
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0300AL381_3
# Molecule2: number of CA atoms   89 (  695),  selected   21 , name T0300
# PARAMETERS: T0300AL381_3.T0300  -3  -ie  -d:4  -o1  -sda  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        57 - 77          1.10     1.10
  LCS_AVERAGE:     23.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        57 - 77          1.10     1.10
  LCS_AVERAGE:     23.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        58 - 77          0.98     1.13
  LCS_AVERAGE:     22.31

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     S      57     S      57     17   21   21     7   13   14   19   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     R      58     R      58     20   21   21     7   13   18   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      59     A      59     20   21   21     7   14   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L      60     L      60     20   21   21     7   14   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G      61     G      61     20   21   21     7   14   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      62     A      62     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     V      63     V      63     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      64     A      64     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     M      65     M      65     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     R      66     R      66     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     K      67     K      67     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     I      68     I      68     20   21   21     5   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     E      69     E      69     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      70     A      70     20   21   21     7   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     K      71     K      71     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     V      72     V      72     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     R      73     R      73     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     S      74     S      74     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     R      75     R      75     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      76     A      76     20   21   21     6   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      77     A      77     20   21   21     8   15   19   20   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:  23.17  (  22.31   23.60   23.60 )

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     15     19     20     21     21     21     21     21     21     21     21     21     21     21     21     21     21     21     21 
GDT PERCENT_CA   8.99  16.85  21.35  22.47  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60  23.60
GDT RMS_LOCAL    0.33   0.59   0.88   0.98   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10
GDT RMS_ALL_CA   1.34   1.83   1.22   1.13   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10

#      Molecule1      Molecule2       DISTANCE
LGA    S      57      S      57          2.306
LGA    R      58      R      58          1.366
LGA    A      59      A      59          0.869
LGA    L      60      L      60          0.599
LGA    G      61      G      61          0.391
LGA    A      62      A      62          0.899
LGA    V      63      V      63          0.422
LGA    A      64      A      64          1.035
LGA    M      65      M      65          1.675
LGA    R      66      R      66          1.200
LGA    K      67      K      67          1.002
LGA    I      68      I      68          1.353
LGA    E      69      E      69          1.538
LGA    A      70      A      70          0.574
LGA    K      71      K      71          0.511
LGA    V      72      V      72          0.412
LGA    R      73      R      73          0.241
LGA    S      74      S      74          1.023
LGA    R      75      R      75          0.995
LGA    A      76      A      76          1.292
LGA    A      77      A      77          1.056

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   89    4.0     21    1.10    21.629    22.817     1.744

LGA_LOCAL      RMSD =  1.104  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.104  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  1.104  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.271634 * X  +   0.804301 * Y  +  -0.528503 * Z  +  70.533028
  Y_new =  -0.245184 * X  +  -0.473196 * Y  +  -0.846150 * Z  +  45.273132
  Z_new =  -0.930645 * X  +   0.359423 * Y  +   0.068666 * Z  +  63.925026 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.382027   -1.759566  [ DEG:    79.1843   -100.8157 ]
  Theta =   1.196171    1.945421  [ DEG:    68.5356    111.4644 ]
  Phi   =  -0.734265    2.407328  [ DEG:   -42.0703    137.9297 ]
 
