
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0352AL381_4
# Molecule2: number of CA atoms  109 ( 1766),  selected   18 , name T0352.pdb
# PARAMETERS: T0352AL381_4.T0352.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:    13        33 - 45          4.90    10.76
  LONGEST_CONTINUOUS_SEGMENT:    13        37 - 49          4.69    10.19
  LONGEST_CONTINUOUS_SEGMENT:    13        38 - 50          4.52    10.89
  LCS_AVERAGE:     11.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        36 - 41          1.56    15.54
  LCS_AVERAGE:      4.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        43 - 47          0.52     9.49
  LCS_AVERAGE:      3.82

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:  109
LCS_GDT     Q      33     Q      33      3    5   13     3    3    3    4    5    8    9   10   10   10   11   12   13   15   15   15   16   16   17   17 
LCS_GDT     F      34     F      34      4    5   13     3    4    4    4    5    8    9   10   10   10   11   12   13   15   15   15   16   16   17   17 
LCS_GDT     N      35     N      35      4    5   13     3    4    4    4    5    6    8   10   10   10   11   12   13   15   15   15   16   16   17   17 
LCS_GDT     S      36     S      36      4    6   13     3    4    4    5    5    8    9   10   10   10   11   12   13   15   15   15   16   16   17   17 
LCS_GDT     T      37     T      37      4    6   13     3    4    4    5    5    8    9   10   10   10   11   12   13   15   15   15   16   16   17   17 
LCS_GDT     Q      38     Q      38      4    6   13     3    3    4    5    5    8    9   10   10   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     P      39     P      39      4    6   13     3    3    4    5    5    8    9   10   10   10   12   12   13   15   15   15   16   16   16   17 
LCS_GDT     F      40     F      40      4    6   13     4    4    4    5    5    8    9   10   10   10   12   12   12   15   15   15   16   16   17   17 
LCS_GDT     F      41     F      41      4    6   13     4    4    4    5    5    8    9   10   10   10   12   12   12   15   15   15   16   16   17   17 
LCS_GDT     M      42     M      42      4    5   13     4    4    4    4    5    6    9   10   10   10   12   12   12   12   13   15   16   16   17   17 
LCS_GDT     D      43     D      43      5    5   13     4    5    5    5    5    6    8    9    9   10   12   12   12   12   13   14   14   15   17   17 
LCS_GDT     T      44     T      44      5    5   13     4    5    5    5    5    6    8    9    9   10   12   12   12   15   15   15   16   16   17   17 
LCS_GDT     M      45     M      45      5    5   13     4    5    5    5    5    6    8    9    9   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     E      46     E      46      5    5   13     4    5    5    5    5    6    8    9    9   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     P      47     P      47      5    5   13     3    5    5    5    5    6    8    9    9   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     L      48     L      48      4    4   13     3    4    4    4    4    5    6    6    8   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     E      49     E      49      4    4   13     3    4    4    4    5    6    8    8    9   10   12   12   13   15   15   15   16   16   17   17 
LCS_GDT     W      50     W      50      3    3   13     3    3    3    3    3    6    8    8    8    9   10   12   13   15   15   15   16   16   17   17 
LCS_AVERAGE  LCS_A:   6.81  (   3.82    4.69   11.93 )

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      5      8      9     10     10     10     12     12     13     15     15     15     16     16     17     17 
GDT PERCENT_CA   3.67   4.59   4.59   4.59   4.59   7.34   8.26   9.17   9.17   9.17  11.01  11.01  11.93  13.76  13.76  13.76  14.68  14.68  15.60  15.60
GDT RMS_LOCAL    0.24   0.52   0.52   0.52   0.52   2.37   2.63   2.87   2.87   2.87   3.91   3.91   4.93   5.42   5.42   5.42   5.78   5.78   6.56   6.56
GDT RMS_ALL_CA  17.38   9.49   9.49   9.49   9.49  13.81  14.64  14.30  14.30  14.30  11.15  11.15   7.41   7.05   7.05   7.05   6.85   6.85   6.81   6.81

