
#######################################################
#                                                     #
#                        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   36 (   36),  selected   36 , name T0301TS464_4_2
# Molecule2: number of CA atoms  391 ( 2894),  selected   36 , name T0301.pdb
# PARAMETERS: T0301TS464_4_2.T0301.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:    16       115 - 148         4.71    25.20
  LCS_AVERAGE:      3.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       134 - 148         1.71    25.34
  LCS_AVERAGE:      2.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       135 - 146         0.78    25.46
  LCS_AVERAGE:      1.68

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:  391
LCS_GDT     F      24     F      24      3    3   10     3    3    3    3    3    4    6    6    6   10   10   10   11   12   17   18   18   21   22   23 
LCS_GDT     R      25     R      25      5    7   10     5    5    5    6    7    7    7    8    8   10   10   10   10   13   19   21   21   23   24   25 
LCS_GDT     L      26     L      26      5    7   10     5    5    5    6    7    7    7    8   10   11   12   15   17   19   22   23   24   24   24   25 
LCS_GDT     E      27     E      27      5    7   10     5    5    5    6    7    7    7    9   10   11   13   15   17   19   22   23   24   24   24   25 
LCS_GDT     D      28     D      28      5    7   10     5    5    5    6    7    7    7    9   10   11   13   15   17   19   22   23   24   24   24   25 
LCS_GDT     L      29     L      29      5    7   10     5    5    5    6    7    7    7    8   10   11   13   15   17   19   22   23   24   24   24   25 
LCS_GDT     P      30     P      30      4    7   10     4    4    4    6    6    7    7    7    8   10   10   12   13   19   22   23   24   24   24   25 
LCS_GDT     E      31     E      31      4    7   10     4    4    4    5    7    7    7    8    8   10   12   12   16   19   22   23   24   24   24   25 
LCS_GDT     S      32     S      32      4    4   10     4    4    4    4    5    5    5    8    8   10   12   12   13   14   22   23   24   24   24   25 
LCS_GDT     C      33     C      33      4    4   10     4    4    4    5    7    7    7    8    8   10   12   12   13   14   17   23   24   24   24   25 
LCS_GDT     G     110     G     110      3    4    9     3    3    3    3    4    4    5    5    6    7    8    9   11   14   18   19   19   19   20   20 
LCS_GDT     A     111     A     111      3    4    7     3    3    3    3    4    4    5    5    6    7    8    9   11   12   18   19   19   19   20   23 
LCS_GDT     G     112     G     112      3    4   11     3    3    3    3    4    4    5    5    6    6    8    9   11   14   18   19   19   19   20   23 
LCS_GDT     A     113     A     113      3    4   12     3    3    3    3    4    5    6    7    9    9    9   12   14   15   18   19   19   20   22   23 
LCS_GDT     F     114     F     114      3    3   12     3    3    3    3    4    6    8    8    9    9   10   12   16   17   19   21   21   23   24   25 
LCS_GDT     A     115     A     115      3    3   16     3    3    3    3    5    6    8    8   10   11   13   15   17   19   22   23   24   24   24   25 
LCS_GDT     V     134     V     134      4   15   16     3    4    8   11   14   15   15   15   15   15   15   15   15   15   15   17   24   24   24   25 
LCS_GDT     R     135     R     135     12   15   16     4    8   12   12   14   15   15   15   15   15   15   15   15   19   22   23   24   24   24   25 
LCS_GDT     I     136     I     136     12   15   16     3   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     W     137     W     137     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     Q     138     Q     138     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     A     139     A     139     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   16   19   22   23   24   24   24   25 
LCS_GDT     N     140     N     140     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     I     141     I     141     12   15   16     3   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     G     142     G     142     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     K     143     K     143     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   18   22   23   24   24   24   25 
LCS_GDT     T     144     T     144     12   15   16     6   11   12   12   14   15   15   15   15   15   15   15   17   18   22   23   24   24   24   25 
LCS_GDT     I     145     I     145     12   15   16     4   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     I     146     I     146     12   15   16     4   11   12   12   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     A     147     A     147      4   15   16     3    4    5    6    7   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     H     148     H     148      4   15   16     3    4    5   11   14   15   15   15   15   15   15   15   17   19   22   23   24   24   24   25 
LCS_GDT     S     353     S     353      3    5    7     0    3    4    4    5    5    5    5    5    5    6    6    6    7   15   16   17   19   19   19 
LCS_GDT     G     354     G     354      4    5    7     3    4    4    4    5    5    5    5    5    5    6    6    6    7    7    8    8   19   19   19 
LCS_GDT     T     355     T     355      4    5    7     3    4    4    4    5    5    5    5    5    5    6    6    6    7    7   13   17   19   19   19 
LCS_GDT     L     356     L     356      4    5    7     3    4    4    4    5    5    5    5    5    5    6    8   10   12   15   16   17   19   19   19 
LCS_GDT     R     357     R     357      4    5    7     3    4    4    4    5    5    5    5    5    5    7    8   10   12   15   16   17   19   19   23 
LCS_AVERAGE  LCS_A:   2.39  (   1.68    2.36    3.14 )

