
#######################################################
#                                                     #
#                        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   26 (  129),  selected   12 , name T0356TS239_4_3
# Molecule2: number of CA atoms  469 ( 3688),  selected   12 , name T0356.pdb
# PARAMETERS: T0356TS239_4_3.T0356.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:    12       480 - 491         4.09     4.09
  LCS_AVERAGE:      2.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       483 - 489         1.02     6.94
  LCS_AVERAGE:      1.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       483 - 488         0.84     6.69
  LONGEST_CONTINUOUS_SEGMENT:     6       484 - 489         0.60     7.34
  LCS_AVERAGE:      1.01

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:  469
LCS_GDT     H     480     H     480      5    5   12     4    4    5    5    5    6    6    7    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     I     481     I     481      5    5   12     4    4    5    5    5    6    7    7    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     D     482     D     482      5    5   12     4    4    5    5    5    6    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     A     483     A     483      6    7   12     4    4    6    7    7    7    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     I     484     I     484      6    7   12     5    6    6    7    7    7    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     W     485     W     485      6    7   12     5    6    6    7    7    7    7    8    8   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     D     486     D     486      6    7   12     5    6    6    7    7    7    7    8    8    9   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     E     487     E     487      6    7   12     5    6    6    7    7    7    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     488     L     488      6    7   12     5    6    6    7    7    7    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     A     489     A     489      6    7   12     3    6    6    7    7    7    7    8    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     I     490     I     490      0    0   12     0    0    0    0    2    4    4    5    7   10   11   12   12   12   12   12   12   12   12   12 
LCS_GDT     F     491     F     491      0    0   12     0    0    0    1    2    4    4    5    9   10   11   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   1.57  (   1.01    1.14    2.56 )

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      5      6      6      7      7      7      7      8      9     10     11     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   1.07   1.28   1.28   1.49   1.49   1.49   1.49   1.71   1.92   2.13   2.35   2.56   2.56   2.56   2.56   2.56   2.56   2.56   2.56   2.56
GDT RMS_LOCAL    0.18   0.60   0.60   1.02   1.02   1.02   1.02   2.51   3.41   3.59   3.83   4.09   4.09   4.09   4.09   4.09   4.09   4.09   4.09   4.09
GDT RMS_ALL_CA   7.00   7.34   7.34   6.94   6.94   6.94   6.94   6.59   4.18   4.38   4.34   4.09   4.09   4.09   4.09   4.09   4.09   4.09   4.09   4.09

#      Molecule1      Molecule2       DISTANCE
LGA    H     480      H     480         10.643
LGA    I     481      I     481          8.529
LGA    D     482      D     482          3.948
LGA    A     483      A     483          2.521
LGA    I     484      I     484          1.252
LGA    W     485      W     485          2.529
LGA    D     486      D     486          1.552
LGA    E     487      E     487          2.677
LGA    L     488      L     488          3.650
LGA    A     489      A     489          3.678
LGA    I     490      I     490         14.775
LGA    F     491      F     491         13.689

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  469    4.0      8    2.51     1.759     1.633     0.306

LGA_LOCAL      RMSD =  2.512  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.405  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  4.085  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.410502 * X  +   0.684808 * Y  +   0.602101 * Z  + 167.162704
  Y_new =   0.044617 * X  +  -0.674593 * Y  +   0.736840 * Z  + 174.724960
  Z_new =   0.910767 * X  +  -0.275611 * Y  +  -0.307476 * Z  +  19.699545 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.410790    0.730802  [ DEG:  -138.1281     41.8719 ]
  Theta =  -1.145139   -1.996454  [ DEG:   -65.6116   -114.3884 ]
  Phi   =   0.108264   -3.033329  [ DEG:     6.2031   -173.7969 ]
 
