
#######################################################
#                                                     #
#                        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:    33       6_C - 38_C        4.93     6.83
  LCS_AVERAGE:     57.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       6_C - 19_C        1.84    10.93
  LCS_AVERAGE:     19.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       9_C - 18_C        0.94    10.20
  LONGEST_CONTINUOUS_SEGMENT:    10      10_C - 19_C        0.73     9.70
  LCS_AVERAGE:     11.76

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   14   33      2    4    8   15   16   17   20   20   22   22   24   28   34   38   42   44   46   47   48   48 
LCS_GDT     T     7_C     T     7_C      3   14   33      3    3    5    5    8   12   16   19   20   22   24   29   35   39   43   44   46   47   48   48 
LCS_GDT     K     8_C     K     8_C      5   14   33      3    4    8   15   16   17   20   20   22   23   27   31   38   39   43   44   46   47   48   48 
LCS_GDT     I     9_C     I     9_C     10   14   33      3    6   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     L    10_C     L    10_C     10   14   33      6    9   10   12   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     P    11_C     P    11_C     10   14   33      6    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     C    12_C     C    12_C     10   14   33      6    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     P    13_C     P    13_C     10   14   33      6    9   10   15   16   17   20   20   22   26   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     R    14_C     R    14_C     10   14   33      6    9   10   15   16   17   20   20   22   23   28   33   38   39   43   44   46   47   48   48 
LCS_GDT     C    15_C     C    15_C     10   14   33      6    9   10   15   16   17   20   20   22   25   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     N    16_C     N    16_C     10   14   33      6    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     S    17_C     S    17_C     10   14   33      3    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     M    18_C     M    18_C     10   14   33      3    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     E    19_C     E    19_C     10   14   33      3    8   10   12   14   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     T    20_C     T    20_C      9   13   33      3    7    9   11   12   13   15   19   22   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     K    21_C     K    21_C      9   13   33      3    7    9   11   12   13   15   16   19   21   26   32   38   39   43   44   46   47   48   48 
LCS_GDT     F    22_C     F    22_C      9   13   33      3    4    9   11   12   13   15   16   19   21   26   32   38   39   43   44   46   47   48   48 
LCS_GDT     C    23_C     C    23_C      4    7   33      3    4    5    6    6    9   13   16   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     Y    24_C     Y    24_C      4    7   33      3    4    5    6    6    9   12   16   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     Y    25_C     Y    25_C      4    7   33      3    3    5    6    6    9   12   15   23   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     N    26_C     N    26_C      4    7   33      3    3    5    6    9   10   12   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     N    27_C     N    27_C      4    7   33      3    3    5    5    6    9   11   16   19   24   29   33   38   39   43   44   46   47   48   48 
LCS_GDT     Y    28_C     Y    28_C      3    7   33      3    4    6    7    9   11   14   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     N    29_C     N    29_C      3    7   33      3    4    6    7    9   11   14   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     V    30_C     V    30_C      3    7   33      3    3    5    5    9   11   14   16   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     N    31_C     N    31_C      3    7   33      3    3    6    7    9   11   14   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     Q    32_C     Q    32_C      4    7   33      3    3    4    6   10   12   13   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     P    33_C     P    33_C      4    7   33      3    3    5    7   10   12   13   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     R    34_C     R    34_C      5    8   33      3    5    6    8   10   12   18   18   20   23   29   33   38   39   43   44   46   47   48   48 
LCS_GDT     H    35_C     H    35_C      5    8   33      3    5    6    8   10   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     F    36_C     F    36_C      5    8   33      3    5    6    8   10   13   20   20   23   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     C    37_C     C    37_C      5    8   33      4    9   10   15   16   17   20   20   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     K    38_C     K    38_C      5    8   33      4    5    7   15   16   17   20   20   22   23   27   34   36   39   43   44   46   47   48   48 
LCS_GDT     A    39_C     A    39_C      5    8   32      4    5    6    8    9   12   20   20   22   22   24   25   31   34   40   44   46   46   48   48 
LCS_GDT     C    40_C     C    40_C      5    8   32      4    5    8   15   16   17   20   20   22   22   24   26   31   34   37   44   46   47   48   48 
LCS_GDT     Q    41_C     Q    41_C      5    8   22      3    5    6   15   16   17   20   20   22   22   24   25   29   33   35   39   43   46   47   48 
LCS_GDT     R    42_C     R    42_C      3    4   22      3    3    3    4    6    9   10   19   22   22   24   31   34   39   41   44   46   47   48   48 
LCS_GDT     Y    43_C     Y    43_C      3    4   22      1    3    4    7    9   15   15   16   18   25   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     W    44_C     W    44_C      3    3   22      3    3    5    9   13   15   15   16   18   26   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     T    45_C     T    45_C      4    5   22      4    4    4    9   13   15   15   16   18   22   28   34   36   39   43   44   46   47   48   48 
LCS_GDT     S    46_C     S    46_C      4   10   22      4    4    6    7    9   11   14   16   17   18   20   21   21   25   28   28   31   36   40   41 
LCS_GDT     G    47_C     G    47_C      4   10   22      4    4    4    5    6    9   11   13   17   18   19   21   21   22   25   27   31   32   36   39 
LCS_GDT     G    48_C     G    48_C      7   10   22      4    4    6    9   13   15   15   16   18   21   27   33   36   39   40   44   46   47   48   48 
LCS_GDT     T    49_C     T    49_C      7   10   22      3    5    6    9   13   15   15   16   18   23   28   34   36   39   43   44   46   47   48   48 
LCS_GDT     M    50_C     M    50_C      7   10   22      3    5    6    9   13   15   15   16   22   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     R    51_C     R    51_C      7   10   22      4    5    6    9   13   15   15   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     S    52_C     S    52_C      7   10   22      4    5    6    9   13   15   15   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     V    53_C     V    53_C      7   10   22      4    5    6    9   13   15   15   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     P    54_C     P    54_C      7   10   22      4    5    6    9   13   15   15   16   24   26   30   33   38   39   43   44   46   47   48   48 
LCS_GDT     I    55_C     I    55_C      4   10   22      3    4    6    7   13   15   15   18   24   27   30   34   38   39   43   44   46   47   48   48 
LCS_GDT     G    56_C     G    56_C      4    9   22      3    4    5    6    7    9   12   15   19   22   30   32   36   38   43   44   46   47   48   48 
LCS_AVERAGE  LCS_A:  29.63  (  11.76   19.26   57.86 )

