
#######################################################
#                                                     #
#                        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   19 (  153),  selected   19 , name T0381TS319_2-D2
# Molecule2: number of CA atoms  176 ( 1314),  selected   19 , name T0381_D2.pdb
# PARAMETERS: T0381TS319_2-D2.T0381_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        90 - 108         1.65     1.65
  LCS_AVERAGE:     10.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        90 - 108         1.65     1.65
  LCS_AVERAGE:     10.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        92 - 106         0.96     1.77
  LCS_AVERAGE:      8.01

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:  176
LCS_GDT     L      90     L      90      3   19   19     0    3    3   12   16   17   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     S      91     S      91     13   19   19     7    7   13   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      92     L      92     15   19   19     7   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     P      93     P      93     15   19   19     7   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      94     E      94     15   19   19     7   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      95     V      95     15   19   19     7    8   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A      96     A      96     15   19   19     7   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q      97     Q      97     15   19   19     7   10   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     P      98     P      98     15   19   19     6   10   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H      99     H      99     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     100     L     100     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E     101     E     101     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     102     K     102     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     103     L     103     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     S     104     S     104     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H     105     H     105     15   19   19     5   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     106     K     106     15   19   19     6   11   15   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V     107     V     107     14   19   19     4    9   14   16   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H     108     H     108     13   19   19     3    4    7   13   17   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:   9.87  (   8.01   10.80   10.80 )

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     11     15     16     17     18     18     19     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   3.98   6.25   8.52   9.09   9.66  10.23  10.23  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80
GDT RMS_LOCAL    0.32   0.67   0.96   1.06   1.18   1.37   1.37   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65
GDT RMS_ALL_CA   4.75   1.81   1.77   1.71   1.78   1.73   1.73   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65

#      Molecule1      Molecule2       DISTANCE
LGA    L      90      L      90          3.772
LGA    S      91      S      91          3.013
LGA    L      92      L      92          1.635
LGA    P      93      P      93          1.229
LGA    E      94      E      94          1.126
