
#######################################################
#                                                     #
#                        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 (   56),  selected   14 , name T0318AL170_1-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318AL170_1-D1.T0318_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       142 - 153         4.42     6.78
  LCS_AVERAGE:      7.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       142 - 150         1.74     7.88
  LCS_AVERAGE:      4.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       143 - 149         0.99     7.84
  LCS_AVERAGE:      3.66

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:  154
LCS_GDT     R     142     R     142      6    9   12     3    5    6    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     E     143     E     143      7    9   12     4    5    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     L     144     L     144      7    9   12     4    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     N     145     N     145      7    9   12     3    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     V     146     V     146      7    9   12     3    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     N     147     N     147      7    9   12     4    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     I     148     I     148      7    9   12     4    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     D     149     D     149      7    9   12     3    6    7    7    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     V     150     V     150      5    9   12     3    3    5    5    8    9    9    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     V     151     V     151      3    4   12     3    3    4    4    5    6    6    7    9   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     C     152     C     152      4    4   12     3    4    4    4    5    6    6    9   10   10   11   12   12   12   12   12   13   13   13   14 
LCS_GDT     D     153     D     153      4    4   12     3    4    4    4    4    5    5    6    6    6    7    8    9    9   10   12   13   13   13   14 
LCS_GDT     K     154     K     154      4    4   11     3    4    4    4    4    5    5    6    6    6    7    8    9    9   10   10   11   12   13   14 
LCS_GDT     L     155     L     155      4    4   11     3    4    4    4    4    6    6    7    7    9   10   12   12   12   12   12   13   13   13   14 
LCS_AVERAGE  LCS_A:   5.35  (   3.66    4.68    7.70 )

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      7      7      8      9      9      9     10     10     11     12     12     12     12     12     13     13     13     14 
GDT PERCENT_CA   2.60   3.90   4.55   4.55   5.19   5.84   5.84   5.84   6.49   6.49   7.14   7.79   7.79   7.79   7.79   7.79   8.44   8.44   8.44   9.09
GDT RMS_LOCAL    0.26   0.82   0.99   0.99   1.32   1.74   1.74   1.74   2.63   2.63   3.17   4.23   4.23   4.23   4.23   4.23   4.82   4.82   4.82   5.48
GDT RMS_ALL_CA   8.16   7.83   7.84   7.84   7.84   7.88   7.88   7.88   7.11   7.11   7.29   5.71   5.71   5.71   5.71   5.71   5.54   5.54   5.54   5.48

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142          2.514
LGA    E     143      E     143          0.749
LGA    L     144      L     144          0.206
LGA    N     145      N     145          2.520
LGA    V     146      V     146          2.123
LGA    N     147      N     147          0.367
LGA    I     148      I     148          1.714
LGA    D     149      D     149          1.002
LGA    V     150      V     150          2.355
LGA    V     151      V     151          8.743
LGA    C     152      C     152          7.527
LGA    D     153      D     153         13.560
LGA    K     154      K     154         16.389
LGA    L     155      L     155         16.015

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0      9    1.74     5.519     5.606     0.488

LGA_LOCAL      RMSD =  1.745  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.881  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  5.475  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.337400 * X  +   0.863927 * Y  +   0.373886 * Z  +  11.137516
  Y_new =  -0.928895 * X  +   0.369969 * Y  +  -0.016627 * Z  +  58.481014
  Z_new =  -0.152691 * X  +  -0.341691 * Y  +   0.927326 * Z  +  65.743080 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.353033    2.788560  [ DEG:   -20.2273    159.7727 ]
  Theta =   0.153291    2.988302  [ DEG:     8.7829    171.2171 ]
  Phi   =  -1.222386    1.919206  [ DEG:   -70.0376    109.9624 ]
 