#      Molecule1      Molecule2       DISTANCE
LGA    Q      33      Q      33          1.470
LGA    F      34      F      34          1.362
LGA    N      35      N      35          3.640
LGA    S      36      S      36          3.748
LGA    T      37      T      37          3.242
LGA    Q      38      Q      38          3.362
LGA    P      39      P      39          1.574
LGA    F      40      F      40          3.966
LGA    F      41      F      41          2.843
LGA    M      42      M      42          2.750
LGA    D      43      D      43          6.377
LGA    T      44      T      44         10.307
LGA    M      45      M      45         13.822
LGA    E      46      E      46         20.606
LGA    P      47      P      47         23.589
LGA    L      48      L      48         24.762
LGA    E      49      E      49         26.864
LGA    W      50      W      50         27.702

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  109    4.0     10    2.87     8.028     7.232     0.337

LGA_LOCAL      RMSD =  2.867  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.961  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  6.670  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.309658 * X  +  -0.883874 * Y  +   0.350541 * Z  + -55.619934
  Y_new =  -0.895039 * X  +  -0.146507 * Y  +   0.421238 * Z  +  -6.273240
  Z_new =  -0.320964 * X  +  -0.444188 * Y  +  -0.836468 * Z  + 135.522827 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.653432    0.488160  [ DEG:  -152.0305     27.9695 ]
  Theta =   0.326747    2.814845  [ DEG:    18.7212    161.2787 ]
  Phi   =  -1.237715    1.903877  [ DEG:   -70.9159    109.0841 ]
 
