
#######################################################
#                                                     #
#                        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   35 (  140),  selected   32 , name T0316AL380_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   32 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_1-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:    19       227 - 245         4.59    12.44
  LONGEST_CONTINUOUS_SEGMENT:    19       228 - 246         4.95    12.19
  LCS_AVERAGE:     27.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       220 - 226         1.79    18.40
  LONGEST_CONTINUOUS_SEGMENT:     7       229 - 235         1.62    13.40
  LCS_AVERAGE:     10.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       220 - 224         0.87    15.06
  LCS_AVERAGE:      6.67

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:   60
LCS_GDT     G     220     G     220      5    7    9     3    4    5    6    7    7    7    7    7    8    8    9    9   12   13   16   17   19   20   20 
LCS_GDT     R     221     R     221      5    7    9     3    4    5    6    7    7    7    7    8    9   10   12   12   14   14   16   17   19   20   22 
LCS_GDT     M     222     M     222      5    7    9     3    4    5    6    7    7    7    7    8    9   10   12   12   14   14   15   17   18   20   23 
LCS_GDT     M     223     M     223      5    7    9     3    4    5    6    7    7    7    7    7    8    8    9   10   12   14   14   17   17   20   23 
LCS_GDT     T     224     T     224      5    7   10     3    4    5    6    7    7    7    7    7    8    8    9   11   14   17   17   19   20   22   23 
LCS_GDT     V     225     V     225      3    7   10     3    3    4    6    7    7    7    8    9   10   11   13   15   16   17   18   20   20   22   23 
LCS_GDT     D     226     D     226      4    7   10     3    4    4    5    7    7    7    8    9    9   10   13   15   16   17   18   19   20   22   23 
LCS_GDT     G     227     G     227      4    5   19     3    4    4    4    5    5    6    6    7    8   10   10   14   17   19   19   20   20   22   23 
LCS_GDT     R     228     R     228      4    5   19     3    4    4    5    7    9   10   10   12   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     D     229     D     229      4    7   19     4    4    4    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     M     230     M     230      4    7   19     4    4    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     G     231     G     231      4    7   19     4    4    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     E     232     E     232      4    7   19     3    4    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     H     233     H     233      4    7   19     3    4    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     A     234     A     234      4    7   19     4    4    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     G     235     G     235      3    7   19     0    3    5    6    7    8   10   11   13   15   16   17   17   18   19   19   20   20   21   23 
LCS_GDT     L     236     L     236      4    5   19     4    4    6    6    6    9   10   11   12   14   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     M     237     M     237      4    5   19     4    4    6    6    6    9   10   11   12   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     Y     238     Y     238      4    5   19     4    4    6    6    6    9   10   11   12   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     Y     239     Y     239      4    5   19     4    4    6    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     T     240     T     240      4    5   19     3    4    6    6    6    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     I     241     I     241      4    5   19     3    4    4    4    5    5    7    9   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     G     242     G     242      4    5   19     3    4    4    4    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     Q     243     Q     243      4    5   19     3    4    6    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     R     244     R     244      3    5   19     3    3    5    6    7    9   10   11   13   15   16   17   17   18   19   19   20   20   22   23 
