
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_1_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         4.91     4.91
  LCS_AVERAGE:      9.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       142 - 149         1.52     7.91
  LCS_AVERAGE:      4.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       142 - 147         0.94     6.96
  LCS_AVERAGE:      2.88

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      6    8   14     3    5    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     E     143     E     143      6    8   14     4    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     L     144     L     144      6    8   14     4    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     N     145     N     145      6    8   14     4    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     V     146     V     146      6    8   14     4    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     N     147     N     147      6    8   14     3    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     I     148     I     148      4    8   14     3    4    5    7    8    8    8    8    8    9   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     D     149     D     149      4    8   14     3    6    7    7    8    8    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     V     150     V     150      3    4   14     3    3    4    4    4    4    5    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     V     151     V     151      3    5   14     3    3    4    4    4    5    5    8    8    8    9    9   11   13   14   14   14   14   14   14 
LCS_GDT     C     152     C     152      3    5   14     3    3    4    4    4    5    5    8    8    8    9   11   12   13   14   14   14   14   14   14 
LCS_GDT     D     153     D     153      3    5   14     3    3    4    4    4    5    5    8    8    8    9   10   11   13   14   14   14   14   14   14 
LCS_GDT     K     154     K     154      3    5   14     3    3    4    4    4    5    5    8    8    8   10   11   12   13   14   14   14   14   14   14 
LCS_GDT     L     155     L     155      3    5   14     0    3    4    4    4    5    8    9    9    9   10   11   12   13   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   5.43  (   2.88    4.31    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      6      7      7      8      8      8      9      9      9     10     11     12     13     14     14     14     14     14     14 
GDT PERCENT_CA   2.60   3.90   4.55   4.55   5.19   5.19   5.19   5.84   5.84   5.84   6.49   7.14   7.79   8.44   9.09   9.09   9.09   9.09   9.09   9.09
GDT RMS_LOCAL    0.40   0.68   0.95   0.95   1.52   1.52   1.52   2.85   2.85   2.85   3.21   4.07   4.24   4.61   4.91   4.91   4.91   4.91   4.91   4.91
GDT RMS_ALL_CA   6.95   7.36   6.84   6.84   7.91   7.91   7.91   5.50   5.50   5.50   5.58   5.02   5.07   4.96   4.91   4.91   4.91   4.91   4.91   4.91

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142          3.606
LGA    E     143      E     143          3.312
LGA    L     144      L     144          3.559
LGA    N     145      N     145          2.745
LGA    V     146      V     146          2.930
LGA    N     147      N     147          3.040
LGA    I     148      I     148          5.478
LGA    D     149      D     149          2.424
LGA    V     150      V     150          3.835
LGA    V     151      V     151          8.154
LGA    C     152      C     152          7.071
LGA    D     153      D     153          8.810
LGA    K     154      K     154          6.524
LGA    L     155      L     155          3.190

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0      9    2.85     5.844     5.413     0.305

LGA_LOCAL      RMSD =  2.850  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.067  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.914  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.534329 * X  +   0.151563 * Y  +  -0.831578 * Z  +  35.839298
  Y_new =   0.038946 * X  +   0.987163 * Y  +   0.154896 * Z  +  60.995667
  Z_new =   0.844379 * X  +   0.050379 * Y  +  -0.533372 * Z  +   5.016960 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.047419   -0.094174  [ DEG:   174.6042     -5.3958 ]
  Theta =  -1.005405   -2.136188  [ DEG:   -57.6055   -122.3945 ]
  Phi   =   3.068834   -0.072758  [ DEG:   175.8313     -4.1687 ]
 
