
#######################################################
#                                                     #
#                        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   10 (   88),  selected   10 , name T0378TS186_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   10 , name T0378_D1.pdb
# PARAMETERS: T0378TS186_4-D1.T0378_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:    10        66 - 75          3.52     3.52
  LCS_AVERAGE:     11.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        67 - 71          1.23     5.26
  LONGEST_CONTINUOUS_SEGMENT:     5        71 - 75          0.92     6.68
  LCS_AVERAGE:      5.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        71 - 75          0.92     6.68
  LCS_AVERAGE:      4.94

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:   89
LCS_GDT     L      66     L      66      3    3   10     0    3    3    3    3    5    6    6    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     P      67     P      67      4    5   10     4    4    4    5    6    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     E      68     E      68      4    5   10     4    4    4    5    6    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     S      69     S      69      4    5   10     4    4    4    5    6    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     F      70     F      70      4    5   10     4    4    4    5    6    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     D      71     D      71      5    5   10     3    4    5    5    6    6    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     F      72     F      72      5    5   10     3    4    5    5    5    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     K      73     K      73      5    5   10     3    4    5    5    5    6    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     R      74     R      74      5    5   10     3    4    5    5    6    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     I      75     I      75      5    5   10     3    3    5    5    5    7    8    9    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   7.19  (   4.94    5.39   11.24 )

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      4      5      5      6      7      8      9      9      9      9     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   4.49   4.49   5.62   5.62   6.74   7.87   8.99  10.11  10.11  10.11  10.11  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24
GDT RMS_LOCAL    0.13   0.13   0.92   0.92   1.71   2.06   2.39   2.67   2.67   2.67   2.67   3.52   3.52   3.52   3.52   3.52   3.52   3.52   3.52   3.52
GDT RMS_ALL_CA   5.09   5.09   6.68   6.68   4.43   3.77   3.74   3.80   3.80   3.80   3.80   3.52   3.52   3.52   3.52   3.52   3.52   3.52   3.52   3.52

#      Molecule1      Molecule2       DISTANCE
LGA    L      66      L      66          8.607
LGA    P      67      P      67          1.938
LGA    E      68      E      68          2.338
LGA    S      69      S      69          2.697
LGA    F      70      F      70          1.342
LGA    D      71      D      71          3.850
LGA    F      72      F      72          2.242
LGA    K      73      K      73          3.877
LGA    R      74      R      74          1.557
LGA    I      75      I      75          3.883

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10   89    4.0      9    2.67     7.865     7.592     0.324

LGA_LOCAL      RMSD =  2.674  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.805  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.520  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.802104 * X  +  -0.074864 * Y  +  -0.592473 * Z  +  63.253513
  Y_new =   0.196882 * X  +  -0.903493 * Y  +   0.380707 * Z  +  18.747799
  Z_new =  -0.563796 * X  +  -0.422014 * Y  +  -0.709956 * Z  + 137.145523 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.605284    0.536309  [ DEG:  -149.2718     30.7282 ]
  Theta =   0.598975    2.542617  [ DEG:    34.3188    145.6812 ]
  Phi   =   0.240699   -2.900894  [ DEG:    13.7910   -166.2090 ]
 
