
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      30_A - 58_A        4.54    14.92
  LCS_AVERAGE:     43.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.56    15.12
  LCS_AVERAGE:     33.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.81    15.12
  LCS_AVERAGE:     28.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     A     1_A     A     1_A      3   14   17      0    4    4   19   26   30   34   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     12   14   17     23   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     12   14   17     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     12   14   17     18   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     12   14   17     18   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     12   14   17     18   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     12   14   25      4    7   17   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     12   14   25      3   11   22   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A      3   17   25     13   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   17   25      3    8   11   14   20   30   34   36   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   17   25     12   14   14   14   15   15   22   25   33   36   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   31   34   41   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   27   30   36   37 
LCS_GDT     P    19_A     P    19_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     F    20_A     F    20_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     K    21_A     K    21_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   27   30 
LCS_GDT     K    22_A     K    22_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   27   30 
LCS_GDT     G    23_A     G    23_A     15   17   25     11   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     E    24_A     E    24_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     I    25_A     I    25_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     L    26_A     L    26_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     R    27_A     R    27_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   25   27   28   30 
LCS_GDT     I    28_A     I    28_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   24   25   28   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   17   19   22   22   22   22   23   23   26   28   32   34   38   39 
LCS_GDT     D    30_A     D    30_A     15   17   29      3    5    8   14   15   15   17   19   22   22   23   24   26   29   32   39   42   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   16   19   22   22   23   24   32   40   43   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    7   29      3    3    4    6   10   15   17   19   22   22   22   22   33   40   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    7   29      3    3    4    5    7    9   12   25   29   35   39   40   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6    9   24   35   38   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     28   34   34   36   36   36   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    7   14   22   26   37   37   39   40   41   41   42   42   42   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.41  (  28.83   33.47   43.94 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     28     34     34     36     36     36     37     37     39     40     41     41     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  48.28  58.62  58.62  62.07  62.07  62.07  63.79  63.79  67.24  68.97  70.69  70.69  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.25   0.42   0.42   0.83   0.83   0.83   1.04   1.04   1.71   2.01   2.32   2.32   2.74   2.74   3.66   3.68   3.68   4.02   4.44   4.44
GDT RMS_ALL_AT  15.13  15.15  15.15  15.20  15.20  15.20  15.18  15.18  15.09  15.05  14.94  14.94  14.91  14.91  14.80  14.77  14.77  14.65  14.54  14.54

