
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0386TS239_3_3-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   23 , name T0386_D1.pdb
# PARAMETERS: T0386TS239_3_3-D1.T0386_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        13 - 24          4.76    12.19
  LONGEST_CONTINUOUS_SEGMENT:    12        21 - 32          4.68    13.16
  LONGEST_CONTINUOUS_SEGMENT:    12        22 - 33          4.85    12.95
  LCS_AVERAGE:      5.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        30 - 35          1.91    24.81
  LCS_AVERAGE:      2.45

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        19 - 23          0.78    13.45
  LCS_AVERAGE:      1.92

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:  206
LCS_GDT     I      13     I      13      4    5   12     3    4    4    5    5    5    5    7    7    9    9    9    9   11   12   13   13   14   14   15 
LCS_GDT     I      14     I      14      4    5   12     3    4    4    5    5    5    6    8    8    9   10   10   11   12   12   13   13   14   14   16 
LCS_GDT     S      15     S      15      4    5   12     3    4    4    5    5    5    6    8    8    9   10   10   11   12   12   13   13   15   17   18 
LCS_GDT     P      16     P      16      4    5   12     3    4    4    5    5    5    6    8    8    9   10   10   11   12   12   13   13   16   17   18 
LCS_GDT     H      17     H      17      4    5   12     3    4    4    5    5    5    6    8    8    9   10   10   11   12   12   14   15   16   17   18 
LCS_GDT     H      18     H      18      3    4   12     3    3    3    4    4    4    6    8    8    9   10   10   11   12   12   14   15   16   17   18 
LCS_GDT     Y      19     Y      19      5    5   12     3    5    5    5    5    5    6    8    8    9   10   10   11   12   12   14   15   16   17   18 
LCS_GDT     V      20     V      20      5    5   12     3    5    5    5    5    5    6    8    8    9   10   10   11   12   13   14   15   16   17   18 
LCS_GDT     Y      21     Y      21      5    5   12     3    5    5    5    5    5    6    8    8    9   10   12   12   13   13   14   15   16   17   18 
LCS_GDT     P      22     P      22      5    5   12     3    5    5    5    5    5    6    6    8    9   10   12   12   13   13   14   15   16   17   18 
LCS_GDT     N      23     N      23      5    5   12     3    5    5    5    5    5    6    6    8    9   10   12   12   13   13   14   15   16   17   18 
LCS_GDT     T      24     T      24      3    4   12     3    3    3    4    4    4    6    6    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     T      25     T      25      3    4   12     3    3    3    4    4    4    6    6    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     T      26     T      26      3    4   12     3    3    3    4    4    4    6    6    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     L      27     L      27      3    4   12     3    4    4    4    4    6    6    6    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     K      28     K      28      3    5   12     3    4    4    4    4    6    6    6    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     N      29     N      29      4    5   12     4    4    5    5    5    6    6    7    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     K      30     K      30      4    6   12     4    4    4    4    5    6    6    7    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     Y      31     Y      31      4    6   12     4    4    4    4    5    6    6    7    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     G      32     G      32      4    6   12     4    4    5    5    5    6    6    7    8    9    9   12   12   13   13   14   15   16   17   18 
LCS_GDT     I      33     I      33      4    6   12     3    3    5    5    5    6    6    7    7    7    9   10   12   13   13   14   15   16   17   18 
LCS_GDT     K      34     K      34      4    6   10     3    3    5    5    5    6    6    7    7    7    7    8    8    9   10   12   13   14   15   15 
LCS_GDT     N      35     N      35      4    6   10     3    3    5    5    5    6    6    7    7    7    7    8    8    9   10   11   13   13   15   15 
LCS_AVERAGE  LCS_A:   3.37  (   1.92    2.45    5.74 )

