
#######################################################
#                                                     #
#                        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    9 (  153),  selected    9 , name T0372TS304_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS304_1-D1.T0372_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:     8       109 - 116         3.36     9.05
  LCS_AVERAGE:      5.64

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       109 - 113         1.96     8.31
  LCS_AVERAGE:      3.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       110 - 113         0.71     9.76
  LCS_AVERAGE:      2.47

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:  126
LCS_GDT     P     109     P     109      3    5    8     3    3    3    5    5    5    5    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     110     E     110      4    5    8     3    4    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     R     111     R     111      4    5    8     3    4    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     F     112     F     112      4    5    8     3    4    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     I     113     I     113      4    5    8     3    4    4    4    4    4    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     F     114     F     114      3    4    8     3    3    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     T     115     T     115      3    3    8     0    3    3    3    3    3    6    7    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     116     E     116      3    3    8     0    3    3    3    3    3    4    4    7    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     117     D     117      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_AVERAGE  LCS_A:   3.73  (   2.47    3.09    5.64 )

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      3      4      4      5      5      5      6      7      7      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.38   3.17   3.17   3.97   3.97   3.97   4.76   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.09   0.71   0.71   1.45   1.45   1.45   2.70   2.80   2.80   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36
GDT RMS_ALL_CA  13.26   9.76   9.76   9.51   9.51   9.51   8.83   8.95   8.95   9.05   9.05   9.05   9.05   9.05   9.05   9.05   9.05   9.05   9.05   9.05

#      Molecule1      Molecule2       DISTANCE
LGA    P     109      P     109          3.976
LGA    E     110      E     110          1.309
LGA    R     111      R     111          2.291
LGA    F     112      F     112          2.036
LGA    I     113      I     113          3.804
LGA    F     114      F     114          3.187
LGA    T     115      T     115          3.228
LGA    E     116      E     116          5.303
LGA    D     117      D     117         25.436

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      7    2.80     4.762     4.406     0.241

LGA_LOCAL      RMSD =  2.803  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.050  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  8.116  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.037463 * X  +  -0.204490 * Y  +   0.978152 * Z  +   8.376495
  Y_new =   0.994113 * X  +  -0.107214 * Y  +   0.015661 * Z  + -13.673893
  Z_new =   0.101669 * X  +   0.972980 * Y  +   0.207302 * Z  + -37.884052 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.360876   -1.780717  [ DEG:    77.9724   -102.0276 ]
  Theta =  -0.101845   -3.039748  [ DEG:    -5.8353   -174.1647 ]
  Phi   =   1.608464   -1.533129  [ DEG:    92.1582    -87.8418 ]
 