# 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: T0356TS239_4_3                                
REMARK     2: T0356.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS239_4_3.T0356.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  469   4.0    8   2.51   1.633     4.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS239_4_3
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1xnv_A
ATOM      1  N   HIS   480      41.522  87.522  74.239  1.00  9.99
ATOM      2  CA  HIS   480      42.689  87.930  73.405  1.00  9.99
ATOM      3  C   HIS   480      43.133  89.300  73.913  1.00  9.99
ATOM      4  O   HIS   480      43.576  89.430  75.056  1.00  9.99
ATOM      5  CB  HIS   480      42.278  88.009  71.929  1.00  9.99
ATOM      6  N   ILE   481      43.009  90.308  73.051  1.00  9.99
ATOM      7  CA  ILE   481      43.385  91.686  73.365  1.00  9.99
ATOM      8  C   ILE   481      42.855  92.451  72.159  1.00  9.99
ATOM      9  O   ILE   481      42.162  93.461  72.298  1.00  9.99
ATOM     10  CB  ILE   481      44.894  91.760  73.671  1.00  9.99
ATOM     11  N   ASP   482      43.203  91.966  70.972  1.00  9.99
ATOM     12  CA  ASP   482      42.752  92.576  69.730  1.00  9.99
ATOM     13  C   ASP   482      41.253  92.471  69.485  1.00  9.99
ATOM     14  O   ASP   482      40.730  92.977  68.493  1.00  9.99
ATOM     15  CB  ASP   482      43.533  91.930  68.584  1.00  9.99
ATOM     16  N   ALA   483      40.573  91.799  70.407  1.00  9.99
ATOM     17  CA  ALA   483      39.131  91.626  70.338  1.00  9.99
ATOM     18  C   ALA   483      38.479  92.587  71.327  1.00  9.99
ATOM     19  O   ALA   483      39.128  93.084  72.246  1.00  9.99
ATOM     20  CB  ALA   483      38.720  90.195  70.709  1.00  9.99
ATOM     21  N   ILE   484      37.197  92.853  71.141  1.00  9.99
ATOM     22  CA  ILE   484      36.504  93.757  72.035  1.00  9.99
ATOM     23  C   ILE   484      36.447  93.195  73.452  1.00  9.99
ATOM     24  O   ILE   484      36.697  93.914  74.428  1.00  9.99
ATOM     25  CB  ILE   484      35.090  94.027  71.528  1.00  9.99
ATOM     26  N   TRP   485      36.121  91.911  73.560  1.00  9.99
ATOM     27  CA  TRP   485      36.035  91.252  74.858  1.00  9.99
ATOM     28  C   TRP   485      37.376  91.345  75.579  1.00  9.99
ATOM     29  O   TRP   485      37.426  91.568  76.788  1.00  9.99
ATOM     30  CB  TRP   485      35.634  89.787  74.682  1.00  9.99
ATOM     31  N   ASP   486      38.460  91.176  74.828  1.00  9.99
ATOM     32  CA  ASP   486      39.785  91.244  75.419  1.00  9.99
ATOM     33  C   ASP   486      40.079  92.625  75.968  1.00  9.99
ATOM     34  O   ASP   486      40.758  92.778  76.986  1.00  9.99
ATOM     35  CB  ASP   486      40.828  90.833  74.367  1.00  9.99
ATOM     36  N   GLU   487      39.575  93.641  75.284  1.00  9.99
ATOM     37  CA  GLU   487      39.777  95.009  75.734  1.00  9.99
ATOM     38  C   GLU   487      38.987  95.261  77.025  1.00  9.99
ATOM     39  O   GLU   487      39.444  95.999  77.899  1.00  9.99
ATOM     40  CB  GLU   487      39.352  95.984  74.636  1.00  9.99
ATOM     41  N   LEU   488      37.810  94.647  77.151  1.00  9.99
ATOM     42  CA  LEU   488      37.005  94.808  78.358  1.00  9.99
ATOM     43  C   LEU   488      37.695  94.118  79.528  1.00  9.99
ATOM     44  O   LEU   488      37.670  94.609  80.651  1.00  9.99
ATOM     45  CB  LEU   488      35.602  94.214  78.180  1.00  9.99
ATOM     46  N   ALA   489      38.309  92.970  79.260  1.00  9.99
ATOM     47  CA  ALA   489      39.012  92.240  80.304  1.00  9.99
ATOM     48  C   ALA   489      40.248  93.034  80.707  1.00  9.99
ATOM     49  O   ALA   489      40.635  93.033  81.876  1.00  9.99
ATOM     50  CB  ALA   489      39.418  90.859  79.811  1.00  9.99
ATOM     51  N   ILE   490      41.442  98.326  86.343  1.00  9.99
ATOM     52  CA  ILE   490      40.595  98.823  87.419  1.00  9.99
ATOM     53  C   ILE   490      41.077  98.257  88.747  1.00  9.99
ATOM     54  O   ILE   490      41.159  98.971  89.749  1.00  9.99
ATOM     55  CB  ILE   490      39.125  98.423  87.211  1.00  9.99
ATOM     56  N   PHE   491      41.395  96.966  88.735  1.00  9.99
ATOM     57  CA  PHE   491      41.871  96.252  89.914  1.00  9.99
ATOM     58  C   PHE   491      43.208  96.821  90.399  1.00  9.99
ATOM     59  O   PHE   491      43.432  96.957  91.599  1.00  9.99
ATOM     60  CB  PHE   491      42.009  94.763  89.577  1.00  9.99
ATOM     61  N   ASN   492      44.092  97.158  89.463  1.00  9.99
ATOM     62  CA  ASN   492      45.388  97.724  89.819  1.00  9.99