# 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_1_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_1_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   2.85   5.413     4.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      32.364  55.826   8.983  1.00  0.00
ATOM   1098  CA  ARG   142      32.643  55.122  10.229  1.00  0.00
ATOM   1099  C   ARG   142      32.132  53.689  10.179  1.00  0.00
ATOM   1100  O   ARG   142      30.965  53.445   9.870  1.00  0.00
ATOM   1101  CB  ARG   142      31.965  55.827  11.407  1.00  0.00
ATOM   1102  CG  ARG   142      32.482  57.231  11.670  1.00  0.00
ATOM   1103  CD  ARG   142      33.866  57.202  12.297  1.00  0.00
ATOM   1104  NE  ARG   142      34.356  58.544  12.604  1.00  0.00
ATOM   1105  CZ  ARG   142      35.508  58.797  13.218  1.00  0.00
ATOM   1106  NH1 ARG   142      35.871  60.050  13.456  1.00  0.00
ATOM   1107  NH2 ARG   142      36.293  57.796  13.591  1.00  0.00
ATOM   1108  N   GLU   143      33.012  52.741  10.483  1.00  0.00
ATOM   1109  CA  GLU   143      32.647  51.329  10.488  1.00  0.00
ATOM   1110  C   GLU   143      33.253  50.607  11.685  1.00  0.00
ATOM   1111  O   GLU   143      34.467  50.630  11.886  1.00  0.00
ATOM   1112  CB  GLU   143      33.148  50.641   9.217  1.00  0.00
ATOM   1113  CG  GLU   143      32.806  49.163   9.134  1.00  0.00
ATOM   1114  CD  GLU   143      33.197  48.548   7.805  1.00  0.00
ATOM   1115  OE1 GLU   143      33.661  49.295   6.918  1.00  0.00
ATOM   1116  OE2 GLU   143      33.041  47.319   7.650  1.00  0.00
ATOM   1117  N   LEU   144      32.400  49.968  12.477  1.00  0.00
ATOM   1118  CA  LEU   144      32.849  49.241  13.659  1.00  0.00
ATOM   1119  C   LEU   144      33.126  47.778  13.333  1.00  0.00
ATOM   1120  O   LEU   144      32.232  47.048  12.907  1.00  0.00
ATOM   1121  CB  LEU   144      31.784  49.288  14.755  1.00  0.00
ATOM   1122  CG  LEU   144      32.109  48.540  16.050  1.00  0.00
ATOM   1123  CD1 LEU   144      33.304  49.169  16.749  1.00  0.00
ATOM   1124  CD2 LEU   144      30.925  48.578  17.004  1.00  0.00
ATOM   1125  N   ASN   145      34.369  47.357  13.538  1.00  0.00
ATOM   1126  CA  ASN   145      34.762  45.977  13.282  1.00  0.00
ATOM   1127  C   ASN   145      34.372  45.069  14.442  1.00  0.00
ATOM   1128  O   ASN   145      34.795  45.281  15.579  1.00  0.00
ATOM   1129  CB  ASN   145      36.277  45.877  13.091  1.00  0.00
ATOM   1130  CG  ASN   145      36.740  46.486  11.782  1.00  0.00
ATOM   1131  OD1 ASN   145      35.967  46.597  10.830  1.00  0.00
ATOM   1132  ND2 ASN   145      38.006  46.883  11.731  1.00  0.00
ATOM   1133  N   VAL   146      33.564  44.056  14.148  1.00  0.00
ATOM   1134  CA  VAL   146      33.125  43.107  15.164  1.00  0.00
ATOM   1135  C   VAL   146      34.159  42.010  15.378  1.00  0.00
ATOM   1136  O   VAL   146      34.505  41.280  14.449  1.00  0.00
ATOM   1137  CB  VAL   146      31.802  42.426  14.767  1.00  0.00
ATOM   1138  CG1 VAL   146      31.402  41.391  15.807  1.00  0.00
ATOM   1139  CG2 VAL   146      30.686  43.454  14.658  1.00  0.00
ATOM   1140  N   ASN   147      34.650  41.898  16.608  1.00  0.00
ATOM   1141  CA  ASN   147      35.645  40.887  16.947  1.00  0.00
ATOM   1142  C   ASN   147      35.185  39.498  16.523  1.00  0.00
ATOM   1143  O   ASN   147      34.001  39.172  16.611  1.00  0.00
ATOM   1144  CB  ASN   147      35.893  40.865  18.456  1.00  0.00
ATOM   1145  CG  ASN   147      37.118  40.054  18.833  1.00  0.00
ATOM   1146  OD1 ASN   147      38.036  39.888  18.030  1.00  0.00
ATOM   1147  ND2 ASN   147      37.135  39.546  20.059  1.00  0.00
ATOM   1148  N   ILE   148      36.202  38.740  16.771  1.00  0.00
ATOM   1149  CA  ILE   148      36.055  37.312  16.517  1.00  0.00
ATOM   1150  C   ILE   148      35.209  36.645  17.595  1.00  0.00
