
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0316AL380_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   28 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_3-D2.T0316_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:    22       223 - 244         4.94     8.13
  LCS_AVERAGE:     33.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       232 - 237         1.78    10.15
  LCS_AVERAGE:      7.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       233 - 237         0.94    11.89
  LONGEST_CONTINUOUS_SEGMENT:     5       243 - 247         0.98    21.13
  LCS_AVERAGE:      6.73

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:   60
LCS_GDT     G     220     G     220      3    3   10     0    3    3    3    5    5    6    7    9    9   10   13   13   14   16   17   18   19   20   20 
LCS_GDT     R     221     R     221      3    3   10     2    3    3    4    5    5    6    7    9    9   11   13   13   14   17   17   18   19   22   24 
LCS_GDT     M     222     M     222      3    3   10     2    3    3    4    5    5    6    7    9    9   11   13   14   16   17   21   22   22   23   25 
LCS_GDT     M     223     M     223      3    5   22     0    4    4    4    4    5    6    8    9   13   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     T     224     T     224      4    5   22     4    4    4    5    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     V     225     V     225      4    5   22     4    4    4    4    4    5    7   10   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     D     226     D     226      4    5   22     4    4    4    4    4    5    6    6    9   10   11   13   18   20   22   22   22   23   23   25 
LCS_GDT     G     227     G     227      4    5   22     4    4    4    4    4    5    6    6    9   10   11   13   16   20   22   22   22   23   23   25 
LCS_GDT     R     228     R     228      3    4   22     3    3    3    3    4    6    8    8    9   12   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     D     229     D     229      3    4   22     3    3    3    4    5    6    8   10   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     M     230     M     230      3    4   22     3    3    3    4    5    6    8    9   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     G     231     G     231      3    4   22     3    3    3    4    5    6    6    7   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     E     232     E     232      3    6   22     3    4    4    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     H     233     H     233      5    6   22     3    3    5    5    5    7    8    8   12   14   16   19   20   20   22   22   22   23   23   25 
LCS_GDT     A     234     A     234      5    6   22     3    4    5    5    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     G     235     G     235      5    6   22     3    4    5    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     L     236     L     236      5    6   22     3    4    5    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     M     237     M     237      5    6   22     3    4    5    5    6    7    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     Y     238     Y     238      4    4   22     3    3    5    5    5    7    8    9   10   14   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     Y     239     Y     239      4    4   22     3    4    5    5    5    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     T     240     T     240      4    5   22     3    4    5    5    6    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     I     241     I     241      4    5   22     3    4    4    5    6    7    8   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     G     242     G     242      4    5   22     3    4    4    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     Q     243     Q     243      5    5   22     3    4    5    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     R     244     R     244      5    5   22     3    4    5    6    8    8    9   12   13   16   17   19   20   20   22   22   22   23   23   25 
