
#######################################################
#                                                     #
#                        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 T0301AL333_3-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   24 , name T0301_D1.pdb
# PARAMETERS: T0301AL333_3-D1.T0301_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:    12       124 - 135         4.06    23.83
  LCS_AVERAGE:      4.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8         4 - 11          1.06    24.44
  LCS_AVERAGE:      3.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7         4 - 10          0.99    24.18
  LONGEST_CONTINUOUS_SEGMENT:     7         5 - 11          0.89    24.32
  LCS_AVERAGE:      2.33

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:  200
LCS_GDT     P       4     P       4      7    8    8     3    5    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     P       5     P       5      7    8    8     3    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     Q       6     Q       6      7    8    8     3    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     I       7     I       7      7    8    8     3    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     R       8     R       8      7    8    8     4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     I       9     I       9      7    8    8     4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     P      10     P      10      7    8    8     4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     A      11     A      11      7    8    8     4    5    8    8    8    8    8    8    8    8    8    8    8    8    8    9   10   10   10   10 
LCS_GDT     G     102     G     102      3    3    4     0    3    3    3    3    4    4    4    4    4    4    8    9    9    9   10   10   10   10   11 
LCS_GDT     N     103     N     103      3    3    4     3    3    4    4    6    7    7    7    8    8    8    8    9    9   10   11   12   13   13   13 
LCS_GDT     C     104     C     104      3    3    4     3    3    4    4    6    7    7    7    8    8    8    8    9    9    9   11   12   13   13   13 
LCS_GDT     G     105     G     105      3    3    4     3    3    4    4    6    7    7    7    8    8    8    8    9    9    9   10   11   13   13   13 
LCS_GDT     A     124     A     124      3    6   12     3    3    3    5    6    9    9   10   11   11   11   11   11   11   11   12   12   12   12   12 
LCS_GDT     R     125     R     125      4    6   12     3    4    4    5    6    8    9    9   11   11   11   11   11   11   11   12   12   12   13   13 
LCS_GDT     I     126     I     126      4    7   12     3    4    4    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     P     127     P     127      4    7   12     3    4    5    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     E     128     E     128      4    7   12     3    4    5    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     D     129     D     129      3    7   12     3    3    5    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     G     130     G     130      3    7   12     3    3    5    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     I     131     I     131      4    7   12     3    4    4    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     C     132     C     132      4    7   12     3    4    5    7    7    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     E     133     E     133      4    4   12     3    4    4    4    6    9    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     V     134     V     134      4    4   12     3    4    4    4    6    7    9   10   11   11   11   11   11   11   11   12   12   13   13   13 
LCS_GDT     R     135     R     135      3    3   12     3    3    4    4    6    6    7    7    8    8    8    8    9    9    9   12   12   13   13   13 
LCS_AVERAGE  LCS_A:   3.36  (   2.33    3.08    4.67 )

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      6      8      8      8      9      9     10     11     11     11     11     11     11     11     12     12     13     13     13 
GDT PERCENT_CA   2.00   3.00   4.00   4.00   4.00   4.50   4.50   5.00   5.50   5.50   5.50   5.50   5.50   5.50   5.50   6.00   6.00   6.50   6.50   6.50
GDT RMS_LOCAL    0.39   0.64   1.06   1.06   1.06   2.36   2.36   2.61   2.90   2.90   2.90   2.90   2.90   2.90   2.90   4.06   4.06   6.39   6.39   6.39
GDT RMS_ALL_CA  24.95  23.96  24.44  24.44  24.44  25.59  25.59  24.92  24.70  24.70  24.70  24.70  24.70  24.70  24.70  23.83  23.83  18.93  18.93  18.93

#      Molecule1      Molecule2       DISTANCE
LGA    P       4      P       4         53.910
LGA    P       5      P       5         48.500
LGA    Q       6      Q       6         43.471
LGA    I       7      I       7         37.945
LGA    R       8      R       8         32.711
LGA    I       9      I       9         26.378
LGA    P      10      P      10         22.598
LGA    A      11      A      11         19.910
LGA    G     102      G     102         30.598
LGA    N     103      N     103         25.867
LGA    C     104      C     104         27.266
LGA    G     105      G     105         28.517
LGA    A     124      A     124          2.976
LGA    R     125      R     125          4.517
LGA    I     126      I     126          2.294
LGA    P     127      P     127          1.740
LGA    E     128      E     128          3.023
LGA    D     129      D     129          2.271
LGA    G     130      G     130          2.694
LGA    I     131      I     131          2.275
LGA    C     132      C     132          2.465
LGA    E     133      E     133          3.029
LGA    V     134      V     134          3.592
LGA    R     135      R     135         11.019

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  200    4.0     10    2.61     4.500     4.266     0.369

