
#######################################################
#                                                     #
#                        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   14 (  112),  selected   14 , name T0318TS193_2_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_2_2-D1.T0318_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:    14       142 - 155         3.05     3.05
  LCS_AVERAGE:      9.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       143 - 151         1.80     5.57
  LONGEST_CONTINUOUS_SEGMENT:     9       144 - 152         1.91     5.44
  LCS_AVERAGE:      5.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       146 - 150         0.88     6.64
  LCS_AVERAGE:      2.78

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:  154
LCS_GDT     R     142     R     142      3    5   14     3    3    3    3    4    5    5   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     143     E     143      4    9   14     4    4    5    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     144     L     144      4    9   14     4    4    5    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     145     N     145      4    9   14     4    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     146     V     146      5    9   14     3    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     147     N     147      5    9   14     3    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     I     148     I     148      5    9   14     4    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     149     D     149      5    9   14     3    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     150     V     150      5    9   14     3    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     151     V     151      4    9   14     3    4    6    7    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     C     152     C     152      4    9   14     3    4    5    6    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     153     D     153      4    6   14     3    4    4    6    8   11   11   12   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     K     154     K     154      4    5   14     3    4    4    4    4    5    5    7   11   13   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     155     L     155      4    5   14     3    4    4    4    4    5    6    9   12   13   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   5.67  (   2.78    5.15    9.09 )

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      4      6      7      8     11     11     12     12     13     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   2.60   2.60   3.90   4.55   5.19   7.14   7.14   7.79   7.79   8.44   9.09   9.09   9.09   9.09   9.09   9.09   9.09   9.09   9.09   9.09
GDT RMS_LOCAL    0.35   0.35   1.08   1.29   1.51   2.20   2.20   2.43   2.43   2.69   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05
GDT RMS_ALL_CA   4.17   4.17   6.73   6.37   4.93   3.10   3.10   3.15   3.15   3.12   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05   3.05

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142          3.909
LGA    E     143      E     143          1.912
LGA    L     144      L     144          2.318
LGA    N     145      N     145          2.392
LGA    V     146      V     146          1.703
LGA    N     147      N     147          2.378
LGA    I     148      I     148          2.745
LGA    D     149      D     149          1.133
LGA    V     150      V     150          2.582
LGA    V     151      V     151          2.663
LGA    C     152      C     152          1.165
LGA    D     153      D     153          2.844
LGA    K     154      K     154          6.387
LGA    L     155      L     155          5.259

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0     12    2.43     6.006     6.240     0.475

LGA_LOCAL      RMSD =  2.426  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.152  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  3.050  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.860795 * X  +   0.428888 * Y  +   0.274020 * Z  +  41.996521
  Y_new =  -0.355287 * X  +  -0.891879 * Y  +   0.279861 * Z  +  50.078457
  Z_new =   0.364422 * X  +   0.143547 * Y  +   0.920104 * Z  +  11.441760 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.154764   -2.986828  [ DEG:     8.8673   -171.1326 ]
  Theta =  -0.373012   -2.768581  [ DEG:   -21.3720   -158.6280 ]
  Phi   =  -2.750149    0.391443  [ DEG:  -157.5720     22.4280 ]
 
