
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0363AL333_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   15 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_5-D1.T0363_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:    13        43 - 55          4.97     5.62
  LONGEST_CONTINUOUS_SEGMENT:    13        44 - 56          4.80     5.61
  LCS_AVERAGE:     27.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        44 - 48          1.83     7.84
  LCS_AVERAGE:      8.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        42 - 44          0.86    17.40
  LONGEST_CONTINUOUS_SEGMENT:     3        44 - 46          0.85    14.90
  LONGEST_CONTINUOUS_SEGMENT:     3        46 - 48          0.49    10.93
  LONGEST_CONTINUOUS_SEGMENT:     3        47 - 49          0.65    10.56
  LONGEST_CONTINUOUS_SEGMENT:     3        48 - 50          0.49    10.35
  LONGEST_CONTINUOUS_SEGMENT:     3        49 - 51          0.37    16.12
  LONGEST_CONTINUOUS_SEGMENT:     3        50 - 52          0.42    12.99
  LONGEST_CONTINUOUS_SEGMENT:     3        51 - 53          0.16    15.84
  LONGEST_CONTINUOUS_SEGMENT:     3        54 - 56          0.11    11.64
  LCS_AVERAGE:      6.52

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:   46
LCS_GDT     I      42     I      42      3    3   10     0    3    3    3    3    3    4    4    5    5    5    5    6    6   12   14   14   15   15   15 
LCS_GDT     T      43     T      43      3    3   13     0    3    3    3    3    4    4    4    5    7    9   11   13   13   14   14   14   15   15   15 
LCS_GDT     Q      44     Q      44      3    5   13     0    3    3    4    6    6    6    6    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     S      45     S      45      3    5   13     0    3    3    4    6    6    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     G      46     G      46      3    5   13     1    3    3    4    6    6    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     I      47     I      47      3    5   13     3    4    4    5    6    6    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     L      48     L      48      3    5   13     0    3    3    5    6    6    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     S      49     S      49      3    3   13     3    3    3    3    3    4    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     Q      50     Q      50      3    4   13     3    3    3    4    4    4    6    6    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     F      51     F      51      3    4   13     3    3    3    4    4    4    5    6    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     P      52     P      52      3    4   13     3    3    3    4    4    4    5    5    7    8   10   11   12   13   14   14   14   15   15   15 
LCS_GDT     E      53     E      53      3    4   13     3    3    3    4    4    4    5    5    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     I      54     I      54      3    3   13     3    4    4    5    5    5    5    5    8    8    9   10   13   13   14   14   14   15   15   15 
LCS_GDT     D      55     D      55      3    3   13     3    4    4    5    5    5    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_GDT     L      56     L      56      3    3   13     3    4    4    5    6    6    6    7    8   10   11   11   13   13   14   14   14   15   15   15 
LCS_AVERAGE  LCS_A:  14.30  (   6.52    8.55   27.83 )

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      6      6      6      7      8     10     11     11     13     13     14     14     14     15     15     15 
GDT PERCENT_CA   6.52   8.70   8.70  10.87  13.04  13.04  13.04  15.22  17.39  21.74  23.91  23.91  28.26  28.26  30.43  30.43  30.43  32.61  32.61  32.61
GDT RMS_LOCAL    0.11   0.52   0.52   1.24   2.05   2.05   2.05   3.01   3.29   3.98   4.14   4.14   4.75   4.75   5.05   5.05   5.05   5.47   5.47   5.47
GDT RMS_ALL_CA  11.64  11.85  11.85  11.15   7.61   7.61   7.61   6.32   6.96   5.65   5.66   5.66   5.54   5.54   5.53   5.53   5.53   5.47   5.47   5.47

#      Molecule1      Molecule2       DISTANCE
LGA    I      42      I      42         10.032
LGA    T      43      T      43         10.049
LGA    Q      44      Q      44          9.054
LGA    S      45      S      45          3.908
LGA    G      46      G      46          3.270
LGA    I      47      I      47          3.235
LGA    L      48      L      48          2.644
LGA    S      49      S      49          3.327
LGA    Q      50      Q      50          9.506
LGA    F      51      F      51          9.198
LGA    P      52      P      52          9.368
LGA    E      53      E      53          9.699
LGA    I      54      I      54          4.036
LGA    D      55      D      55          2.222
LGA    L      56      L      56          3.316

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   46    4.0      7    3.01    16.304    14.657     0.225

LGA_LOCAL      RMSD =  3.006  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.962  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  5.465  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.405517 * X  +   0.854467 * Y  +  -0.324719 * Z  +  44.518440
  Y_new =  -0.871264 * X  +  -0.468766 * Y  +  -0.145457 * Z  +  23.292061
  Z_new =  -0.276506 * X  +   0.223930 * Y  +   0.934559 * Z  +  24.527065 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.235177   -2.906415  [ DEG:    13.4747   -166.5253 ]
  Theta =   0.280156    2.861437  [ DEG:    16.0518    163.9482 ]
  Phi   =  -2.006412    1.135180  [ DEG:  -114.9590     65.0410 ]
 
