
#######################################################
#                                                     #
#                        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   71 (  560),  selected   69 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   69 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       3_B - 71_B        0.78     0.78
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       3_B - 71_B        0.78     0.78
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       3_B - 71_B        0.78     0.78
  LCS_AVERAGE:     97.18

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   69
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     V     3_B     V     3_B     69   69   69     44   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S     4_B     S     4_B     69   69   69     41   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K     5_B     K     5_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     W     6_B     W     6_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S     7_B     S     7_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T     8_B     T     8_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D     9_B     D     9_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    10_B     E    10_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    11_B     V    11_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    12_B     S    12_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    13_B     E    13_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    14_B     F    14_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    15_B     I    15_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    16_B     Q    16_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    17_B     S    17_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    18_B     L    18_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     P    19_B     P    19_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    20_B     G    20_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     C    21_B     C    21_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    22_B     E    22_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    23_B     E    23_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     H    24_B     H    24_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    25_B     G    25_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    26_B     K    26_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    27_B     V    27_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    28_B     F    28_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    29_B     K    29_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    30_B     D    30_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    31_B     E    31_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    32_B     Q    32_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    33_B     I    33_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    34_B     D    34_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    35_B     G    35_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    36_B     E    36_B     69   69   69     41   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    37_B     A    37_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    38_B     F    38_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    39_B     L    39_B     69   69   69     41   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    40_B     L    40_B     69   69   69     37   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    41_B     M    41_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T    42_B     T    42_B     69   69   69     13   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    43_B     Q    43_B     69   69   69     13   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T    44_B     T    44_B     69   69   69     22   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    45_B     D    45_B     69   69   69     45   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    46_B     I    46_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    47_B     V    47_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    48_B     K    48_B     69   69   69     24   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    49_B     I    49_B     69   69   69     24   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    50_B     M    50_B     69   69   69     24   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    51_B     S    51_B     69   69   69     32   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    52_B     I    52_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    53_B     K    53_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    54_B     E    54_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    55_B     G    55_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     P    56_B     P    56_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    57_B     A    57_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    58_B     E    58_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    59_B     K    59_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    60_B     I    60_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    61_B     F    61_B     69   69   69     46   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     N    62_B     N    62_B     69   69   69     44   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    63_B     S    63_B     69   69   69     37   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    64_B     I    64_B     69   69   69     31   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    65_B     L    65_B     69   69   69     32   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    66_B     M    66_B     69   69   69     19   64   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    67_B     F    67_B     69   69   69     19   46   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    68_B     K    68_B     69   69   69      8   42   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    69_B     A    69_B     69   69   69      8   42   57   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    70_B     A    70_B     69   69   69      8   20   57   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    71_B     E    71_B     69   69   69      8   13   39   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_AVERAGE  LCS_A:  97.18  (  97.18   97.18   97.18 )

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     46     64     66     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69 
GDT PERCENT_AT  64.79  90.14  92.96  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18
GDT RMS_LOCAL    0.33   0.49   0.57   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78
GDT RMS_ALL_AT   0.93   0.85   0.82   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78   0.78