LCS_GDT     G     245     G     245      5    5   18     3    4    5    5    6    7    8    9    9   11   13   14   17   19   21   21   22   23   23   25 
LCS_GDT     G     246     G     246      5    5   15     3    4    5    5    6    7    8    9    9   10   10   13   13   13   16   17   19   19   23   25 
LCS_GDT     L     247     L     247      5    5   13     3    4    5    5    6    7    8    9    9    9   10   13   13   13   15   16   18   18   18   20 
LCS_AVERAGE  LCS_A:  16.01  (   6.73    7.98   33.33 )

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      5      6      8      8      9     12     13     16     17     19     20     20     22     22     22     23     23     25 
GDT PERCENT_CA   6.67   6.67   8.33  10.00  13.33  13.33  15.00  20.00  21.67  26.67  28.33  31.67  33.33  33.33  36.67  36.67  36.67  38.33  38.33  41.67
GDT RMS_LOCAL    0.19   0.19   0.94   1.58   1.83   1.83   2.14   2.76   3.23   3.87   4.00   4.25   4.41   4.41   4.94   4.94   4.94   5.30   5.30   6.04
GDT RMS_ALL_CA  19.16  19.16  11.89   8.31   8.32   8.32   8.19   8.33   8.25   8.10   8.00   8.11   7.99   7.99   8.13   8.13   8.13   7.96   7.96   7.73

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         16.971
LGA    R     221      R     221         13.030
LGA    M     222      M     222         10.452
LGA    M     223      M     223          6.685
LGA    T     224      T     224          3.403
LGA    V     225      V     225          5.446
LGA    D     226      D     226         10.688
LGA    G     227      G     227          9.970
LGA    R     228      R     228          7.337
LGA    D     229      D     229          6.802
LGA    M     230      M     230          7.097
LGA    G     231      G     231          6.401
LGA    E     232      E     232          1.794
LGA    H     233      H     233          5.031
LGA    A     234      A     234          2.633
LGA    G     235      G     235          1.080
LGA    L     236      L     236          1.655
LGA    M     237      M     237          3.758
LGA    Y     238      Y     238          6.509
LGA    Y     239      Y     239          3.962
LGA    T     240      T     240          3.520
LGA    I     241      I     241          3.329
LGA    G     242      G     242          2.733
LGA    Q     243      Q     243          2.144
LGA    R     244      R     244          3.860
LGA    G     245      G     245         10.832
LGA    G     246      G     246         13.659
LGA    L     247      L     247         19.498

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   60    4.0     12    2.76    18.333    16.227     0.419

LGA_LOCAL      RMSD =  2.765  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.247  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  7.511  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.651315 * X  +  -0.221923 * Y  +   0.725630 * Z  +  53.444073
  Y_new =  -0.757446 * X  +   0.132872 * Y  +  -0.639235 * Z  + -14.295531
  Z_new =   0.045445 * X  +  -0.965969 * Y  +  -0.254636 * Z  + -16.426449 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.828540    1.313053  [ DEG:  -104.7676     75.2324 ]
  Theta =  -0.045461   -3.096132  [ DEG:    -2.6047   -177.3953 ]
  Phi   =  -2.281000    0.860593  [ DEG:  -130.6917     49.3083 ]
 
# 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: T0316AL380_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_3-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   60   4.0   12   2.76  16.227     7.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_3-D2
REMARK Aligment from pdb entry: 1xngA
ATOM    705  N   GLY   220      30.693  10.070 -22.405  1.00  0.00              
ATOM    706  CA  GLY   220      32.012  10.672 -22.245  1.00  0.00              
ATOM    707  C   GLY   220      32.252  11.837 -23.192  1.00  0.00              
ATOM    708  O   GLY   220      32.707  12.900 -22.773  1.00  0.00              
ATOM    709  N   ARG   221      31.935  11.638 -24.467  1.00  0.00              
ATOM    710  CA  ARG   221      32.164  12.663 -25.481  1.00  0.00              
ATOM    711  C   ARG   221      31.546  14.035 -25.237  1.00  0.00              
ATOM    712  O   ARG   221      32.177  15.057 -25.508  1.00  0.00              
