
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0304AL586_1
# Molecule2: number of CA atoms  107 (  848),  selected   12 , name T0304.pdb
# PARAMETERS: T0304AL586_1.T0304.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       112 - 121         4.14     7.66
  LCS_AVERAGE:      9.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       114 - 121         1.98     9.52
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       110 - 114         0.70    15.60
  LONGEST_CONTINUOUS_SEGMENT:     5       115 - 119         0.43    11.28
  LCS_AVERAGE:      4.36

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:  107
LCS_GDT     V     110     V     110      5    6    9     3    5    5    5    6    6    6    6    7    8    8    8    8    8    8    9    9    9   10   10 
LCS_GDT     Y     111     Y     111      5    6    9     3    5    5    5    6    6    6    7    7    8    8    8    8    9    9   10   10   11   11   11 
LCS_GDT     L     112     L     112      5    6   10     3    5    5    5    6    6    6    7    7    8    8    8    8    9    9   10   10   11   11   11 
LCS_GDT     A     113     A     113      5    6   10     3    5    5    5    6    6    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     V     114     V     114      5    8   10     3    5    5    5    6    6    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     Y     115     Y     115      5    8   10     3    5    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     P     116     P     116      5    8   10     4    5    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     T     117     T     117      5    8   10     4    5    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     P     118     P     118      5    8   10     4    5    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     E     119     E     119      5    8   10     4    5    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     M     120     M     120      3    8   10     3    3    5    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_GDT     K     121     K     121      3    8   10     0    3    6    7    7    7    9    9    9    9    9    9    9    9    9   10   10   11   11   11 
LCS_AVERAGE  LCS_A:   6.80  (   4.36    6.85    9.19 )

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      5      6      7      7      7      9      9      9      9      9      9      9      9      9     10     10     11     11     11 
GDT PERCENT_CA   3.74   4.67   5.61   6.54   6.54   6.54   8.41   8.41   8.41   8.41   8.41   8.41   8.41   8.41   8.41   9.35   9.35  10.28  10.28  10.28
GDT RMS_LOCAL    0.21   0.43   0.85   1.21   1.21   1.21   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   4.14   4.14   5.25   5.25   5.25
GDT RMS_ALL_CA  11.88  11.28  10.41  10.19  10.19  10.19   8.66   8.66   8.66   8.66   8.66   8.66   8.66   8.66   8.66   7.66   7.66   6.88   6.88   6.88

#      Molecule1      Molecule2       DISTANCE
LGA    V     110      V     110         19.198
LGA    Y     111      Y     111         12.824
LGA    L     112      L     112          9.806
LGA    A     113      A     113          3.025
LGA    V     114      V     114          2.425
LGA    Y     115      Y     115          2.711
LGA    P     116      P     116          1.852
LGA    T     117      T     117          2.649
LGA    P     118      P     118          3.444
LGA    E     119      E     119          2.835
LGA    M     120      M     120          3.491
LGA    K     121      K     121          3.172

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  107    4.0      9    2.54     7.243     7.202     0.341

LGA_LOCAL      RMSD =  2.537  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.660  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  6.508  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.712250 * X  +   0.651098 * Y  +  -0.262244 * Z  +  44.293869
  Y_new =   0.545496 * X  +  -0.278316 * Y  +   0.790553 * Z  +  36.397247
  Z_new =   0.441741 * X  +  -0.706124 * Y  +  -0.553402 * Z  +  38.446781 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.235529    0.906063  [ DEG:  -128.0864     51.9136 ]
  Theta =  -0.457538   -2.684055  [ DEG:   -26.2150   -153.7850 ]
  Phi   =   0.653585   -2.488008  [ DEG:    37.4477   -142.5523 ]
 