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      6      6      8      8      9     10     12     12     13     13     14     15     16     17     18 
GDT PERCENT_CA   1.94   2.43   2.43   2.43   2.43   2.91   2.91   3.88   3.88   4.37   4.85   5.83   5.83   6.31   6.31   6.80   7.28   7.77   8.25   8.74
GDT RMS_LOCAL    0.20   0.78   0.78   0.78   0.78   1.91   1.91   3.17   3.17   3.48   3.90   4.68   4.68   5.01   5.01   5.47   6.16   6.34   6.60   6.96
GDT RMS_ALL_CA  19.79  13.45  13.45  13.45  13.45  24.81  24.81  12.32  12.32  12.66  12.62  13.16  13.16  12.87  12.87  11.46  10.28  10.09   9.95   9.72

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13          6.001
LGA    I      14      I      14          3.895
LGA    S      15      S      15          2.933
LGA    P      16      P      16          2.392
LGA    H      17      H      17          2.179
LGA    H      18      H      18          3.839
LGA    Y      19      Y      19          3.025
LGA    V      20      V      20          2.788
LGA    Y      21      Y      21          3.828
LGA    P      22      P      22          7.168
LGA    N      23      N      23          8.000
LGA    T      24      T      24          9.168
LGA    T      25      T      25         13.765
LGA    T      26      T      26         10.942
LGA    L      27      L      27         15.797
LGA    K      28      K      28         18.607
LGA    N      29      N      29         16.931
LGA    K      30      K      30         17.553
LGA    Y      31      Y      31         17.780
LGA    G      32      G      32         17.361
LGA    I      33      I      33         17.525
LGA    K      34      K      34         18.742
LGA    N      35      N      35         19.995

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  206    4.0      8    3.17     3.883     3.442     0.244

LGA_LOCAL      RMSD =  3.173  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.321  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  9.067  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.388496 * X  +   0.107551 * Y  +   0.915152 * Z  + -28.249907
  Y_new =  -0.850417 * X  +   0.424231 * Y  +   0.311159 * Z  +  60.284031
  Z_new =  -0.354770 * X  +  -0.899145 * Y  +   0.256275 * Z  +  37.574677 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.293138    1.848455  [ DEG:   -74.0913    105.9087 ]
  Theta =   0.362668    2.778924  [ DEG:    20.7794    159.2206 ]
  Phi   =  -1.142277    1.999316  [ DEG:   -65.4476    114.5524 ]
 
