
#######################################################
#                                                     #
#                        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   13 (  104),  selected   13 , name T0299TS677_2_2-D1
# Molecule2: number of CA atoms   91 (  726),  selected   13 , name T0299_D1.pdb
# PARAMETERS: T0299TS677_2_2-D1.T0299_D1.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:    13       168 - 180         1.97     1.97
  LCS_AVERAGE:     14.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       168 - 180         1.97     1.97
  LCS_AVERAGE:     14.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       168 - 177         0.99     2.15
  LCS_AVERAGE:      9.64

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:   91
LCS_GDT     A     168     A     168     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     169     K     169     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     T     170     T     170     10   13   13     5    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     171     F     171     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     172     D     172     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     173     K     173     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     174     I     174     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     G     175     G     175     10   13   13     6    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     Q     176     Q     176     10   13   13     4    8    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     M     177     M     177     10   13   13     4    5    9   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     178     L     178      5   13   13     4    4    5   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     179     K     179      5   13   13     4    4    5    9   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     180     K     180      4   13   13     0    3    4    5    7    7   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:  12.74  (   9.64   14.29   14.29 )

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      6      8      9     10     12     12     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   6.59   8.79   9.89  10.99  13.19  13.19  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29
GDT RMS_LOCAL    0.25   0.48   0.69   0.99   1.48   1.48   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97
GDT RMS_ALL_CA   2.23   2.42   2.21   2.15   2.13   2.13   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97

#      Molecule1      Molecule2       DISTANCE
LGA    A     168      A     168          2.858
LGA    K     169      K     169          1.158
LGA    T     170      T     170          1.532
LGA    F     171      F     171          1.485
LGA    D     172      D     172          1.265
LGA    K     173      K     173          1.117
LGA    I     174      I     174          1.208
LGA    G     175      G     175          1.040
LGA    Q     176      Q     176          0.639
LGA    M     177      M     177          1.449
LGA    L     178      L     178          2.829
LGA    K     179      K     179          2.722
LGA    K     180      K     180          3.962

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   91    4.0     13    1.97    12.088    13.153     0.627

LGA_LOCAL      RMSD =  1.973  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.020  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  1.973  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.935373 * X  +  -0.229278 * Y  +   0.269274 * Z  + -35.748676
  Y_new =  -0.161536 * X  +   0.400352 * Y  +   0.902011 * Z  +  17.818933
  Z_new =  -0.314615 * X  +  -0.887215 * Y  +   0.337442 * Z  + -28.961319 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.207354    1.934239  [ DEG:   -69.1763    110.8237 ]
  Theta =   0.320051    2.821541  [ DEG:    18.3376    161.6624 ]
  Phi   =  -0.171010    2.970582  [ DEG:    -9.7982    170.2018 ]
 
