
#######################################################
#                                                     #
#                        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   43 (   43),  selected   43 , name T0319TS464_4_2
# Molecule2: number of CA atoms  135 ( 1055),  selected   43 , name T0319.pdb
# PARAMETERS: T0319TS464_4_2.T0319.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:    25        57 - 99          4.74    18.91
  LCS_AVERAGE:     13.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        57 - 72          1.61    17.26
  LCS_AVERAGE:      8.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        57 - 69          0.86    16.95
  LCS_AVERAGE:      6.39

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:  135
LCS_GDT     P      57     P      57     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     A      58     A      58     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     V      59     V      59     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     L      60     L      60     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     T      61     T      61     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     V      62     V      62     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     A      63     A      63     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     A      64     A      64     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     E      65     E      65     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     L      66     L      66     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     G      67     G      67     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     N      68     N      68     13   16   25     9   12   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     N      69     N      69     13   16   25     3    5   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     A      70     A      70      3   16   25     3    3    5    7    9   10   16   16   16   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     L      71     L      71      3   16   25     3    3   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     P      72     P      72      3   16   25     0    5   13   15   15   15   16   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     A      91     A      91     11   12   25     9   10   11   11   12   12   13   13   14   14   15   18   20   22   24   24   26   28   28   28 
LCS_GDT     I      92     I      92     11   12   25     9   10   11   11   12   12   13   13   16   18   20   21   23   25   26   27   27   28   28   28 
LCS_GDT     L      93     L      93     11   12   25     9   10   11   11   12   12   13   13   14   14   17   20   23   25   26   27   27   28   28   28 
LCS_GDT     N      94     N      94     11   12   25     9   10   11   11   12   12   13   13   14   16   20   21   23   24   26   27   27   28   28   28 
LCS_GDT     D      95     D      95     11   12   25     9   10   11   11   12   12   13   13   16   19   20   21   23   25   26   27   27   28   28   28 
LCS_GDT     L      96     L      96     11   12   25     9   10   11   11   12   12   15   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     H      97     H      97     11   12   25     9   10   11   11   12   12   13   13   14   19   21   21   23   25   26   27   27   28   28   28 
LCS_GDT     T      98     T      98     11   12   25     9   10   11   11   12   12   14   17   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     L      99     L      99     11   12   25     9   10   11   11   12   12   13   14   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     L     100     L     100     11   12   18     4   10   11   11   12   12   13   13   16   19   21   22   23   23   25   27   27   28   28   28 
LCS_GDT     L     101     L     101     11   12   18     4    6   11   11   12   12   13   14   16   19   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     Q     102     Q     102      4   12   18     0    4    4    8   12   12   13   16   17   20   21   22   23   25   26   27   27   28   28   28 
LCS_GDT     R     113     R     113      3    4   15     0    3    3    3    4    4    4    5    7    8   10   11   13   14   16   17   18   18   19   21 
LCS_GDT     N     114     N     114      4    7    8     3    3    4    5    6    7    7    7    7    9   10   12   13   14   16   17   18   18   19   21 
LCS_GDT     C     115     C     115      4    7    8     3    3    4    4    6    7    7    7    7    9   10   12   13   14   16   17   18   18   19   21 
LCS_GDT     G     116     G     116      5    7    8     3    4    5    5    6    7    7    7    7    9   10   12   13   14   16   17   18   18   19   21 
LCS_GDT     H     117     H     117      5    7    8     4    4    5    5    6    7    7    7    7    9   10   12   13   14   16   17   17   18   19   21 
LCS_GDT     I     118     I     118      5    7    8     4    4    5    5    6    7    7    7    7    8   10   12   13   14   16   17   17   18   19   21 
LCS_GDT     Y     119     Y     119      5    7    8     4    4    5    5    6    7    7    7    8    9   10   12   13   14   16   17   17   18   19   21 
LCS_GDT     Y     120     Y     120      5    7    8     4    4    5    5    6    7    7    7    8    9   10   12   13   14   16   17   17   18   19   20 
LCS_GDT     P     126     P     126      3    4    7     1    4    4    4    5    7    9   11   13   14   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     N     127     N     127      4    6    7     3    3    5    6    6    6    7    9   13   14   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     L     128     L     128      5    6    7     3    5    5    6    6    6    7    9   13   14   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     L     129     L     129      5    6    7     3    5    5    6    6    6    7    7   10   11   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     L     130     L     130      5    6    7     3    5    5    6    6    6    7    7    8    9   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     P     131     P     131      5    6    7     3    5    5    6    6    6    7    9   10   11   14   16   17   17   18   18   18   18   19   21 
LCS_GDT     P     132     P     132      5    6    7     3    5    5    6    6    6    7    7    8    9    9   16   17   17   18   18   18   18   19   21 
LCS_AVERAGE  LCS_A:   9.55  (   6.39    8.49   13.76 )