# 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: T0372TS304_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS304_1-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    7   2.80   4.406     8.12
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS304_1-D1
PFRMAT TS
TARGET T0372
MODEL 1 REFINED
PARENT 1P62_B
ATOM      1  N   PRO   109      21.031  55.252  -5.108  1.00 10.00
ATOM      2  CA  PRO   109      20.214  54.061  -4.719  1.00 10.00
ATOM      3  C   PRO   109      19.969  53.079  -5.880  1.00 10.00
ATOM      4  O   PRO   109      19.811  51.890  -5.666  1.00 10.00
ATOM      5  CB  PRO   109      18.882  54.675  -4.260  1.00 10.00
ATOM      6  CG  PRO   109      18.874  56.149  -4.871  1.00 10.00
ATOM      7  CD  PRO   109      20.301  56.537  -4.919  1.00 10.00
ATOM      8 HA   PRO   109      20.699  53.531  -3.870  1.00 10.00
ATOM      9 HB1  PRO   109      18.839  54.716  -3.150  1.00 10.00
ATOM     10 HB2  PRO   109      18.028  54.086  -4.660  1.00 10.00
ATOM     11 HG1  PRO   109      18.305  56.841  -4.210  1.00 10.00
ATOM     12 HG2  PRO   109      18.439  56.143  -5.896  1.00 10.00
ATOM     13 HD1  PRO   109      20.606  57.018  -3.964  1.00 10.00
ATOM     14 HD2  PRO   109      20.490  57.218  -5.779  1.00 10.00
ATOM     15  N   GLU   110      19.852  53.586  -7.107  1.00 10.00
ATOM     16  CA  GLU   110      19.756  52.709  -8.280  1.00 10.00
ATOM     17  C   GLU   110      20.982  51.829  -8.564  1.00 10.00
ATOM     18  O   GLU   110      20.839  50.763  -9.218  1.00 10.00
ATOM     19  CB  GLU   110      19.193  53.453  -9.532  1.00 10.00
ATOM     20  CG  GLU   110      20.249  54.211 -10.310  1.00 10.00
ATOM     21  CD  GLU   110      20.558  55.600  -9.736  1.00 10.00
ATOM     22  OE1 GLU   110      20.230  55.915  -8.542  1.00 10.00
ATOM     23  OE2 GLU   110      21.209  56.375 -10.478  1.00 10.00
ATOM     24 HN   GLU   110      19.595  54.540  -7.203  1.00 10.00
ATOM     25 HA   GLU   110      18.961  51.973  -8.021  1.00 10.00
ATOM     26 HB1  GLU   110      18.412  54.172  -9.198  1.00 10.00
ATOM     27 HB2  GLU   110      18.722  52.706 -10.208  1.00 10.00
ATOM     28 HG1  GLU   110      21.186  53.612 -10.314  1.00 10.00
ATOM     29 HG2  GLU   110      19.900  54.331 -11.360  1.00 10.00
ATOM     30  N   ARG   111      22.150  52.211  -8.053  1.00 10.00
ATOM     31  CA  ARG   111      23.371  51.453  -8.164  1.00 10.00
ATOM     32  C   ARG   111      23.529  50.435  -7.011  1.00 10.00
ATOM     33  O   ARG   111      24.003  49.331  -7.231  1.00 10.00
ATOM     34  CB  ARG   111      24.611  52.362  -8.231  1.00 10.00
ATOM     35  CG  ARG   111      25.993  51.653  -8.295  1.00 10.00
ATOM     36  CD  ARG   111      26.150  50.675  -9.439  1.00 10.00
ATOM     37  NE  ARG   111      27.416  49.955  -9.430  1.00 10.00
ATOM     38  CZ  ARG   111      27.662  48.815  -8.774  1.00 10.00
ATOM     39 HN   ARG   111      22.157  53.014  -7.467  1.00 10.00
ATOM     40 HA   ARG   111      23.327  50.874  -9.115  1.00 10.00
ATOM     41 HB1  ARG   111      24.514  53.008  -9.132  1.00 10.00
ATOM     42 HB2  ARG   111      24.603  53.020  -7.333  1.00 10.00
ATOM     43 HG1  ARG   111      26.151  51.105  -7.340  1.00 10.00
ATOM     44 HG2  ARG   111      26.783  52.432  -8.389  1.00 10.00
ATOM     45 HD1  ARG   111      26.066  51.234 -10.397  1.00 10.00
ATOM     46 HD2  ARG   111      25.320  49.935  -9.387  1.00 10.00
ATOM     47 HE   ARG   111      28.182  50.382  -9.896  1.00 10.00
ATOM     48  NH1 ARG   111      27.334  47.680  -9.304  1.00 10.00