# 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: T0300AL381_3                                  
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300AL381_3.T0300 -3 -ie -d:4 -o1 -sda 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   89   4.0   21   1.10  22.817     1.10
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL381_3
REMARK Aligment from pdb entry: 1cs4A
ATOM      1  N   SER    57      43.383 -13.356  -4.843  1.00  0.00              
ATOM      2  CA  SER    57      43.140 -11.963  -5.206  1.00  0.00              
ATOM      3  C   SER    57      42.520 -11.187  -4.041  1.00  0.00              
ATOM      4  O   SER    57      41.896 -11.779  -3.162  1.00  0.00              
ATOM      5  N   ARG    58      42.707  -9.869  -4.026  1.00  0.00              
ATOM      6  CA  ARG    58      42.167  -9.027  -2.957  1.00  0.00              
ATOM      7  C   ARG    58      40.641  -9.078  -2.881  1.00  0.00              
ATOM      8  O   ARG    58      40.056  -8.865  -1.820  1.00  0.00              
ATOM      9  N   ALA    59      40.009  -9.366  -4.016  1.00  0.00              
ATOM     10  CA  ALA    59      38.554  -9.465  -4.120  1.00  0.00              
ATOM     11  C   ALA    59      38.060 -10.706  -3.375  1.00  0.00              
ATOM     12  O   ALA    59      37.219 -10.607  -2.487  1.00  0.00              
ATOM     13  N   LEU    60      38.622 -11.862  -3.725  1.00  0.00              
ATOM     14  CA  LEU    60      38.273 -13.151  -3.121  1.00  0.00              
ATOM     15  C   LEU    60      38.458 -13.169  -1.602  1.00  0.00              
ATOM     16  O   LEU    60      37.616 -13.704  -0.880  1.00  0.00              
ATOM     17  N   GLY    61      39.561 -12.582  -1.133  1.00  0.00              
ATOM     18  CA  GLY    61      39.886 -12.516   0.295  1.00  0.00              
ATOM     19  C   GLY    61      38.795 -11.829   1.108  1.00  0.00              
ATOM     20  O   GLY    61      38.380 -12.331   2.154  1.00  0.00              
ATOM     21  N   ALA    62      38.346 -10.674   0.625  1.00  0.00              
ATOM     22  CA  ALA    62      37.314  -9.908   1.306  1.00  0.00              
ATOM     23  C   ALA    62      35.968 -10.634   1.323  1.00  0.00              
ATOM     24  O   ALA    62      35.186 -10.479   2.259  1.00  0.00              
ATOM     25  N   VAL    63      35.707 -11.444   0.301  1.00  0.00              
ATOM     26  CA  VAL    63      34.460 -12.203   0.245  1.00  0.00              
ATOM     27  C   VAL    63      34.496 -13.275   1.335  1.00  0.00              
ATOM     28  O   VAL    63      33.510 -13.483   2.044  1.00  0.00              
ATOM     29  N   ALA    64      35.653 -13.921   1.480  1.00  0.00              
ATOM     30  CA  ALA    64      35.860 -14.971   2.479  1.00  0.00              
ATOM     31  C   ALA    64      35.774 -14.414   3.898  1.00  0.00              
ATOM     32  O   ALA    64      35.263 -15.071   4.803  1.00  0.00              
ATOM     33  N   MET    65      36.291 -13.203   4.082  1.00  0.00              
ATOM     34  CA  MET    65      36.278 -12.536   5.381  1.00  0.00              
ATOM     35  C   MET    65      34.892 -12.003   5.737  1.00  0.00              
ATOM     36  O   MET    65      34.470 -12.101   6.888  1.00  0.00              
ATOM     37  N   ARG    66      34.197 -11.430   4.755  1.00  0.00              
ATOM     38  CA  ARG    66      32.860 -10.879   4.974  1.00  0.00              
ATOM     39  C   ARG    66      31.865 -11.992   5.264  1.00  0.00              
ATOM     40  O   ARG    66      30.938 -11.816   6.048  1.00  0.00              
ATOM     41  N   LYS    67      32.062 -13.134   4.616  1.00  0.00              
ATOM     42  CA  LYS    67      31.200 -14.286   4.816  1.00  0.00              
ATOM     43  C   LYS    67      31.385 -14.771   6.252  1.00  0.00              
ATOM     44  O   LYS    67      30.422 -15.070   6.956  1.00  0.00              
ATOM     45  N   ILE    68      32.636 -14.761   6.696  1.00  0.00              
ATOM     46  CA  ILE    68      33.003 -15.201   8.032  1.00  0.00              