# 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: T0386TS239_3_3-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_3_3-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  206   4.0    8   3.17   3.442     9.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_3_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0386
PARENT 1gz5_A
ATOM     61  N   ILE    13      19.972  53.363  25.388  1.00  9.99
ATOM     62  CA  ILE    13      20.811  53.110  26.560  1.00  9.99
ATOM     63  C   ILE    13      20.261  53.886  27.756  1.00  9.99
ATOM     64  O   ILE    13      19.685  54.966  27.594  1.00  9.99
ATOM     65  CB  ILE    13      22.253  53.527  26.256  1.00  9.99
ATOM     66  N   ILE    14      20.405  53.334  28.954  1.00  9.99
ATOM     67  CA  ILE    14      20.042  54.055  30.159  1.00  9.99
ATOM     68  C   ILE    14      21.242  54.160  31.065  1.00  9.99
ATOM     69  O   ILE    14      22.137  53.329  30.968  1.00  9.99
ATOM     70  CB  ILE    14      18.890  53.395  30.920  1.00  9.99
ATOM     71  N   SER    15      21.271  55.201  31.914  1.00  9.99
ATOM     72  CA  SER    15      22.414  55.478  32.795  1.00  9.99
ATOM     73  C   SER    15      22.081  56.504  33.864  1.00  9.99
ATOM     74  O   SER    15      21.074  57.223  33.773  1.00  9.99
ATOM     75  CB  SER    15      23.642  55.900  31.968  1.00  9.99
ATOM     76  N   PRO    16      22.894  56.560  34.903  1.00  9.99
ATOM     77  CA  PRO    16      22.622  57.428  36.046  1.00  9.99
ATOM     78  C   PRO    16      23.676  58.507  36.101  1.00  9.99
ATOM     79  O   PRO    16      24.849  58.216  36.060  1.00  9.99
ATOM     80  CB  PRO    16      22.635  56.631  37.390  1.00  9.99
ATOM     81  N   HIS    17      23.259  59.776  36.164  1.00  9.99
ATOM     82  CA  HIS    17      24.212  60.893  36.275  1.00  9.99
ATOM     83  C   HIS    17      23.689  61.881  37.295  1.00  9.99
ATOM     84  O   HIS    17      23.011  62.807  36.927  1.00  9.99
ATOM     85  CB  HIS    17      24.352  61.634  34.931  1.00  9.99
ATOM     86  N   HIS    18      23.993  61.714  38.567  1.00  9.99
ATOM     87  CA  HIS    18      23.488  62.693  39.551  1.00  9.99
ATOM     88  C   HIS    18      24.065  64.097  39.266  1.00  9.99
ATOM     89  O   HIS    18      25.244  64.230  39.198  1.00  9.99
ATOM     90  CB  HIS    18      23.851  62.081  40.933  1.00  9.99
ATOM     91  N   TYR    19      23.216  65.089  39.007  1.00  9.99
ATOM     92  CA  TYR    19      23.604  66.456  38.655  1.00  9.99
ATOM     93  C   TYR    19      24.257  67.164  39.852  1.00  9.99
ATOM     94  O   TYR    19      23.896  66.909  41.010  1.00  9.99
ATOM     95  CB  TYR    19      22.390  67.244  38.133  1.00  9.99
ATOM     96  N   VAL    20      25.273  67.998  39.557  1.00  9.99
ATOM     97  CA  VAL    20      26.089  68.608  40.585  1.00  9.99
ATOM     98  C   VAL    20      26.171  70.094  40.397  1.00  9.99
ATOM     99  O   VAL    20      25.386  70.687  39.654  1.00  9.99
ATOM    100  CB  VAL    20      27.489  67.971  40.572  1.00  9.99
ATOM    101  N   TYR    21      27.198  70.657  41.009  1.00  9.99
ATOM    102  CA  TYR    21      27.341  72.048  41.293  1.00  9.99
ATOM    103  C   TYR    21      28.838  72.407  40.957  1.00  9.99
ATOM    104  O   TYR    21      29.647  71.510  40.718  1.00  9.99
ATOM    105  CB  TYR    21      26.932  72.147  42.824  1.00  9.99
ATOM    106  N   PRO    22      29.180  73.693  40.883  1.00  9.99
ATOM    107  CA  PRO    22      30.584  74.144  40.681  1.00  9.99
ATOM    108  C   PRO    22      31.197  74.548  42.018  1.00  9.99
ATOM    109  O   PRO    22      31.041  75.690  42.407  1.00  9.99
ATOM    110  CB  PRO    22      30.713  75.359  39.715  1.00  9.99
ATOM    111  N   ASN    23      31.887  73.640  42.714  1.00  9.99
ATOM    112  CA  ASN    23      32.227  73.858  44.138  1.00  9.99
ATOM    113  C   ASN    23      33.192  75.001  44.284  1.00  9.99
ATOM    114  O   ASN    23      33.114  75.731  45.283  1.00  9.99
