
#######################################################
#                                                     #
#                        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   14 (  121),  selected   14 , name T0347TS105_5_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   14 , name T0347_D1.pdb
# PARAMETERS: T0347TS105_5_2-D1.T0347_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:    14        95 - 108         0.87     0.87
  LCS_AVERAGE:     15.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        95 - 108         0.87     0.87
  LCS_AVERAGE:     15.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        95 - 108         0.87     0.87
  LCS_AVERAGE:     15.73

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:   89
LCS_GDT     G      95     G      95     14   14   14     9   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     K      96     K      96     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D      97     D      97     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E      98     E      98     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     F      99     F      99     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     W     100     W     100     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     101     S     101     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     102     V     102     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     M     103     M     103     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     104     D     104     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     H     105     H     105     14   14   14    10   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     R     106     R     106     14   14   14     8   12   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     107     N     107     14   14   14     3    5   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     108     L     108     14   14   14     0    9   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:  15.73  (  15.73   15.73   15.73 )

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     10     12     13     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA  11.24  13.48  14.61  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73  15.73
GDT RMS_LOCAL    0.29   0.41   0.61   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87
GDT RMS_ALL_CA   0.91   0.89   0.93   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87   0.87

#      Molecule1      Molecule2       DISTANCE
LGA    G      95      G      95          0.653
LGA    K      96      K      96          0.531
LGA    D      97      D      97          0.410
LGA    E      98      E      98          0.150
LGA    F      99      F      99          0.214
LGA    W     100      W     100          0.310
LGA    S     101      S     101          0.271
LGA    V     102      V     102          0.336
LGA    M     103      M     103          0.359
LGA    D     104      D     104          0.440
LGA    H     105      H     105          0.573
LGA    R     106      R     106          0.772
LGA    N     107      N     107          2.093
LGA    L     108      L     108          1.922

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14   89    4.0     14    0.87    15.169    15.469     1.446

LGA_LOCAL      RMSD =  0.868  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.868  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  0.868  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.990323 * X  +  -0.010698 * Y  +  -0.138366 * Z  +  37.458797
  Y_new =   0.106571 * X  +  -0.697264 * Y  +  -0.708848 * Z  +  -2.452732
  Z_new =  -0.088894 * X  +  -0.716735 * Y  +   0.691657 * Z  +   3.901600 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.803202    2.338390  [ DEG:   -46.0201    133.9799 ]
  Theta =   0.089012    3.052581  [ DEG:     5.1000    174.9000 ]
  Phi   =   3.034393   -0.107200  [ DEG:   173.8579     -6.1421 ]
 