ATOM     49  NH2 ARG   111      28.222  48.847  -7.608  1.00 10.00
ATOM     50 HH11 ARG   111      26.415  47.584  -9.667  1.00 10.00
ATOM     51 HH12 ARG   111      27.794  46.863  -8.975  1.00 10.00
ATOM     52 HH21 ARG   111      27.634  48.916  -6.810  1.00 10.00
ATOM     53 HH22 ARG   111      29.141  49.217  -7.542  1.00 10.00
ATOM     54  N   PHE   112      23.182  50.860  -5.795  1.00 10.00
ATOM     55  CA  PHE   112      23.615  50.200  -4.560  1.00 10.00
ATOM     56  C   PHE   112      22.494  49.574  -3.687  1.00 10.00
ATOM     57  O   PHE   112      22.839  48.916  -2.711  1.00 10.00
ATOM     58  CB  PHE   112      24.493  51.149  -3.692  1.00 10.00
ATOM     59  CG  PHE   112      25.827  51.529  -4.347  1.00 10.00
ATOM     60 HN   PHE   112      22.725  51.739  -5.721  1.00 10.00
ATOM     61 HA   PHE   112      24.273  49.355  -4.865  1.00 10.00
ATOM     62 HB1  PHE   112      23.918  52.080  -3.493  1.00 10.00
ATOM     63 HB2  PHE   112      24.704  50.648  -2.722  1.00 10.00
ATOM     64  CD1 PHE   112      26.169  52.864  -4.242  1.00 10.00
ATOM     65  CD2 PHE   112      26.782  50.630  -4.796  1.00 10.00
ATOM     66  CE1 PHE   112      27.495  53.182  -4.040  1.00 10.00
ATOM     67  CE2 PHE   112      28.104  51.053  -4.910  1.00 10.00
ATOM     68  CZ  PHE   112      28.433  52.378  -4.655  1.00 10.00
ATOM     69 HD1  PHE   112      25.404  53.636  -4.247  1.00 10.00
ATOM     70 HD2  PHE   112      26.505  49.616  -5.071  1.00 10.00
ATOM     71 HE1  PHE   112      27.786  53.961  -3.337  1.00 10.00
ATOM     72 HE2  PHE   112      28.884  50.351  -5.194  1.00 10.00
ATOM     73 HZ   PHE   112      29.380  52.797  -4.991  1.00 10.00
ATOM     74  N   ILE   113      21.213  49.729  -4.012  1.00 10.00
ATOM     75  CA  ILE   113      20.128  49.239  -3.141  1.00 10.00
ATOM     76  C   ILE   113      20.187  47.723  -3.034  1.00 10.00
ATOM     77  O   ILE   113      20.043  47.233  -1.953  1.00 10.00
ATOM     78  CB  ILE   113      18.751  49.651  -3.656  1.00 10.00
ATOM     79 HN   ILE   113      20.984  50.351  -4.751  1.00 10.00
ATOM     80 HA   ILE   113      20.266  49.670  -2.124  1.00 10.00
ATOM     81 HB   ILE   113      18.404  50.526  -3.064  1.00 10.00
ATOM     82  CG1 ILE   113      17.740  48.533  -3.496  1.00 10.00
ATOM     83 HG11 ILE   113      16.743  48.979  -3.278  1.00 10.00
ATOM     84 HG12 ILE   113      18.040  47.874  -2.651  1.00 10.00
ATOM     85  CG2 ILE   113      18.853  50.067  -5.109  1.00 10.00
ATOM     86 HG21 ILE   113      17.840  50.069  -5.568  1.00 10.00
ATOM     87 HG22 ILE   113      19.511  49.358  -5.658  1.00 10.00
ATOM     88 HG23 ILE   113      19.285  51.092  -5.165  1.00 10.00
ATOM     89  CD1 ILE   113      17.648  47.720  -4.769  1.00 10.00
ATOM     90 HD1  ILE   113      17.936  48.352  -5.638  1.00 10.00
ATOM     91 HD2  ILE   113      16.602  47.363  -4.903  1.00 10.00
ATOM     92 HD3  ILE   113      18.331  46.846  -4.700  1.00 10.00
ATOM     93  N   PHE   114      20.361  47.000  -4.154  1.00 10.00
ATOM     94  CA  PHE   114      20.421  45.504  -4.100  1.00 10.00
ATOM     95  C   PHE   114      21.547  45.028  -3.144  1.00 10.00
ATOM     96  O   PHE   114      21.343  44.134  -2.273  1.00 10.00
ATOM     97  CB  PHE   114      20.620  44.879  -5.471  1.00 10.00
ATOM     98  CG  PHE   114      20.894  43.408  -5.411  1.00 10.00
ATOM     99  CD1 PHE   114      19.853  42.498  -5.383  1.00 10.00
ATOM    100  CD2 PHE   114      22.178  42.938  -5.348  1.00 10.00