# 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: T0378TS186_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS186_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10   89   4.0    9   2.67   7.592     3.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS186_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT 1zjr_A
ATOM      1  N   LEU    66      -7.487  34.638  40.133  1.00  0.00
ATOM      2  CA  LEU    66      -6.336  35.578  40.255  1.00  0.00
ATOM      3  C   LEU    66      -5.317  35.067  41.268  1.00  0.00
ATOM      4  O   LEU    66      -4.112  35.262  41.102  1.00  0.00
ATOM      5  CB  LEU    66      -6.830  36.962  40.687  1.00  0.00
ATOM      6  CG  LEU    66      -7.830  37.661  39.764  1.00  0.00
ATOM      7  CD1 LEU    66      -8.246  38.990  40.376  1.00  0.00
ATOM      8  CD2 LEU    66      -7.205  37.875  38.394  1.00  0.00
ATOM      9  N   PRO    67      -5.809  34.417  42.318  1.00  0.00
ATOM     10  CA  PRO    67      -4.945  33.881  43.362  1.00  0.00
ATOM     11  C   PRO    67      -3.908  32.930  42.774  1.00  0.00
ATOM     12  O   PRO    67      -2.726  32.998  43.112  1.00  0.00
ATOM     13  CB  PRO    67      -5.907  33.150  44.301  1.00  0.00
ATOM     14  CG  PRO    67      -7.196  33.889  44.162  1.00  0.00
ATOM     15  CD  PRO    67      -7.324  34.234  42.705  1.00  0.00
ATOM     16  N   GLU    68      -4.358  32.047  41.891  1.00  0.00
ATOM     17  CA  GLU    68      -3.471  31.079  41.261  1.00  0.00
ATOM     18  C   GLU    68      -2.377  31.789  40.467  1.00  0.00
ATOM     19  O   GLU    68      -1.283  31.252  40.286  1.00  0.00
ATOM     20  CB  GLU    68      -4.254  30.179  40.303  1.00  0.00
ATOM     21  CG  GLU    68      -5.182  29.194  40.996  1.00  0.00
ATOM     22  CD  GLU    68      -6.009  28.385  40.017  1.00  0.00
ATOM     23  OE1 GLU    68      -5.909  28.643  38.800  1.00  0.00
ATOM     24  OE2 GLU    68      -6.758  27.492  40.467  1.00  0.00
ATOM     25  N   SER    69      -2.678  32.997  39.998  1.00  0.00
ATOM     26  CA  SER    69      -1.717  33.786  39.234  1.00  0.00
ATOM     27  C   SER    69      -0.577  34.202  40.155  1.00  0.00
ATOM     28  O   SER    69       0.583  34.258  39.744  1.00  0.00
ATOM     29  CB  SER    69      -2.385  35.037  38.662  1.00  0.00
ATOM     30  OG  SER    69      -3.366  34.695  37.698  1.00  0.00
ATOM     31  N   PHE    70      -0.924  34.495  41.405  1.00  0.00
ATOM     32  CA  PHE    70       0.051  34.916  42.401  1.00  0.00
ATOM     33  C   PHE    70       1.068  33.820  42.698  1.00  0.00
ATOM     34  O   PHE    70       2.269  34.082  42.771  1.00  0.00
ATOM     35  CB  PHE    70      -0.645  35.272  43.716  1.00  0.00
ATOM     36  CG  PHE    70      -1.301  36.624  43.708  1.00  0.00
ATOM     37  CD1 PHE    70      -2.668  36.746  43.528  1.00  0.00
ATOM     38  CD2 PHE    70      -0.549  37.774  43.880  1.00  0.00
ATOM     39  CE1 PHE    70      -3.270  37.990  43.520  1.00  0.00
ATOM     40  CE2 PHE    70      -1.152  39.017  43.872  1.00  0.00
ATOM     41  CZ  PHE    70      -2.507  39.129  43.694  1.00  0.00
ATOM     42  N   ASP    71       0.586  32.593  42.866  1.00  0.00
ATOM     43  CA  ASP    71       1.468  31.469  43.160  1.00  0.00
ATOM     44  C   ASP    71       2.413  31.228  41.985  1.00  0.00
ATOM     45  O   ASP    71       3.601  30.972  42.178  1.00  0.00
ATOM     46  CB  ASP    71       0.653  30.198  43.403  1.00  0.00
ATOM     47  CG  ASP    71      -0.073  30.216  44.734  1.00  0.00
ATOM     48  OD1 ASP    71       0.236  31.094  45.567  1.00  0.00
ATOM     49  OD2 ASP    71      -0.951  29.353  44.944  1.00  0.00
ATOM     50  N   PHE    72       1.883  31.318  40.769  1.00  0.00
ATOM     51  CA  PHE    72       2.691  31.124  39.568  1.00  0.00
ATOM     52  C   PHE    72       3.711  32.247  39.450  1.00  0.00
ATOM     53  O   PHE    72       4.842  32.032  39.008  1.00  0.00
ATOM     54  CB  PHE    72       1.805  31.127  38.320  1.00  0.00
ATOM     55  CG  PHE    72       2.562  30.917  37.040  1.00  0.00
ATOM     56  CD1 PHE    72       2.990  29.653  36.672  1.00  0.00
ATOM     57  CD2 PHE    72       2.846  31.982  36.203  1.00  0.00
ATOM     58  CE1 PHE    72       3.687  29.459  35.494  1.00  0.00
ATOM     59  CE2 PHE    72       3.542  31.788  35.025  1.00  0.00
ATOM     60  CZ  PHE    72       3.962  30.533  34.669  1.00  0.00
ATOM     61  N   LYS    73       3.300  33.446  39.849  1.00  0.00
ATOM     62  CA  LYS    73       4.170  34.612  39.810  1.00  0.00
ATOM     63  C   LYS    73       5.325  34.344  40.767  1.00  0.00
ATOM     64  O   LYS    73       6.492  34.572  40.448  1.00  0.00
ATOM     65  CB  LYS    73       3.402  35.853  40.273  1.00  0.00
ATOM     66  CG  LYS    73       4.165  37.162  40.142  1.00  0.00
ATOM     67  CD  LYS    73       3.965  37.797  38.770  1.00  0.00
ATOM     68  CE  LYS    73       2.508  38.189  38.541  1.00  0.00
ATOM     69  NZ  LYS    73       2.301  38.873  37.232  1.00  0.00
ATOM     70  N   ARG    74       4.979  33.844  41.947  1.00  0.00
ATOM     71  CA  ARG    74       5.966  33.541  42.969  1.00  0.00
ATOM     72  C   ARG    74       6.849  32.381  42.524  1.00  0.00
ATOM     73  O   ARG    74       8.051  32.365  42.790  1.00  0.00
ATOM     74  CB  ARG    74       5.249  33.203  44.280  1.00  0.00
ATOM     75  CG  ARG    74       6.123  33.278  45.516  1.00  0.00
ATOM     76  CD  ARG    74       5.266  33.511  46.748  1.00  0.00
ATOM     77  NE  ARG    74       4.462  34.723  46.599  1.00  0.00
ATOM     78  CZ  ARG    74       3.605  35.177  47.509  1.00  0.00
ATOM     79  NH1 ARG    74       3.429  34.520  48.648  1.00  0.00
ATOM     80  NH2 ARG    74       2.924  36.291  47.277  1.00  0.00
ATOM     81  N   ILE    75       6.247  31.417  41.836  1.00  0.00
ATOM     82  CA  ILE    75       6.973  30.252  41.349  1.00  0.00
ATOM     83  C   ILE    75       8.034  30.730  40.360  1.00  0.00
ATOM     84  O   ILE    75       9.160  30.243  40.350  1.00  0.00
ATOM     85  CB  ILE    75       6.035  29.258  40.639  1.00  0.00
ATOM     86  CG1 ILE    75       5.070  28.625  41.644  1.00  0.00
ATOM     87  CG2 ILE    75       6.837  28.148  39.977  1.00  0.00
ATOM     88  CD1 ILE    75       3.946  27.842  41.002  1.00  0.00
TER
END
