
#######################################################
#                                                     #
#                        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 (  104),  selected   15 , name T0298TS319_4-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected   15 , name T0298_D2.pdb
# PARAMETERS: T0298TS319_4-D2.T0298_D2.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:    15       130 - 144         2.96     2.96
  LCS_AVERAGE:      8.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       131 - 144         1.78     3.15
  LCS_AVERAGE:      7.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       132 - 144         0.99     3.54
  LCS_AVERAGE:      6.27

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:  186
LCS_GDT     C     130     C     130      3    4   15     3    3    4    4    4    4    4    5    5    8    8   10   12   12   15   15   15   15   15   15 
LCS_GDT     A     131     A     131      3   14   15     3    3    4    5    9   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     V     132     V     132     13   14   15     3    9   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     133     A     133     13   14   15     6    9   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     134     A     134     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     E     135     E     135     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     136     L     136     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     C     137     C     137     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     E     138     E     138     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     V     139     V     139     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     140     L     140     13   14   15     7   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     141     A     141     13   14   15     6   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     P     142     P     142     13   14   15     6   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     143     L     143     13   14   15     6   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     144     L     144     13   14   15     6   11   13   13   13   14   14   14   14   14   14   14   14   14   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   7.17  (   6.27    7.17    8.06 )

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      7     11     13     13     13     14     14     14     14     14     14     14     14     14     15     15     15     15     15     15 
GDT PERCENT_CA   3.76   5.91   6.99   6.99   6.99   7.53   7.53   7.53   7.53   7.53   7.53   7.53   7.53   7.53   8.06   8.06   8.06   8.06   8.06   8.06
GDT RMS_LOCAL    0.34   0.75   0.99   0.99   0.99   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   2.96   2.96   2.96   2.96   2.96   2.96
GDT RMS_ALL_CA   3.61   3.89   3.54   3.54   3.54   3.15   3.15   3.15   3.15   3.15   3.15   3.15   3.15   3.15   2.96   2.96   2.96   2.96   2.96   2.96

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130          8.560
LGA    A     131      A     131          3.100
LGA    V     132      V     132          2.795
LGA    A     133      A     133          1.654
LGA    A     134      A     134          2.342
LGA    E     135      E     135          2.522
LGA    L     136      L     136          1.923
LGA    C     137      C     137          1.893
LGA    E     138      E     138          1.981
LGA    V     139      V     139          1.451
LGA    L     140      L     140          0.924
LGA    A     141      A     141          0.922
LGA    P     142      P     142          1.886
LGA    L     143      L     143          1.957
LGA    L     144      L     144          2.026

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  186    4.0     14    1.78     7.124     7.232     0.745

LGA_LOCAL      RMSD =  1.779  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.964  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.964  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.840790 * X  +   0.387428 * Y  +   0.378115 * Z  + -77.259521
  Y_new =  -0.381871 * X  +   0.919522 * Y  +  -0.093027 * Z  +  62.588470
  Z_new =  -0.383727 * X  +  -0.066175 * Y  +   0.921073 * Z  +  11.799294 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.071723    3.069870  [ DEG:    -4.1094    175.8906 ]
  Theta =   0.393828    2.747764  [ DEG:    22.5647    157.4353 ]
  Phi   =  -0.426326    2.715267  [ DEG:   -24.4267    155.5733 ]
 
