
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_4_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:    11       145 - 155         4.20    10.02
  LCS_AVERAGE:      6.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       147 - 153         1.74    10.67
  LCS_AVERAGE:      3.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       147 - 151         0.84    10.95
  LCS_AVERAGE:      2.60

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      4    5    8     3    3    4    4    4    5    5    6    6    6    6    7    7    8    9    9   10   10   10   11 
LCS_GDT     E     143     E     143      4    5    8     3    3    4    4    4    5    5    6    6    6    6    7    7    8    9    9   10   10   10   11 
LCS_GDT     L     144     L     144      4    5    8     3    3    4    4    4    5    5    6    6    6    6    8    8    8    9    9   10   10   10   11 
LCS_GDT     N     145     N     145      4    5   11     0    3    4    4    4    5    5    6    6    6    7    8    8    9    9   11   11   11   11   11 
LCS_GDT     V     146     V     146      3    5   11     3    3    3    4    5    6    7    8   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     N     147     N     147      5    7   11     3    4    5    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     I     148     I     148      5    7   11     4    4    5    5    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     D     149     D     149      5    7   11     4    4    5    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     V     150     V     150      5    7   11     4    4    5    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     V     151     V     151      5    7   11     4    4    5    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     C     152     C     152      3    7   11     3    3    4    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     D     153     D     153      3    7   11     3    3    4    6    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     K     154     K     154      3    6   11     3    3    3    5    6    6    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_GDT     L     155     L     155      3    6   11     3    3    3    5    7    8    8    9   10   10   10   10   10   10   10   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   4.44  (   2.60    3.99    6.73 )

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      5      6      7      8      8      9     10     10     10     10     10     10     10     11     11     11     11     11 
GDT PERCENT_CA   2.60   2.60   3.25   3.90   4.55   5.19   5.19   5.84   6.49   6.49   6.49   6.49   6.49   6.49   6.49   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.33   0.33   0.84   1.53   1.74   2.03   2.03   2.36   2.81   2.81   2.81   2.81   2.81   2.81   2.81   4.20   4.20   4.20   4.20   4.20
GDT RMS_ALL_CA  10.63  10.63  10.95  10.77  10.67  10.85  10.85  11.08  10.55  10.55  10.55  10.55  10.55  10.55  10.55  10.02  10.02  10.02  10.02  10.02

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142         26.360
LGA    E     143      E     143         20.809
LGA    L     144      L     144         18.362
LGA    N     145      N     145         12.756
LGA    V     146      V     146          6.256
LGA    N     147      N     147          2.377
LGA    I     148      I     148          2.495
LGA    D     149      D     149          2.182
LGA    V     150      V     150          2.568
LGA    V     151      V     151          1.573
LGA    C     152      C     152          1.630
LGA    D     153      D     153          2.040
LGA    K     154      K     154          3.720
LGA    L     155      L     155          1.985

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0      9    2.36     4.870     4.848     0.365

LGA_LOCAL      RMSD =  2.364  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.075  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  8.435  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.010616 * X  +  -0.367148 * Y  +  -0.930102 * Z  +  23.234016
  Y_new =  -0.751923 * X  +   0.616091 * Y  +  -0.234613 * Z  +  29.357597
  Z_new =   0.659165 * X  +   0.696875 * Y  +  -0.282608 * Z  +  11.535775 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.956066   -1.185527  [ DEG:   112.0743    -67.9257 ]
  Theta =  -0.719708   -2.421885  [ DEG:   -41.2362   -138.7638 ]
  Phi   =  -1.584914    1.556679  [ DEG:   -90.8089     89.1911 ]
 
