
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0356AL044_2-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   24 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_2-D2.T0356_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:    17       290 - 306         4.85     9.08
  LONGEST_CONTINUOUS_SEGMENT:    17       293 - 309         5.00     8.86
  LCS_AVERAGE:      8.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.86    31.40
  LONGEST_CONTINUOUS_SEGMENT:     6       300 - 305         1.98    16.94
  LCS_AVERAGE:      2.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       294 - 298         0.57    29.52
  LONGEST_CONTINUOUS_SEGMENT:     5       299 - 303         0.99    20.60
  LCS_AVERAGE:      2.21

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:  192
LCS_GDT     D     290     D     290      4    4   17     4    4    5    5    6    7    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     H     291     H     291      4    6   17     4    4    5    5    6    7    8    9   11   13   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     T     292     T     292      4    6   17     4    4    4    4    5    7    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     G     293     G     293      4    6   17     4    4    4    4    5    8    9   10   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     Y     294     Y     294      5    6   17     3    5    5    5    7    8    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     Y     295     Y     295      5    6   17     4    5    5    5    5    8    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     N     296     N     296      5    6   17     4    5    5    5    7    8    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     E     297     E     297      5    5   17     4    5    5    5    7    8    9    9   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     V     298     V     298      5    5   17     4    5    5    5    7    8    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     D     299     D     299      5    5   17     4    4    4    5    6    7    8    9   12   14   14   15   16   17   19   21   21   22   22   23 
LCS_GDT     S     300     S     300      5    6   17     4    4    4    5    6    7    8    9   12   14   14   15   16   17   18   21   21   22   22   23 
LCS_GDT     F     301     F     301      5    6   17     4    4    4    5    6    7    8    9   12   14   14   15   16   17   19   21   21   22   22   23 
LCS_GDT     P     302     P     302      5    6   17     4    4    4    5    6    7    8    9   11   14   14   15   16   17   19   21   21   22   22   23 
LCS_GDT     V     303     V     303      5    6   17     3    4    4    5    5    7    8    9   12   14   15   17   17   19   19   21   21   22   22   23 
LCS_GDT     F     304     F     304      4    6   17     3    4    4    4    7    8    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     T     305     T     305      4    6   17     3    4    4    4    7    8    9   10   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     V     306     V     306      4    5   17     3    4    4    4    7    8    9    9   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     T     307     T     307      4    4   17     3    3    4    4    4    4    6    7    8    8    8   10   13   19   19   21   21   22   22   23 
LCS_GDT     H     308     H     308      4    5   17     3    3    4    4    4    7    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     I     309     I     309      4    5   17     3    3    5    5    6    7    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     T     310     T     310      3    5   11     3    3    4    4    6    7    9   11   12   14   16   17   17   19   19   21   21   22   22   23 
LCS_GDT     Q     311     Q     311      3    5   11     3    3    5    5    6    7    9   11   12   14   16   17   17   19   19   19   21   22   22   23 
LCS_GDT     R     312     R     312      3    5   11     3    3    4    4    4    5    5    6    7   11   13   16   17   19   19   19   19   22   22   23 
LCS_GDT     E     313     E     313      3    5   10     3    3    3    4    4    5    5    6    6    6    6    7    9    9   10   10   10   11   17   20 
LCS_AVERAGE  LCS_A:   4.45  (   2.21    2.82    8.31 )

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      5      5      5      7      8      9     11     12     14     16     17     17     19     19     21     21     22     22     23 
GDT PERCENT_CA   2.08   2.60   2.60   2.60   3.65   4.17   4.69   5.73   6.25   7.29   8.33   8.85   8.85   9.90   9.90  10.94  10.94  11.46  11.46  11.98
GDT RMS_LOCAL    0.06   0.57   0.57   0.57   1.87   2.04   2.23   3.20   3.32   3.68   4.00   4.18   4.18   4.59   4.59   5.57   5.57   5.78   5.78   6.09
GDT RMS_ALL_CA  13.22  29.52  29.52  29.52   9.44   9.06   9.18   7.28   7.90   7.36   7.23   7.01   7.01   7.14   7.14   7.31   7.31   6.91   6.91   6.70

#      Molecule1      Molecule2       DISTANCE
LGA    D     290      D     290          3.209
LGA    H     291      H     291          6.717
LGA    T     292      T     292          3.663
LGA    G     293      G     293          4.366
LGA    Y     294      Y     294          2.320
LGA    Y     295      Y     295          3.901
LGA    N     296      N     296          2.054
LGA    E     297      E     297          5.011
LGA    V     298      V     298          3.796
LGA    D     299      D     299         11.662
LGA    S     300      S     300         13.624
LGA    F     301      F     301         12.294
LGA    P     302      P     302         12.468
LGA    V     303      V     303          6.288
LGA    F     304      F     304          2.706
LGA    T     305      T     305          5.113
LGA    V     306      V     306          5.694
LGA    T     307      T     307          7.612
LGA    H     308      H     308          3.859
LGA    I     309      I     309          2.629
LGA    T     310      T     310          3.958
LGA    Q     311      Q     311          3.772
LGA    R     312      R     312          7.531
LGA    E     313      E     313         12.503