# 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: T0352AL381_4                                  
REMARK     2: T0352.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_4.T0352.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  109   4.0   10   2.87   7.232     6.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_4
REMARK Aligment from pdb entry: 2mev2
ATOM      1  N   GLN    33      -6.164  22.583  -7.725  1.00  0.00              
ATOM      2  CA  GLN    33      -6.332  22.704  -9.172  1.00  0.00              
ATOM      3  C   GLN    33      -6.201  21.433 -10.023  1.00  0.00              
ATOM      4  O   GLN    33      -7.053  21.005 -10.840  1.00  0.00              
ATOM      5  N   PHE    34      -5.050  20.825  -9.814  1.00  0.00              
ATOM      6  CA  PHE    34      -4.518  19.607 -10.373  1.00  0.00              
ATOM      7  C   PHE    34      -5.131  18.334  -9.788  1.00  0.00              
ATOM      8  O   PHE    34      -5.197  17.327 -10.529  1.00  0.00              
ATOM      9  N   ASN    35      -5.479  18.453  -8.505  1.00  0.00              
ATOM     10  CA  ASN    35      -6.139  17.313  -7.854  1.00  0.00              
ATOM     11  C   ASN    35      -7.494  17.156  -8.589  1.00  0.00              
ATOM     12  O   ASN    35      -8.590  17.574  -8.198  1.00  0.00              
ATOM     13  N   SER    36      -7.330  16.554  -9.753  1.00  0.00              
ATOM     14  CA  SER    36      -8.342  16.246 -10.754  1.00  0.00              
ATOM     15  C   SER    36      -9.306  15.151 -10.288  1.00  0.00              
ATOM     16  O   SER    36     -10.536  15.255 -10.493  1.00  0.00              
ATOM     17  N   THR    37      -8.682  14.129  -9.690  1.00  0.00              
ATOM     18  CA  THR    37      -9.501  12.986  -9.252  1.00  0.00              
ATOM     19  C   THR    37      -9.677  12.956  -7.754  1.00  0.00              
ATOM     20  O   THR    37     -10.388  12.009  -7.352  1.00  0.00              
ATOM     21  N   GLN    38      -9.156  13.905  -7.001  1.00  0.00              
ATOM     22  CA  GLN    38      -9.344  13.817  -5.528  1.00  0.00              
ATOM     23  C   GLN    38     -10.801  13.763  -5.120  1.00  0.00              
ATOM     24  O   GLN    38     -11.509  14.613  -5.670  1.00  0.00              
ATOM     25  N   PRO    39     -11.163  12.849  -4.234  1.00  0.00              
ATOM     26  CA  PRO    39     -12.545  12.729  -3.799  1.00  0.00              
ATOM     27  C   PRO    39     -13.073  13.962  -3.106  1.00  0.00              
ATOM     28  O   PRO    39     -14.248  14.248  -3.360  1.00  0.00              
ATOM     29  N   PHE    40     -12.312  14.611  -2.247  1.00  0.00              
ATOM     30  CA  PHE    40     -12.807  15.800  -1.532  1.00  0.00              
ATOM     31  C   PHE    40     -11.690  16.434  -0.703  1.00  0.00              
ATOM     32  O   PHE    40     -10.632  15.809  -0.693  1.00  0.00              
ATOM     33  N   PHE    41     -11.961  17.590  -0.122  1.00  0.00              
ATOM     34  CA  PHE    41     -10.958  18.268   0.708  1.00  0.00              
ATOM     35  C   PHE    41     -11.542  18.350   2.135  1.00  0.00              
ATOM     36  O   PHE    41     -12.762  18.174   2.335  1.00  0.00              
ATOM     37  N   MET    42     -10.687  18.591   3.128  1.00  0.00              
ATOM     38  CA  MET    42     -11.085  18.641   4.545  1.00  0.00              
ATOM     39  C   MET    42     -11.954  19.821   4.926  1.00  0.00              
ATOM     40  O   MET    42     -12.539  19.911   6.054  1.00  0.00              
ATOM     41  N   ASP    43     -12.197  20.712   3.973  1.00  0.00              
ATOM     42  CA  ASP    43     -13.088  21.877   4.294  1.00  0.00              
ATOM     43  C   ASP    43     -14.458  21.587   3.693  1.00  0.00              
ATOM     44  O   ASP    43     -15.186  22.561   3.381  1.00  0.00              
ATOM     45  N   THR    44     -14.698  20.274   3.583  1.00  0.00              
ATOM     46  CA  THR    44     -16.007  19.869   3.038  1.00  0.00              
ATOM     47  C   THR    44     -17.078  20.284   4.055  1.00  0.00              
ATOM     48  O   THR    44     -16.821  20.427   5.262  1.00  0.00              
ATOM     49  N   MET    45     -18.247  20.533   3.519  1.00  0.00              
ATOM     50  CA  MET    45     -19.475  20.938   4.165  1.00  0.00              
ATOM     51  C   MET    45     -20.755  20.443   3.474  1.00  0.00              
ATOM     52  O   MET    45     -21.241  21.182   2.611  1.00  0.00              
ATOM     53  N   GLU    46     -21.240  19.275   3.852  1.00  0.00              
ATOM     54  CA  GLU    46     -22.480  18.730   3.272  1.00  0.00              
ATOM     55  C   GLU    46     -23.664  19.501   3.817  1.00  0.00              
ATOM     56  O   GLU    46     -24.231  19.057   4.828  1.00  0.00              
ATOM     57  N   PRO    47     -24.014  20.583   3.189  1.00  0.00              
ATOM     58  CA  PRO    47     -25.124  21.427   3.701  1.00  0.00              
ATOM     59  C   PRO    47     -26.439  20.691   3.900  1.00  0.00              
ATOM     60  O   PRO    47     -27.266  21.271   4.639  1.00  0.00              
ATOM     61  N   LEU    48     -26.699  19.534   3.349  1.00  0.00              
ATOM     62  CA  LEU    48     -27.969  18.808   3.585  1.00  0.00              
ATOM     63  C   LEU    48     -28.111  18.523   5.087  1.00  0.00              
ATOM     64  O   LEU    48     -29.234  18.317   5.592  1.00  0.00              
ATOM     65  N   GLU    49     -27.004  18.518   5.804  1.00  0.00              
ATOM     66  CA  GLU    49     -26.957  18.235   7.219  1.00  0.00              
ATOM     67  C   GLU    49     -26.618  19.422   8.109  1.00  0.00              
ATOM     68  O   GLU    49     -26.303  19.175   9.313  1.00  0.00              
ATOM     69  N   TRP    50     -26.685  20.613   7.499  1.00  0.00              
ATOM     70  CA  TRP    50     -26.362  21.794   8.333  1.00  0.00              
ATOM     71  C   TRP    50     -27.216  21.836   9.589  1.00  0.00              
ATOM     72  O   TRP    50     -26.724  22.525  10.491  1.00  0.00              
END