LCS_GDT     G     245     G     245      3    4   19     3    3    4    4    4    5    8   10   12   14   15   17   17   18   19   19   20   20   22   23 
LCS_GDT     G     246     G     246      4    6   19     3    3    4    5    5    6   10   11   12   14   14   15   15   16   17   18   19   20   22   23 
LCS_GDT     L     247     L     247      4    6   16     3    4    4    5    5    9   10   11   12   14   14   15   15   15   16   16   17   19   21   21 
LCS_GDT     G     248     G     248      4    6   16     3    4    4    5    6    9   10   11   12   14   14   15   15   15   16   16   17   19   20   20 
LCS_GDT     I     249     I     249      4    6   16     3    4    4    5    6    9   10   11   12   14   14   15   15   15   16   16   17   19   20   20 
LCS_GDT     G     250     G     250      4    6   16     3    4    4    5    5    9   10   11   12   14   14   15   15   15   16   16   17   19   20   20 
LCS_GDT     G     251     G     251      3    6   16     0    0    3    3    5    6    6    6    6   14   14   15   15   15   16   16   16   19   19   20 
LCS_AVERAGE  LCS_A:  14.70  (   6.67   10.05   27.40 )

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      6      7      9     10     11     13     15     16     17     17     18     19     19     20     20     22     23 
GDT PERCENT_CA   6.67   6.67  10.00  10.00  11.67  15.00  16.67  18.33  21.67  25.00  26.67  28.33  28.33  30.00  31.67  31.67  33.33  33.33  36.67  38.33
GDT RMS_LOCAL    0.13   0.13   1.16   1.16   1.52   2.00   2.17   2.37   3.10   3.51   3.66   3.85   3.85   4.24   4.59   4.59   5.25   5.20   6.19   6.38
GDT RMS_ALL_CA  15.09  15.09  18.19  18.19  12.43  12.65  12.74  12.73  13.12  12.97  12.99  12.87  12.87  12.50  12.44  12.44  12.20  12.12  11.76  11.73

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         16.522
LGA    R     221      R     221         17.160
LGA    M     222      M     222         14.769
LGA    M     223      M     223         16.832
LGA    T     224      T     224         16.527
LGA    V     225      V     225         14.619
LGA    D     226      D     226         14.458
LGA    G     227      G     227          9.342
LGA    R     228      R     228          5.486
LGA    D     229      D     229          2.540
LGA    M     230      M     230          1.171
LGA    G     231      G     231          1.293
LGA    E     232      E     232          1.739
LGA    H     233      H     233          2.784
LGA    A     234      A     234          1.797
LGA    G     235      G     235          3.578
LGA    L     236      L     236          7.763
LGA    M     237      M     237          7.031
LGA    Y     238      Y     238          5.149
LGA    Y     239      Y     239          3.415
LGA    T     240      T     240          6.391
LGA    I     241      I     241          6.415
LGA    G     242      G     242          2.096
LGA    Q     243      Q     243          1.878
LGA    R     244      R     244          2.412
LGA    G     245      G     245          8.735
LGA    G     246      G     246         13.460
LGA    L     247      L     247         16.690
LGA    G     248      G     248         20.308
LGA    I     249      I     249         20.735
LGA    G     250      G     250         26.966
LGA    G     251      G     251         30.296

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   60    4.0     11    2.37    16.667    16.080     0.446

LGA_LOCAL      RMSD =  2.368  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.730  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 10.583  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.420514 * X  +   0.772273 * Y  +   0.476195 * Z  +  -1.457983