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  192    4.0     11    3.20     5.469     4.849     0.333

LGA_LOCAL      RMSD =  3.204  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.096  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  6.645  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.671860 * X  +   0.019645 * Y  +   0.740417 * Z  +   7.629940
  Y_new =  -0.490999 * X  +   0.760253 * Y  +   0.425365 * Z  +  84.732727
  Z_new =  -0.554548 * X  +  -0.649330 * Y  +   0.520430 * Z  + 130.734787 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.895149    2.246444  [ DEG:   -51.2882    128.7118 ]
  Theta =   0.587820    2.553773  [ DEG:    33.6796    146.3204 ]
  Phi   =  -0.631103    2.510490  [ DEG:   -36.1595    143.8405 ]
 
# 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: T0356AL044_2-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  192   4.0   11   3.20   4.849     6.65
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D2
REMARK Aligment from pdb entry: 1xov_A
ATOM      1  N   ASP   290      59.176  54.876  84.182  1.00  0.00              
ATOM      2  CA  ASP   290      58.622  53.580  83.794  1.00  0.00              
ATOM      3  C   ASP   290      57.121  53.683  83.621  1.00  0.00              
ATOM      4  O   ASP   290      56.564  53.150  82.697  1.00  0.00              
ATOM      5  N   HIS   291      56.484  54.394  84.537  1.00  0.00              
ATOM      6  CA  HIS   291      55.048  54.641  84.443  1.00  0.00              
ATOM      7  C   HIS   291      54.675  55.481  83.224  1.00  0.00              
ATOM      8  O   HIS   291      53.719  55.168  82.536  1.00  0.00              
ATOM      9  N   THR   292      55.441  56.523  82.923  1.00  0.00              
ATOM     10  CA  THR   292      55.171  57.324  81.714  1.00  0.00              
ATOM     11  C   THR   292      55.297  56.498  80.438  1.00  0.00              
ATOM     12  O   THR   292      54.455  56.600  79.536  1.00  0.00              
ATOM     13  N   GLY   293      56.349  55.683  80.362  1.00  0.00              
ATOM     14  CA  GLY   293      56.683  54.917  79.145  1.00  0.00              
ATOM     15  C   GLY   293      55.832  53.671  78.971  1.00  0.00              
ATOM     16  O   GLY   293      55.646  53.176  77.853  1.00  0.00              
ATOM     17  N   TYR   294      55.295  53.190  80.091  1.00  0.00              
ATOM     18  CA  TYR   294      54.527  51.963  80.145  1.00  0.00              
ATOM     19  C   TYR   294      55.433  50.754  79.999  1.00  0.00              
ATOM     20  O   TYR   294      55.027  49.744  79.384  1.00  0.00              
ATOM     21  N   TYR   295      56.639  50.852  80.535  1.00  0.00              
ATOM     22  CA  TYR   295      57.637  49.787  80.515  1.00  0.00              
ATOM     23  C   TYR   295      57.934  49.322  81.906  1.00  0.00              
ATOM     24  O   TYR   295      57.668  50.044  82.884  1.00  0.00              
ATOM     25  N   ASN   296      58.554  48.157  82.058  1.00  0.00              
ATOM     26  CA  ASN   296      59.002  47.752  83.387  1.00  0.00              
ATOM     27  C   ASN   296      60.016  48.659  84.061  1.00  0.00              
ATOM     28  O   ASN   296      60.870  49.248  83.420  1.00  0.00              
ATOM     29  N   GLU   297      59.923  48.756  85.371  1.00  0.00              
ATOM     30  CA  GLU   297      60.894  49.415  86.170  1.00  0.00              
ATOM     31  C   GLU   297      61.961  48.440  86.631  1.00  0.00              
ATOM     32  O   GLU   297      61.736  47.568  87.500  1.00  0.00              
ATOM     33  N   VAL   298      63.157  48.579  86.065  1.00  0.00              
ATOM     34  CA  VAL   298      64.278  47.786  86.515  1.00  0.00              
ATOM     35  C   VAL   298      64.849  48.294  87.840  1.00  0.00              
ATOM     36  O   VAL   298      65.621  47.615  88.530  1.00  0.00              
ATOM     37  N   ASP   299      69.717  51.537  91.007  1.00  0.00              
ATOM     38  CA  ASP   299      70.859  50.649  91.125  1.00  0.00              
ATOM     39  C   ASP   299      72.067  51.414  91.620  1.00  0.00              
ATOM     40  O   ASP   299      72.385  52.450  91.062  1.00  0.00              
ATOM     41  N   SER   300      72.719  50.882  92.661  1.00  0.00              
ATOM     42  CA  SER   300      73.872  51.476  93.317  1.00  0.00              