LGA    V      95      V      95          1.358
LGA    A      96      A      96          0.683
LGA    Q      97      Q      97          1.698
LGA    P      98      P      98          1.681
LGA    H      99      H      99          0.413
LGA    L     100      L     100          0.934
LGA    E     101      E     101          1.112
LGA    K     102      K     102          0.852
LGA    L     103      L     103          0.642
LGA    S     104      S     104          0.367
LGA    H     105      H     105          1.082
LGA    K     106      K     106          0.456
LGA    V     107      V     107          1.553
LGA    H     108      H     108          2.792

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  176    4.0     19    1.65     9.233    10.005     1.084

LGA_LOCAL      RMSD =  1.653  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.653  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  1.653  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.090694 * X  +   0.901285 * Y  +  -0.423628 * Z  +  15.441292
  Y_new =   0.940942 * X  +   0.216882 * Y  +   0.259980 * Z  +  -5.860192
  Z_new =   0.326193 * X  +  -0.375031 * Y  +  -0.867727 * Z  +  21.478619 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.733640    0.407952  [ DEG:  -156.6261     23.3739 ]
  Theta =  -0.332273   -2.809319  [ DEG:   -19.0379   -160.9621 ]
  Phi   =   1.666886   -1.474707  [ DEG:    95.5055    -84.4945 ]
 
# 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: T0381TS319_2-D2                               
REMARK     2: T0381_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS319_2-D2.T0381_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  176   4.0   19   1.65  10.005     1.65
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS319_2-D2
PFRMAT TS
TARGET T0381
MODEL 2
PARENT N/A
ATOM    564  N   LEU    90      22.326  28.576  24.964  1.00120.55       1SG 565
ATOM    565  CA  LEU    90      22.245  29.006  26.329  1.00120.55       1SG 566
ATOM    566  CB  LEU    90      23.263  30.124  26.643  1.00120.55       1SG 567
ATOM    567  CG  LEU    90      23.299  30.562  28.123  1.00120.55       1SG 568
ATOM    568  CD2 LEU    90      24.122  31.849  28.306  1.00120.55       1SG 569
ATOM    569  CD1 LEU    90      23.789  29.425  29.035  1.00120.55       1SG 570
ATOM    570  C   LEU    90      20.876  29.528  26.638  1.00120.55       1SG 571
ATOM    571  O   LEU    90      20.326  29.249  27.703  1.00120.55       1SG 572
ATOM    572  N   SER    91      20.278  30.296  25.712  1.00 71.73       1SG 573
ATOM    573  CA  SER    91      19.017  30.909  26.013  1.00 71.73       1SG 574
ATOM    574  CB  SER    91      18.542  31.899  24.939  1.00 71.73       1SG 575
ATOM    575  OG  SER    91      18.272  31.216  23.725  1.00 71.73       1SG 576
ATOM    576  C   SER    91      17.962  29.866  26.183  1.00 71.73       1SG 577
ATOM    577  O   SER    91      17.020  30.054  26.951  1.00 71.73       1SG 578
ATOM    578  N   LEU    92      18.090  28.725  25.482  1.00103.41       1SG 579
ATOM    579  CA  LEU    92      17.049  27.749  25.580  1.00103.41       1SG 580
ATOM    580  CB  LEU    92      17.303  26.549  24.630  1.00103.41       1SG 581
ATOM    581  CG  LEU    92      16.159  25.523  24.452  1.00103.41       1SG 582
ATOM    582  CD2 LEU    92      15.517  25.082  25.777  1.00103.41       1SG 583
ATOM    583  CD1 LEU    92      16.637  24.334  23.605  1.00103.41       1SG 584
ATOM    584  C   LEU    92      16.963  27.311  27.017  1.00103.41       1SG 585
ATOM    585  O   LEU    92      15.875  27.366  27.592  1.00103.41       1SG 586