  Y_new =  -0.727386 * X  +   0.600674 * Y  +  -0.331815 * Z  +  47.839069
  Z_new =  -0.542290 * X  +  -0.206845 * Y  +   0.814332 * Z  +   5.831369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.248745    2.892847  [ DEG:   -14.2521    165.7479 ]
  Theta =   0.573160    2.568433  [ DEG:    32.8396    147.1604 ]
  Phi   =  -1.046623    2.094969  [ DEG:   -59.9671    120.0329 ]
 
# 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_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_1-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   60   4.0   11   2.37  16.080    10.58
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_1-D2
REMARK Aligment from pdb entry: 1vl2A
ATOM    737  N   GLY   220      48.107  14.251  -6.707  1.00  0.00              
ATOM    738  CA  GLY   220      46.744  14.405  -6.288  1.00  0.00              
ATOM    739  C   GLY   220      46.179  15.799  -6.414  1.00  0.00              
ATOM    740  O   GLY   220      45.007  16.031  -6.037  1.00  0.00              
ATOM    741  N   ARG   221      46.966  16.728  -6.952  1.00  0.00              
ATOM    742  CA  ARG   221      46.531  18.130  -7.115  1.00  0.00              
ATOM    743  C   ARG   221      46.245  18.387  -8.572  1.00  0.00              
ATOM    744  O   ARG   221      47.097  18.084  -9.383  1.00  0.00              
ATOM    745  N   MET   222      45.076  18.943  -8.931  1.00  0.00              
ATOM    746  CA  MET   222      44.755  19.282 -10.304  1.00  0.00              
ATOM    747  C   MET   222      45.706  20.351 -10.802  1.00  0.00              
ATOM    748  O   MET   222      45.935  21.379 -10.080  1.00  0.00              
ATOM    749  N   MET   223      46.278  20.120 -11.982  1.00  0.00              
ATOM    750  CA  MET   223      47.252  21.078 -12.555  1.00  0.00              
ATOM    751  C   MET   223      46.957  21.525 -13.988  1.00  0.00              
ATOM    752  O   MET   223      47.664  22.417 -14.523  1.00  0.00              
ATOM    753  N   THR   224      46.006  20.879 -14.675  1.00  0.00              
ATOM    754  CA  THR   224      45.614  21.310 -16.021  1.00  0.00              
ATOM    755  C   THR   224      44.223  20.763 -16.337  1.00  0.00              
ATOM    756  O   THR   224      43.912  19.632 -15.947  1.00  0.00              
ATOM    757  N   VAL   225      43.405  21.573 -17.018  1.00  0.00              
ATOM    758  CA  VAL   225      42.192  21.063 -17.672  1.00  0.00              
ATOM    759  C   VAL   225      42.256  21.458 -19.151  1.00  0.00              
ATOM    760  O   VAL   225      42.622  22.584 -19.488  1.00  0.00              
ATOM    761  N   ASP   226      41.931  20.506 -20.003  1.00  0.00              
ATOM    762  CA  ASP   226      41.912  20.707 -21.458  1.00  0.00              
ATOM    763  C   ASP   226      40.558  20.236 -21.990  1.00  0.00              
ATOM    764  O   ASP   226      40.111  19.115 -21.707  1.00  0.00              
ATOM    765  N   GLY   227      39.903  21.093 -22.768  1.00  0.00              
ATOM    766  CA  GLY   227      38.669  20.716 -23.448  1.00  0.00              
ATOM    767  C   GLY   227      39.122  20.128 -24.785  1.00  0.00              
ATOM    768  O   GLY   227      39.810  20.815 -25.602  1.00  0.00              
ATOM    769  N   ARG   228      38.819  18.841 -25.002  1.00  0.00              
ATOM    770  CA  ARG   228      39.359  18.115 -26.180  1.00  0.00              
ATOM    771  C   ARG   228      38.601  18.453 -27.462  1.00  0.00              
ATOM    772  O   ARG   228      39.064  18.133 -28.580  1.00  0.00              
ATOM    773  N   ASP   229      37.470  19.119 -27.311  1.00  0.00              
ATOM    774  CA  ASP   229      36.637  19.550 -28.449  1.00  0.00              
ATOM    775  C   ASP   229      37.041  20.943 -28.893  1.00  0.00              
ATOM    776  O   ASP   229      37.303  21.166 -30.087  1.00  0.00              
ATOM    777  N   MET   230      37.105  21.883 -27.945  1.00  0.00              