ATOM   1151  O   ILE   148      34.328  35.839  17.296  1.00  0.00
ATOM   1152  CB  ILE   148      37.420  36.600  16.494  1.00  0.00
ATOM   1153  CG1 ILE   148      38.251  37.078  15.300  1.00  0.00
ATOM   1154  CG2 ILE   148      37.234  35.094  16.378  1.00  0.00
ATOM   1155  CD1 ILE   148      39.691  36.616  15.335  1.00  0.00
ATOM   1156  N   ASP   149      35.480  36.987  18.850  1.00  0.00
ATOM   1157  CA  ASP   149      34.747  36.419  19.974  1.00  0.00
ATOM   1158  C   ASP   149      33.286  36.849  19.952  1.00  0.00
ATOM   1159  O   ASP   149      32.391  36.059  20.259  1.00  0.00
ATOM   1160  CB  ASP   149      35.357  36.880  21.299  1.00  0.00
ATOM   1161  CG  ASP   149      34.698  36.232  22.501  1.00  0.00
ATOM   1162  OD1 ASP   149      33.841  35.344  22.302  1.00  0.00
ATOM   1163  OD2 ASP   149      35.037  36.613  23.641  1.00  0.00
ATOM   1164  N   VAL   150      33.156  38.166  20.064  1.00  0.00
ATOM   1165  CA  VAL   150      31.849  38.779  20.274  1.00  0.00
ATOM   1166  C   VAL   150      30.876  38.394  19.168  1.00  0.00
ATOM   1167  O   VAL   150      29.699  38.138  19.425  1.00  0.00
ATOM   1168  CB  VAL   150      31.942  40.316  20.296  1.00  0.00
ATOM   1169  CG1 VAL   150      30.553  40.934  20.317  1.00  0.00
ATOM   1170  CG2 VAL   150      32.697  40.786  21.531  1.00  0.00
ATOM   1171  N   VAL   151      31.372  38.356  17.936  1.00  0.00
ATOM   1172  CA  VAL   151      30.541  38.024  16.785  1.00  0.00
ATOM   1173  C   VAL   151      30.074  36.575  16.844  1.00  0.00
ATOM   1174  O   VAL   151      28.912  36.276  16.566  1.00  0.00
ATOM   1175  CB  VAL   151      31.307  38.211  15.462  1.00  0.00
ATOM   1176  CG1 VAL   151      30.491  37.682  14.294  1.00  0.00
ATOM   1177  CG2 VAL   151      31.596  39.684  15.218  1.00  0.00
ATOM   1178  N   CYS   152      30.984  35.679  17.205  1.00  0.00
ATOM   1179  CA  CYS   152      30.669  34.258  17.290  1.00  0.00
ATOM   1180  C   CYS   152      29.850  33.948  18.537  1.00  0.00
ATOM   1181  O   CYS   152      29.325  32.845  18.689  1.00  0.00
ATOM   1182  CB  CYS   152      31.952  33.427  17.347  1.00  0.00
ATOM   1183  SG  CYS   152      32.927  33.453  15.826  1.00  0.00
ATOM   1184  N   ASP   153      29.860  34.731  19.792  1.00  0.00
ATOM   1185  CA  ASP   153      28.736  34.643  20.717  1.00  0.00
ATOM   1186  C   ASP   153      27.419  34.939  20.012  1.00  0.00
ATOM   1187  O   ASP   153      26.349  34.558  20.488  1.00  0.00
ATOM   1188  CB  ASP   153      28.900  35.650  21.858  1.00  0.00
ATOM   1189  CG  ASP   153      27.866  35.465  22.950  1.00  0.00
ATOM   1190  OD1 ASP   153      27.031  34.544  22.829  1.00  0.00
ATOM   1191  OD2 ASP   153      27.889  36.242  23.928  1.00  0.00
ATOM   1192  N   LYS   154      26.864  32.391  20.811  1.00  0.00
ATOM   1193  CA  LYS   154      26.383  31.966  19.502  1.00  0.00
ATOM   1194  C   LYS   154      24.910  32.311  19.317  1.00  0.00
ATOM   1195  O   LYS   154      24.421  32.398  18.192  1.00  0.00
ATOM   1196  CB  LYS   154      26.541  30.453  19.339  1.00  0.00
ATOM   1197  CG  LYS   154      27.984  29.981  19.284  1.00  0.00
ATOM   1198  CD  LYS   154      28.065  28.475  19.091  1.00  0.00
ATOM   1199  CE  LYS   154      29.509  28.001  19.055  1.00  0.00
ATOM   1200  NZ  LYS   154      29.604  26.526  18.881  1.00  0.00
ATOM   1201  N   LEU   155      23.870  30.339  17.473  1.00  0.00
ATOM   1202  CA  LEU   155      24.833  30.342  16.378  1.00  0.00
ATOM   1203  C   LEU   155      24.476  31.393  15.334  1.00  0.00
ATOM   1204  O   LEU   155      25.346  32.110  14.839  1.00  0.00
ATOM   1205  CB  LEU   155      24.863  28.978  15.686  1.00  0.00
ATOM   1206  CG  LEU   155      25.844  28.829  14.522  1.00  0.00
ATOM   1207  CD1 LEU   155      27.275  29.040  14.995  1.00  0.00
ATOM   1208  CD2 LEU   155      25.746  27.440  13.911  1.00  0.00
TER
END