# 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: T0299TS677_2_2-D1                             
REMARK     2: T0299_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299TS677_2_2-D1.T0299_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   91   4.0   13   1.97  13.153     1.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS677_2_2-D1
REMARK PARENT number 2
PFRMAT     TS
TARGET     T0299
PARENT     1zzmA
ATOM    659  N   ALA   168       4.597  53.581 -15.375  1.00   .37       1SG 660
ATOM    660  CA  ALA   168       3.469  54.107 -14.660  1.00   .37       1SG 661
ATOM    661  CB  ALA   168       2.730  55.187 -15.466  1.00   .37       1SG 662
ATOM    662  C   ALA   168       2.481  53.007 -14.414  1.00   .37       1SG 663
ATOM    663  O   ALA   168       1.323  53.274 -14.100  1.00   .37       1SG 664
ATOM    664  N   LYS   169       2.904  51.738 -14.537  1.00   .72       1SG 665
ATOM    665  CA  LYS   169       1.973  50.647 -14.474  1.00   .72       1SG 666
ATOM    666  CB  LYS   169       2.664  49.283 -14.646  1.00   .72       1SG 667
ATOM    667  CG  LYS   169       3.589  48.927 -13.481  1.00   .72       1SG 668
ATOM    668  CD  LYS   169       4.707  49.947 -13.247  1.00   .72       1SG 669
ATOM    669  CE  LYS   169       5.594  49.621 -12.043  1.00   .72       1SG 670
ATOM    670  NZ  LYS   169       6.488  48.486 -12.367  1.00   .72       1SG 671
ATOM    671  C   LYS   169       1.251  50.604 -13.163  1.00   .72       1SG 672
ATOM    672  O   LYS   169       0.032  50.437 -13.126  1.00   .72       1SG 673
ATOM    673  N   THR   170       1.979  50.777 -12.048  1.00   .70       1SG 674
ATOM    674  CA  THR   170       1.382  50.602 -10.757  1.00   .70       1SG 675
ATOM    675  CB  THR   170       2.375  50.726  -9.635  1.00   .70       1SG 676
ATOM    676  OG1 THR   170       1.781  50.320  -8.412  1.00   .70       1SG 677
ATOM    677  CG2 THR   170       2.859  52.183  -9.538  1.00   .70       1SG 678
ATOM    678  C   THR   170       0.278  51.584 -10.524  1.00   .70       1SG 679
ATOM    679  O   THR   170      -0.791  51.214 -10.039  1.00   .70       1SG 680
ATOM    680  N   PHE   171       0.470  52.863 -10.885  1.00   .46       1SG 681
ATOM    681  CA  PHE   171      -0.570  53.780 -10.532  1.00   .46       1SG 682
ATOM    682  CB  PHE   171      -0.006  55.104 -10.006  1.00   .46       1SG 683
ATOM    683  CG  PHE   171       1.130  55.456 -10.893  1.00   .46       1SG 684
ATOM    684  CD1 PHE   171       0.948  56.092 -12.097  1.00   .46       1SG 685
ATOM    685  CD2 PHE   171       2.405  55.126 -10.491  1.00   .46       1SG 686
ATOM    686  CE1 PHE   171       2.038  56.401 -12.877  1.00   .46       1SG 687
ATOM    687  CE2 PHE   171       3.494  55.434 -11.269  1.00   .46       1SG 688
ATOM    688  CZ  PHE   171       3.307  56.074 -12.470  1.00   .46       1SG 689
ATOM    689  C   PHE   171      -1.504  54.026 -11.668  1.00   .46       1SG 690
ATOM    690  O   PHE   171      -2.541  54.662 -11.489  1.00   .46       1SG 691
ATOM    691  N   ASP   172      -1.203  53.520 -12.870  1.00   .42       1SG 692
ATOM    692  CA  ASP   172      -2.228  53.649 -13.855  1.00   .42       1SG 693
ATOM    693  CB  ASP   172      -1.748  53.405 -15.292  1.00   .42       1SG 694
ATOM    694  CG  ASP   172      -0.983  54.669 -15.666  1.00   .42       1SG 695
ATOM    695  OD1 ASP   172      -0.214  55.167 -14.801  1.00   .42       1SG 696
ATOM    696  OD2 ASP   172      -1.160  55.162 -16.811  1.00   .42       1SG 697
ATOM    697  C   ASP   172      -3.266  52.660 -13.448  1.00   .42       1SG 698
ATOM    698  O   ASP   172      -4.465  52.874 -13.619  1.00   .42       1SG 699
ATOM    699  N   LYS   173      -2.796  51.543 -12.864  1.00   .63       1SG 700
ATOM    700  CA  LYS   173      -3.655  50.496 -12.403  1.00   .63       1SG 701
ATOM    701  CB  LYS   173      -2.871  49.298 -11.824  1.00   .63       1SG 702
ATOM    702  CG  LYS   173      -3.715  48.072 -11.443  1.00   .63       1SG 703
ATOM    703  CD  LYS   173      -4.693  48.294 -10.284  1.00   .63       1SG 704
ATOM    704  CE  LYS   173      -5.629  47.113 -10.025  1.00   .63       1SG 705
ATOM    705  NZ  LYS   173      -6.530  47.423  -8.892  1.00   .63       1SG 706
ATOM    706  C   LYS   173      -4.525  51.041 -11.318  1.00   .63       1SG 707
ATOM    707  O   LYS   173      -5.724  50.764 -11.274  1.00   .63       1SG 708