ATOM    586  N   PRO    93      18.031  26.908  27.667  1.00161.47       1SG 587
ATOM    587  CA  PRO    93      17.836  26.580  29.044  1.00161.47       1SG 588
ATOM    588  CD  PRO    93      18.952  25.952  27.073  1.00161.47       1SG 589
ATOM    589  CB  PRO    93      19.040  25.751  29.481  1.00161.47       1SG 590
ATOM    590  CG  PRO    93      19.412  25.006  28.195  1.00161.47       1SG 591
ATOM    591  C   PRO    93      17.533  27.737  29.930  1.00161.47       1SG 592
ATOM    592  O   PRO    93      16.911  27.528  30.970  1.00161.47       1SG 593
ATOM    593  N   GLU    94      17.966  28.953  29.558  1.00 42.31       1SG 594
ATOM    594  CA  GLU    94      17.747  30.075  30.420  1.00 42.31       1SG 595
ATOM    595  CB  GLU    94      18.334  31.375  29.853  1.00 42.31       1SG 596
ATOM    596  CG  GLU    94      19.860  31.418  29.826  1.00 42.31       1SG 597
ATOM    597  CD  GLU    94      20.255  32.701  29.110  1.00 42.31       1SG 598
ATOM    598  OE1 GLU    94      19.650  32.991  28.045  1.00 42.31       1SG 599
ATOM    599  OE2 GLU    94      21.176  33.405  29.606  1.00 42.31       1SG 600
ATOM    600  C   GLU    94      16.284  30.318  30.565  1.00 42.31       1SG 601
ATOM    601  O   GLU    94      15.774  30.483  31.669  1.00 42.31       1SG 602
ATOM    602  N   VAL    95      15.540  30.348  29.454  1.00 39.45       1SG 603
ATOM    603  CA  VAL    95      14.157  30.665  29.612  1.00 39.45       1SG 604
ATOM    604  CB  VAL    95      13.452  30.805  28.294  1.00 39.45       1SG 605
ATOM    605  CG1 VAL    95      11.941  30.945  28.542  1.00 39.45       1SG 606
ATOM    606  CG2 VAL    95      14.067  32.001  27.548  1.00 39.45       1SG 607
ATOM    607  C   VAL    95      13.486  29.583  30.384  1.00 39.45       1SG 608
ATOM    608  O   VAL    95      12.776  29.841  31.356  1.00 39.45       1SG 609
ATOM    609  N   ALA    96      13.735  28.328  29.982  1.00 43.05       1SG 610
ATOM    610  CA  ALA    96      12.994  27.246  30.548  1.00 43.05       1SG 611
ATOM    611  CB  ALA    96      13.327  25.898  29.894  1.00 43.05       1SG 612
ATOM    612  C   ALA    96      13.238  27.082  32.015  1.00 43.05       1SG 613
ATOM    613  O   ALA    96      12.286  26.967  32.784  1.00 43.05       1SG 614
ATOM    614  N   GLN    97      14.512  27.089  32.451  1.00119.84       1SG 615
ATOM    615  CA  GLN    97      14.777  26.745  33.816  1.00119.84       1SG 616
ATOM    616  CB  GLN    97      16.280  26.499  34.081  1.00119.84       1SG 617
ATOM    617  CG  GLN    97      16.602  25.896  35.451  1.00119.84       1SG 618
ATOM    618  CD  GLN    97      17.029  27.004  36.402  1.00119.84       1SG 619
ATOM    619  OE1 GLN    97      17.968  27.751  36.128  1.00119.84       1SG 620
ATOM    620  NE2 GLN    97      16.332  27.100  37.565  1.00119.84       1SG 621
ATOM    621  C   GLN    97      14.212  27.760  34.769  1.00119.84       1SG 622
ATOM    622  O   GLN    97      13.525  27.374  35.710  1.00119.84       1SG 623
ATOM    623  N   PRO    98      14.440  29.036  34.582  1.00130.38       1SG 624
ATOM    624  CA  PRO    98      13.833  29.948  35.506  1.00130.38       1SG 625
ATOM    625  CD  PRO    98      15.793  29.471  34.282  1.00130.38       1SG 626
ATOM    626  CB  PRO    98      14.542  31.285  35.318  1.00130.38       1SG 627
ATOM    627  CG  PRO    98      15.969  30.844  34.958  1.00130.38       1SG 628
ATOM    628  C   PRO    98      12.343  29.991  35.485  1.00130.38       1SG 629