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      6     11     12     12     14     15     15     15     15     15     15     15     17     19     22     23     24     24     24     25 
GDT PERCENT_CA   1.53   2.81   3.07   3.07   3.58   3.84   3.84   3.84   3.84   3.84   3.84   3.84   4.35   4.86   5.63   5.88   6.14   6.14   6.14   6.39
GDT RMS_LOCAL    0.27   0.60   0.78   0.78   1.48   1.71   1.71   1.71   1.71   1.71   1.71   1.71   4.71   5.22   5.68   5.80   5.96   5.96   5.96   6.23
GDT RMS_ALL_CA  25.62  25.52  25.46  25.46  25.26  25.34  25.34  25.34  25.34  25.34  25.34  25.34  12.71  13.00  13.01  13.08  13.19  13.19  13.19  13.04

#      Molecule1      Molecule2       DISTANCE
LGA    F      24      F      24         39.601
LGA    R      25      R      25         40.272
LGA    L      26      L      26         36.604
LGA    E      27      E      27         38.281
LGA    D      28      D      28         42.642
LGA    L      29      L      29         41.282
LGA    P      30      P      30         40.274
LGA    E      31      E      31         39.540
LGA    S      32      S      32         41.546
LGA    C      33      C      33         37.556
LGA    G     110      G     110         26.421
LGA    A     111      A     111         25.293
LGA    G     112      G     112         23.389
LGA    A     113      A     113         23.720
LGA    F     114      F     114         22.332
LGA    A     115      A     115         18.408
LGA    V     134      V     134          1.852
LGA    R     135      R     135          0.881
LGA    I     136      I     136          2.065
LGA    W     137      W     137          2.004
LGA    Q     138      Q     138          0.685
LGA    A     139      A     139          0.385
LGA    N     140      N     140          1.390
LGA    I     141      I     141          1.161
LGA    G     142      G     142          1.178
LGA    K     143      K     143          0.411
LGA    T     144      T     144          0.738
LGA    I     145      I     145          1.987
LGA    I     146      I     146          2.318
LGA    A     147      A     147          3.275
LGA    H     148      H     148          2.320
LGA    S     353      S     353         32.228
LGA    G     354      G     354         29.214
LGA    T     355      T     355         27.648
LGA    L     356      L     356         26.596
LGA    R     357      R     357         24.029

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36  391    4.0     15    1.71     3.900     3.437     0.828