LGA_LOCAL      RMSD =  2.611  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 24.696  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 14.170  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.711514 * X  +   0.644490 * Y  +   0.279967 * Z  +  61.179161
  Y_new =  -0.648958 * X  +   0.449930 * Y  +   0.613528 * Z  +  26.027287
  Z_new =   0.269447 * X  +  -0.618220 * Y  +   0.738378 * Z  +  18.421009 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.697056    2.444537  [ DEG:   -39.9384    140.0616 ]
  Theta =  -0.272818   -2.868774  [ DEG:   -15.6313   -164.3687 ]
  Phi   =  -0.739450    2.402143  [ DEG:   -42.3674    137.6326 ]
 
# 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: T0301AL333_3-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL333_3-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  200   4.0   10   2.61   4.266    14.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL333_3-D1
REMARK Aligment from pdb entry: 1lv3_A
ATOM      1  N   PRO     4      57.237   5.907  30.275  1.00  0.00              
ATOM      2  CA  PRO     4      58.327   6.038  29.265  1.00  0.00              
ATOM      3  C   PRO     4      57.680   6.420  27.921  1.00  0.00              
ATOM      4  O   PRO     4      58.050   5.941  26.862  1.00  0.00              
ATOM      5  N   PRO     5      56.685   7.278  27.991  1.00  0.00              
ATOM      6  CA  PRO     5      55.931   7.729  26.787  1.00  0.00              
ATOM      7  C   PRO     5      56.842   8.432  25.786  1.00  0.00              
ATOM      8  O   PRO     5      57.453   9.447  26.078  1.00  0.00              
ATOM      9  N   GLN     6      56.890   7.914  24.594  1.00  0.00              
ATOM     10  CA  GLN     6      57.705   8.546  23.529  1.00  0.00              
ATOM     11  C   GLN     6      56.739   9.337  22.648  1.00  0.00              
ATOM     12  O   GLN     6      56.032   8.776  21.824  1.00  0.00              
ATOM     13  N   ILE     7      56.679  10.632  22.835  1.00  0.00              
ATOM     14  CA  ILE     7      55.733  11.456  22.025  1.00  0.00              
ATOM     15  C   ILE     7      56.326  11.648  20.630  1.00  0.00              
ATOM     16  O   ILE     7      57.529  11.649  20.456  1.00  0.00              
ATOM     17  N   ARG     8      55.489  11.769  19.632  1.00  0.00              
ATOM     18  CA  ARG     8      56.000  11.921  18.237  1.00  0.00              
ATOM     19  C   ARG     8      55.514  13.241  17.628  1.00  0.00              
ATOM     20  O   ARG     8      54.324  13.476  17.498  1.00  0.00              
ATOM     21  N   ILE     9      56.435  14.090  17.240  1.00  0.00              
ATOM     22  CA  ILE     9      56.058  15.396  16.615  1.00  0.00              
ATOM     23  C   ILE     9      55.841  15.172  15.111  1.00  0.00              
ATOM     24  O   ILE     9      56.637  14.527  14.450  1.00  0.00              
ATOM     25  N   PRO    10      54.763  15.681  14.572  1.00  0.00              
ATOM     26  CA  PRO    10      54.485  15.483  13.120  1.00  0.00              
ATOM     27  C   PRO    10      55.078  16.637  12.303  1.00  0.00              
ATOM     28  O   PRO    10      54.938  17.795  12.651  1.00  0.00              
ATOM     29  N   ALA    11      55.729  16.315  11.209  1.00  0.00              
ATOM     30  CA  ALA    11      56.336  17.362  10.331  1.00  0.00              
ATOM     31  C   ALA    11      55.209  18.191   9.698  1.00  0.00              
ATOM     32  O   ALA    11      54.390  17.655   8.978  1.00  0.00              
ATOM     33  N   GLY   102      55.191  19.472   9.994  1.00  0.00              
ATOM     34  CA  GLY   102      54.161  20.394   9.470  1.00  0.00              
ATOM     35  C   GLY   102      54.417  20.763   7.996  1.00  0.00              
ATOM     36  O   GLY   102      53.539  21.281   7.328  1.00  0.00              
ATOM     37  N   ASN   103      55.605  20.513   7.486  1.00  0.00              
ATOM     38  CA  ASN   103      55.903  20.868   6.061  1.00  0.00              
ATOM     39  C   ASN   103      55.360  19.793   5.110  1.00  0.00              
ATOM     40  O   ASN   103      54.679  20.105   4.150  1.00  0.00              
ATOM     41  N   CYS   104      55.661  18.542   5.357  1.00  0.00              
ATOM     42  CA  CYS   104      55.167  17.456   4.451  1.00  0.00              