# 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: T0298TS319_4-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS319_4-D2.T0298_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  186   4.0   14   1.78   7.232     2.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS319_4-D2
PFRMAT TS
TARGET T0298
MODEL 4
PARENT N/A
ATOM    905  N   CYS   130      -9.582  73.639   9.046  1.00 85.90       1SG 906
ATOM    906  CA  CYS   130     -10.487  73.208   8.032  1.00 85.90       1SG 907
ATOM    907  CB  CYS   130     -11.024  74.356   7.158  1.00 85.90       1SG 908
ATOM    908  SG  CYS   130     -12.123  75.467   8.088  1.00 85.90       1SG 909
ATOM    909  C   CYS   130      -9.800  72.247   7.135  1.00 85.90       1SG 910
ATOM    910  O   CYS   130      -8.622  71.932   7.323  1.00 85.90       1SG 911
ATOM    911  N   ALA   131     -10.629  71.625   6.275  1.00158.83       1SG 912
ATOM    912  CA  ALA   131     -10.226  70.817   5.165  1.00158.83       1SG 913
ATOM    913  CB  ALA   131     -11.373  69.939   4.635  1.00158.83       1SG 914
ATOM    914  C   ALA   131      -9.700  71.648   3.965  1.00158.83       1SG 915
ATOM    915  O   ALA   131      -8.632  71.287   3.470  1.00158.83       1SG 916
ATOM    916  N   VAL   132     -10.397  72.755   3.491  1.00260.98       1SG 917
ATOM    917  CA  VAL   132     -10.044  73.634   2.356  1.00260.98       1SG 918
ATOM    918  CB  VAL   132     -10.681  73.144   1.070  1.00260.98       1SG 919
ATOM    919  CG1 VAL   132     -10.251  73.991  -0.146  1.00260.98       1SG 920
ATOM    920  CG2 VAL   132     -10.311  71.656   0.923  1.00260.98       1SG 921
ATOM    921  C   VAL   132     -10.501  75.076   2.682  1.00260.98       1SG 922
ATOM    922  O   VAL   132     -10.858  75.348   3.821  1.00260.98       1SG 923
ATOM    923  N   ALA   133     -10.454  76.056   1.720  1.00115.36       1SG 924
ATOM    924  CA  ALA   133     -10.715  77.484   1.883  1.00115.36       1SG 925
ATOM    925  CB  ALA   133     -10.326  78.298   0.633  1.00115.36       1SG 926
ATOM    926  C   ALA   133     -12.126  77.902   2.253  1.00115.36       1SG 927
ATOM    927  O   ALA   133     -12.311  78.714   3.162  1.00115.36       1SG 928
ATOM    928  N   ALA   134     -13.169  77.337   1.615  1.00 53.22       1SG 929
ATOM    929  CA  ALA   134     -14.505  77.855   1.783  1.00 53.22       1SG 930
ATOM    930  CB  ALA   134     -15.553  77.043   1.007  1.00 53.22       1SG 931
ATOM    931  C   ALA   134     -14.909  77.851   3.222  1.00 53.22       1SG 932
ATOM    932  O   ALA   134     -15.533  78.795   3.702  1.00 53.22       1SG 933
ATOM    933  N   GLU   135     -14.550  76.793   3.961  1.00 95.64       1SG 934
ATOM    934  CA  GLU   135     -14.936  76.690   5.337  1.00 95.64       1SG 935
ATOM    935  CB  GLU   135     -14.501  75.360   5.973  1.00 95.64       1SG 936
ATOM    936  CG  GLU   135     -15.367  74.167   5.554  1.00 95.64       1SG 937
ATOM    937  CD  GLU   135     -15.217  73.951   4.053  1.00 95.64       1SG 938
ATOM    938  OE1 GLU   135     -15.914  74.661   3.280  1.00 95.64       1SG 939
ATOM    939  OE2 GLU   135     -14.405  73.072   3.659  1.00 95.64       1SG 940
ATOM    940  C   GLU   135     -14.325  77.805   6.132  1.00 95.64       1SG 941
ATOM    941  O   GLU   135     -14.943  78.302   7.072  1.00 95.64       1SG 942
ATOM    942  N   LEU   136     -13.084  78.218   5.799  1.00 66.89       1SG 943
ATOM    943  CA  LEU   136     -12.426  79.255   6.551  1.00 66.89       1SG 944
ATOM    944  CB  LEU   136     -11.003  79.548   6.039  1.00 66.89       1SG 945
ATOM    945  CG  LEU   136     -10.052  78.342   6.122  1.00 66.89       1SG 946
ATOM    946  CD2 LEU   136     -10.098  77.702   7.516  1.00 66.89       1SG 947
ATOM    947  CD1 LEU   136      -8.629  78.714   5.679  1.00 66.89       1SG 948
ATOM    948  C   LEU   136     -13.190  80.528   6.394  1.00 66.89       1SG 949
ATOM    949  O   LEU   136     -13.498  81.226   7.361  1.00 66.89       1SG 950
ATOM    950  N   CYS   137     -13.568  80.837   5.147  1.00 48.19       1SG 951
ATOM    951  CA  CYS   137     -14.226  82.074   4.864  1.00 48.19       1SG 952
ATOM    952  CB  CYS   137     -14.616  82.171   3.381  1.00 48.19       1SG 953
ATOM    953  SG  CYS   137     -15.417  83.740   2.954  1.00 48.19       1SG 954
ATOM    954  C   CYS   137     -15.475  82.128   5.684  1.00 48.19       1SG 955