# 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: T0318TS193_2_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_2_2-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  154   4.0   12   2.43   6.240     3.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      35.506  53.526  14.062  1.00  0.00
ATOM   1098  CA  ARG   142      34.413  54.356  13.572  1.00  0.00
ATOM   1099  C   ARG   142      34.513  54.566  12.066  1.00  0.00
ATOM   1100  O   ARG   142      33.500  54.665  11.375  1.00  0.00
ATOM   1101  CB  ARG   142      34.441  55.730  14.244  1.00  0.00
ATOM   1102  CG  ARG   142      34.048  55.710  15.713  1.00  0.00
ATOM   1103  CD  ARG   142      34.179  57.089  16.338  1.00  0.00
ATOM   1104  NE  ARG   142      33.827  57.082  17.757  1.00  0.00
ATOM   1105  CZ  ARG   142      33.959  58.130  18.564  1.00  0.00
ATOM   1106  NH1 ARG   142      33.612  58.031  19.840  1.00  0.00
ATOM   1107  NH2 ARG   142      34.437  59.273  18.093  1.00  0.00
ATOM   1108  N   GLU   143      35.742  54.635  11.564  1.00  0.00
ATOM   1109  CA  GLU   143      35.981  54.657  10.126  1.00  0.00
ATOM   1110  C   GLU   143      35.634  53.318   9.489  1.00  0.00
ATOM   1111  O   GLU   143      34.996  53.265   8.438  1.00  0.00
ATOM   1112  CB  GLU   143      37.453  54.954   9.832  1.00  0.00
ATOM   1113  CG  GLU   143      37.875  56.378  10.155  1.00  0.00
ATOM   1114  CD  GLU   143      39.363  56.601   9.969  1.00  0.00
ATOM   1115  OE1 GLU   143      40.075  55.624   9.657  1.00  0.00
ATOM   1116  OE2 GLU   143      39.817  57.753  10.136  1.00  0.00
ATOM   1117  N   LEU   144      36.058  52.235  10.132  1.00  0.00
ATOM   1118  CA  LEU   144      35.779  50.892   9.638  1.00  0.00
ATOM   1119  C   LEU   144      34.286  50.594   9.669  1.00  0.00
ATOM   1120  O   LEU   144      33.750  49.966   8.756  1.00  0.00
ATOM   1121  CB  LEU   144      36.489  49.845  10.499  1.00  0.00
ATOM   1122  CG  LEU   144      38.014  49.949  10.572  1.00  0.00
ATOM   1123  CD1 LEU   144      38.577  48.918  11.537  1.00  0.00
ATOM   1124  CD2 LEU   144      38.635  49.709   9.203  1.00  0.00
ATOM   1125  N   ASN   145      33.089  49.650  10.883  1.00  0.00
ATOM   1126  CA  ASN   145      33.287  48.205  10.848  1.00  0.00
ATOM   1127  C   ASN   145      32.002  47.465  11.193  1.00  0.00
ATOM   1128  O   ASN   145      31.388  47.716  12.230  1.00  0.00
ATOM   1129  CB  ASN   145      34.360  47.787  11.856  1.00  0.00
ATOM   1130  CG  ASN   145      33.952  48.060  13.290  1.00  0.00
ATOM   1131  OD1 ASN   145      32.851  48.546  13.549  1.00  0.00
ATOM   1132  ND2 ASN   145      34.840  47.748  14.226  1.00  0.00
ATOM   1133  N   VAL   146      32.986  46.135  12.333  1.00  0.00
ATOM   1134  CA  VAL   146      32.175  45.208  13.114  1.00  0.00
ATOM   1135  C   VAL   146      32.980  44.600  14.255  1.00  0.00
ATOM   1136  O   VAL   146      34.208  44.678  14.271  1.00  0.00
ATOM   1137  CB  VAL   146      31.650  44.049  12.247  1.00  0.00
ATOM   1138  CG1 VAL   146      30.764  44.580  11.128  1.00  0.00
ATOM   1139  CG2 VAL   146      32.806  43.284  11.622  1.00  0.00
ATOM   1140  N   ASN   147      32.280  43.994  15.208  1.00  0.00
ATOM   1141  CA  ASN   147      32.931  43.348  16.342  1.00  0.00
ATOM   1142  C   ASN   147      32.827  41.832  16.246  1.00  0.00
ATOM   1143  O   ASN   147      31.729  41.274  16.224  1.00  0.00
ATOM   1144  CB  ASN   147      32.277  43.785  17.655  1.00  0.00
ATOM   1145  CG  ASN   147      32.406  45.276  17.901  1.00  0.00
ATOM   1146  OD1 ASN   147      33.512  45.796  18.051  1.00  0.00
ATOM   1147  ND2 ASN   147      31.275  45.968  17.943  1.00  0.00
ATOM   1148  N   ILE   148      33.976  41.167  16.189  1.00  0.00
ATOM   1149  CA  ILE   148      34.016  39.712  16.098  1.00  0.00
ATOM   1150  C   ILE   148      34.434  39.088  17.423  1.00  0.00