ATOM    629  O   PRO    98      11.760  30.265  36.531  1.00130.38       1SG 630
ATOM    630  N   HIS    99      11.690  29.745  34.334  1.00 72.05       1SG 631
ATOM    631  CA  HIS    99      10.257  29.738  34.373  1.00 72.05       1SG 632
ATOM    632  ND1 HIS    99      10.258  31.914  31.844  1.00 72.05       1SG 633
ATOM    633  CG  HIS    99       9.343  31.150  32.533  1.00 72.05       1SG 634
ATOM    634  CB  HIS    99       9.568  29.741  32.999  1.00 72.05       1SG 635
ATOM    635  NE2 HIS    99       8.475  33.204  32.166  1.00 72.05       1SG 636
ATOM    636  CD2 HIS    99       8.258  31.955  32.719  1.00 72.05       1SG 637
ATOM    637  CE1 HIS    99       9.690  33.131  31.651  1.00 72.05       1SG 638
ATOM    638  C   HIS    99       9.826  28.568  35.187  1.00 72.05       1SG 639
ATOM    639  O   HIS    99       8.825  28.626  35.901  1.00 72.05       1SG 640
ATOM    640  N   LEU   100      10.602  27.476  35.118  1.00120.48       1SG 641
ATOM    641  CA  LEU   100      10.273  26.320  35.892  1.00120.48       1SG 642
ATOM    642  CB  LEU   100      11.336  25.222  35.792  1.00120.48       1SG 643
ATOM    643  CG  LEU   100      11.058  24.074  36.768  1.00120.48       1SG 644
ATOM    644  CD2 LEU   100      12.297  23.188  36.952  1.00120.48       1SG 645
ATOM    645  CD1 LEU   100       9.793  23.308  36.360  1.00120.48       1SG 646
ATOM    646  C   LEU   100      10.267  26.738  37.323  1.00120.48       1SG 647
ATOM    647  O   LEU   100       9.397  26.338  38.096  1.00120.48       1SG 648
ATOM    648  N   GLU   101      11.248  27.575  37.706  1.00 66.45       1SG 649
ATOM    649  CA  GLU   101      11.374  28.022  39.059  1.00 66.45       1SG 650
ATOM    650  CB  GLU   101      12.571  28.967  39.254  1.00 66.45       1SG 651
ATOM    651  CG  GLU   101      13.912  28.245  39.144  1.00 66.45       1SG 652
ATOM    652  CD  GLU   101      14.056  27.379  40.385  1.00 66.45       1SG 653
ATOM    653  OE1 GLU   101      14.372  27.950  41.461  1.00 66.45       1SG 654
ATOM    654  OE2 GLU   101      13.844  26.141  40.277  1.00 66.45       1SG 655
ATOM    655  C   GLU   101      10.138  28.771  39.410  1.00 66.45       1SG 656
ATOM    656  O   GLU   101       9.635  28.664  40.525  1.00 66.45       1SG 657
ATOM    657  N   LYS   102       9.603  29.551  38.459  1.00112.87       1SG 658
ATOM    658  CA  LYS   102       8.428  30.314  38.743  1.00112.87       1SG 659
ATOM    659  CB  LYS   102       8.012  31.202  37.556  1.00112.87       1SG 660
ATOM    660  CG  LYS   102       7.071  32.345  37.949  1.00112.87       1SG 661
ATOM    661  CD  LYS   102       7.725  33.374  38.879  1.00112.87       1SG 662
ATOM    662  CE  LYS   102       8.811  34.222  38.210  1.00112.87       1SG 663
ATOM    663  NZ  LYS   102       8.203  35.400  37.553  1.00112.87       1SG 664
ATOM    664  C   LYS   102       7.325  29.350  39.065  1.00112.87       1SG 665
ATOM    665  O   LYS   102       6.556  29.556  40.002  1.00112.87       1SG 666
ATOM    666  N   LEU   103       7.250  28.237  38.312  1.00110.48       1SG 667
ATOM    667  CA  LEU   103       6.224  27.255  38.520  1.00110.48       1SG 668
ATOM    668  CB  LEU   103       6.335  26.084  37.520  1.00110.48       1SG 669
ATOM    669  CG  LEU   103       5.196  25.050  37.598  1.00110.48       1SG 670
ATOM    670  CD2 LEU   103       5.515  23.815  36.740  1.00110.48       1SG 671
ATOM    671  CD1 LEU   103       3.847  25.685  37.227  1.00110.48       1SG 672
ATOM    672  C   LEU   103       6.398  26.707  39.903  1.00110.48       1SG 673