ATOM    955  O   CYS   137     -15.806  83.162   6.265  1.00 48.19       1SG 956
ATOM    956  N   GLU   138     -16.201  80.999   5.755  1.00 49.49       1SG 957
ATOM    957  CA  GLU   138     -17.423  80.945   6.501  1.00 49.49       1SG 958
ATOM    958  CB  GLU   138     -18.196  79.625   6.324  1.00 49.49       1SG 959
ATOM    959  CG  GLU   138     -18.783  79.439   4.927  1.00 49.49       1SG 960
ATOM    960  CD  GLU   138     -19.532  78.116   4.912  1.00 49.49       1SG 961
ATOM    961  OE1 GLU   138     -19.739  77.539   6.014  1.00 49.49       1SG 962
ATOM    962  OE2 GLU   138     -19.911  77.666   3.800  1.00 49.49       1SG 963
ATOM    963  C   GLU   138     -17.163  81.098   7.965  1.00 49.49       1SG 964
ATOM    964  O   GLU   138     -17.889  81.823   8.628  1.00 49.49       1SG 965
ATOM    965  N   VAL   139     -16.119  80.455   8.521  1.00 96.16       1SG 966
ATOM    966  CA  VAL   139     -15.924  80.495   9.949  1.00 96.16       1SG 967
ATOM    967  CB  VAL   139     -14.762  79.675  10.430  1.00 96.16       1SG 968
ATOM    968  CG1 VAL   139     -13.460  80.315   9.936  1.00 96.16       1SG 969
ATOM    969  CG2 VAL   139     -14.865  79.541  11.961  1.00 96.16       1SG 970
ATOM    970  C   VAL   139     -15.695  81.908  10.368  1.00 96.16       1SG 971
ATOM    971  O   VAL   139     -16.155  82.340  11.425  1.00 96.16       1SG 972
ATOM    972  N   LEU   140     -14.987  82.673   9.523  1.00 59.64       1SG 973
ATOM    973  CA  LEU   140     -14.670  84.031   9.835  1.00 59.64       1SG 974
ATOM    974  CB  LEU   140     -13.959  84.748   8.673  1.00 59.64       1SG 975
ATOM    975  CG  LEU   140     -13.666  86.241   8.924  1.00 59.64       1SG 976
ATOM    976  CD2 LEU   140     -13.182  86.937   7.640  1.00 59.64       1SG 977
ATOM    977  CD1 LEU   140     -12.693  86.436  10.095  1.00 59.64       1SG 978
ATOM    978  C   LEU   140     -15.945  84.781  10.058  1.00 59.64       1SG 979
ATOM    979  O   LEU   140     -16.037  85.579  10.990  1.00 59.64       1SG 980
ATOM    980  N   ALA   141     -16.978  84.537   9.229  1.00 47.92       1SG 981
ATOM    981  CA  ALA   141     -18.162  85.342   9.338  1.00 47.92       1SG 982
ATOM    982  CB  ALA   141     -19.233  84.997   8.287  1.00 47.92       1SG 983
ATOM    983  C   ALA   141     -18.777  85.215  10.704  1.00 47.92       1SG 984
ATOM    984  O   ALA   141     -19.080  86.245  11.302  1.00 47.92       1SG 985
ATOM    985  N   PRO   142     -18.979  84.048  11.265  1.00159.08       1SG 986
ATOM    986  CA  PRO   142     -19.524  84.049  12.593  1.00159.08       1SG 987
ATOM    987  CD  PRO   142     -19.593  82.975  10.502  1.00159.08       1SG 988
ATOM    988  CB  PRO   142     -19.983  82.623  12.868  1.00159.08       1SG 989
ATOM    989  CG  PRO   142     -20.443  82.152  11.483  1.00159.08       1SG 990
ATOM    990  C   PRO   142     -18.639  84.633  13.637  1.00159.08       1SG 991
ATOM    991  O   PRO   142     -19.153  85.073  14.664  1.00159.08       1SG 992
ATOM    992  N   LEU   143     -17.316  84.625  13.426  1.00 48.32       1SG 993
ATOM    993  CA  LEU   143     -16.433  85.185  14.401  1.00 48.32       1SG 994
ATOM    994  CB  LEU   143     -14.952  84.932  14.073  1.00 48.32       1SG 995
ATOM    995  CG  LEU   143     -14.584  83.438  14.088  1.00 48.32       1SG 996
ATOM    996  CD2 LEU   143     -15.138  82.745  15.344  1.00 48.32       1SG 997
ATOM    997  CD1 LEU   143     -13.072  83.236  13.897  1.00 48.32       1SG 998
ATOM    998  C   LEU   143     -16.649  86.663  14.449  1.00 48.32       1SG 999
ATOM    999  O   LEU   143     -16.630  87.270  15.520  1.00 48.32       1SG1000
ATOM   1000  N   LEU   144     -16.876  87.281  13.275  1.00 75.36       1SG1001
ATOM   1001  CA  LEU   144     -16.989  88.709  13.212  1.00 75.36       1SG1002
ATOM   1002  CB  LEU   144     -18.186  89.313  13.978  1.00 75.36       1SG1003
ATOM   1003  CG  LEU   144     -19.581  88.970  13.416  1.00 75.36       1SG1004
ATOM   1004  CD2 LEU   144     -19.914  87.485  13.599  1.00 75.36       1SG1005
ATOM   1005  CD1 LEU   144     -19.758  89.477  11.974  1.00 75.36       1SG1006
ATOM   1006  C   LEU   144     -15.727  89.272  13.851  1.00 75.36       1SG1007
ATOM   1007  O   LEU   144     -14.615  88.844  13.440  1.00 75.36       1SG1008
ATOM   1008  OXT LEU   144     -15.854  90.136  14.759  1.00 75.36       1SG1009
TER
END