ATOM    101  CE1 PHE   114      20.123  41.063  -5.262  1.00 10.00
ATOM    102  CE2 PHE   114      22.439  41.587  -5.275  1.00 10.00
ATOM    103  CZ  PHE   114      21.422  40.666  -5.239  1.00 10.00
ATOM    104 HN   PHE   114      20.685  47.460  -4.971  1.00 10.00
ATOM    105 HA   PHE   114      19.454  45.134  -3.694  1.00 10.00
ATOM    106 HB1  PHE   114      21.475  45.383  -5.972  1.00 10.00
ATOM    107 HB2  PHE   114      19.701  45.048  -6.076  1.00 10.00
ATOM    108 HD1  PHE   114      18.826  42.851  -5.451  1.00 10.00
ATOM    109 HD2  PHE   114      23.005  43.643  -5.357  1.00 10.00
ATOM    110 HE1  PHE   114      19.313  40.341  -5.193  1.00 10.00
ATOM    111 HE2  PHE   114      23.471  41.244  -5.243  1.00 10.00
ATOM    112 HZ   PHE   114      21.659  39.606  -5.193  1.00 10.00
ATOM    113  N   THR   115      22.729  45.628  -3.288  1.00 10.00
ATOM    114  CA  THR   115      23.889  45.193  -2.506  1.00 10.00
ATOM    115  C   THR   115      23.651  45.480  -1.006  1.00 10.00
ATOM    116  O   THR   115      23.929  44.650  -0.141  1.00 10.00
ATOM    117  CB  THR   115      25.128  45.954  -3.007  1.00 10.00
ATOM    118  OG1 THR   115      25.375  45.617  -4.370  1.00 10.00
ATOM    119  CG2 THR   115      26.361  45.636  -2.263  1.00 10.00
ATOM    120 HN   THR   115      22.878  46.202  -4.085  1.00 10.00
ATOM    121 HA   THR   115      24.043  44.101  -2.651  1.00 10.00
ATOM    122 HB   THR   115      24.933  47.047  -2.933  1.00 10.00
ATOM    123 HG1  THR   115      26.374  45.840  -4.514  1.00 10.00
ATOM    124 HG21 THR   115      27.195  45.471  -2.981  1.00 10.00
ATOM    125 HG22 THR   115      26.616  46.483  -1.588  1.00 10.00
ATOM    126 HG23 THR   115      26.203  44.716  -1.659  1.00 10.00
ATOM    127  N   GLU   116      23.180  46.704  -0.737  1.00 10.00
ATOM    128  CA  GLU   116      22.806  47.095   0.609  1.00 10.00
ATOM    129  C   GLU   116      21.759  46.169   1.240  1.00 10.00
ATOM    130  O   GLU   116      21.926  45.639   2.388  1.00 10.00
ATOM    131  CB  GLU   116      22.394  48.611   0.708  1.00 10.00
ATOM    132  CG  GLU   116      21.997  48.992   2.115  1.00 10.00
ATOM    133 HN   GLU   116      22.889  47.278  -1.494  1.00 10.00
ATOM    134 HA   GLU   116      23.720  46.985   1.234  1.00 10.00
ATOM    135 HB1  GLU   116      21.536  48.799   0.025  1.00 10.00
ATOM    136 HB2  GLU   116      23.254  49.242   0.391  1.00 10.00
ATOM    137 HG1  GLU   116      22.407  49.996   2.363  1.00 10.00
ATOM    138 HG2  GLU   116      20.888  49.007   2.201  1.00 10.00
ATOM    139  CD  GLU   116      22.559  47.977   3.048  1.00 10.00
ATOM    140  OE1 GLU   116      23.461  48.322   3.927  1.00 10.00
ATOM    141  OE2 GLU   116      22.155  46.733   2.978  1.00 10.00
ATOM    142  N   ASP   117      11.047  28.620  23.508  1.00 10.00
ATOM    143  CA  ASP   117      11.425  28.987  24.929  1.00 10.00
ATOM    144  C   ASP   117      11.685  30.489  25.113  1.00 10.00
ATOM    145  O   ASP   117      11.110  31.129  25.982  1.00 10.00
ATOM    146  CB  ASP   117      12.685  28.219  25.368  1.00 10.00
ATOM    147  CG  ASP   117      12.475  27.258  26.548  1.00 10.00
ATOM    148 HN   ASP   117      10.454  27.847  23.317  1.00 10.00
ATOM    149 HA   ASP   117      10.587  28.696  25.602  1.00 10.00
ATOM    150 HB1  ASP   117      13.059  27.632  24.500  1.00 10.00
ATOM    151 HB2  ASP   117      13.466  28.959  25.653  1.00 10.00
ATOM    152  OD1 ASP   117      11.669  26.235  26.423  1.00 10.00
ATOM    153  OD2 ASP   117      13.103  27.462  27.677  1.00 10.00
TER
END