ATOM    673  O   LEU   103       5.431  26.528  40.640  1.00110.48       1SG 674
ATOM    674  N   SER   104       7.655  26.432  40.298  1.00 27.70       1SG 675
ATOM    675  CA  SER   104       7.934  25.886  41.597  1.00 27.70       1SG 676
ATOM    676  CB  SER   104       9.406  25.488  41.770  1.00 27.70       1SG 677
ATOM    677  OG  SER   104       9.757  24.485  40.832  1.00 27.70       1SG 678
ATOM    678  C   SER   104       7.662  26.925  42.638  1.00 27.70       1SG 679
ATOM    679  O   SER   104       7.383  26.614  43.794  1.00 27.70       1SG 680
ATOM    680  N   HIS   105       7.730  28.206  42.247  1.00 60.15       1SG 681
ATOM    681  CA  HIS   105       7.587  29.263  43.201  1.00 60.15       1SG 682
ATOM    682  ND1 HIS   105       8.618  32.381  44.135  1.00 60.15       1SG 683
ATOM    683  CG  HIS   105       7.539  31.793  43.512  1.00 60.15       1SG 684
ATOM    684  CB  HIS   105       7.646  30.650  42.545  1.00 60.15       1SG 685
ATOM    685  NE2 HIS   105       6.808  33.471  44.830  1.00 60.15       1SG 686
ATOM    686  CD2 HIS   105       6.442  32.470  43.948  1.00 60.15       1SG 687
ATOM    687  CE1 HIS   105       8.124  33.380  44.912  1.00 60.15       1SG 688
ATOM    688  C   HIS   105       6.249  29.136  43.839  1.00 60.15       1SG 689
ATOM    689  O   HIS   105       6.123  29.215  45.059  1.00 60.15       1SG 690
ATOM    690  N   LYS   106       5.205  28.910  43.024  1.00111.42       1SG 691
ATOM    691  CA  LYS   106       3.894  28.841  43.588  1.00111.42       1SG 692
ATOM    692  CB  LYS   106       2.768  28.767  42.532  1.00111.42       1SG 693
ATOM    693  CG  LYS   106       2.603  27.443  41.791  1.00111.42       1SG 694
ATOM    694  CD  LYS   106       1.903  26.358  42.607  1.00111.42       1SG 695
ATOM    695  CE  LYS   106       1.404  25.202  41.738  1.00111.42       1SG 696
ATOM    696  NZ  LYS   106       0.775  24.169  42.587  1.00111.42       1SG 697
ATOM    697  C   LYS   106       3.815  27.674  44.514  1.00111.42       1SG 698
ATOM    698  O   LYS   106       3.273  27.806  45.611  1.00111.42       1SG 699
ATOM    699  N   VAL   107       4.377  26.504  44.135  1.00 90.84       1SG 700
ATOM    700  CA  VAL   107       4.247  25.400  45.046  1.00 90.84       1SG 701
ATOM    701  CB  VAL   107       4.813  24.082  44.569  1.00 90.84       1SG 702
ATOM    702  CG1 VAL   107       4.080  23.653  43.288  1.00 90.84       1SG 703
ATOM    703  CG2 VAL   107       6.339  24.163  44.429  1.00 90.84       1SG 704
ATOM    704  C   VAL   107       4.938  25.759  46.324  1.00 90.84       1SG 705
ATOM    705  O   VAL   107       4.383  25.576  47.408  1.00 90.84       1SG 706
ATOM    706  N   HIS   108       6.163  26.312  46.243  1.00 85.97       1SG 707
ATOM    707  CA  HIS   108       6.832  26.683  47.453  1.00 85.97       1SG 708
ATOM    708  ND1 HIS   108       8.182  23.387  47.139  1.00 85.97       1SG 709
ATOM    709  CG  HIS   108       7.810  24.390  48.006  1.00 85.97       1SG 710
ATOM    710  CB  HIS   108       8.083  25.848  47.767  1.00 85.97       1SG 711
ATOM    711  NE2 HIS   108       7.192  22.397  48.865  1.00 85.97       1SG 712
ATOM    712  CD2 HIS   108       7.203  23.769  49.054  1.00 85.97       1SG 713
ATOM    713  CE1 HIS   108       7.789  22.216  47.701  1.00 85.97       1SG 714
ATOM    714  C   HIS   108       7.317  28.110  47.264  1.00 85.97       1SG 715
ATOM    715  O   HIS   108       6.767  29.023  47.933  1.00 85.97       1SG 716
ATOM    716  OXT HIS   108       8.238  28.310  46.429  1.00 85.97       1SG 717
TER
END