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    30_A      D    30_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     5.911     0    0.062   0.070     7.857   33.929   29.810
LGA    E     2_A      E     2_A     0.884     0    0.632   1.235     6.938   86.905   52.222
LGA    Y     3_A      Y     3_A     0.282     0    0.071   0.133     0.750  100.000   93.651
LGA    V     4_A      V     4_A     0.277     0    0.036   0.089     0.460  100.000  100.000
LGA    R     5_A      R     5_A     0.329     0    0.028   1.088     4.039  100.000   84.545
LGA    A     6_A      A     6_A     0.385     0    0.032   0.045     0.410  100.000  100.000
LGA    L     7_A      L     7_A     0.441     0    0.108   0.977     2.629   95.238   87.857
LGA    F     8_A      F     8_A     0.449     0    0.043   0.158     2.156   97.619   86.017
LGA    D     9_A      D     9_A     0.852     0    0.024   0.922     3.004   92.857   80.060
LGA    H    10_A      H    10_A     0.653     0    0.017   1.129     2.608   88.214   81.905
LGA    T    11_A      T    11_A     0.642     0    0.588   1.039     2.461   86.429   80.816
LGA    G    12_A      G    12_A     2.876     0    0.075   0.075     2.876   65.119   65.119
LGA    H    13_A      H    13_A     2.832     0    0.579   1.288     4.958   52.262   47.810
LGA    D    14_A      D    14_A     0.954     0    0.025   1.105     5.786   63.333   51.012
LGA    E    15_A      E    15_A     6.897     0    0.632   0.960    12.928   16.905    8.201
LGA    Q    16_A      Q    16_A     8.350     0    0.629   1.000    10.813    3.810    2.804
LGA    E    17_A      E    17_A    12.189     0    0.071   0.649    15.816    0.000    0.000
LGA    L    18_A      L    18_A    19.337     0    0.075   1.393    23.706    0.000    0.000
LGA    P    19_A      P    19_A    24.802     0    0.035   0.041    27.451    0.000    0.000
LGA    F    20_A      F    20_A    30.614     0    0.032   1.432    32.664    0.000    0.000
LGA    K    21_A      K    21_A    37.279     0    0.050   0.539    39.976    0.000    0.000
LGA    K    22_A      K    22_A    40.258     0    0.030   0.830    46.111    0.000    0.000
LGA    G    23_A      G    23_A    42.364     0    0.062   0.062    42.364    0.000    0.000
LGA    E    24_A      E    24_A    38.578     0    0.032   1.095    39.379    0.000    0.000
LGA    I    25_A      I    25_A    36.402     0    0.064   0.605    41.412    0.000    0.000
LGA    L    26_A      L    26_A    30.065     0    0.047   0.118    32.048    0.000    0.000
LGA    R    27_A      R    27_A    28.238     0    0.031   0.107    32.316    0.000    0.000
LGA    I    28_A      I    28_A    21.152     0    0.047   0.108    23.887    0.000    0.000
LGA    R    29_A      R    29_A    20.999     0    0.616   1.263    27.551    0.000    0.000
LGA    D    30_A      D    30_A    17.045     0    0.666   1.078    19.452    0.000    0.000
LGA    K    31_A      K    31_A    15.033     0    0.319   0.649    21.391    0.000    0.000
LGA    P    32_A      P    32_A    14.068     0    0.043   0.363    16.319    0.000    0.000
LGA    E    33_A      E    33_A    11.188     0    0.718   1.296    14.495    0.476    0.212
LGA    E    34_A      E    34_A     7.111     0    0.253   0.841    11.112   17.500    8.995
LGA    Q    35_A      Q    35_A     0.709     0    0.637   1.260     4.941   82.143   64.074
LGA    L    36_A      L    36_A     0.798     0    0.079   1.282     2.809   88.214   81.964
LGA    W    37_A      W    37_A     0.739     0    0.000   0.204     1.459   92.857   87.925
LGA    N    38_A      N    38_A     0.655     0    0.029   0.778     3.067   90.476   79.048
LGA    A    39_A      A    39_A     0.260     0    0.019   0.034     0.417  100.000  100.000
LGA    E    40_A      E    40_A     0.234     0    0.025   0.161     0.808  100.000   96.825
LGA    N    41_A      N    41_A     0.344     0    0.032   0.240     1.186  100.000   96.488
LGA    V    42_A      V    42_A     0.684     0    0.057   0.126     1.344   90.476   87.891
LGA    E    43_A      E    43_A     0.359     0    0.201   0.379     1.321   92.976   92.698
LGA    G    44_A      G    44_A     0.453     0    0.047   0.047     0.561   97.619   97.619
LGA    K    45_A      K    45_A     0.496     0    0.082   0.888     5.592   97.619   75.397
LGA    R    46_A      R    46_A     0.196     0    0.042   0.108     0.965  100.000   95.671
LGA    G    47_A      G    47_A     0.339     0    0.022   0.022     0.379  100.000  100.000
LGA    L    48_A      L    48_A     0.489     0    0.023   0.110     0.726   95.238   92.857
LGA    I    49_A      I    49_A     0.556     0    0.015   0.603     1.618   95.238   90.655
LGA    H    50_A      H    50_A     0.556     0    0.010   0.087     0.781   90.476   91.429
LGA    V    51_A      V    51_A     0.551     0    0.038   0.113     0.611   95.238   93.197
LGA    V    52_A      V    52_A     0.574     0    0.121   1.089     3.134   92.857   84.762
LGA    L    53_A      L    53_A     0.508     0    0.095   1.044     3.146   95.238   84.464
LGA    V    54_A      V    54_A     0.357     0    0.035   0.104     0.519  100.000   98.639
LGA    E    55_A      E    55_A     0.127     0    0.035   0.337     1.751  100.000   91.799
LGA    K    56_A      K    56_A     0.078     0    0.100   0.828     3.353  100.000   84.709
LGA    Y    57_A      Y    57_A     0.261     0    0.594   0.490     3.373   90.833   75.873
LGA    G    58_A      G    58_A     3.761     0    0.112   0.112     6.887   32.024   32.024

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.040         12.958                 13.360           58.968   54.087

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    1.04    65.086    57.264     3.246

LGA_LOCAL      RMSD:   1.040  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.180  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.040  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.548590 * X  +   0.410360 * Y  +  -0.728460 * Z  + -127.357719
  Y_new =   0.200454 * X  +  -0.910410 * Y  +  -0.361900 * Z  + 123.765144
  Z_new =  -0.811706 * X  +   0.052512 * Y  +  -0.581700 * Z  +  78.363197 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.350326  0.947068  3.051564   [DEG:   20.0722   54.2630  174.8417 ]
ZXZ: -1.109711  2.191614 -1.506193   [DEG:  -63.5818  125.5702  -86.2985 ]
 
# END of job