ATOM     43  C   CYS   104      54.111  16.593   5.160  1.00  0.00              
ATOM     44  O   CYS   104      53.272  15.989   4.514  1.00  0.00              
ATOM     45  N   GLY   105      54.146  16.521   6.472  1.00  0.00              
ATOM     46  CA  GLY   105      53.152  15.685   7.212  1.00  0.00              
ATOM     47  C   GLY   105      53.746  14.297   7.439  1.00  0.00              
ATOM     48  O   GLY   105      53.377  13.341   6.783  1.00  0.00              
ATOM     49  N   ALA   124      54.676  14.193   8.357  1.00  0.00              
ATOM     50  CA  ALA   124      55.325  12.881   8.641  1.00  0.00              
ATOM     51  C   ALA   124      55.527  12.725  10.154  1.00  0.00              
ATOM     52  O   ALA   124      56.064  13.598  10.808  1.00  0.00              
ATOM     53  N   ARG   125      55.088  11.621  10.709  1.00  0.00              
ATOM     54  CA  ARG   125      55.236  11.397  12.182  1.00  0.00              
ATOM     55  C   ARG   125      56.711  11.158  12.524  1.00  0.00              
ATOM     56  O   ARG   125      57.307  10.182  12.100  1.00  0.00              
ATOM     57  N   ILE   126      57.296  12.044  13.291  1.00  0.00              
ATOM     58  CA  ILE   126      58.729  11.884  13.678  1.00  0.00              
ATOM     59  C   ILE   126      58.818  11.717  15.197  1.00  0.00              
ATOM     60  O   ILE   126      58.349  12.551  15.949  1.00  0.00              
ATOM     61  N   PRO   127      59.411  10.637  15.645  1.00  0.00              
ATOM     62  CA  PRO   127      59.537  10.383  17.114  1.00  0.00              
ATOM     63  C   PRO   127      60.179  11.596  17.813  1.00  0.00              
ATOM     64  O   PRO   127      61.131  12.178  17.324  1.00  0.00              
ATOM     65  N   GLU   128      59.648  11.979  18.954  1.00  0.00              
ATOM     66  CA  GLU   128      60.196  13.151  19.707  1.00  0.00              
ATOM     67  C   GLU   128      60.843  12.673  21.015  1.00  0.00              
ATOM     68  O   GLU   128      60.519  11.620  21.535  1.00  0.00              
ATOM     69  N   ASP   129      61.756  13.455  21.546  1.00  0.00              
ATOM     70  CA  ASP   129      62.442  13.081  22.815  1.00  0.00              
ATOM     71  C   ASP   129      63.932  12.896  22.535  1.00  0.00              
ATOM     72  O   ASP   129      64.674  13.857  22.430  1.00  0.00              
ATOM     73  N   GLY   130      64.368  11.668  22.404  1.00  0.00              
ATOM     74  CA  GLY   130      65.808  11.401  22.118  1.00  0.00              
ATOM     75  C   GLY   130      65.951  10.000  21.504  1.00  0.00              
ATOM     76  O   GLY   130      66.655   9.145  22.013  1.00  0.00              
ATOM     77  N   ILE   131      65.273   9.766  20.406  1.00  0.00              
ATOM     78  CA  ILE   131      65.342   8.436  19.734  1.00  0.00              
ATOM     79  C   ILE   131      65.874   8.613  18.308  1.00  0.00              
ATOM     80  O   ILE   131      66.820   7.960  17.904  1.00  0.00              
ATOM     81  N   CYS   132      65.271   9.495  17.551  1.00  0.00              
ATOM     82  CA  CYS   132      65.726   9.732  16.144  1.00  0.00              
ATOM     83  C   CYS   132      66.729  10.892  16.105  1.00  0.00              
ATOM     84  O   CYS   132      66.858  11.633  17.062  1.00  0.00              
ATOM     85  N   GLU   133      67.403  11.025  14.986  1.00  0.00              
ATOM     86  CA  GLU   133      68.391  12.098  14.780  1.00  0.00              
ATOM     87  C   GLU   133      67.668  13.416  14.464  1.00  0.00              
ATOM     88  O   GLU   133      68.126  14.484  14.826  1.00  0.00              
ATOM     89  N   VAL   134      66.539  13.333  13.794  1.00  0.00              
ATOM     90  CA  VAL   134      65.764  14.557  13.442  1.00  0.00              
ATOM     91  C   VAL   134      64.427  14.546  14.194  1.00  0.00              
ATOM     92  O   VAL   134      63.372  14.438  13.597  1.00  0.00              
ATOM     93  N   ARG   135      64.463  14.661  15.502  1.00  0.00              
ATOM     94  CA  ARG   135      63.193  14.665  16.302  1.00  0.00              
ATOM     95  C   ARG   135      62.226  15.709  15.717  1.00  0.00              
ATOM     96  O   ARG   135      61.119  15.367  15.350  1.00  0.00              
END