# 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: T0318AL170_1-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL170_1-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  154   4.0    9   1.74   5.606     5.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL170_1-D1
REMARK Aligment from pdb entry: 1GYT_A
ATOM      1  N   ARG   142      36.312  56.776   8.139  1.00  0.00              
ATOM      2  CA  ARG   142      35.239  57.465   8.832  1.00  0.00              
ATOM      3  C   ARG   142      34.425  56.600   9.765  1.00  0.00              
ATOM      4  O   ARG   142      33.737  57.103  10.651  1.00  0.00              
ATOM      5  N   GLU   143      34.505  55.294   9.559  1.00  0.00              
ATOM      6  CA  GLU   143      33.773  54.346  10.383  1.00  0.00              
ATOM      7  C   GLU   143      34.667  53.138  10.498  1.00  0.00              
ATOM      8  O   GLU   143      35.404  52.809   9.572  1.00  0.00              
ATOM      9  N   LEU   144      34.595  52.479  11.640  1.00  0.00              
ATOM     10  CA  LEU   144      35.390  51.300  11.891  1.00  0.00              
ATOM     11  C   LEU   144      34.522  50.286  12.639  1.00  0.00              
ATOM     12  O   LEU   144      33.953  50.596  13.685  1.00  0.00              
ATOM     13  N   ASN   145      34.418  49.079  12.088  1.00  0.00              
ATOM     14  CA  ASN   145      33.636  48.009  12.695  1.00  0.00              
ATOM     15  C   ASN   145      34.541  46.969  13.344  1.00  0.00              
ATOM     16  O   ASN   145      35.404  46.387  12.683  1.00  0.00              
ATOM     17  N   VAL   146      34.348  46.744  14.643  1.00  0.00              
ATOM     18  CA  VAL   146      35.138  45.752  15.367  1.00  0.00              
ATOM     19  C   VAL   146      34.313  44.494  15.355  1.00  0.00              
ATOM     20  O   VAL   146      33.130  44.514  15.693  1.00  0.00              
ATOM     21  N   ASN   147      34.937  43.400  14.952  1.00  0.00              
ATOM     22  CA  ASN   147      34.245  42.143  14.894  1.00  0.00              
ATOM     23  C   ASN   147      34.383  41.359  16.192  1.00  0.00              
ATOM     24  O   ASN   147      35.486  41.160  16.712  1.00  0.00              
ATOM     25  N   ILE   148      33.254  40.904  16.710  1.00  0.00              
ATOM     26  CA  ILE   148      33.247  40.104  17.932  1.00  0.00              
ATOM     27  C   ILE   148      32.949  38.649  17.551  1.00  0.00              
ATOM     28  O   ILE   148      32.214  38.387  16.600  1.00  0.00              
ATOM     29  N   ASP   149      33.519  37.688  18.289  1.00  0.00              
ATOM     30  CA  ASP   149      33.352  36.243  18.057  1.00  0.00              
ATOM     31  C   ASP   149      31.964  35.771  17.636  1.00  0.00              
ATOM     32  O   ASP   149      31.795  35.197  16.553  1.00  0.00              
ATOM     33  N   VAL   150      30.978  35.992  18.501  1.00  0.00              
ATOM     34  CA  VAL   150      29.611  35.593  18.207  1.00  0.00              
ATOM     35  C   VAL   150      28.636  36.654  18.646  1.00  0.00              
ATOM     36  O   VAL   150      29.004  37.595  19.334  1.00  0.00              
ATOM     37  N   VAL   151      27.385  36.502  18.244  1.00  0.00              
ATOM     38  CA  VAL   151      26.374  37.480  18.594  1.00  0.00              
ATOM     39  C   VAL   151      26.248  37.641  20.102  1.00  0.00              
ATOM     40  O   VAL   151      25.652  38.611  20.575  1.00  0.00              
ATOM     41  N   CYS   152      26.807  36.697  20.855  1.00  0.00              
ATOM     42  CA  CYS   152      26.726  36.771  22.307  1.00  0.00              
ATOM     43  C   CYS   152      27.331  38.062  22.809  1.00  0.00              
ATOM     44  O   CYS   152      26.653  38.828  23.501  1.00  0.00              
ATOM     45  N   ASP   153      28.593  38.313  22.450  1.00  0.00              
ATOM     46  CA  ASP   153      29.260  39.534  22.880  1.00  0.00              
ATOM     47  C   ASP   153      28.991  40.746  21.994  1.00  0.00              
ATOM     48  O   ASP   153      29.801  41.666  21.924  1.00  0.00              
ATOM     49  N   LYS   154      27.850  40.747  21.317  1.00  0.00              
ATOM     50  CA  LYS   154      27.475  41.891  20.515  1.00  0.00              
ATOM     51  C   LYS   154      26.950  42.981  21.458  1.00  0.00              
ATOM     52  O   LYS   154      27.085  44.175  21.178  1.00  0.00              
ATOM     53  N   LEU   155      26.357  42.564  22.578  1.00  0.00              
ATOM     54  CA  LEU   155      25.805  43.495  23.563  1.00  0.00              
ATOM     55  C   LEU   155      26.907  44.146  24.416  1.00  0.00              
ATOM     56  O   LEU   155      26.903  45.366  24.641  1.00  0.00              
END