ATOM    778  CA  MET   230      37.256  23.307 -28.313  1.00  0.00              
ATOM    779  C   MET   230      38.583  23.927 -27.981  1.00  0.00              
ATOM    780  O   MET   230      38.820  25.108 -28.297  1.00  0.00              
ATOM    781  N   GLY   231      39.466  23.120 -27.388  1.00  0.00              
ATOM    782  CA  GLY   231      40.826  23.497 -27.142  1.00  0.00              
ATOM    783  C   GLY   231      41.141  24.348 -25.924  1.00  0.00              
ATOM    784  O   GLY   231      42.326  24.625 -25.676  1.00  0.00              
ATOM    785  N   GLU   232      40.121  24.815 -25.195  1.00  0.00              
ATOM    786  CA  GLU   232      40.344  25.567 -23.985  1.00  0.00              
ATOM    787  C   GLU   232      41.338  24.817 -23.096  1.00  0.00              
ATOM    788  O   GLU   232      41.186  23.599 -22.922  1.00  0.00              
ATOM    789  N   HIS   233      42.318  25.528 -22.530  1.00  0.00              
ATOM    790  CA  HIS   233      43.267  24.946 -21.560  1.00  0.00              
ATOM    791  C   HIS   233      43.420  25.910 -20.420  1.00  0.00              
ATOM    792  O   HIS   233      43.584  27.119 -20.639  1.00  0.00              
ATOM    793  N   ALA   234      43.461  25.379 -19.208  1.00  0.00              
ATOM    794  CA  ALA   234      43.624  26.182 -17.993  1.00  0.00              
ATOM    795  C   ALA   234      44.587  25.416 -17.106  1.00  0.00              
ATOM    796  O   ALA   234      44.425  24.178 -16.946  1.00  0.00              
ATOM    797  N   GLY   235      45.585  26.106 -16.560  1.00  0.00              
ATOM    798  CA  GLY   235      46.512  25.552 -15.564  1.00  0.00              
ATOM    799  C   GLY   235      46.473  26.218 -14.181  1.00  0.00              
ATOM    800  O   GLY   235      46.794  25.571 -13.156  1.00  0.00              
ATOM    801  N   LEU   236      37.196  27.236 -11.781  1.00  0.00              
ATOM    802  CA  LEU   236      36.091  28.018 -12.349  1.00  0.00              
ATOM    803  C   LEU   236      35.611  27.471 -13.696  1.00  0.00              
ATOM    804  O   LEU   236      34.408  27.407 -13.959  1.00  0.00              
ATOM    805  N   MET   237      36.549  27.019 -14.507  1.00  0.00              
ATOM    806  CA  MET   237      36.203  26.391 -15.768  1.00  0.00              
ATOM    807  C   MET   237      35.426  25.095 -15.563  1.00  0.00              
ATOM    808  O   MET   237      34.417  24.897 -16.254  1.00  0.00              
ATOM    809  N   TYR   238      35.863  24.247 -14.620  1.00  0.00              
ATOM    810  CA  TYR   238      35.097  23.025 -14.292  1.00  0.00              
ATOM    811  C   TYR   238      33.682  23.402 -13.816  1.00  0.00              
ATOM    812  O   TYR   238      32.712  22.718 -14.169  1.00  0.00              
ATOM    813  N   TYR   239      33.555  24.485 -13.031  1.00  0.00              
ATOM    814  CA  TYR   239      32.240  24.988 -12.593  1.00  0.00              
ATOM    815  C   TYR   239      31.381  25.333 -13.806  1.00  0.00              
ATOM    816  O   TYR   239      30.220  24.957 -13.887  1.00  0.00              
ATOM    817  N   THR   240      31.979  26.058 -14.752  1.00  0.00              
ATOM    818  CA  THR   240      31.261  26.474 -15.960  1.00  0.00              
ATOM    819  C   THR   240      30.787  25.270 -16.775  1.00  0.00              
ATOM    820  O   THR   240      29.619  25.204 -17.199  1.00  0.00              
ATOM    821  N   ILE   241      31.706  24.357 -17.070  1.00  0.00              
ATOM    822  CA  ILE   241      31.368  23.173 -17.865  1.00  0.00              
ATOM    823  C   ILE   241      30.308  22.354 -17.153  1.00  0.00              
ATOM    824  O   ILE   241      29.331  21.889 -17.735  1.00  0.00              
ATOM    825  N   GLY   242      30.514  22.144 -15.864  1.00  0.00              
ATOM    826  CA  GLY   242      29.534  21.383 -15.111  1.00  0.00              