# 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: T0304AL586_1                                  
REMARK     2: T0304.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304AL586_1.T0304.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  107   4.0    9   2.54   7.202     6.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL586_1
REMARK Aligment from pdb entry: 1fmb
ATOM      1  N   VAL   110      36.190  36.857  34.111  1.00  0.00              
ATOM      2  CA  VAL   110      36.215  35.375  34.260  1.00  0.00              
ATOM      3  C   VAL   110      37.620  34.991  34.733  1.00  0.00              
ATOM      4  O   VAL   110      38.577  35.738  34.611  1.00  0.00              
ATOM      5  N   TYR   111      37.648  33.810  35.294  1.00  0.00              
ATOM      6  CA  TYR   111      38.836  33.238  35.906  1.00  0.00              
ATOM      7  C   TYR   111      39.285  31.993  35.182  1.00  0.00              
ATOM      8  O   TYR   111      38.480  31.127  34.940  1.00  0.00              
ATOM      9  N   LEU   112      40.582  31.908  34.875  1.00  0.00              
ATOM     10  CA  LEU   112      41.141  30.729  34.225  1.00  0.00              
ATOM     11  C   LEU   112      42.023  30.093  35.292  1.00  0.00              
ATOM     12  O   LEU   112      42.964  30.735  35.766  1.00  0.00              
ATOM     13  N   ALA   113      41.734  28.881  35.632  1.00  0.00              
ATOM     14  CA  ALA   113      42.388  28.076  36.658  1.00  0.00              
ATOM     15  C   ALA   113      43.561  27.252  36.122  1.00  0.00              
ATOM     16  O   ALA   113      44.176  26.469  36.866  1.00  0.00              
ATOM     17  N   VAL   114      43.798  27.430  34.806  1.00  0.00              
ATOM     18  CA  VAL   114      44.952  26.805  34.150  1.00  0.00              
ATOM     19  C   VAL   114      44.996  25.320  33.990  1.00  0.00              
ATOM     20  O   VAL   114      45.990  24.759  33.513  1.00  0.00              
ATOM     21  N   TYR   115      43.845  24.634  34.174  1.00  0.00              
ATOM     22  CA  TYR   115      43.698  23.224  33.837  1.00  0.00              
ATOM     23  C   TYR   115      43.788  23.070  32.301  1.00  0.00              
ATOM     24  O   TYR   115      44.234  22.022  31.834  1.00  0.00              
ATOM     25  N   PRO   116      43.365  24.101  31.594  1.00  0.00              
ATOM     26  CA  PRO   116      43.462  24.072  30.119  1.00  0.00              
ATOM     27  C   PRO   116      44.175  25.323  29.658  1.00  0.00              
ATOM     28  O   PRO   116      44.438  26.273  30.453  1.00  0.00              
ATOM     29  N   THR   117      44.641  25.378  28.376  1.00  0.00              
ATOM     30  CA  THR   117      45.336  26.647  28.032  1.00  0.00              
ATOM     31  C   THR   117      44.272  27.754  28.118  1.00  0.00              
ATOM     32  O   THR   117      43.134  27.496  27.659  1.00  0.00              
ATOM     33  N   PRO   118      44.628  28.913  28.596  1.00  0.00              
ATOM     34  CA  PRO   118      43.674  30.026  28.753  1.00  0.00              
ATOM     35  C   PRO   118      43.512  30.729  27.398  1.00  0.00              
ATOM     36  O   PRO   118      44.283  31.567  26.904  1.00  0.00              
ATOM     37  N   GLU   119      42.408  30.344  26.734  1.00  0.00              
ATOM     38  CA  GLU   119      42.082  30.911  25.432  1.00  0.00              
ATOM     39  C   GLU   119      40.749  31.679  25.483  1.00  0.00              
ATOM     40  O   GLU   119      39.899  31.318  26.297  1.00  0.00              
ATOM     41  N   MET   120      40.673  32.664  24.571  1.00  0.00              
ATOM     42  CA  MET   120      39.398  33.404  24.520  1.00  0.00              
ATOM     43  C   MET   120      39.218  33.903  23.096  1.00  0.00              
ATOM     44  O   MET   120      40.178  33.883  22.315  1.00  0.00              
ATOM     45  N   LYS   121      37.978  34.264  22.760  1.00  0.00              
ATOM     46  CA  LYS   121      37.705  34.823  21.441  1.00  0.00              
ATOM     47  C   LYS   121      37.749  36.334  21.554  1.00  0.00              
ATOM     48  O   LYS   121      37.123  36.974  22.435  1.00  0.00              
END