ATOM    713  N   MET   222      30.301  14.092 -24.746  1.00  0.00              
ATOM    714  CA  MET   222      29.739  15.423 -24.511  1.00  0.00              
ATOM    715  C   MET   222      30.582  16.196 -23.487  1.00  0.00              
ATOM    716  O   MET   222      30.794  17.400 -23.627  1.00  0.00              
ATOM    717  N   MET   223      31.072  15.490 -22.471  1.00  0.00              
ATOM    718  CA  MET   223      31.903  16.096 -21.434  1.00  0.00              
ATOM    719  C   MET   223      33.269  16.467 -22.001  1.00  0.00              
ATOM    720  O   MET   223      33.783  17.556 -21.744  1.00  0.00              
ATOM    721  N   THR   224      33.861  15.561 -22.774  1.00  0.00              
ATOM    722  CA  THR   224      35.156  15.854 -23.366  1.00  0.00              
ATOM    723  C   THR   224      35.069  17.072 -24.288  1.00  0.00              
ATOM    724  O   THR   224      36.002  17.873 -24.361  1.00  0.00              
ATOM    725  N   VAL   225      33.951  17.224 -24.993  1.00  0.00              
ATOM    726  CA  VAL   225      33.803  18.368 -25.886  1.00  0.00              
ATOM    727  C   VAL   225      33.806  19.691 -25.115  1.00  0.00              
ATOM    728  O   VAL   225      34.427  20.666 -25.547  1.00  0.00              
ATOM    729  N   ASP   226      33.118  19.733 -23.979  1.00  0.00              
ATOM    730  CA  ASP   226      33.104  20.952 -23.178  1.00  0.00              
ATOM    731  C   ASP   226      34.476  21.223 -22.570  1.00  0.00              
ATOM    732  O   ASP   226      34.897  22.374 -22.454  1.00  0.00              
ATOM    733  N   GLY   227      35.174  20.163 -22.180  1.00  0.00              
ATOM    734  CA  GLY   227      36.505  20.314 -21.611  1.00  0.00              
ATOM    735  C   GLY   227      37.464  20.847 -22.678  1.00  0.00              
ATOM    736  O   GLY   227      38.287  21.719 -22.408  1.00  0.00              
ATOM    737  N   ARG   228      37.346  20.346 -23.906  1.00  0.00              
ATOM    738  CA  ARG   228      38.229  20.814 -24.964  1.00  0.00              
ATOM    739  C   ARG   228      37.952  22.275 -25.315  1.00  0.00              
ATOM    740  O   ARG   228      38.872  23.026 -25.643  1.00  0.00              
ATOM    741  N   ASP   229      36.687  22.677 -25.239  1.00  0.00              
ATOM    742  CA  ASP   229      36.307  24.045 -25.579  1.00  0.00              
ATOM    743  C   ASP   229      36.637  25.039 -24.476  1.00  0.00              
ATOM    744  O   ASP   229      37.089  26.155 -24.745  1.00  0.00              
ATOM    745  N   MET   230      36.421  24.616 -23.237  1.00  0.00              
ATOM    746  CA  MET   230      36.654  25.469 -22.079  1.00  0.00              
ATOM    747  C   MET   230      38.078  25.461 -21.549  1.00  0.00              
ATOM    748  O   MET   230      38.616  26.514 -21.198  1.00  0.00              
ATOM    749  N   GLY   231      38.685  24.280 -21.488  1.00  0.00              
ATOM    750  CA  GLY   231      40.035  24.150 -20.954  1.00  0.00              
ATOM    751  C   GLY   231      40.983  23.404 -21.886  1.00  0.00              
ATOM    752  O   GLY   231      41.453  22.312 -21.559  1.00  0.00              
ATOM    753  N   GLU   232      41.274  23.989 -23.039  1.00  0.00              
ATOM    754  CA  GLU   232      42.174  23.346 -23.981  1.00  0.00              
ATOM    755  C   GLU   232      43.623  23.621 -23.596  1.00  0.00              
ATOM    756  O   GLU   232      44.481  22.747 -23.719  1.00  0.00              
ATOM    757  N   HIS   233      43.888  24.836 -23.124  1.00  0.00              
ATOM    758  CA  HIS   233      45.239  25.224 -22.733  1.00  0.00              
ATOM    759  C   HIS   233      45.268  25.774 -21.308  1.00  0.00              
ATOM    760  O   HIS   233      46.182  26.507 -20.934  1.00  0.00              
ATOM    761  N   ALA   234      44.258  25.422 -20.520  1.00  0.00              
ATOM    762  CA  ALA   234      44.168  25.878 -19.139  1.00  0.00              
ATOM    763  C   ALA   234      43.688  24.727 -18.260  1.00  0.00              
ATOM    764  O   ALA   234      43.120  23.752 -18.755  1.00  0.00              
