5456   -148.4544 ]
  Phi   =  -0.971634    2.169958  [ DEG:   -55.6706    124.3295 ]
 
# 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: T0386TS261_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS261_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   81   4.0   10   2.91  11.918     6.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS261_1-D2
PFRMAT TS
TARGET T0386
MODEL  1
PARENT 2f6s_A
ATOM    724  N   LYS   222      17.405  92.453  78.947  1.00  6.52
ATOM    725  CA  LYS   222      17.203  91.103  79.420  1.00  6.52
ATOM    726  C   LYS   222      15.929  91.007  80.252  1.00  6.52
ATOM    727  O   LYS   222      15.173  90.054  80.091  1.00  6.52
ATOM    728  CB  LYS   222      18.454  90.500  80.150  1.00  6.52
ATOM    729  N   ILE   223      15.668  91.994  81.113  1.00  6.44
ATOM    730  CA  ILE   223      14.445  91.975  81.925  1.00  6.44
ATOM    731  C   ILE   223      13.216  91.940  81.030  1.00  6.44
ATOM    732  O   ILE   223      12.310  91.152  81.260  1.00  6.44
ATOM    733  CB  ILE   223      14.346  93.183  82.852  1.00  6.44
ATOM    734  N   ARG   224      13.193  92.780  79.998  1.00  6.76
ATOM    735  CA  ARG   224      12.048  92.876  79.092  1.00  6.76
ATOM    736  C   ARG   224      11.883  91.596  78.289  1.00  6.76
ATOM    737  O   ARG   224      10.767  91.103  78.110  1.00  6.76
ATOM    738  CB  ARG   224      12.220  94.081  78.125  1.00  6.76
ATOM    739  N   LEU   225      12.999  91.058  77.809  1.00  4.98
ATOM    740  CA  LEU   225      12.987  89.889  76.951  1.00  4.98
ATOM    741  C   LEU   225      12.443  88.686  77.705  1.00  4.98
ATOM    742  O   LEU   225      11.558  87.981  77.208  1.00  4.98
ATOM    743  CB  LEU   225      14.396  89.601  76.444  1.00  4.98
ATOM    744  N   LEU   226      12.970  88.460  78.908  1.00  5.03
ATOM    745  CA  LEU   226      12.507  87.362  79.757  1.00  5.03
ATOM    746  C   LEU   226      11.061  87.508  80.201  1.00  5.03
ATOM    747  O   LEU   226      10.321  86.530  80.179  1.00  5.03
ATOM    748  CB  LEU   226      13.415  87.184  80.976  1.00  5.03
ATOM    749  N   LYS   227      10.649  88.718  80.581  1.00  5.51
ATOM    750  CA  LYS   227       9.295  88.911  81.122  1.00  5.51
ATOM    751  C   LYS   227       8.213  88.520  80.124  1.00  5.51
ATOM    752  O   LYS   227       7.127  88.130  80.512  1.00  5.51
ATOM    753  CB  LYS   227       9.079  90.335  81.614  1.00  5.51
ATOM    754  N   GLU   228       8.538  88.594  78.839  1.00  5.26
ATOM    755  CA  GLU   228       7.584  88.321  77.764  1.00  5.26
ATOM    756  C   GLU   228       7.430  86.848  77.394  1.00  5.26
ATOM    757  O   GLU   228       6.583  86.518  76.583  1.00  5.26
ATOM    758  CB  GLU   228       7.976  89.102  76.509  1.00  5.26
ATOM    759  N   PHE   229      10.017  71.676  78.935  1.00  2.98
ATOM    760  CA  PHE   229      11.317  71.792  79.564  1.00  2.98
ATOM    761  C   PHE   229      12.436  71.350  78.621  1.00  2.98
ATOM    762  O   PHE   229      13.473  72.006  78.534  1.00  2.98
ATOM    763  CB  PHE   229      11.333  70.996  80.871  1.00  2.98
ATOM    764  N   MET   230      12.212  70.258  77.899  1.00  3.96