ATOM    115  CB  ASN    23      32.873  72.532  44.583  1.00  9.99
ATOM    116  N   THR    24      34.068  75.155  43.303  1.00  9.99
ATOM    117  CA  THR    24      35.071  76.200  43.326  1.00  9.99
ATOM    118  C   THR    24      34.402  77.563  43.181  1.00  9.99
ATOM    119  O   THR    24      34.755  78.490  43.907  1.00  9.99
ATOM    120  CB  THR    24      36.144  76.007  42.212  1.00  9.99
ATOM    121  N   THR    25      33.467  77.697  42.236  1.00  9.99
ATOM    122  CA  THR    25      32.796  78.975  42.048  1.00  9.99
ATOM    123  C   THR    25      31.926  79.377  43.257  1.00  9.99
ATOM    124  O   THR    25      31.934  80.568  43.654  1.00  9.99
ATOM    125  CB  THR    25      31.966  79.001  40.765  1.00  9.99
ATOM    126  N   THR    26      31.203  78.425  43.869  1.00  9.99
ATOM    127  CA  THR    26      30.438  78.813  45.038  1.00  9.99
ATOM    128  C   THR    26      31.303  79.186  46.221  1.00  9.99
ATOM    129  O   THR    26      30.958  80.133  46.938  1.00  9.99
ATOM    130  CB  THR    26      29.222  77.918  45.408  1.00  9.99
ATOM    131  N   LEU    27      32.449  78.507  46.373  1.00  9.99
ATOM    132  CA  LEU    27      33.443  78.906  47.366  1.00  9.99
ATOM    133  C   LEU    27      33.694  80.390  47.189  1.00  9.99
ATOM    134  O   LEU    27      33.488  81.153  48.127  1.00  9.99
ATOM    135  CB  LEU    27      34.755  78.110  47.227  1.00  9.99
ATOM    136  N   LYS    28      34.066  80.790  45.969  1.00  9.99
ATOM    137  CA  LYS    28      34.400  82.192  45.636  1.00  9.99
ATOM    138  C   LYS    28      33.233  83.092  45.975  1.00  9.99
ATOM    139  O   LYS    28      33.416  84.096  46.678  1.00  9.99
ATOM    140  CB  LYS    28      34.778  82.381  44.163  1.00  9.99
ATOM    141  N   ASN    29      32.023  82.736  45.535  1.00  9.99
ATOM    142  CA  ASN    29      30.942  83.689  45.757  1.00  9.99
ATOM    143  C   ASN    29      30.555  83.761  47.234  1.00  9.99
ATOM    144  O   ASN    29      30.256  84.858  47.719  1.00  9.99
ATOM    145  CB  ASN    29      29.764  83.556  44.762  1.00  9.99
ATOM    146  N   LYS    30      30.626  82.624  47.939  1.00  9.99
ATOM    147  CA  LYS    30      30.283  82.542  49.367  1.00  9.99
ATOM    148  C   LYS    30      31.241  83.381  50.256  1.00  9.99
ATOM    149  O   LYS    30      30.858  83.809  51.337  1.00  9.99
ATOM    150  CB  LYS    30      30.265  81.096  49.825  1.00  9.99
ATOM    151  N   TYR    31      32.457  83.631  49.781  1.00  9.99
ATOM    152  CA  TYR    31      33.465  84.332  50.579  1.00  9.99
ATOM    153  C   TYR    31      33.516  85.842  50.264  1.00  9.99
ATOM    154  O   TYR    31      34.251  86.593  50.900  1.00  9.99
ATOM    155  CB  TYR    31      34.873  83.695  50.345  1.00  9.99
ATOM    156  N   GLY    32      32.737  86.283  49.282  1.00  9.99
ATOM    157  CA  GLY    32      32.662  87.689  48.923  1.00  9.99
ATOM    158  C   GLY    32      31.969  88.481  50.016  1.00  9.99
ATOM    159  O   GLY    32      31.246  87.911  50.842  1.00  9.99
ATOM    160  N   ILE    33      32.159  89.795  50.046  1.00  9.99
ATOM    161  CA  ILE    33      31.627  90.597  51.158  1.00  9.99
ATOM    162  C   ILE    33      30.091  90.551  51.207  1.00  9.99
ATOM    163  O   ILE    33      29.442  90.380  50.156  1.00  9.99
ATOM    164  CB  ILE    33      32.112  91.989  50.835  1.00  9.99
ATOM    165  N   LYS    34      29.506  90.662  52.410  1.00  9.99
ATOM    166  CA  LYS    34      28.043  90.702  52.497  1.00  9.99
ATOM    167  C   LYS    34      27.531  92.099  52.158  1.00  9.99
ATOM    168  O   LYS    34      28.208  93.085  52.460  1.00  9.99
ATOM    169  CB  LYS    34      27.586  90.322  53.902  1.00  9.99
ATOM    170  N   ASN    35      26.343  92.202  51.567  1.00  9.99
ATOM    171  CA  ASN    35      25.663  93.506  51.432  1.00  9.99
ATOM    172  C   ASN    35      25.567  94.178  52.819  1.00  9.99
ATOM    173  O   ASN    35      25.341  93.447  53.821  1.00  9.99
ATOM    174  CB  ASN    35      24.243  93.150  50.970  1.00  9.99
TER
END