ATOM     43  C   SER   300      75.158  51.007  92.641  1.00  0.00              
ATOM     44  O   SER   300      75.278  49.841  92.224  1.00  0.00              
ATOM     45  N   PHE   301      76.123  51.895  92.522  1.00  0.00              
ATOM     46  CA  PHE   301      77.423  51.506  92.012  1.00  0.00              
ATOM     47  C   PHE   301      78.518  52.466  92.447  1.00  0.00              
ATOM     48  O   PHE   301      78.254  53.644  92.731  1.00  0.00              
ATOM     49  N   PRO   302      79.749  51.949  92.506  1.00  0.00              
ATOM     50  CA  PRO   302      80.918  52.805  92.668  1.00  0.00              
ATOM     51  C   PRO   302      81.844  52.691  91.450  1.00  0.00              
ATOM     52  O   PRO   302      83.067  52.966  91.530  1.00  0.00              
ATOM     53  N   VAL   303      81.301  52.196  90.360  1.00  0.00              
ATOM     54  CA  VAL   303      82.089  51.868  89.192  1.00  0.00              
ATOM     55  C   VAL   303      81.920  52.838  88.027  1.00  0.00              
ATOM     56  O   VAL   303      82.562  52.654  87.001  1.00  0.00              
ATOM     57  N   PHE   304      81.081  53.860  88.171  1.00  0.00              
ATOM     58  CA  PHE   304      80.825  54.779  87.051  1.00  0.00              
ATOM     59  C   PHE   304      81.523  56.090  87.261  1.00  0.00              
ATOM     60  O   PHE   304      81.332  56.756  88.276  1.00  0.00              
ATOM     61  N   THR   305      82.353  56.474  86.292  1.00  0.00              
ATOM     62  CA  THR   305      83.168  57.674  86.425  1.00  0.00              
ATOM     63  C   THR   305      82.319  58.926  86.687  1.00  0.00              
ATOM     64  O   THR   305      82.674  59.770  87.523  1.00  0.00              
ATOM     65  N   VAL   306      81.223  59.027  85.952  1.00  0.00              
ATOM     66  CA  VAL   306      80.298  60.167  86.114  1.00  0.00              
ATOM     67  C   VAL   306      79.857  60.350  87.578  1.00  0.00              
ATOM     68  O   VAL   306      79.961  61.444  88.134  1.00  0.00              
ATOM     69  N   THR   307      79.387  59.267  88.198  1.00  0.00              
ATOM     70  CA  THR   307      78.947  59.293  89.595  1.00  0.00              
ATOM     71  C   THR   307      80.104  59.444  90.575  1.00  0.00              
ATOM     72  O   THR   307      79.944  60.047  91.623  1.00  0.00              
ATOM     73  N   HIS   308      81.270  58.885  90.251  1.00  0.00              
ATOM     74  CA  HIS   308      82.400  58.909  91.154  1.00  0.00              
ATOM     75  C   HIS   308      83.061  60.263  91.231  1.00  0.00              
ATOM     76  O   HIS   308      83.567  60.645  92.240  1.00  0.00              
ATOM     77  N   ILE   309      83.088  60.962  90.116  1.00  0.00              
ATOM     78  CA  ILE   309      83.915  62.138  89.931  1.00  0.00              
ATOM     79  C   ILE   309      83.171  63.469  89.993  1.00  0.00              
ATOM     80  O   ILE   309      83.783  64.490  90.140  1.00  0.00              
ATOM     81  N   THR   310      81.852  63.430  89.865  1.00  0.00              
ATOM     82  CA  THR   310      81.015  64.605  90.011  1.00  0.00              
ATOM     83  C   THR   310      80.898  64.842  91.511  1.00  0.00              
ATOM     84  O   THR   310      80.533  63.940  92.236  1.00  0.00              
ATOM     85  N   GLN   311      81.256  66.030  91.988  1.00  0.00              
ATOM     86  CA  GLN   311      81.272  66.322  93.428  1.00  0.00              
ATOM     87  C   GLN   311      79.896  66.308  94.084  1.00  0.00              
ATOM     88  O   GLN   311      79.744  65.833  95.193  1.00  0.00              
ATOM     89  N   ARG   312      78.880  66.813  93.406  1.00  0.00              
ATOM     90  CA  ARG   312      77.600  66.956  94.046  1.00  0.00              
ATOM     91  C   ARG   312      76.813  65.687  93.935  1.00  0.00              
ATOM     92  O   ARG   312      77.287  64.660  93.390  1.00  0.00              
ATOM     93  N   GLU   313      75.571  65.749  94.395  1.00  0.00              
ATOM     94  CA  GLU   313      74.673  64.616  94.254  1.00  0.00              
ATOM     95  C   GLU   313      74.371  64.329  92.805  1.00  0.00              
ATOM     96  O   GLU   313      73.891  65.205  92.064  1.00  0.00              
END