# 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: T0347TS105_5_2-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS105_5_2-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14   89   4.0   14   0.87  15.469     0.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS105_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0347
PARENT 1vz0_A
ATOM    768  N   GLY    95      -5.256  27.661   8.669  1.00 85.64       1SG 769
ATOM    769  CA  GLY    95      -3.939  27.528   8.124  1.00 85.64       1SG 770
ATOM    770  C   GLY    95      -3.469  28.856   7.628  1.00 85.64       1SG 771
ATOM    771  O   GLY    95      -2.302  29.205   7.789  1.00 85.64       1SG 772
ATOM    772  N   LYS    96      -4.365  29.634   7.000  1.00125.01       1SG 773
ATOM    773  CA  LYS    96      -3.962  30.891   6.446  1.00125.01       1SG 774
ATOM    774  CB  LYS    96      -5.099  31.610   5.698  1.00125.01       1SG 775
ATOM    775  CG  LYS    96      -4.674  32.947   5.083  1.00125.01       1SG 776
ATOM    776  CD  LYS    96      -5.625  33.457   3.997  1.00125.01       1SG 777
ATOM    777  CE  LYS    96      -5.333  32.868   2.614  1.00125.01       1SG 778
ATOM    778  NZ  LYS    96      -3.995  33.306   2.151  1.00125.01       1SG 779
ATOM    779  C   LYS    96      -3.492  31.760   7.566  1.00125.01       1SG 780
ATOM    780  O   LYS    96      -2.501  32.477   7.441  1.00125.01       1SG 781
ATOM    781  N   ASP    97      -4.199  31.703   8.707  1.00 38.53       1SG 782
ATOM    782  CA  ASP    97      -3.858  32.510   9.839  1.00 38.53       1SG 783
ATOM    783  CB  ASP    97      -4.814  32.255  11.013  1.00 38.53       1SG 784
ATOM    784  CG  ASP    97      -6.211  32.598  10.528  1.00 38.53       1SG 785
ATOM    785  OD1 ASP    97      -6.318  33.421   9.580  1.00 38.53       1SG 786
ATOM    786  OD2 ASP    97      -7.192  32.039  11.087  1.00 38.53       1SG 787
ATOM    787  C   ASP    97      -2.497  32.101  10.303  1.00 38.53       1SG 788
ATOM    788  O   ASP    97      -1.635  32.936  10.574  1.00 38.53       1SG 789
ATOM    789  N   GLU    98      -2.271  30.779  10.386  1.00 60.28       1SG 790
ATOM    790  CA  GLU    98      -1.026  30.264  10.867  1.00 60.28       1SG 791
ATOM    791  CB  GLU    98      -1.019  28.728  10.953  1.00 60.28       1SG 792
ATOM    792  CG  GLU    98      -1.985  28.171  12.002  1.00 60.28       1SG 793
ATOM    793  CD  GLU    98      -1.422  28.505  13.375  1.00 60.28       1SG 794
ATOM    794  OE1 GLU    98      -0.326  29.125  13.424  1.00 60.28       1SG 795
ATOM    795  OE2 GLU    98      -2.075  28.147  14.392  1.00 60.28       1SG 796
ATOM    796  C   GLU    98       0.054  30.661   9.919  1.00 60.28       1SG 797
ATOM    797  O   GLU    98       1.152  31.033  10.331  1.00 60.28       1SG 798
ATOM    798  N   PHE    99      -0.239  30.603   8.610  1.00 79.88       1SG 799
ATOM    799  CA  PHE    99       0.760  30.885   7.627  1.00 79.88       1SG 800
ATOM    800  CB  PHE    99       0.277  30.653   6.189  1.00 79.88       1SG 801
ATOM    801  CG  PHE    99       1.489  30.740   5.328  1.00 79.88       1SG 802
ATOM    802  CD1 PHE    99       2.295  29.638   5.143  1.00 79.88       1SG 803
ATOM    803  CD2 PHE    99       1.827  31.924   4.714  1.00 79.88       1SG 804
ATOM    804  CE1 PHE    99       3.417  29.711   4.351  1.00 79.88       1SG 805
ATOM    805  CE2 PHE    99       2.948  32.007   3.922  1.00 79.88       1SG 806
ATOM    806  CZ  PHE    99       3.742  30.899   3.742  1.00 79.88       1SG 807
ATOM    807  C   PHE    99       1.182  32.314   7.756  1.00 79.88       1SG 808
ATOM    808  O   PHE    99       2.367  32.630   7.671  1.00 79.88       1SG 809
ATOM    809  N   TRP   100       0.216  33.221   7.976  1.00 68.95       1SG 810
ATOM    810  CA  TRP   100       0.523  34.614   8.066  1.00 68.95       1SG 811
ATOM    811  CB  TRP   100      -0.717  35.472   8.335  1.00 68.95       1SG 812
ATOM    812  CG  TRP   100      -1.703  35.460   7.200  1.00 68.95       1SG 813
ATOM    813  CD2 TRP   100      -1.321  35.328   5.824  1.00 68.95       1SG 814
ATOM    814  CD1 TRP   100      -3.065  35.511   7.222  1.00 68.95       1SG 815
ATOM    815  NE1 TRP   100      -3.552  35.466   5.939  1.00 68.95       1SG 816
ATOM    816  CE2 TRP   100      -2.491  35.343   5.069  1.00 68.95       1SG 817
ATOM    817  CE3 TRP   100      -0.097  35.188   5.240  1.00 68.95       1SG 818
ATOM    818  CZ2 TRP   100      -2.453  35.228   3.710  1.00 68.95       1SG 819
ATOM    819  CZ3 TRP   100      -0.058  35.089   3.866  1.00 68.95       1SG 820
ATOM    820  CH2 TRP   100      -1.215  35.111   3.116  1.00 68.95       1SG 821
ATOM    821  C   TRP   100       1.466  34.825   9.207  1.00 68.95       1SG 822
ATOM    822  O   TRP   100       2.464  35.533   9.078  1.00 68.95       1SG 823
ATOM    823  N   SER   101       1.178  34.199  10.360  1.00 67.85       1SG 824
ATOM    824  CA  SER   101       2.007  34.382  11.514  1.00 67.85       1SG 825
ATOM    825  CB  SER   101       1.492  33.610  12.741  1.00 67.85       1SG 826