LGA_LOCAL      RMSD =  1.711  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 25.337  Number of atoms =   36 
Std_ALL_ATOMS  RMSD = 10.929  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.047894 * X  +  -0.854613 * Y  +   0.517052 * Z  + 109.811310
  Y_new =  -0.935248 * X  +  -0.220135 * Y  +  -0.277221 * Z  +  26.185556
  Z_new =   0.350738 * X  +  -0.470295 * Y  +  -0.809818 * Z  +  26.550982 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.615454    0.526138  [ DEG:  -149.8545     30.1455 ]
  Theta =  -0.358359   -2.783234  [ DEG:   -20.5325   -159.4675 ]
  Phi   =  -1.519631    1.621961  [ DEG:   -87.0685     92.9315 ]
 
# 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: T0301TS464_4_2                                
REMARK     2: T0301.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_4_2.T0301.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   36  391   4.0   15   1.71   3.437    10.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  PHE    24      90.943  -0.285  -3.080  1.00  0.00
ATOM      2  CA  ARG    25      88.794  -3.183  -1.882  1.00  0.00
ATOM      3  CA  LEU    26      86.558  -0.682  -0.092  1.00  0.00
ATOM      4  CA  GLU    27      86.057   1.312  -3.298  1.00  0.00
ATOM      5  CA  ASP    28      84.968  -1.854  -5.146  1.00  0.00
ATOM      6  CA  LEU    29      82.398  -2.528  -2.411  1.00  0.00
ATOM      7  CA  PRO    30      81.146   1.067  -2.215  1.00  0.00
ATOM      8  CA  GLU    31      80.933   1.338  -6.016  1.00  0.00
ATOM      9  CA  SER    32      79.132  -1.982  -6.370  1.00  0.00
ATOM     10  CA  CYS    33      77.060  -1.148  -3.289  1.00  0.00
ATOM     11  CA  GLY   110      87.254   8.956  -4.534  1.00  0.00
ATOM     12  CA  ALA   111      86.845   5.686  -2.631  1.00  0.00
ATOM     13  CA  GLY   112      83.051   5.703  -2.888  1.00  0.00
ATOM     14  CA  ALA   113      82.208   6.932   0.597  1.00  0.00
ATOM     15  CA  PHE   114      78.634   8.244   0.532  1.00  0.00
ATOM     16  CA  ALA   115      78.118   8.701   4.246  1.00  0.00
ATOM     17  CA  VAL   134      66.042  13.329   9.566  1.00  0.00
ATOM     18  CA  ARG   135      69.068  13.500   7.358  1.00  0.00
ATOM     19  CA  ILE   136      71.697  16.250   7.349  1.00  0.00
ATOM     20  CA  TRP   137      72.504  16.734   3.687  1.00  0.00
ATOM     21  CA  GLN   138      75.456  18.613   2.175  1.00  0.00
ATOM     22  CA  ALA   139      73.964  20.177  -0.912  1.00  0.00
ATOM     23  CA  ASN   140      77.411  20.807  -2.412  1.00  0.00
ATOM     24  CA  ILE   141      78.794  17.290  -2.118  1.00  0.00
ATOM     25  CA  GLY   142      75.392  15.593  -2.583  1.00  0.00
ATOM     26  CA  LYS   143      76.591  13.602   0.561  1.00  0.00
ATOM     27  CA  THR   144      74.863  12.046   3.575  1.00  0.00
ATOM     28  CA  ILE   145      76.801  13.561   6.496  1.00  0.00
ATOM     29  CA  ILE   146      74.598  12.496   9.589  1.00  0.00
ATOM     30  CA  ALA   147      71.289  10.871  10.531  1.00  0.00
ATOM     31  CA  HIS   148      69.499  12.296  13.557  1.00  0.00
ATOM     32  CA  SER   353      73.470  27.582   5.811  1.00  0.00
ATOM     33  CA  GLY   354      75.880  24.666   5.509  1.00  0.00
ATOM     34  CA  THR   355      73.598  21.647   5.567  1.00  0.00
ATOM     35  CA  LEU   356      70.271  20.419   4.249  1.00  0.00
ATOM     36  CA  ARG   357      68.116  18.804   6.936  1.00  0.00
TER
END
