
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , 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:    61       1_B - 61_B        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37      23_B - 59_B        1.00     2.01
  LCS_AVERAGE:     43.29

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     10   61   61      8   30   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     10   61   61      8   10   44   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     10   61   61      8   10   16   50   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     10   61   61      8   29   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     10   61   61      9   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     10   61   61      8   31   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     10   61   61      8   10   43   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     10   61   61      8   30   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     10   61   61      8   26   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     10   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B      6   61   61      5    5    6   34   39   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B      6   61   61      5    5    6    6    7    8   16   23   55   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B      6   61   61      5    5    6    6    7    8   10   14   21   42   56   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B      6   61   61      5    5    6   23   32   39   52   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B      7   61   61      5   23   43   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B      7   61   61      8   19   45   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B      7   61   61      5   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B      7   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B      7   61   61     11   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B      7   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B      7   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B      9   61   61      3    4   17   28   40   53   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     37   61   61     12   29   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     37   61   61     11   31   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     37   61   61      8   31   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     37   61   61      9   31   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     37   61   61      8   31   45   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     37   61   61      8   27   44   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     37   61   61      6   27   45   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     37   61   61     12   31   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     37   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     37   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     37   61   61     12   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     37   61   61     14   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     37   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     37   61   61     13   27   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     37   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     37   61   61     13   32   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     37   61   61     13   26   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     37   61   61     13   19   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     37   61   61     12   30   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     30   61   61     13   30   46   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     30   61   61     13   19   45   55   56   56   57   59   59   59   60   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  81.10  (  43.29  100.00  100.00 )