ATOM    708  N   ILE   174      -3.950  51.853 -10.415  1.00   .61       1SG 709
ATOM    709  CA  ILE   174      -4.718  52.305  -9.294  1.00   .61       1SG 710
ATOM    710  CB  ILE   174      -3.934  53.130  -8.309  1.00   .61       1SG 711
ATOM    711  CG2 ILE   174      -3.582  54.474  -8.963  1.00   .61       1SG 712
ATOM    712  CG1 ILE   174      -4.725  53.285  -7.000  1.00   .61       1SG 713
ATOM    713  CD1 ILE   174      -4.902  51.975  -6.232  1.00   .61       1SG 714
ATOM    714  C   ILE   174      -5.875  53.121  -9.765  1.00   .61       1SG 715
ATOM    715  O   ILE   174      -6.976  52.996  -9.234  1.00   .61       1SG 716
ATOM    716  N   GLY   175      -5.679  53.971 -10.791  1.00   .47       1SG 717
ATOM    717  CA  GLY   175      -6.778  54.823 -11.127  1.00   .47       1SG 718
ATOM    718  C   GLY   175      -7.546  54.319 -12.302  1.00   .47       1SG 719
ATOM    719  O   GLY   175      -8.564  54.912 -12.654  1.00   .47       1SG 720
ATOM    720  N   GLN   176      -7.150  53.206 -12.944  1.00   .69       1SG 721
ATOM    721  CA  GLN   176      -7.968  52.938 -14.086  1.00   .69       1SG 722
ATOM    722  CB  GLN   176      -7.170  52.514 -15.334  1.00   .69       1SG 723
ATOM    723  CG  GLN   176      -6.477  51.158 -15.250  1.00   .69       1SG 724
ATOM    724  CD  GLN   176      -7.420  50.136 -15.865  1.00   .69       1SG 725
ATOM    725  OE1 GLN   176      -7.083  48.961 -15.988  1.00   .69       1SG 726
ATOM    726  NE2 GLN   176      -8.631  50.594 -16.281  1.00   .69       1SG 727
ATOM    727  C   GLN   176      -8.948  51.889 -13.744  1.00   .69       1SG 728
ATOM    728  O   GLN   176     -10.158  52.069 -13.859  1.00   .69       1SG 729
ATOM    729  N   MET   177      -8.453  50.753 -13.273  1.00   .89       1SG 730
ATOM    730  CA  MET   177      -9.386  49.748 -12.924  1.00   .89       1SG 731
ATOM    731  CB  MET   177      -8.707  48.417 -12.705  1.00   .89       1SG 732
ATOM    732  CG  MET   177      -7.309  48.532 -12.098  1.00   .89       1SG 733
ATOM    733  SD  MET   177      -6.016  48.797 -13.340  1.00   .89       1SG 734
ATOM    734  CE  MET   177      -5.773  47.043 -13.737  1.00   .89       1SG 735
ATOM    735  C   MET   177     -10.033  50.127 -11.646  1.00   .89       1SG 736
ATOM    736  O   MET   177     -11.101  50.739 -11.628  1.00   .89       1SG 737
ATOM    737  N   LEU   178      -9.349  49.724 -10.559  1.00   .81       1SG 738
ATOM    738  CA  LEU   178      -9.696  49.842  -9.179  1.00   .81       1SG 739
ATOM    739  CB  LEU   178      -8.450  50.038  -8.287  1.00   .81       1SG 740
ATOM    740  CG  LEU   178      -8.713  50.166  -6.768  1.00   .81       1SG 741
ATOM    741  CD2 LEU   178      -9.517  48.962  -6.248  1.00   .81       1SG 742
ATOM    742  CD1 LEU   178      -9.341  51.515  -6.379  1.00   .81       1SG 743
ATOM    743  C   LEU   178     -10.658  50.959  -8.946  1.00   .81       1SG 744
ATOM    744  O   LEU   178     -11.668  50.771  -8.272  1.00   .81       1SG 745
ATOM    745  N   LYS   179     -10.406  52.144  -9.531  1.00   .67       1SG 746
ATOM    746  CA  LYS   179     -11.295  53.225  -9.227  1.00   .67       1SG 747
ATOM    747  CB  LYS   179     -10.556  54.550  -8.951  1.00   .67       1SG 748
ATOM    748  CG  LYS   179      -9.497  54.929  -9.991  1.00   .67       1SG 749
ATOM    749  CD  LYS   179      -9.017  56.377  -9.871  1.00   .67       1SG 750
ATOM    750  CE  LYS   179      -8.193  56.651  -8.610  1.00   .67       1SG 751
ATOM    751  NZ  LYS   179      -7.774  58.070  -8.579  1.00   .67       1SG 752
ATOM    752  C   LYS   179     -12.266  53.417 -10.350  1.00   .67       1SG 753
ATOM    753  O   LYS   179     -13.305  52.757 -10.380  1.00   .67       1SG 754
ATOM    754  N   LYS   180     -11.943  54.355 -11.266  1.00   .55       1SG 755
ATOM    755  CA  LYS   180     -12.701  54.770 -12.417  1.00   .55       1SG 756
ATOM    756  CB  LYS   180     -11.807  55.273 -13.562  1.00   .55       1SG 757
ATOM    757  CG  LYS   180     -10.969  56.479 -13.135  1.00   .55       1SG 758
ATOM    758  CD  LYS   180     -11.811  57.627 -12.572  1.00   .55       1SG 759
ATOM    759  CE  LYS   180     -10.985  58.723 -11.894  1.00   .55       1SG 760
ATOM    760  NZ  LYS   180     -11.883  59.707 -11.249  1.00   .55       1SG 761
ATOM    761  C   LYS   180     -13.585  53.679 -12.930  1.00   .55       1SG 762
ATOM    762  O   LYS   180     -14.739  53.932 -13.275  1.00   .55       1SG 763
TER
END