ATOM    765  N   GLY   235      43.911  24.822 -16.941  1.00  0.00              
ATOM    766  CA  GLY   235      43.491  23.769 -16.013  1.00  0.00              
ATOM    767  C   GLY   235      41.980  23.563 -15.960  1.00  0.00              
ATOM    768  O   GLY   235      41.208  24.518 -16.021  1.00  0.00              
ATOM    769  N   LEU   236      41.565  22.308 -15.842  1.00  0.00              
ATOM    770  CA  LEU   236      40.149  21.980 -15.780  1.00  0.00              
ATOM    771  C   LEU   236      39.516  22.435 -14.463  1.00  0.00              
ATOM    772  O   LEU   236      40.077  22.225 -13.387  1.00  0.00              
ATOM    773  N   MET   237      38.351  23.071 -14.561  1.00  0.00              
ATOM    774  CA  MET   237      37.620  23.547 -13.388  1.00  0.00              
ATOM    775  C   MET   237      36.419  22.629 -13.201  1.00  0.00              
ATOM    776  O   MET   237      35.391  22.792 -13.861  1.00  0.00              
ATOM    777  N   TYR   238      36.558  21.661 -12.302  1.00  0.00              
ATOM    778  CA  TYR   238      35.495  20.699 -12.045  1.00  0.00              
ATOM    779  C   TYR   238      34.201  21.352 -11.577  1.00  0.00              
ATOM    780  O   TYR   238      33.113  20.820 -11.800  1.00  0.00              
ATOM    781  N   TYR   239      34.320  22.506 -10.932  1.00  0.00              
ATOM    782  CA  TYR   239      33.148  23.212 -10.440  1.00  0.00              
ATOM    783  C   TYR   239      32.342  23.755 -11.614  1.00  0.00              
ATOM    784  O   TYR   239      31.113  23.712 -11.605  1.00  0.00              
ATOM    785  N   THR   240      33.040  24.259 -12.625  1.00  0.00              
ATOM    786  CA  THR   240      32.382  24.794 -13.809  1.00  0.00              
ATOM    787  C   THR   240      31.645  23.666 -14.520  1.00  0.00              
ATOM    788  O   THR   240      30.512  23.837 -14.966  1.00  0.00              
ATOM    789  N   ILE   241      32.292  22.509 -14.617  1.00  0.00              
ATOM    790  CA  ILE   241      31.688  21.354 -15.270  1.00  0.00              
ATOM    791  C   ILE   241      30.471  20.883 -14.477  1.00  0.00              
ATOM    792  O   ILE   241      29.488  20.407 -15.048  1.00  0.00              
ATOM    793  N   GLY   242      30.545  21.028 -13.157  1.00  0.00              
ATOM    794  CA  GLY   242      29.451  20.628 -12.279  1.00  0.00              
ATOM    795  C   GLY   242      28.221  21.483 -12.564  1.00  0.00              
ATOM    796  O   GLY   242      27.093  20.991 -12.557  1.00  0.00              
ATOM    797  N   GLN   243      28.449  22.766 -12.818  1.00  0.00              
ATOM    798  CA  GLN   243      27.367  23.698 -13.105  1.00  0.00              
ATOM    799  C   GLN   243      26.695  23.392 -14.438  1.00  0.00              
ATOM    800  O   GLN   243      25.528  23.724 -14.644  1.00  0.00              
ATOM    801  N   ARG   244      27.435  22.760 -15.344  1.00  0.00              
ATOM    802  CA  ARG   244      26.892  22.413 -16.650  1.00  0.00              
ATOM    803  C   ARG   244      25.922  21.243 -16.549  1.00  0.00              
ATOM    804  O   ARG   244      25.262  20.887 -17.526  1.00  0.00              
ATOM    805  N   GLY   245      25.848  20.644 -15.365  1.00  0.00              
ATOM    806  CA  GLY   245      24.941  19.530 -15.156  1.00  0.00              
ATOM    807  C   GLY   245      25.565  18.152 -15.255  1.00  0.00              
ATOM    808  O   GLY   245      24.847  17.160 -15.376  1.00  0.00              
ATOM    809  N   GLY   246      26.892  18.077 -15.206  1.00  0.00              
ATOM    810  CA  GLY   246      27.570  16.788 -15.291  1.00  0.00              
ATOM    811  C   GLY   246      27.697  16.122 -13.928  1.00  0.00              
ATOM    812  O   GLY   246      27.914  16.790 -12.919  1.00  0.00              
ATOM    813  N   LEU   247      27.560  14.801 -13.916  1.00  0.00              
ATOM    814  CA  LEU   247      27.661  14.012 -12.692  1.00  0.00              
ATOM    815  C   LEU   247      29.001  14.262 -12.012  1.00  0.00              
ATOM    816  O   LEU   247      30.043  14.278 -12.668  1.00  0.00              
END