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     14     32     46     55     56     56     57     59     59     59     60     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  22.95  52.46  75.41  90.16  91.80  91.80  93.44  96.72  96.72  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.68   0.95   1.15   1.18   1.18   1.25   1.48   1.48   1.48   1.68   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91
GDT RMS_ALL_AT   2.04   2.01   1.96   1.93   1.93   1.93   1.94   1.92   1.92   1.92   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  D    22_B      D    22_B
#   possible swapping detected:  F    37_B      F    37_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     1.484     0    0.474   1.264     4.223   76.429   66.250
LGA    Y     2_B      Y     2_B     1.545     0    0.047   1.460    10.338   75.000   43.214
LGA    I     3_B      I     3_B     2.362     0    0.028   1.241     6.117   68.810   56.190
LGA    R     4_B      R     4_B     1.615     0    0.071   1.174     3.369   77.143   64.589
LGA    E     5_B      E     5_B     0.652     0    0.047   0.932     2.406   90.476   85.608
LGA    L     6_B      L     6_B     1.219     0    0.085   1.393     5.155   83.690   69.464
LGA    R     7_B      R     7_B     1.752     0    0.131   1.077     9.267   83.810   43.636
LGA    A     8_B      A     8_B     1.516     0    0.076   0.073     1.933   77.143   76.286
LGA    A     9_B      A     9_B     1.419     0    0.063   0.076     1.584   81.429   79.714
LGA    L    10_B      L    10_B     0.502     0    0.601   1.203     3.054   88.452   80.179
LGA    I    11_B      I    11_B     3.431     0    0.053   1.276    10.963   59.286   33.631
LGA    L    12_B      L    12_B     6.520     0    0.070   1.427    13.243   18.810    9.762
LGA    L    13_B      L    13_B     7.305     0    0.089   0.290    11.479   13.929    7.798
LGA    A    14_B      A    14_B     4.704     0    0.071   0.090     4.950   38.929   37.429
LGA    L    15_B      L    15_B     2.149     0    0.414   1.064     7.789   72.976   51.548
LGA    K    16_B      K    16_B     1.759     0    0.113   0.924     3.702   75.000   67.937
LGA    K    17_B      K    17_B     0.755     0    0.068   0.992     4.399   85.952   77.037
LGA    Q    18_B      Q    18_B     1.242     0    0.597   1.416     3.887   72.024   65.132
LGA    H    19_B      H    19_B     1.075     0    0.158   1.166     2.978   77.262   72.476
LGA    A    20_B      A    20_B     0.519     0    0.142   0.143     0.903   90.476   92.381
LGA    E    21_B      E    21_B     0.659     0    0.065   0.632     6.012   83.810   58.307
LGA    D    22_B      D    22_B     3.999     0    0.500   1.372     9.292   59.524   33.036
LGA    P    23_B      P    23_B     0.605     0    0.713   0.706     3.348   75.833   74.558
LGA    D    24_B      D    24_B     0.998     0    0.261   0.670     3.475   95.238   76.369
LGA    A    25_B      A    25_B     0.520     0    0.034   0.046     0.960   92.857   92.381
LGA    Q    26_B      Q    26_B     1.138     0    0.041   1.183     6.469   83.690   63.333
LGA    R    27_B      R    27_B     1.473     0    0.038   1.396     6.051   81.429   58.225
LGA    V    28_B      V    28_B     0.907     0    0.020   1.176     2.423   88.214   81.837
LGA    A    29_B      A    29_B     0.755     0    0.054   0.071     0.994   90.476   90.476
LGA    D    30_B      D    30_B     1.590     0    0.047   0.437     3.447   77.143   68.155
LGA    E    31_B      E    31_B     1.529     0    0.048   0.959     4.205   77.143   64.974
LGA    L    32_B      L    32_B     0.565     0    0.065   1.471     4.543   92.857   75.417
LGA    M    33_B      M    33_B     0.634     0    0.035   1.095     4.638   90.476   73.214
LGA    K    34_B      K    34_B     0.786     0    0.067   0.882     5.611   92.857   71.481
LGA    K    35_B      K    35_B     0.562     0    0.090   0.766     2.851   95.238   81.323
LGA    L    36_B      L    36_B     0.734     0    0.023   1.405     3.001   90.476   80.119
LGA    F    37_B      F    37_B     1.267     0    0.034   1.358     4.985   81.548   69.351
LGA    D    38_B      D    38_B     1.262     0    0.048   0.265     1.815   79.286   80.357
LGA    A    39_B      A    39_B     1.119     0    0.023   0.037     1.435   81.429   83.238
LGA    A    40_B      A    40_B     1.591     0    0.097   0.097     1.777   75.000   74.571
LGA    H    41_B      H    41_B     2.146     0    0.128   0.828     2.820   64.881   62.524
LGA    R    42_B      R    42_B     1.640     0    0.143   1.559     3.519   75.000   64.632
LGA    N    43_B      N    43_B     0.962     0    0.047   1.049     2.650   88.214   82.976
LGA    D    44_B      D    44_B     0.454     0    0.101   0.290     1.131   97.619   92.917
LGA    K    45_B      K    45_B     0.980     0    0.084   0.748     4.944   90.476   65.608
LGA    D    46_B      D    46_B     1.066     0    0.031   0.079     1.966   88.214   81.607
LGA    K    47_B      K    47_B     0.426     0    0.026   0.861     1.555   97.619   87.725
LGA    V    48_B      V    48_B     0.639     0    0.023   0.089     1.255   92.857   87.959
LGA    K    49_B      K    49_B     0.832     0    0.028   1.136     8.209   90.476   62.540
LGA    K    50_B      K    50_B     0.460     0    0.038   0.813     5.482   97.619   71.587
LGA    V    51_B      V    51_B     0.503     0    0.025   0.086     1.128   92.857   89.252
LGA    V    52_B      V    52_B     0.715     0    0.038   1.247     3.903   95.238   81.497
LGA    E    53_B      E    53_B     0.683     0    0.034   0.065     2.227   92.857   81.852
LGA    E    54_B      E    54_B     1.045     0    0.051   0.339     3.780   85.952   72.063
LGA    A    55_B      A    55_B     0.779     0    0.036   0.052     0.868   90.476   90.476
LGA    K    56_B      K    56_B     0.514     0    0.044   0.588     1.585   92.857   89.577
LGA    K    57_B      K    57_B     1.126     0    0.037   0.735     5.818   83.690   64.127
LGA    V    58_B      V    58_B     1.601     0    0.085   0.118     2.563   77.143   71.905
LGA    V    59_B      V    59_B     1.403     0    0.078   0.254     1.926   81.429   80.204
LGA    S    60_B      S    60_B     1.027     0    0.180   0.208     2.075   77.262   83.254
LGA    T    61_B      T    61_B     1.670     0    0.035   0.973     4.016   70.952   63.401

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     1.906          1.803                  3.072           80.578   69.814

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     59    1.48    84.836    91.767     3.734

LGA_LOCAL      RMSD:   1.480  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.921  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.906  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.171812 * X  +  -0.661977 * Y  +  -0.729566 * Z  +  10.427645
  Y_new =  -0.186625 * X  +   0.705297 * Y  +  -0.683906 * Z  +   2.679257
  Z_new =   0.967291 * X  +   0.253659 * Y  +  -0.002363 * Z  +  -2.472331 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.826701 -1.314324  1.580112   [DEG:  -47.3665  -75.3052   90.5338 ]
ZXZ: -0.817690  1.573159  1.314335   [DEG:  -46.8502   90.1354   75.3058 ]
 
# END of job