ATOM    826  OG  SER   101       2.351  33.824  13.852  1.00 67.85       1SG 827
ATOM    827  C   SER   101       3.373  33.867  11.190  1.00 67.85       1SG 828
ATOM    828  O   SER   101       4.379  34.450  11.592  1.00 67.85       1SG 829
ATOM    829  N   VAL   102       3.444  32.758  10.436  1.00 35.12       1SG 830
ATOM    830  CA  VAL   102       4.714  32.179  10.114  1.00 35.12       1SG 831
ATOM    831  CB  VAL   102       4.599  30.929   9.294  1.00 35.12       1SG 832
ATOM    832  CG1 VAL   102       6.019  30.468   8.923  1.00 35.12       1SG 833
ATOM    833  CG2 VAL   102       3.791  29.885  10.083  1.00 35.12       1SG 834
ATOM    834  C   VAL   102       5.509  33.147   9.297  1.00 35.12       1SG 835
ATOM    835  O   VAL   102       6.694  33.355   9.552  1.00 35.12       1SG 836
ATOM    836  N   MET   103       4.866  33.787   8.304  1.00121.66       1SG 837
ATOM    837  CA  MET   103       5.580  34.644   7.402  1.00121.66       1SG 838
ATOM    838  CB  MET   103       4.686  35.262   6.311  1.00121.66       1SG 839
ATOM    839  CG  MET   103       4.374  34.337   5.132  1.00121.66       1SG 840
ATOM    840  SD  MET   103       5.827  34.003   4.086  1.00121.66       1SG 841
ATOM    841  CE  MET   103       4.950  33.669   2.531  1.00121.66       1SG 842
ATOM    842  C   MET   103       6.211  35.782   8.129  1.00121.66       1SG 843
ATOM    843  O   MET   103       7.375  36.096   7.883  1.00121.66       1SG 844
ATOM    844  N   ASP   104       5.484  36.436   9.052  1.00109.83       1SG 845
ATOM    845  CA  ASP   104       6.107  37.576   9.653  1.00109.83       1SG 846
ATOM    846  CB  ASP   104       5.193  38.379  10.598  1.00109.83       1SG 847
ATOM    847  CG  ASP   104       4.765  37.503  11.762  1.00109.83       1SG 848
ATOM    848  OD1 ASP   104       5.506  37.460  12.781  1.00109.83       1SG 849
ATOM    849  OD2 ASP   104       3.672  36.886  11.657  1.00109.83       1SG 850
ATOM    850  C   ASP   104       7.314  37.140  10.416  1.00109.83       1SG 851
ATOM    851  O   ASP   104       8.398  37.695  10.241  1.00109.83       1SG 852
ATOM    852  N   HIS   105       7.177  36.104  11.259  1.00 42.22       1SG 853
ATOM    853  CA  HIS   105       8.313  35.725  12.042  1.00 42.22       1SG 854
ATOM    854  ND1 HIS   105       7.451  35.725  15.272  1.00 42.22       1SG 855
ATOM    855  CG  HIS   105       7.068  35.034  14.144  1.00 42.22       1SG 856
ATOM    856  CB  HIS   105       8.011  34.610  13.059  1.00 42.22       1SG 857
ATOM    857  NE2 HIS   105       5.259  35.401  15.441  1.00 42.22       1SG 858
ATOM    858  CD2 HIS   105       5.725  34.844  14.264  1.00 42.22       1SG 859
ATOM    859  CE1 HIS   105       6.330  35.919  16.012  1.00 42.22       1SG 860
ATOM    860  C   HIS   105       9.409  35.221  11.161  1.00 42.22       1SG 861
ATOM    861  O   HIS   105      10.545  35.686  11.247  1.00 42.22       1SG 862
ATOM    862  N   ARG   106       9.098  34.262  10.269  1.00165.12       1SG 863
ATOM    863  CA  ARG   106      10.164  33.659   9.525  1.00165.12       1SG 864
ATOM    864  CB  ARG   106       9.655  32.553   8.584  1.00165.12       1SG 865
ATOM    865  CG  ARG   106      10.745  31.852   7.773  1.00165.12       1SG 866
ATOM    866  CD  ARG   106      10.208  30.668   6.964  1.00165.12       1SG 867
ATOM    867  NE  ARG   106       9.312  31.215   5.904  1.00165.12       1SG 868
ATOM    868  CZ  ARG   106       8.283  30.463   5.413  1.00165.12       1SG 869
ATOM    869  NH1 ARG   106       8.060  29.208   5.899  1.00165.12       1SG 870
ATOM    870  NH2 ARG   106       7.471  30.971   4.441  1.00165.12       1SG 871
ATOM    871  C   ARG   106      10.862  34.680   8.695  1.00165.12       1SG 872
ATOM    872  O   ARG   106      12.011  35.020   8.968  1.00165.12       1SG 873
ATOM    873  N   ASN   107      10.155  35.247   7.699  1.00188.69       1SG 874
ATOM    874  CA  ASN   107      10.757  36.234   6.856  1.00188.69       1SG 875
ATOM    875  CB  ASN   107      11.670  35.654   5.760  1.00188.69       1SG 876
ATOM    876  CG  ASN   107      12.938  35.104   6.396  1.00188.69       1SG 877
ATOM    877  OD1 ASN   107      13.182  33.900   6.372  1.00188.69       1SG 878
ATOM    878  ND2 ASN   107      13.765  36.008   6.990  1.00188.69       1SG 879
ATOM    879  C   ASN   107       9.650  36.915   6.135  1.00188.69       1SG 880
ATOM    880  O   ASN   107       9.018  36.324   5.263  1.00188.69       1SG 881
ATOM    881  N   LEU   108       9.376  38.186   6.469  1.00211.13       1SG 882
ATOM    882  CA  LEU   108       8.346  38.804   5.704  1.00211.13       1SG 883
ATOM    883  CB  LEU   108       7.053  39.096   6.481  1.00211.13       1SG 884
ATOM    884  CG  LEU   108       6.007  39.800   5.597  1.00211.13       1SG 885
ATOM    885  CD1 LEU   108       6.219  41.321   5.521  1.00211.13       1SG 886
ATOM    886  CD2 LEU   108       6.014  39.177   4.190  1.00211.13       1SG 887
ATOM    887  C   LEU   108       8.852  40.084   5.157  1.00211.13       1SG 888
ATOM    888  O   LEU   108       8.943  41.078   5.872  1.00211.13       1SG 889
TER
END