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      9     12     13     15     15     15     16     17     17     20     21     22     23     25     26     27     27     28     28     28 
GDT PERCENT_CA   6.67   8.89   9.63  11.11  11.11  11.11  11.85  12.59  12.59  14.81  15.56  16.30  17.04  18.52  19.26  20.00  20.00  20.74  20.74  20.74
GDT RMS_LOCAL    0.18   0.44   0.69   1.09   1.09   1.09   1.61   2.18   2.18   3.07   3.41   3.62   3.79   4.54   4.79   4.98   4.98   5.41   5.41   5.41
GDT RMS_ALL_CA  20.22  16.68  16.85  17.13  17.13  17.13  17.26  17.60  17.60  17.37  17.39  17.35  17.52  18.20  18.38  18.29  18.29  18.44  18.44  18.44

#      Molecule1      Molecule2       DISTANCE
LGA    P      57      P      57          3.587
LGA    A      58      A      58          2.571
LGA    V      59      V      59          3.520
LGA    L      60      L      60          2.399
LGA    T      61      T      61          0.468
LGA    V      62      V      62          2.627
LGA    A      63      A      63          1.775
LGA    A      64      A      64          1.284
LGA    E      65      E      65          3.473
LGA    L      66      L      66          3.770
LGA    G      67      G      67          2.258
LGA    N      68      N      68          0.602
LGA    N      69      N      69          1.713
LGA    A      70      A      70          5.012
LGA    L      71      L      71          3.398
LGA    P      72      P      72          2.455
LGA    A      91      A      91         16.757
LGA    I      92      I      92         10.300
LGA    L      93      L      93         10.504
LGA    N      94      N      94         11.553
LGA    D      95      D      95          7.626
LGA    L      96      L      96          2.631
LGA    H      97      H      97          5.930
LGA    T      98      T      98          3.496
LGA    L      99      L      99          5.007
LGA    L     100      L     100          7.794
LGA    L     101      L     101          7.306
LGA    Q     102      Q     102          5.774
LGA    R     113      R     113         32.815
LGA    N     114      N     114         33.072
LGA    C     115      C     115         32.080
LGA    G     116      G     116         30.939
LGA    H     117      H     117         29.049
LGA    I     118      I     118         26.431
LGA    Y     119      Y     119         27.810
LGA    Y     120      Y     120         27.629
LGA    P     126      P     126         27.389
LGA    N     127      N     127         31.399
LGA    L     128      L     128         28.331
LGA    L     129      L     129         29.078
LGA    L     130      L     130         23.020
LGA    P     131      P     131         24.281
LGA    P     132      P     132         26.397

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   43  135    4.0     17    2.18    13.148    11.837     0.746

LGA_LOCAL      RMSD =  2.180  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.705  Number of atoms =   43 
Std_ALL_ATOMS  RMSD = 12.910  (standard rmsd on all 43 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.353566 * X  +   0.655982 * Y  +   0.666842 * Z  + -66.058060
  Y_new =  -0.842568 * X  +   0.532977 * Y  +  -0.077560 * Z  +  22.227747
  Z_new =  -0.406290 * X  +  -0.534437 * Y  +   0.741152 * Z  + -22.291109 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.624740    2.516852  [ DEG:   -35.7950    144.2050 ]
  Theta =   0.418390    2.723203  [ DEG:    23.9720    156.0280 ]
  Phi   =  -1.173484    1.968109  [ DEG:   -67.2357    112.7643 ]
 
