
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       6_C - 51_C        4.45     6.81
  LCS_AVERAGE:     86.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       6_C - 29_C        1.93     7.89
  LCS_AVERAGE:     33.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       8_C - 24_C        0.97     7.93
  LCS_AVERAGE:     18.80

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3   24   46      3    3   21   26   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     T     7_C     T     7_C      8   24   46      3    7    7    9   20   31   35   37   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     K     8_C     K     8_C     17   24   46      7   14   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     I     9_C     I     9_C     17   24   46      7   14   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     L    10_C     L    10_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     P    11_C     P    11_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     C    12_C     C    12_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     P    13_C     P    13_C     17   24   46      3   11   19   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     R    14_C     R    14_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     C    15_C     C    15_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     N    16_C     N    16_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     S    17_C     S    17_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     M    18_C     M    18_C     17   24   46      4   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     E    19_C     E    19_C     17   24   46      3   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     T    20_C     T    20_C     17   24   46      7   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     K    21_C     K    21_C     17   24   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     F    22_C     F    22_C     17   24   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     C    23_C     C    23_C     17   24   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Y    24_C     Y    24_C     17   24   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Y    25_C     Y    25_C      8   24   46      3    4    8   13   22   32   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     N    26_C     N    26_C      3   24   46      6   15   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     N    27_C     N    27_C      3   24   46      3   12   22   27   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Y    28_C     Y    28_C      5   24   46      3    5   11   19   29   32   35   37   38   39   40   41   43   43   44   45   45   46   49   49 
LCS_GDT     N    29_C     N    29_C      5   24   46      3    5   21   27   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     V    30_C     V    30_C      5   23   46      3    5    8   16   22   29   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     N    31_C     N    31_C      5   11   46      4    5    8   16   17   21   33   38   38   39   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Q    32_C     Q    32_C      5   13   46      4   11   19   24   32   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     P    33_C     P    33_C      5   13   46      4   10   19   27   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     R    34_C     R    34_C      9   13   46      5   13   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     H    35_C     H    35_C      9   13   46      3    9   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     F    36_C     F    36_C      9   13   46      5    7   14   26   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     C    37_C     C    37_C      9   13   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     K    38_C     K    38_C      9   13   46      6   16   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     A    39_C     A    39_C      9   13   46      4    8   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     C    40_C     C    40_C      9   13   46      6   13   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Q    41_C     Q    41_C      9   13   46      4   11   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     R    42_C     R    42_C      9   13   46      3    7   18   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     Y    43_C     Y    43_C      7   13   46      6    8   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     W    44_C     W    44_C      7   13   46      6    9   22   28   33   34   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     T    45_C     T    45_C      5   13   46      4    5    7   19   28   33   35   38   38   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     S    46_C     S    46_C      5   10   46      4    5    5    7   10   16   22   26   37   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     G    47_C     G    47_C      5    8   46      3    5    5    6    9   12   16   21   26   28   36   42   43   43   44   45   45   46   49   49 
LCS_GDT     G    48_C     G    48_C      5    8   46      4    5    5    7   10   13   18   23   32   40   41   42   43   43   44   45   45   46   49   49 
LCS_GDT     T    49_C     T    49_C      4    8   46      4    4    5    7   10   12   14   20   23   28   34   42   43   43   44   45   45   46   49   49 
LCS_GDT     M    50_C     M    50_C      4    8   46      4    4    5    7   10   11   13   16   18   21   26   29   37   42   44   45   45   46   49   49 
LCS_GDT     R    51_C     R    51_C      4    8   46      3    4    5    7   10   11   13   14   17   18   19   21   26   29   34   40   43   45   49   49 
LCS_GDT     S    52_C     S    52_C      4    8   25      3    4    4    5    7    9    9   13   16   18   19   20   21   23   24   28   29   35   38   40 
LCS_GDT     V    53_C     V    53_C      4    8   25      3    4    4    7   10   11   13   14   17   18   19   21   23   27   31   35   37   44   49   49 
LCS_GDT     P    54_C     P    54_C      4    8   25      3    4    4    7   10   11   13   14   17   18   19   20   21   24   31   34   35   40   41   46 
LCS_GDT     I    55_C     I    55_C      3    8   25      3    3    4    7   10   11   13   14   17   18   19   21   24   27   34   35   42   44   49   49 
LCS_GDT     G    56_C     G    56_C      3    6   25      3    3    4    5    7    8   10   12   16   17   23   25   28   33   36   40   43   46   49   49 
LCS_AVERAGE  LCS_A:  46.26  (  18.80   33.83   86.16 )

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      7     16     22     28     33     34     35     38     38     40     41     42     43     43     44     45     45     46     49     49 
GDT PERCENT_AT  13.73  31.37  43.14  54.90  64.71  66.67  68.63  74.51  74.51  78.43  80.39  82.35  84.31  84.31  86.27  88.24  88.24  90.20  96.08  96.08
GDT RMS_LOCAL    0.26   0.72   0.98   1.26   1.49   1.56   1.69   2.13   2.08   2.72   2.82   3.13   3.22   3.22   3.56   3.93   3.93   4.52   5.55   5.55
GDT RMS_ALL_AT   7.39   8.12   8.30   8.09   7.95   7.90   7.84   7.87   7.87   7.52   7.51   7.40   7.46   7.46   7.26   7.05   7.05   6.74   6.32   6.32