ATOM   1151  O   ILE   148      35.362  39.562  18.078  1.00  0.00
ATOM   1152  CB  ILE   148      35.018  39.241  15.027  1.00  0.00
ATOM   1153  CG1 ILE   148      35.016  37.714  14.930  1.00  0.00
ATOM   1154  CG2 ILE   148      36.426  39.701  15.376  1.00  0.00
ATOM   1155  CD1 ILE   148      35.769  37.178  13.733  1.00  0.00
ATOM   1156  N   ASP   149      33.742  38.023  17.814  1.00  0.00
ATOM   1157  CA  ASP   149      34.009  37.360  19.083  1.00  0.00
ATOM   1158  C   ASP   149      33.472  35.934  19.085  1.00  0.00
ATOM   1159  O   ASP   149      32.875  35.485  18.106  1.00  0.00
ATOM   1160  CB  ASP   149      33.345  38.118  20.234  1.00  0.00
ATOM   1161  CG  ASP   149      34.010  37.849  21.570  1.00  0.00
ATOM   1162  OD1 ASP   149      34.901  36.974  21.625  1.00  0.00
ATOM   1163  OD2 ASP   149      33.641  38.512  22.562  1.00  0.00
ATOM   1164  N   VAL   150      33.688  35.227  20.188  1.00  0.00
ATOM   1165  CA  VAL   150      33.213  33.854  20.324  1.00  0.00
ATOM   1166  C   VAL   150      32.215  33.728  21.468  1.00  0.00
ATOM   1167  O   VAL   150      32.574  33.872  22.637  1.00  0.00
ATOM   1168  CB  VAL   150      34.372  32.881  20.609  1.00  0.00
ATOM   1169  CG1 VAL   150      33.849  31.463  20.774  1.00  0.00
ATOM   1170  CG2 VAL   150      35.373  32.895  19.465  1.00  0.00
ATOM   1171  N   VAL   151      30.961  33.455  21.125  1.00  0.00
ATOM   1172  CA  VAL   151      29.907  33.314  22.123  1.00  0.00
ATOM   1173  C   VAL   151      29.173  31.989  21.964  1.00  0.00
ATOM   1174  O   VAL   151      28.683  31.666  20.881  1.00  0.00
ATOM   1175  CB  VAL   151      28.863  34.440  22.004  1.00  0.00
ATOM   1176  CG1 VAL   151      27.758  34.252  23.032  1.00  0.00
ATOM   1177  CG2 VAL   151      29.513  35.795  22.239  1.00  0.00
ATOM   1178  N   CYS   152      29.098  31.226  23.049  1.00  0.00
ATOM   1179  CA  CYS   152      28.439  29.925  23.026  1.00  0.00
ATOM   1180  C   CYS   152      29.122  28.980  22.046  1.00  0.00
ATOM   1181  O   CYS   152      28.470  28.144  21.419  1.00  0.00
ATOM   1182  CB  CYS   152      26.977  30.072  22.604  1.00  0.00
ATOM   1183  SG  CYS   152      26.009  31.196  23.638  1.00  0.00
ATOM   1184  N   ASP   153      30.437  29.116  21.918  1.00  0.00
ATOM   1185  CA  ASP   153      31.215  28.256  21.034  1.00  0.00
ATOM   1186  C   ASP   153      30.933  28.571  19.570  1.00  0.00
ATOM   1187  O   ASP   153      31.308  27.811  18.679  1.00  0.00
ATOM   1188  CB  ASP   153      30.870  26.786  21.277  1.00  0.00
ATOM   1189  CG  ASP   153      31.154  26.347  22.701  1.00  0.00
ATOM   1190  OD1 ASP   153      32.245  26.671  23.215  1.00  0.00
ATOM   1191  OD2 ASP   153      30.284  25.682  23.302  1.00  0.00
ATOM   1192  N   LYS   154      30.269  29.697  19.330  1.00  0.00
ATOM   1193  CA  LYS   154      29.939  30.118  17.974  1.00  0.00
ATOM   1194  C   LYS   154      30.513  31.496  17.670  1.00  0.00
ATOM   1195  O   LYS   154      30.675  32.323  18.568  1.00  0.00
ATOM   1196  CB  LYS   154      28.423  30.184  17.787  1.00  0.00
ATOM   1197  CG  LYS   154      27.722  28.841  17.920  1.00  0.00
ATOM   1198  CD  LYS   154      26.229  28.970  17.664  1.00  0.00
ATOM   1199  CE  LYS   154      25.515  27.647  17.886  1.00  0.00
ATOM   1200  NZ  LYS   154      24.048  27.762  17.660  1.00  0.00
ATOM   1201  N   LEU   155      29.078  33.169  19.908  1.00  0.00
ATOM   1202  CA  LEU   155      28.153  33.449  18.818  1.00  0.00
ATOM   1203  C   LEU   155      28.714  34.503  17.874  1.00  0.00
ATOM   1204  O   LEU   155      28.522  34.432  16.660  1.00  0.00
ATOM   1205  CB  LEU   155      26.820  33.964  19.364  1.00  0.00
ATOM   1206  CG  LEU   155      25.960  32.949  20.121  1.00  0.00
ATOM   1207  CD1 LEU   155      24.761  33.633  20.762  1.00  0.00
ATOM   1208  CD2 LEU   155      25.446  31.872  19.179  1.00  0.00
TER
END