# 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: T0319TS464_4_2                                
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319TS464_4_2.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   43  135   4.0   17   2.18  11.837    12.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0319
PARENT N/A
ATOM      1  CA  PRO    57      16.591  -6.374   0.898  1.00  0.00
ATOM      2  CA  ALA    58      15.628  -5.480   4.455  1.00  0.00
ATOM      3  CA  VAL    59      19.443  -5.326   4.520  1.00  0.00
ATOM      4  CA  LEU    60      19.592  -3.106   1.468  1.00  0.00
ATOM      5  CA  THR    61      17.187  -0.650   3.126  1.00  0.00
ATOM      6  CA  VAL    62      19.011  -0.839   6.464  1.00  0.00
ATOM      7  CA  ALA    63      22.334  -0.040   4.859  1.00  0.00
ATOM      8  CA  ALA    64      21.094   2.769   2.668  1.00  0.00
ATOM      9  CA  GLU    65      19.415   4.281   5.728  1.00  0.00
ATOM     10  CA  LEU    66      22.864   4.537   7.388  1.00  0.00
ATOM     11  CA  GLY    67      24.003   6.188   4.195  1.00  0.00
ATOM     12  CA  ASN    68      25.953   3.078   3.286  1.00  0.00
ATOM     13  CA  ASN    69      25.290   0.114   0.983  1.00  0.00
ATOM     14  CA  ALA    70      24.721  -3.683   1.020  1.00  0.00
ATOM     15  CA  LEU    71      28.051  -4.360  -0.709  1.00  0.00
ATOM     16  CA  PRO    72      27.182  -8.063  -1.079  1.00  0.00
ATOM     17  CA  ALA    91      21.929  -5.878  15.888  1.00  0.00
ATOM     18  CA  ILE    92      24.589  -6.454  13.237  1.00  0.00
ATOM     19  CA  LEU    93      23.355  -3.325  11.427  1.00  0.00
ATOM     20  CA  ASN    94      23.565  -1.398  14.710  1.00  0.00
ATOM     21  CA  ASP    95      27.152  -2.659  15.199  1.00  0.00
ATOM     22  CA  LEU    96      28.122  -1.480  11.702  1.00  0.00
ATOM     23  CA  HIS    97      26.654   1.915  12.636  1.00  0.00
ATOM     24  CA  THR    98      28.739   1.927  15.839  1.00  0.00
ATOM     25  CA  LEU    99      31.881   1.290  13.784  1.00  0.00
ATOM     26  CA  LEU   100      31.033   3.988  11.262  1.00  0.00
ATOM     27  CA  LEU   101      30.444   6.390  14.182  1.00  0.00
ATOM     28  CA  GLN   102      34.082   5.836  15.244  1.00  0.00
ATOM     29  CA  ARG   113      37.677   5.692   9.771  1.00  0.00
ATOM     30  CA  ASN   114      34.687   5.108   7.510  1.00  0.00
ATOM     31  CA  CYS   115      32.097   2.391   6.776  1.00  0.00
ATOM     32  CA  GLY   116      32.736   0.692   3.406  1.00  0.00
ATOM     33  CA  HIS   117      29.512  -1.294   3.627  1.00  0.00
ATOM     34  CA  ILE   118      27.257  -3.931   5.225  1.00  0.00
ATOM     35  CA  TYR   119      27.551  -7.635   4.318  1.00  0.00
ATOM     36  CA  TYR   120      24.483  -9.865   4.699  1.00  0.00
ATOM     37  CA  PRO   126      36.562   0.786   8.138  1.00  0.00
ATOM     38  CA  ASN   127      35.241  -2.786   7.763  1.00  0.00
ATOM     39  CA  LEU   128      32.264  -4.487   9.417  1.00  0.00
ATOM     40  CA  LEU   129      31.171  -8.097   8.953  1.00  0.00
ATOM     41  CA  LEU   130      27.438  -8.527   9.457  1.00  0.00
ATOM     42  CA  PRO   131      27.985 -12.253   9.023  1.00  0.00
ATOM     43  CA  PRO   132      25.991 -14.681   6.862  1.00  0.00
TER
END