ATOM     47  C   ILE    68      32.594 -14.238   9.153  1.00  0.00              
ATOM     48  O   ILE    68      31.935 -14.646  10.110  1.00  0.00              
ATOM     49  N   GLU    69      32.967 -12.965   9.030  1.00  0.00              
ATOM     50  CA  GLU    69      32.657 -11.976  10.066  1.00  0.00              
ATOM     51  C   GLU    69      31.189 -11.567  10.197  1.00  0.00              
ATOM     52  O   GLU    69      30.780 -11.047  11.236  1.00  0.00              
ATOM     53  N   ALA    70      30.405 -11.770   9.140  1.00  0.00              
ATOM     54  CA  ALA    70      28.982 -11.440   9.185  1.00  0.00              
ATOM     55  C   ALA    70      28.311 -12.436  10.135  1.00  0.00              
ATOM     56  O   ALA    70      27.525 -12.048  11.010  1.00  0.00              
ATOM     57  N   LYS    71      28.664 -13.711   9.973  1.00  0.00              
ATOM     58  CA  LYS    71      28.146 -14.777  10.818  1.00  0.00              
ATOM     59  C   LYS    71      28.563 -14.539  12.270  1.00  0.00              
ATOM     60  O   LYS    71      27.741 -14.653  13.181  1.00  0.00              
ATOM     61  N   VAL    72      29.834 -14.202  12.484  1.00  0.00              
ATOM     62  CA  VAL    72      30.334 -13.939  13.831  1.00  0.00              
ATOM     63  C   VAL    72      29.529 -12.820  14.495  1.00  0.00              
ATOM     64  O   VAL    72      29.159 -12.915  15.673  1.00  0.00              
ATOM     65  N   ARG    73      29.256 -11.761  13.735  1.00  0.00              
ATOM     66  CA  ARG    73      28.505 -10.626  14.262  1.00  0.00              
ATOM     67  C   ARG    73      27.083 -10.999  14.696  1.00  0.00              
ATOM     68  O   ARG    73      26.552 -10.417  15.644  1.00  0.00              
ATOM     69  N   SER    74      26.486 -11.984  14.020  1.00  0.00              
ATOM     70  CA  SER    74      25.135 -12.455  14.345  1.00  0.00              
ATOM     71  C   SER    74      25.197 -13.374  15.573  1.00  0.00              
ATOM     72  O   SER    74      24.353 -13.289  16.469  1.00  0.00              
ATOM     73  N   ARG    75      26.218 -14.230  15.611  1.00  0.00              
ATOM     74  CA  ARG    75      26.434 -15.153  16.727  1.00  0.00              
ATOM     75  C   ARG    75      26.736 -14.370  17.997  1.00  0.00              
ATOM     76  O   ARG    75      26.508 -14.857  19.100  1.00  0.00              
ATOM     77  N   ALA    76      27.277 -13.165  17.835  1.00  0.00              
ATOM     78  CA  ALA    76      27.615 -12.309  18.966  1.00  0.00              
ATOM     79  C   ALA    76      26.361 -11.796  19.649  1.00  0.00              
ATOM     80  O   ALA    76      26.326 -11.667  20.871  1.00  0.00              
ATOM     81  N   ALA    77      25.337 -11.500  18.851  1.00  0.00              
ATOM     82  CA  ALA    77      24.060 -11.006  19.367  1.00  0.00              
ATOM     83  C   ALA    77      23.315 -12.112  20.114  1.00  0.00              
ATOM     84  O   ALA    77      22.680 -11.857  21.142  1.00  0.00              
END
   74      24.353 -13.289  16.469  1.00  0.00              
ATOM     73  N   ARG    75      26.218 -14.230  15.611  1.00  0.00              
ATOM     74  CA  ARG    75      26.434 -15.153  16.727  1.00  0.00              
ATOM     75  C   ARG    75      26.736 -14.370  17.997  1.00  0.00              
ATOM     76  O   ARG    75      26.508 -14.857  19.100  1.00  0.00              
ATOM     77  N   ALA    76      27.277 -13.165  17.835  1.00  0.00              
ATOM     78  CA  ALA    76      27.615 -12.309  18.966  1.00  0.00              
ATOM     79  C   ALA    76      26.361 -11.796  19.649  1.00  0.00              
ATOM     80  O   ALA    76      26.326 -11.667  20.871  1.00  0.00              
ATOM     81  N   ALA    77      25.337 -11.500  18.851  1.00  0.00              
ATOM     82  CA  ALA    77      24.060 -11.006  19.367  1.00  0.00              
ATOM     83  C   ALA    77      23.315 -12.112  20.114  1.00  0.00              
ATOM     84  O   ALA    77      22.680 -11.857  21.142  1.00  0.00              
END