# 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: T0363AL333_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_5-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   46   4.0    7   3.01  14.657     5.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_5-D1
REMARK Aligment from pdb entry: 1a62
ATOM      5  N   ILE    42      23.557  16.278  14.279  1.00  0.00              
ATOM      6  CA  ILE    42      23.499  16.596  12.870  1.00  0.00              
ATOM      7  C   ILE    42      24.580  15.729  12.217  1.00  0.00              
ATOM      8  O   ILE    42      25.658  15.512  12.793  1.00  0.00              
ATOM      9  N   THR    43      24.280  15.212  11.036  1.00  0.00              
ATOM     10  CA  THR    43      25.212  14.335  10.354  1.00  0.00              
ATOM     11  C   THR    43      25.652  14.862   9.011  1.00  0.00              
ATOM     12  O   THR    43      25.027  15.762   8.437  1.00  0.00              
ATOM     13  N   GLN    44      26.730  14.269   8.506  1.00  0.00              
ATOM     14  CA  GLN    44      27.262  14.640   7.208  1.00  0.00              
ATOM     15  C   GLN    44      28.062  13.475   6.632  1.00  0.00              
ATOM     16  O   GLN    44      28.340  12.498   7.331  1.00  0.00              
ATOM     17  N   SER    45      28.421  13.562   5.359  1.00  0.00              
ATOM     18  CA  SER    45      29.198  12.496   4.751  1.00  0.00              
ATOM     19  C   SER    45      29.915  13.004   3.517  1.00  0.00              
ATOM     20  O   SER    45      29.628  14.086   3.010  1.00  0.00              
ATOM     21  N   GLY    46      30.872  12.228   3.036  1.00  0.00              
ATOM     22  CA  GLY    46      31.596  12.656   1.856  1.00  0.00              
ATOM     23  C   GLY    46      32.829  11.827   1.604  1.00  0.00              
ATOM     24  O   GLY    46      33.130  10.895   2.351  1.00  0.00              
ATOM     25  N   ILE    47      33.536  12.166   0.535  1.00  0.00              
ATOM     26  CA  ILE    47      34.755  11.463   0.172  1.00  0.00              
ATOM     27  C   ILE    47      35.914  12.246   0.747  1.00  0.00              
ATOM     28  O   ILE    47      36.038  13.447   0.526  1.00  0.00              
ATOM     29  N   LEU    48      36.760  11.550   1.491  1.00  0.00              
ATOM     30  CA  LEU    48      37.885  12.193   2.129  1.00  0.00              
ATOM     31  C   LEU    48      39.074  12.408   1.220  1.00  0.00              
ATOM     32  O   LEU    48      39.425  11.544   0.406  1.00  0.00              
ATOM     33  N   SER    49      39.681  13.584   1.355  1.00  0.00              
ATOM     34  CA  SER    49      40.903  13.928   0.638  1.00  0.00              
ATOM     35  C   SER    49      41.800  14.547   1.695  1.00  0.00              
ATOM     36  O   SER    49      41.458  15.567   2.281  1.00  0.00              
ATOM     37  N   GLN    50      42.927  13.907   1.967  1.00  0.00              
ATOM     38  CA  GLN    50      43.879  14.422   2.941  1.00  0.00              
ATOM     39  C   GLN    50      44.821  15.356   2.187  1.00  0.00              
ATOM     40  O   GLN    50      45.430  14.966   1.190  1.00  0.00              
ATOM     41  N   PHE    51      44.932  16.595   2.649  1.00  0.00              
ATOM     42  CA  PHE    51      45.799  17.560   2.000  1.00  0.00              
ATOM     43  C   PHE    51      47.212  17.534   2.566  1.00  0.00              
ATOM     44  O   PHE    51      47.517  16.758   3.470  1.00  0.00              
ATOM     45  N   PRO    52      48.065  18.390   2.017  1.00  0.00              
ATOM     46  CA  PRO    52      49.466  18.483   2.425  1.00  0.00              
ATOM     47  C   PRO    52      49.693  18.635   3.926  1.00  0.00              
ATOM     48  O   PRO    52      50.452  17.869   4.528  1.00  0.00              
ATOM     49  N   GLU    53      49.045  19.626   4.524  1.00  0.00              
ATOM     50  CA  GLU    53      49.198  19.885   5.948  1.00  0.00              
ATOM     51  C   GLU    53      48.842  18.700   6.851  1.00  0.00              
ATOM     52  O   GLU    53      49.146  18.717   8.042  1.00  0.00              
ATOM     53  N   ILE    54      33.413  19.230   4.694  1.00  0.00              
ATOM     54  CA  ILE    54      33.508  18.909   6.118  1.00  0.00              
ATOM     55  C   ILE    54      34.967  18.682   6.505  1.00  0.00              
ATOM     56  O   ILE    54      35.650  17.832   5.940  1.00  0.00              
ATOM     57  N   ASP    55      35.436  19.469   7.467  1.00  0.00              
ATOM     58  CA  ASP    55      36.809  19.377   7.947  1.00  0.00              
ATOM     59  C   ASP    55      37.063  18.120   8.755  1.00  0.00              
ATOM     60  O   ASP    55      36.275  17.774   9.635  1.00  0.00              
ATOM     61  N   LEU    56      38.176  17.447   8.464  1.00  0.00              
ATOM     62  CA  LEU    56      38.574  16.245   9.174  1.00  0.00              
ATOM     63  C   LEU    56      39.966  16.471   9.738  1.00  0.00              
ATOM     64  O   LEU    56      40.897  16.760   8.996  1.00  0.00              
END