# 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_4_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_4_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    9   2.36   4.848     8.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      25.908  33.681  10.114  1.00  0.00
ATOM   1098  CA  ARG   142      26.695  32.525  10.529  1.00  0.00
ATOM   1099  C   ARG   142      27.428  32.798  11.836  1.00  0.00
ATOM   1100  O   ARG   142      27.526  31.924  12.699  1.00  0.00
ATOM   1101  CB  ARG   142      27.738  32.177   9.465  1.00  0.00
ATOM   1102  CG  ARG   142      28.581  30.957   9.798  1.00  0.00
ATOM   1103  CD  ARG   142      29.514  30.601   8.651  1.00  0.00
ATOM   1104  NE  ARG   142      30.361  29.455   8.971  1.00  0.00
ATOM   1105  CZ  ARG   142      31.299  28.970   8.163  1.00  0.00
ATOM   1106  NH1 ARG   142      32.022  27.924   8.539  1.00  0.00
ATOM   1107  NH2 ARG   142      31.511  29.533   6.981  1.00  0.00
ATOM   1108  N   GLU   143      27.941  34.015  11.977  1.00  0.00
ATOM   1109  CA  GLU   143      28.662  34.408  13.184  1.00  0.00
ATOM   1110  C   GLU   143      27.719  34.527  14.374  1.00  0.00
ATOM   1111  O   GLU   143      28.042  34.094  15.479  1.00  0.00
ATOM   1112  CB  GLU   143      29.346  35.762  12.982  1.00  0.00
ATOM   1113  CG  GLU   143      30.391  35.771  11.879  1.00  0.00
ATOM   1114  CD  GLU   143      30.948  37.157  11.616  1.00  0.00
ATOM   1115  OE1 GLU   143      30.496  38.114  12.280  1.00  0.00
ATOM   1116  OE2 GLU   143      31.834  37.285  10.746  1.00  0.00
ATOM   1117  N   LEU   144      25.863  34.505  15.854  1.00  0.00
ATOM   1118  CA  LEU   144      25.848  35.742  15.082  1.00  0.00
ATOM   1119  C   LEU   144      26.237  36.935  15.945  1.00  0.00
ATOM   1120  O   LEU   144      25.605  37.207  16.967  1.00  0.00
ATOM   1121  CB  LEU   144      24.451  36.003  14.515  1.00  0.00
ATOM   1122  CG  LEU   144      24.309  37.217  13.594  1.00  0.00
ATOM   1123  CD1 LEU   144      25.131  37.031  12.328  1.00  0.00
ATOM   1124  CD2 LEU   144      22.856  37.419  13.192  1.00  0.00
ATOM   1125  N   ASN   145      27.281  37.645  15.531  1.00  0.00
ATOM   1126  CA  ASN   145      27.768  38.798  16.276  1.00  0.00
ATOM   1127  C   ASN   145      28.099  39.957  15.344  1.00  0.00
ATOM   1128  O   ASN   145      28.345  39.759  14.155  1.00  0.00
ATOM   1129  CB  ASN   145      29.036  38.437  17.053  1.00  0.00
ATOM   1130  CG  ASN   145      28.781  37.414  18.143  1.00  0.00
ATOM   1131  OD1 ASN   145      28.991  36.218  17.945  1.00  0.00
ATOM   1132  ND2 ASN   145      28.327  37.885  19.298  1.00  0.00
ATOM   1133  N   VAL   146      28.104  41.168  15.893  1.00  0.00
ATOM   1134  CA  VAL   146      28.453  42.356  15.122  1.00  0.00
ATOM   1135  C   VAL   146      29.961  42.560  15.076  1.00  0.00
ATOM   1136  O   VAL   146      30.612  42.697  16.112  1.00  0.00
ATOM   1137  CB  VAL   146      27.831  43.626  15.732  1.00  0.00
ATOM   1138  CG1 VAL   146      28.200  44.849  14.905  1.00  0.00
ATOM   1139  CG2 VAL   146      26.315  43.512  15.769  1.00  0.00
ATOM   1140  N   ASN   147      32.485  41.965  15.105  1.00  0.00
ATOM   1141  CA  ASN   147      31.792  41.488  13.914  1.00  0.00
ATOM   1142  C   ASN   147      32.179  40.050  13.591  1.00  0.00
ATOM   1143  O   ASN   147      33.341  39.665  13.721  1.00  0.00
ATOM   1144  CB  ASN   147      32.143  42.357  12.706  1.00  0.00
ATOM   1145  CG  ASN   147      31.267  42.065  11.503  1.00  0.00
ATOM   1146  OD1 ASN   147      30.148  41.572  11.644  1.00  0.00
ATOM   1147  ND2 ASN   147      31.775  42.371  10.315  1.00  0.00
ATOM   1148  N   ILE   148      32.386  39.879  15.746  1.00  0.00
ATOM   1149  CA  ILE   148      33.024  38.689  16.297  1.00  0.00
ATOM   1150  C   ILE   148      32.084  37.946  17.238  1.00  0.00