ATOM    827  C   GLY   242      28.146  21.978 -15.103  1.00  0.00              
ATOM    828  O   GLY   242      27.122  21.271 -15.310  1.00  0.00              
ATOM    829  N   GLN   243      28.068  23.271 -14.819  1.00  0.00              
ATOM    830  CA  GLN   243      26.805  23.953 -14.692  1.00  0.00              
ATOM    831  C   GLN   243      26.063  23.891 -16.025  1.00  0.00              
ATOM    832  O   GLN   243      24.899  23.639 -16.026  1.00  0.00              
ATOM    833  N   ARG   244      26.774  24.133 -17.125  1.00  0.00              
ATOM    834  CA  ARG   244      26.166  24.153 -18.473  1.00  0.00              
ATOM    835  C   ARG   244      25.592  22.769 -18.835  1.00  0.00              
ATOM    836  O   ARG   244      24.576  22.671 -19.587  1.00  0.00              
ATOM    837  N   GLY   245      26.257  21.705 -18.332  1.00  0.00              
ATOM    838  CA  GLY   245      25.918  20.332 -18.683  1.00  0.00              
ATOM    839  C   GLY   245      25.119  19.600 -17.604  1.00  0.00              
ATOM    840  O   GLY   245      24.905  18.388 -17.733  1.00  0.00              
ATOM    841  N   GLY   246      24.586  20.309 -16.637  1.00  0.00              
ATOM    842  CA  GLY   246      23.620  19.752 -15.663  1.00  0.00              
ATOM    843  C   GLY   246      24.247  18.866 -14.566  1.00  0.00              
ATOM    844  O   GLY   246      23.564  18.012 -13.987  1.00  0.00              
ATOM    845  N   LEU   247      25.545  19.092 -14.312  1.00  0.00              
ATOM    846  CA  LEU   247      26.319  18.254 -13.407  1.00  0.00              
ATOM    847  C   LEU   247      26.274  18.800 -11.994  1.00  0.00              
ATOM    848  O   LEU   247      26.378  19.966 -11.772  1.00  0.00              
ATOM    849  N   GLY   248      26.109  17.912 -11.022  1.00  0.00              
ATOM    850  CA  GLY   248      26.370  18.274  -9.632  1.00  0.00              
ATOM    851  C   GLY   248      25.202  18.536  -8.721  1.00  0.00              
ATOM    852  O   GLY   248      25.387  19.082  -7.627  1.00  0.00              
ATOM    853  N   ILE   249      24.003  18.084  -9.104  1.00  0.00              
ATOM    854  CA  ILE   249      22.840  18.223  -8.246  1.00  0.00              
ATOM    855  C   ILE   249      22.765  17.049  -7.270  1.00  0.00              
ATOM    856  O   ILE   249      23.074  15.891  -7.640  1.00  0.00              
ATOM    857  N   GLY   250      22.378  17.386  -6.038  1.00  0.00              
ATOM    858  CA  GLY   250      22.249  16.424  -4.918  1.00  0.00              
ATOM    859  C   GLY   250      21.070  16.849  -4.057  1.00  0.00              
ATOM    860  O   GLY   250      20.932  18.001  -3.658  1.00  0.00              
ATOM    861  N   GLY   251      20.238  15.869  -3.750  1.00  0.00              
ATOM    862  CA  GLY   251      19.103  16.043  -2.835  1.00  0.00              
ATOM    863  C   GLY   251      19.209  14.940  -1.793  1.00  0.00              
ATOM    864  O   GLY   251      19.166  13.762  -2.131  1.00  0.00              
ATOM    865  N   GLN   252      19.471  15.307  -0.553  1.00  0.00              
ATOM    866  CA  GLN   252      19.659  14.322   0.513  1.00  0.00              
ATOM    867  C   GLN   252      19.198  14.820   1.855  1.00  0.00              
ATOM    868  O   GLN   252      18.984  16.005   2.060  1.00  0.00              
ATOM    869  N   HIS   253      19.022  13.874   2.781  1.00  0.00              
ATOM    870  CA  HIS   253      18.855  14.157   4.212  1.00  0.00              
ATOM    871  C   HIS   253      20.153  13.759   4.877  1.00  0.00              
ATOM    872  O   HIS   253      20.650  12.599   4.738  1.00  0.00              
ATOM    873  N   GLY   254      20.704  14.739   5.591  1.00  0.00              
ATOM    874  CA  GLY   254      21.981  14.573   6.290  1.00  0.00              
ATOM    875  C   GLY   254      21.777  14.688   7.804  1.00  0.00              
ATOM    876  O   GLY   254      20.874  15.364   8.256  1.00  0.00              
END
