
#######################################################
#                                                     #
#                        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   38 (   38),  selected   38 , name T0318TS464_5_2
# Molecule2: number of CA atoms  489 ( 3665),  selected   38 , name T0318.pdb
# PARAMETERS: T0318TS464_5_2.T0318.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:    24        77 - 100         4.50    18.33
  LCS_AVERAGE:      4.15

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        87 - 100         1.86    15.42
  LCS_AVERAGE:      2.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        89 - 100         0.88    15.20
  LCS_AVERAGE:      1.80

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:  489
LCS_GDT     V      77     V      77      3    3   24     0    3    3    3    3    3    5    6    8   10   16   19   23   23   24   24   24   24   24   25 
LCS_GDT     P      78     P      78      3    4   24     3    3    3    4    4    6    9   12   15   18   21   22   23   23   24   24   24   24   24   25 
LCS_GDT     D      79     D      79      3    4   24     3    3    3    4    4    4    5   14   16   18   21   22   23   23   24   24   24   28   29   31 
LCS_GDT     A      80     A      80      3    4   24     3    3    3    4    4    4    9   10   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     S      81     S      81      3    4   24     0    3    3    4    5    7   10   13   15   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     S      82     S      82      3    4   24     3    3    3    3    5    9   10   13   15   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     R      83     R      83      3    7   24     3    3    5    6    6    7    7   10   13   16   20   22   22   23   24   24   25   28   29   31 
LCS_GDT     G      84     G      84      6    7   24     4    6    6    6    7    9   10   13   15   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     N      85     N      85      6    7   24     4    6    6    6    8   10   11   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     T      86     T      86      6    7   24     4    6    6    6   12   13   13   15   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     P      87     P      87      6   14   24     4    6    6    6    7   11   13   14   16   18   21   22   23   23   24   24   24   28   29   31 
LCS_GDT     T      88     T      88      6   14   24     4    6    6    6    7    9   11   14   15   18   21   22   23   23   24   24   24   25   28   31 
LCS_GDT     N      89     N      89     12   14   24     4    7   11   12   12   13   13   15   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     A      90     A      90     12   14   24     8   10   11   12   12   13   13   15   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     H      91     H      91     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     S      92     S      92     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     I      93     I      93     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     Y      94     Y      94     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     K      95     K      95     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     E      96     E      96     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   25   28   29   31 
LCS_GDT     L      97     L      97     12   14   24     5   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   24   28   29   30 
LCS_GDT     K      98     K      98     12   14   24     4   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   24   26   27   28 
LCS_GDT     P      99     P      99     12   14   24     4    6   11   12   12   13   13   14   16   18   21   22   23   23   24   24   24   26   27   28 
LCS_GDT     I     100     I     100     12   14   24     8   10   11   12   12   13   13   14   16   18   21   22   23   23   24   24   24   26   27   28 
LCS_GDT     D     153     D     153      4   13   14     4    5   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   25   28   31 
LCS_GDT     K     154     K     154     11   13   14     4    5    9   12   13   13   13   15   16   17   20   21   22   22   23   24   25   25   28   31 
LCS_GDT     L     155     L     155     11   13   14     4   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     T     156     T     156     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     N     157     N     157     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     E     158     E     158     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     D     159     D     159     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     A     160     A     160     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     V     161     V     161     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     F     162     F     162     11   13   14     8   10   10   12   13   13   13   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     L     163     L     163     11   13   14     6   10   10   12   13   13   13   14   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_GDT     T     164     T     164     11   13   14     8   10   10   12   13   13   13   13   15   16   18   18   21   22   23   24   24   25   28   31 
LCS_GDT     D     165     D     165     11   13   14     3    8   10   11   13   13   13   15   16   17   20   21   22   22   23   24   25   26   29   31 
LCS_GDT     L     166     L     166      3    3   14     0    3    3    7    9   10   12   15   16   17   20   21   22   22   23   24   25   28   29   31 
LCS_AVERAGE  LCS_A:   2.74  (   1.80    2.25    4.15 )

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      8     10     11     12     13     13     13     15     16     18     21     22     23     23     24     24     25     28     29     31 
GDT PERCENT_CA   1.64   2.04   2.25   2.45   2.66   2.66   2.66   3.07   3.27   3.68   4.29   4.50   4.70   4.70   4.91   4.91   5.11   5.73   5.93   6.34
GDT RMS_LOCAL    0.32   0.51   0.76   0.88   1.29   1.25   1.25   2.73   2.82   3.65   4.04   4.18   4.32   4.32   4.50   4.50   5.66   6.96   7.04   6.94
GDT RMS_ALL_CA  15.03  14.78  15.25  15.20  13.55  15.17  15.17  11.56  11.42  16.55  17.40  17.89  18.02  18.02  18.33  18.33   9.87   8.81   8.82   9.42