ATOM     63  C   ASN   492      45.241  99.142  90.372  1.00  9.99
ATOM     64  O   ASN   492      45.971  99.544  91.278  1.00  9.99
ATOM     65  CB  ASN   492      46.311  97.761  88.597  1.00  9.99
ATOM     66  N   ASN   493      44.294  99.894  89.819  1.00  9.99
ATOM     67  CA  ASN   493      44.055 101.273  90.236  1.00  9.99
ATOM     68  C   ASN   493      43.507 101.376  91.654  1.00  9.99
ATOM     69  O   ASN   493      43.962 102.205  92.440  1.00  9.99
ATOM     70  CB  ASN   493      43.097 101.947  89.261  1.00  9.99
ATOM     71  N   GLY   494      50.829  99.654  97.955  1.00  9.99
ATOM     72  CA  GLY   494      51.284  98.300  98.278  1.00  9.99
ATOM     73  C   GLY   494      50.584  97.767  99.521  1.00  9.99
ATOM     74  O   GLY   494      50.202  98.532 100.409  1.00  9.99
ATOM     75  N   LYS   495      50.427  96.449  99.578  1.00  9.99
ATOM     76  CA  LYS   495      49.773  95.798 100.706  1.00  9.99
ATOM     77  C   LYS   495      50.435  96.190 102.020  1.00  9.99
ATOM     78  O   LYS   495      49.763  96.356 103.036  1.00  9.99
ATOM     79  CB  LYS   495      49.813  94.285 100.532  1.00  9.99
ATOM     80  N   SER   496      51.754  96.346 101.998  1.00  9.99
ATOM     81  CA  SER   496      52.471  96.714 103.208  1.00  9.99
ATOM     82  C   SER   496      52.117  98.140 103.614  1.00  9.99
ATOM     83  O   SER   496      51.869  98.412 104.788  1.00  9.99
ATOM     84  CB  SER   496      53.986  96.587 103.007  1.00  9.99
ATOM     85  N   ALA   497      52.081  99.041 102.638  1.00  9.99
ATOM     86  CA  ALA   497      51.753 100.439 102.901  1.00  9.99
ATOM     87  C   ALA   497      50.372 100.549 103.540  1.00  9.99
ATOM     88  O   ALA   497      50.170 101.315 104.480  1.00  9.99
ATOM     89  CB  ALA   497      51.798 101.236 101.607  1.00  9.99
ATOM     90  N   LEU   498      49.427  99.779 103.015  1.00  9.99
ATOM     91  CA  LEU   498      48.067  99.767 103.537  1.00  9.99
ATOM     92  C   LEU   498      48.063  99.244 104.977  1.00  9.99
ATOM     93  O   LEU   498      47.330  99.748 105.829  1.00  9.99
ATOM     94  CB  LEU   498      47.153  98.873 102.662  1.00  9.99
ATOM     95  N   GLU   499      48.889  98.236 105.242  1.00  9.99
ATOM     96  CA  GLU   499      48.983  97.657 106.580  1.00  9.99
ATOM     97  C   GLU   499      49.465  98.688 107.582  1.00  9.99
ATOM     98  O   GLU   499      48.891  98.822 108.662  1.00  9.99
ATOM     99  CB  GLU   499      49.946  96.469 106.604  1.00  9.99
ATOM    100  N   HIS   500      50.526  99.410 107.232  1.00  9.99
ATOM    101  CA  HIS   500      51.057 100.419 108.132  1.00  9.99
ATOM    102  C   HIS   500      49.977 101.456 108.397  1.00  9.99
ATOM    103  O   HIS   500      49.742 101.829 109.541  1.00  9.99
ATOM    104  CB  HIS   500      52.299 101.081 107.533  1.00  9.99
ATOM    105  N   HIS   501      49.309 101.906 107.340  1.00  9.99
ATOM    106  CA  HIS   501      48.243 102.893 107.477  1.00  9.99
ATOM    107  C   HIS   501      47.214 102.421 108.506  1.00  9.99
ATOM    108  O   HIS   501      46.826 103.172 109.400  1.00  9.99
ATOM    109  CB  HIS   501      47.563 103.112 106.128  1.00  9.99
ATOM    110  N   HIS   502      46.777 101.171 108.382  1.00  9.99
ATOM    111  CA  HIS   502      45.810 100.616 109.319  1.00  9.99
ATOM    112  C   HIS   502      46.396 100.465 110.720  1.00  9.99
ATOM    113  O   HIS   502      45.697 100.654 111.716  1.00  9.99
ATOM    114  CB  HIS   502      45.311  99.269 108.805  1.00  9.99
ATOM    115  N   HIS   503      47.682 100.135 110.798  1.00  9.99
ATOM    116  CA  HIS   503      48.342  99.966 112.092  1.00  9.99
ATOM    117  C   HIS   503      48.363 101.279 112.869  1.00  9.99
ATOM    118  O   HIS   503      48.330 101.285 114.100  1.00  9.99
ATOM    119  CB  HIS   503      49.763  99.449 111.894  1.00  9.99
ATOM    120  N   HIS   504      48.420 102.393 112.147  1.00  9.99
ATOM    121  CA  HIS   504      48.446 103.702 112.782  1.00  9.99
ATOM    122  C   HIS   504      47.033 104.146 113.137  1.00  9.99
ATOM    123  O   HIS   504      46.818 105.281 113.562  1.00  9.99
ATOM    124  CB  HIS   504      49.095 104.725 111.849  1.00  9.99
ATOM    125  N   HIS   505      46.072 103.244 112.964  1.00  9.99
ATOM    126  CA  HIS   505      44.695 103.576 113.271  1.00  9.99
ATOM    127  C   HIS   505      44.092 104.540 112.259  1.00  9.99
ATOM    128  O   HIS   505      43.122 105.242 112.559  1.00  9.99
ATOM    129  CB  HIS   505      44.632 104.159 114.693  1.00  9.99
TER
END