ATOM   1151  O   ILE   148      31.063  38.485  17.665  1.00  0.00
ATOM   1152  CB  ILE   148      34.291  39.047  17.096  1.00  0.00
ATOM   1153  CG1 ILE   148      33.941  39.962  18.272  1.00  0.00
ATOM   1154  CG2 ILE   148      35.295  39.767  16.208  1.00  0.00
ATOM   1155  CD1 ILE   148      35.091  40.198  19.226  1.00  0.00
ATOM   1156  N   ASP   149      32.436  36.705  17.558  1.00  0.00
ATOM   1157  CA  ASP   149      31.663  35.911  18.505  1.00  0.00
ATOM   1158  C   ASP   149      32.346  35.857  19.866  1.00  0.00
ATOM   1159  O   ASP   149      33.573  35.892  19.957  1.00  0.00
ATOM   1160  CB  ASP   149      31.505  34.476  17.997  1.00  0.00
ATOM   1161  CG  ASP   149      30.415  33.717  18.726  1.00  0.00
ATOM   1162  OD1 ASP   149      30.593  33.431  19.929  1.00  0.00
ATOM   1163  OD2 ASP   149      29.383  33.407  18.095  1.00  0.00
ATOM   1164  N   VAL   150      31.544  35.771  20.921  1.00  0.00
ATOM   1165  CA  VAL   150      32.069  35.732  22.281  1.00  0.00
ATOM   1166  C   VAL   150      31.687  34.434  22.982  1.00  0.00
ATOM   1167  O   VAL   150      30.508  34.090  23.071  1.00  0.00
ATOM   1168  CB  VAL   150      31.524  36.897  23.130  1.00  0.00
ATOM   1169  CG1 VAL   150      32.304  37.017  24.430  1.00  0.00
ATOM   1170  CG2 VAL   150      31.645  38.210  22.373  1.00  0.00
ATOM   1171  N   VAL   151      31.403  32.889  24.749  1.00  0.00
ATOM   1172  CA  VAL   151      32.290  32.124  23.879  1.00  0.00
ATOM   1173  C   VAL   151      31.497  31.246  22.920  1.00  0.00
ATOM   1174  O   VAL   151      31.937  30.976  21.802  1.00  0.00
ATOM   1175  CB  VAL   151      33.220  31.202  24.690  1.00  0.00
ATOM   1176  CG1 VAL   151      34.014  30.297  23.761  1.00  0.00
ATOM   1177  CG2 VAL   151      34.200  32.025  25.512  1.00  0.00
ATOM   1178  N   CYS   152      30.835  30.266  23.631  1.00  0.00
ATOM   1179  CA  CYS   152      30.774  28.877  23.192  1.00  0.00
ATOM   1180  C   CYS   152      29.657  28.670  22.176  1.00  0.00
ATOM   1181  O   CYS   152      28.533  29.132  22.372  1.00  0.00
ATOM   1182  CB  CYS   152      30.512  27.951  24.381  1.00  0.00
ATOM   1183  SG  CYS   152      31.851  27.893  25.593  1.00  0.00
ATOM   1184  N   ASP   153      27.168  27.455  22.995  1.00  0.00
ATOM   1185  CA  ASP   153      27.836  26.455  22.171  1.00  0.00
ATOM   1186  C   ASP   153      27.606  26.719  20.688  1.00  0.00
ATOM   1187  O   ASP   153      26.526  27.149  20.285  1.00  0.00
ATOM   1188  CB  ASP   153      27.306  25.055  22.491  1.00  0.00
ATOM   1189  CG  ASP   153      28.127  23.959  21.842  1.00  0.00
ATOM   1190  OD1 ASP   153      29.177  24.277  21.245  1.00  0.00
ATOM   1191  OD2 ASP   153      27.721  22.781  21.931  1.00  0.00
ATOM   1192  N   LYS   154      28.484  26.391  19.477  1.00  0.00
ATOM   1193  CA  LYS   154      28.848  27.649  18.834  1.00  0.00
ATOM   1194  C   LYS   154      28.407  27.670  17.377  1.00  0.00
ATOM   1195  O   LYS   154      28.776  28.568  16.620  1.00  0.00
ATOM   1196  CB  LYS   154      30.364  27.851  18.874  1.00  0.00
ATOM   1197  CG  LYS   154      30.829  29.173  18.286  1.00  0.00
ATOM   1198  CD  LYS   154      32.334  29.341  18.423  1.00  0.00
ATOM   1199  CE  LYS   154      32.800  30.658  17.826  1.00  0.00
ATOM   1200  NZ  LYS   154      34.272  30.837  17.956  1.00  0.00
ATOM   1201  N   LEU   155      27.783  30.357  17.556  1.00  0.00
ATOM   1202  CA  LEU   155      26.465  30.052  17.014  1.00  0.00
ATOM   1203  C   LEU   155      26.420  30.286  15.509  1.00  0.00
ATOM   1204  O   LEU   155      26.685  31.391  15.036  1.00  0.00
ATOM   1205  CB  LEU   155      25.400  30.937  17.664  1.00  0.00
ATOM   1206  CG  LEU   155      25.201  30.764  19.171  1.00  0.00
ATOM   1207  CD1 LEU   155      24.179  31.760  19.697  1.00  0.00
ATOM   1208  CD2 LEU   155      24.704  29.361  19.489  1.00  0.00
TER
END