#      Molecule1      Molecule2       DISTANCE
LGA    V      77      V      77         18.346
LGA    P      78      P      78         20.277
LGA    D      79      D      79         16.068
LGA    A      80      A      80         15.438
LGA    S      81      S      81         15.212
LGA    S      82      S      82         15.331
LGA    R      83      R      83          9.790
LGA    G      84      G      84          6.839
LGA    N      85      N      85          4.589
LGA    T      86      T      86          3.859
LGA    P      87      P      87          9.504
LGA    T      88      T      88          6.650
LGA    N      89      N      89          2.208
LGA    A      90      A      90          3.961
LGA    H      91      H      91          7.060
LGA    S      92      S      92          7.848
LGA    I      93      I      93          9.696
LGA    Y      94      Y      94         12.614
LGA    K      95      K      95         15.041
LGA    E      96      E      96         16.098
LGA    L      97      L      97         18.075
LGA    K      98      K      98         20.107
LGA    P      99      P      99         23.904
LGA    I     100      I     100         25.494
LGA    D     153      D     153          2.528
LGA    K     154      K     154          1.244
LGA    L     155      L     155          1.775
LGA    T     156      T     156          1.263
LGA    N     157      N     157          2.018
LGA    E     158      E     158          1.399
LGA    D     159      D     159          1.610
LGA    A     160      A     160          3.372
LGA    V     161      V     161          3.530
LGA    F     162      F     162          2.683
LGA    L     163      L     163          4.873
LGA    T     164      T     164          6.203
LGA    D     165      D     165          3.974
LGA    L     166      L     166          3.099

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   38  489    4.0     15    2.73     3.119     2.968     0.531

LGA_LOCAL      RMSD =  2.727  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.455  Number of atoms =   38 
Std_ALL_ATOMS  RMSD =  8.759  (standard rmsd on all 38 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.764154 * X  +   0.641380 * Y  +   0.068555 * Z  +   4.765035
  Y_new =  -0.644272 * X  +   0.753767 * Y  +   0.129416 * Z  +  38.253712
  Z_new =   0.031330 * X  +  -0.143062 * Y  +   0.989218 * Z  + -24.101795 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.143625    2.997967  [ DEG:    -8.2291    171.7709 ]
  Theta =  -0.031335   -3.110257  [ DEG:    -1.7954   -178.2046 ]
  Phi   =  -0.700485    2.441108  [ DEG:   -40.1348    139.8652 ]
 
# 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: T0318TS464_5_2                                
REMARK     2: T0318.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS464_5_2.T0318.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   38  489   4.0   15   2.73   2.968     8.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM      1  CA  VAL    77      13.722  41.207  20.052  1.00  0.00
ATOM      2  CA  PRO    78      12.982  37.499  19.896  1.00  0.00
ATOM      3  CA  ASP    79      15.209  36.775  22.924  1.00  0.00
ATOM      4  CA  ALA    80      13.220  39.207  25.133  1.00  0.00
ATOM      5  CA  SER    81      10.010  37.576  23.906  1.00  0.00
ATOM      6  CA  SER    82      10.786  33.893  24.424  1.00  0.00
ATOM      7  CA  ARG    83      12.595  34.485  27.757  1.00  0.00
ATOM      8  CA  GLY    84      11.080  37.718  29.042  1.00  0.00
ATOM      9  CA  ASN    85      14.453  39.461  29.342  1.00  0.00
ATOM     10  CA  THR    86      15.626  43.074  29.445  1.00  0.00
ATOM     11  CA  PRO    87      17.173  44.278  26.178  1.00  0.00
ATOM     12  CA  THR    88      20.644  44.226  27.837  1.00  0.00
ATOM     13  CA  ASN    89      20.423  40.570  29.062  1.00  0.00
ATOM     14  CA  ALA    90      19.477  39.625  25.473  1.00  0.00
ATOM     15  CA  HIS    91      22.684  41.261  24.121  1.00  0.00
ATOM     16  CA  SER    92      25.081  39.864  26.713  1.00  0.00
ATOM     17  CA  ILE    93      23.658  36.340  26.229  1.00  0.00
ATOM     18  CA  TYR    94      24.410  36.638  22.503  1.00  0.00
ATOM     19  CA  LYS    95      27.998  37.658  23.220  1.00  0.00
ATOM     20  CA  GLU    96      28.679  34.666  25.505  1.00  0.00
ATOM     21  CA  LEU    97      27.407  32.469  22.667  1.00  0.00
ATOM     22  CA  LYS    98      30.011  33.770  20.232  1.00  0.00
ATOM     23  CA  PRO    99      32.580  32.455  22.675  1.00  0.00
ATOM     24  CA  ILE   100      31.112  28.966  22.300  1.00  0.00
ATOM     25  CA  ASP   153      31.166  25.952  19.945  1.00  0.00
ATOM     26  CA  LYS   154      27.435  25.123  20.157  1.00  0.00
ATOM     27  CA  LEU   155      26.241  27.063  17.133  1.00  0.00
ATOM     28  CA  THR   156      27.849  27.479  13.733  1.00  0.00
ATOM     29  CA  ASN   157      28.602  30.980  12.519  1.00  0.00
ATOM     30  CA  GLU   158      25.384  30.862  10.488  1.00  0.00
ATOM     31  CA  ASP   159      23.368  29.760  13.508  1.00  0.00
ATOM     32  CA  ALA   160      24.850  32.614  15.522  1.00  0.00
ATOM     33  CA  VAL   161      24.030  35.038  12.725  1.00  0.00
ATOM     34  CA  PHE   162      20.345  34.106  12.854  1.00  0.00
ATOM     35  CA  LEU   163      20.239  34.912  16.553  1.00  0.00
ATOM     36  CA  THR   164      22.136  38.235  16.477  1.00  0.00
ATOM     37  CA  ASP   165      20.972  39.842  13.246  1.00  0.00
ATOM     38  CA  LEU   166      21.488  43.618  13.120  1.00  0.00
TER
END