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     3.049     2    0.033   0.040     5.580   39.524   27.891
LGA    T     7_C      T     7_C     5.564     0    0.096   1.128     9.286   29.405   20.884
LGA    K     8_C      K     8_C     2.595     4    0.096   0.144     3.404   59.167   31.852
LGA    I     9_C      I     9_C     1.647     0    0.053   0.719     3.961   72.857   72.440
LGA    L    10_C      L    10_C     1.336     0    0.064   0.120     1.758   81.429   79.286
LGA    P    11_C      P    11_C     0.771     0    0.018   0.053     1.008   90.476   89.184
LGA    C    12_C      C    12_C     0.898     0    0.039   0.092     1.401   90.476   88.968
LGA    P    13_C      P    13_C     1.445     0    0.046   0.114     2.205   81.429   75.442
LGA    R    14_C      R    14_C     0.696     0    0.079   1.417     9.605   90.476   54.156
LGA    C    15_C      C    15_C     0.871     0    0.036   0.876     2.487   90.476   86.190
LGA    N    16_C      N    16_C     0.555     0    0.178   0.278     1.581   90.476   86.012
LGA    S    17_C      S    17_C     0.807     0    0.040   0.422     1.072   88.214   89.048
LGA    M    18_C      M    18_C     1.358     0    0.738   1.043     3.025   73.571   70.179
LGA    E    19_C      E    19_C     1.480     4    0.046   0.044     1.858   79.286   43.333
LGA    T    20_C      T    20_C     0.839     0    0.008   0.095     1.377   95.238   89.320
LGA    K    21_C      K    21_C     0.513     0    0.082   1.062     3.792   86.071   72.063
LGA    F    22_C      F    22_C     0.660     0    0.065   1.312     8.446   92.857   55.498
LGA    C    23_C      C    23_C     1.723     0    0.572   0.926     4.801   60.714   62.381
LGA    Y    24_C      Y    24_C     1.697     0    0.148   1.322    12.666   71.071   33.968
LGA    Y    25_C      Y    25_C     3.843     0    0.616   1.167    12.436   51.905   20.079
LGA    N    26_C      N    26_C     1.792     0    0.314   0.706     5.430   77.143   58.512
LGA    N    27_C      N    27_C     0.891     0    0.303   1.010     6.516   88.214   59.524
LGA    Y    28_C      Y    28_C     5.426     0    0.336   1.430    15.422   34.524   12.817
LGA    N    29_C      N    29_C     2.090     0    0.614   0.797     3.464   57.381   62.262
LGA    V    30_C      V    30_C     4.457     0    0.197   0.178     6.994   37.619   28.912
LGA    N    31_C      N    31_C     5.078     0    0.306   0.503     9.016   34.524   20.536
LGA    Q    32_C      Q    32_C     2.403     0    0.110   0.841     5.290   67.262   54.286
LGA    P    33_C      P    33_C     1.694     0    0.623   0.574     2.759   71.071   69.524
LGA    R    34_C      R    34_C     3.073     0    0.344   0.972     8.182   47.381   31.126
LGA    H    35_C      H    35_C     2.666     0    0.089   0.983     4.876   55.357   48.524
LGA    F    36_C      F    36_C     2.585     0    0.093   1.342     5.853   69.048   52.294
LGA    C    37_C      C    37_C     0.748     0    0.155   0.824     1.800   83.810   84.524
LGA    K    38_C      K    38_C     1.194     0    0.034   0.698     5.444   77.381   65.026
LGA    A    39_C      A    39_C     2.181     0    0.528   0.550     3.565   61.429   60.571
LGA    C    40_C      C    40_C     1.565     0    0.323   0.910     2.781   70.833   70.317
LGA    Q    41_C      Q    41_C     2.139     0    0.077   0.763     3.459   70.833   62.434
LGA    R    42_C      R    42_C     2.044     0    0.620   1.160     7.748   56.548   49.307
LGA    Y    43_C      Y    43_C     1.410     0    0.385   0.337     2.467   77.381   73.690
LGA    W    44_C      W    44_C     1.388     0    0.391   1.280     8.343   75.119   42.857
LGA    T    45_C      T    45_C     3.567     0    0.626   0.899     6.565   38.333   32.789
LGA    S    46_C      S    46_C     7.676     0    0.446   0.750     9.738    6.905    5.635
LGA    G    47_C      G    47_C    10.844     0    0.443   0.443    11.473    0.357    0.357
LGA    G    48_C      G    48_C     9.609     0    0.502   0.502    12.549    0.238    0.238
LGA    T    49_C      T    49_C    12.672     0    0.057   1.158    13.892    0.000    0.000
LGA    M    50_C      M    50_C    14.159     0    0.555   1.185    18.229    0.000    0.000
LGA    R    51_C      R    51_C    17.719     0    0.648   0.920    19.595    0.000    0.000
LGA    S    52_C      S    52_C    21.201     0    0.499   0.770    23.705    0.000    0.000
LGA    V    53_C      V    53_C    18.019     0    0.206   1.272    20.656    0.000    0.000
LGA    P    54_C      P    54_C    22.016     0    0.445   0.513    22.990    0.000    0.000
LGA    I    55_C      I    55_C    19.021     0    0.600   1.086    20.745    0.000    0.000
LGA    G    56_C      G    56_C    18.898     0    0.533   0.533    20.039    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     6.238          6.256                  6.896           54.388   44.985

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     38    2.13    62.255    57.908     1.702

LGA_LOCAL      RMSD:   2.132  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.865  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.238  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.601784 * X  +   0.185108 * Y  +  -0.776911 * Z  + -18.137678
  Y_new =  -0.775649 * X  +   0.367277 * Y  +  -0.513299 * Z  + -24.285780
  Z_new =   0.190326 * X  +   0.911506 * Y  +   0.364601 * Z  +  -1.377684 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.910958 -0.191494  1.190292   [DEG:  -52.1941  -10.9718   68.1987 ]
ZXZ: -0.986942  1.197592  0.205846   [DEG:  -56.5476   68.6170   11.7941 ]
 
# END of job