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    28_B      F    28_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    61_B      F    61_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V     3_B      V     3_B     0.405     0    0.086   0.096     0.591   92.857   95.918
LGA    S     4_B      S     4_B     0.814     0    0.023   0.074     1.002   90.476   88.968
LGA    K     5_B      K     5_B     0.698     0    0.025   0.878     4.119   90.476   73.810
LGA    W     6_B      W     6_B     0.827     0    0.061   0.132     0.934   90.476   90.476
LGA    S     7_B      S     7_B     0.786     0    0.010   0.099     0.983   90.476   90.476
LGA    T     8_B      T     8_B     0.798     0    0.025   1.068     2.737   90.476   82.041
LGA    D     9_B      D     9_B     0.480     0    0.074   0.777     3.429   97.619   83.750
LGA    E    10_B      E    10_B     0.427     0    0.025   0.229     1.527  100.000   90.741
LGA    V    11_B      V    11_B     0.574     0    0.016   0.037     0.727   92.857   91.837
LGA    S    12_B      S    12_B     0.583     0    0.023   0.095     0.691   95.238   93.651
LGA    E    13_B      E    13_B     0.251     0    0.030   0.780     3.695  100.000   82.646
LGA    F    14_B      F    14_B     0.500     0    0.017   0.231     1.822   92.857   84.069
LGA    I    15_B      I    15_B     0.545     0    0.013   0.635     1.491   95.238   91.726
LGA    Q    16_B      Q    16_B     0.407     0    0.033   0.187     0.584   97.619   97.884
LGA    S    17_B      S    17_B     0.659     0    0.035   0.057     0.794   90.476   90.476
LGA    L    18_B      L    18_B     0.616     0    0.083   0.132     0.616   92.857   91.667
LGA    P    19_B      P    19_B     0.834     0    0.081   0.380     2.215   90.476   84.218
LGA    G    20_B      G    20_B     0.700     0    0.106   0.106     0.973   90.476   90.476
LGA    C    21_B      C    21_B     0.284     0    0.021   0.084     0.593  100.000   98.413
LGA    E    22_B      E    22_B     0.402     0    0.050   0.151     1.005  100.000   95.820
LGA    E    23_B      E    23_B     0.437     0    0.067   0.962     5.486   97.619   73.175
LGA    H    24_B      H    24_B     0.210     0    0.033   0.104     0.633  100.000   97.143
LGA    G    25_B      G    25_B     0.197     0    0.021   0.021     0.319  100.000  100.000
LGA    K    26_B      K    26_B     0.315     0    0.013   0.538     2.065  100.000   96.085
LGA    V    27_B      V    27_B     0.638     0    0.055   1.127     3.425   92.857   83.537
LGA    F    28_B      F    28_B     0.264     0    0.015   0.042     0.406  100.000  100.000
LGA    K    29_B      K    29_B     0.486     0    0.031   0.791     2.509   95.238   86.190
LGA    D    30_B      D    30_B     0.899     0    0.090   0.129     1.384   90.476   87.083
LGA    E    31_B      E    31_B     0.972     0    0.017   0.100     1.251   90.476   87.460
LGA    Q    32_B      Q    32_B     0.995     0    0.042   0.735     2.353   90.476   81.746
LGA    I    33_B      I    33_B     0.679     0    0.050   0.618     1.768   90.476   88.274
LGA    D    34_B      D    34_B     0.731     0    0.019   0.128     1.393   92.857   89.405
LGA    G    35_B      G    35_B     0.572     0    0.056   0.056     0.649   95.238   95.238
LGA    E    36_B      E    36_B     0.547     0    0.028   0.780     2.727   90.476   83.810
LGA    A    37_B      A    37_B     0.506     0    0.042   0.044     0.552   95.238   96.190
LGA    F    38_B      F    38_B     0.382     0    0.022   0.271     0.581  100.000   98.268
LGA    L    39_B      L    39_B     0.407     0    0.061   0.209     0.574   97.619   97.619
LGA    L    40_B      L    40_B     0.297     0    0.082   0.163     0.777   97.619   95.238
LGA    M    41_B      M    41_B     0.350     0    0.091   0.113     0.448  100.000  100.000
LGA    T    42_B      T    42_B     0.896     0    0.011   0.146     1.178   90.476   89.184
LGA    Q    43_B      Q    43_B     0.848     0    0.017   0.991     3.462   90.476   79.153
LGA    T    44_B      T    44_B     0.738     0    0.034   0.108     1.183   92.857   90.544
LGA    D    45_B      D    45_B     0.504     0    0.019   0.104     0.608   95.238   92.857
LGA    I    46_B      I    46_B     0.429     0    0.033   0.047     0.818  100.000   95.238
LGA    V    47_B      V    47_B     0.385     0    0.051   0.060     0.529  100.000   98.639
LGA    K    48_B      K    48_B     0.787     0    0.040   0.816     4.592   90.476   77.354
LGA    I    49_B      I    49_B     0.842     0    0.030   0.100     0.925   90.476   90.476
LGA    M    50_B      M    50_B     0.809     0    0.021   0.691     1.828   90.476   88.333
LGA    S    51_B      S    51_B     0.557     0    0.030   0.045     0.675   95.238   93.651
LGA    I    52_B      I    52_B     0.298     0    0.016   0.027     0.585  100.000   98.810
LGA    K    53_B      K    53_B     0.154     0    0.033   0.694     2.806  100.000   90.476
LGA    E    54_B      E    54_B     0.124     0    0.077   1.066     4.124  100.000   83.069
LGA    G    55_B      G    55_B     0.144     0    0.052   0.052     0.193  100.000  100.000
LGA    P    56_B      P    56_B     0.160     0    0.016   0.288     1.011  100.000   97.347
LGA    A    57_B      A    57_B     0.155     0    0.029   0.030     0.270  100.000  100.000
LGA    E    58_B      E    58_B     0.312     0    0.035   0.771     3.090  100.000   86.455
LGA    K    59_B      K    59_B     0.380     0    0.031   0.047     0.473  100.000  100.000
LGA    I    60_B      I    60_B     0.253     0    0.012   0.035     0.312  100.000  100.000
LGA    F    61_B      F    61_B     0.308     0    0.043   0.084     0.542  100.000   98.268
LGA    N    62_B      N    62_B     0.532     0    0.018   0.113     0.779   92.857   91.667
LGA    S    63_B      S    63_B     0.411     0    0.023   0.077     0.433  100.000  100.000
LGA    I    64_B      I    64_B     0.592     0    0.015   0.069     0.721   90.476   90.476
LGA    L    65_B      L    65_B     0.519     0    0.018   0.160     0.859   90.476   94.048
LGA    M    66_B      M    66_B     0.737     0    0.025   0.792     3.234   88.214   75.952
LGA    F    67_B      F    67_B     1.114     0    0.028   0.243     1.623   81.548   85.584
LGA    K    68_B      K    68_B     1.546     0    0.051   0.970     2.051   75.000   76.720
LGA    A    69_B      A    69_B     1.740     0    0.073   0.077     2.110   68.810   69.619
LGA    A    70_B      A    70_B     2.380     0    0.134   0.144     3.416   59.167   61.905
LGA    E    71_B      E    71_B     3.059     0    0.052   0.635     4.067   50.119   46.508

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       69     276    276  100.00     543    543  100.00                71
SUMMARY(RMSD_GDC):     0.784          0.812                  1.182           90.563   86.871

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   71   71    4.0     69    0.78    95.423    96.312     7.805

LGA_LOCAL      RMSD:   0.784  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.784  Number of assigned atoms:   69 
Std_ASGN_ATOMS RMSD:   0.784  Standard rmsd on all 69 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.235275 * X  +  -0.910983 * Y  +   0.338755 * Z  +  18.900333
  Y_new =   0.729524 * X  +   0.064779 * Y  +   0.680881 * Z  +  40.018250
  Z_new =  -0.642215 * X  +   0.407324 * Y  +   0.649343 * Z  +   3.150524 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.882770  0.697385  0.560242   [DEG:  107.8748   39.9572   32.0995 ]
ZXZ:  2.679927  0.864076 -1.005574   [DEG:  153.5485   49.5079  -57.6152 ]
 
# END of job