ATOM    765  CA  MET   230      13.189  69.754  76.938  1.00  3.96
ATOM    766  C   MET   230      13.372  70.731  75.767  1.00  3.96
ATOM    767  O   MET   230      14.503  71.020  75.382  1.00  3.96
ATOM    768  CB  MET   230      12.839  68.302  76.446  1.00  3.96
ATOM    769  N   HIS   231      12.269  71.245  75.225  1.00  5.48
ATOM    770  CA  HIS   231      12.334  72.305  74.217  1.00  5.48
ATOM    771  C   HIS   231      13.149  73.498  74.706  1.00  5.48
ATOM    772  O   HIS   231      13.958  74.055  73.960  1.00  5.48
ATOM    773  CB  HIS   231      10.947  72.778  73.823  1.00  5.48
ATOM    774  N   THR   232      12.942  73.867  75.966  1.00  3.05
ATOM    775  CA  THR   232      13.682  74.929  76.599  1.00  3.05
ATOM    776  C   THR   232      15.173  74.660  76.652  1.00  3.05
ATOM    777  O   THR   232      15.987  75.523  76.276  1.00  3.05
ATOM    778  CB  THR   232      13.112  75.149  78.011  1.00  3.05
ATOM    779  N   MET   233      15.547  73.470  77.110  1.00  5.81
ATOM    780  CA  MET   233      16.959  73.153  77.280  1.00  5.81
ATOM    781  C   MET   233      17.648  72.978  75.937  1.00  5.81
ATOM    782  O   MET   233      18.800  73.345  75.794  1.00  5.81
ATOM    783  CB  MET   233      17.164  71.931  78.188  1.00  5.81
ATOM    784  N   LYS   234      16.937  72.439  74.948  1.00  5.54
ATOM    785  CA  LYS   234      17.465  72.324  73.599  1.00  5.54
ATOM    786  C   LYS   234      17.822  73.721  73.074  1.00  5.54
ATOM    787  O   LYS   234      18.848  73.901  72.433  1.00  5.54
ATOM    788  CB  LYS   234      16.461  71.607  72.657  1.00  5.54
ATOM    789  N   ASN   235      16.988  74.713  73.359  1.00  4.31
ATOM    790  CA  ASN   235      17.243  76.061  72.890  1.00  4.31
ATOM    791  C   ASN   235      18.433  76.659  73.634  1.00  4.31
ATOM    792  O   ASN   235      19.279  77.329  73.029  1.00  4.31
ATOM    793  CB  ASN   235      16.022  76.929  73.092  1.00  4.31
ATOM    794  N   THR   236      18.506  76.393  74.941  1.00  1.91
ATOM    795  CA  THR   236      19.624  76.842  75.742  1.00  1.91
ATOM    796  C   THR   236      20.945  76.367  75.117  1.00  1.91
ATOM    797  O   THR   236      21.892  77.144  74.992  1.00  1.91
ATOM    798  CB  THR   236      19.484  76.332  77.181  1.00  1.91
ATOM    799  N   GLY   237      20.999  75.094  74.723  1.00  1.75
ATOM    800  CA  GLY   237      22.192  74.529  74.079  1.00  1.75
ATOM    801  C   GLY   237      22.412  75.099  72.683  1.00  1.75
ATOM    802  O   GLY   237      23.553  75.247  72.229  1.00  1.75
ATOM    803  N   ARG   238      21.311  75.440  72.020  1.00  7.65
ATOM    804  CA  ARG   238      21.384  76.091  70.737  1.00  7.65
ATOM    805  C   ARG   238      22.045  77.465  70.825  1.00  7.65
ATOM    806  O   ARG   238      22.703  77.889  69.870  1.00  7.65
ATOM    807  CB  ARG   238      19.997  76.200  70.099  1.00  7.65
ATOM    808  N   ASN   239      23.496  72.724  66.995  1.00  5.57
ATOM    809  CA  ASN   239      22.437  72.779  65.979  1.00  5.57
ATOM    810  C   ASN   239      21.854  71.417  65.653  1.00  5.57
ATOM    811  O   ASN   239      21.092  70.849  66.444  1.00  5.57
ATOM    812  CB  ASN   239      22.997  73.442  64.709  1.00  5.57
TER
END