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      6      9     10     15     16     17     20     20     24     27     30     34     38     39     43     44     46     47     48     48 
GDT PERCENT_AT  11.76  17.65  19.61  29.41  31.37  33.33  39.22  39.22  47.06  52.94  58.82  66.67  74.51  76.47  84.31  86.27  90.20  92.16  94.12  94.12
GDT RMS_LOCAL    0.23   0.52   0.65   1.58   1.63   1.76   2.10   2.10   3.64   3.81   4.01   4.45   4.75   4.81   5.13   5.24   5.42   5.56   5.70   5.70
GDT RMS_ALL_AT   9.43   9.62   9.74  11.73  11.67  11.49  11.39  11.39   6.79   6.64   6.76   6.48   6.61   6.60   6.52   6.49   6.47   6.45   6.44   6.44

# Checking swapping
#   possible swapping detected:  Y    25_C      Y    25_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     1.890     2    0.653   0.621     5.648   50.595   39.320
LGA    T     7_C      T     7_C     5.295     0    0.682   1.376     8.537   42.381   26.667
LGA    K     8_C      K     8_C     1.639     4    0.581   0.582     2.926   65.000   35.238
LGA    I     9_C      I     9_C     1.391     0    0.088   0.152     4.293   79.405   65.000
LGA    L    10_C      L    10_C     2.338     0    0.060   0.960     6.802   75.119   51.964
LGA    P    11_C      P    11_C     2.205     0    0.065   0.134     3.287   60.952   57.279
LGA    C    12_C      C    12_C     1.281     0    0.057   0.148     1.480   81.429   82.937
LGA    P    13_C      P    13_C     1.988     0    0.041   0.147     2.317   72.857   70.544
LGA    R    14_C      R    14_C     1.272     0    0.085   1.418     9.359   81.429   49.740
LGA    C    15_C      C    15_C     1.609     0    0.103   0.568     2.555   72.976   70.317
LGA    N    16_C      N    16_C     2.207     0    0.136   0.311     4.552   72.976   56.726
LGA    S    17_C      S    17_C     1.234     0    0.094   0.176     2.435   81.429   77.222
LGA    M    18_C      M    18_C     1.427     0    0.213   1.297     5.180   77.143   62.440
LGA    E    19_C      E    19_C     3.427     4    0.296   0.297     4.876   43.929   23.016
LGA    T    20_C      T    20_C     5.712     0    0.110   1.051     7.337   25.476   23.537
LGA    K    21_C      K    21_C     9.193     0    0.608   1.220    13.715    1.786    0.847
LGA    F    22_C      F    22_C    10.533     0    0.035   1.335    18.893    0.476    0.173
LGA    C    23_C      C    23_C     8.260     0    0.604   0.912     8.877    3.333    8.254
LGA    Y    24_C      Y    24_C    10.444     0    0.072   1.395    11.396    0.238    4.048
LGA    Y    25_C      Y    25_C    11.105     0    0.208   1.067    13.371    0.000    0.000
LGA    N    26_C      N    26_C    10.629     0    0.211   0.516    11.005    0.000    0.357
LGA    N    27_C      N    27_C    12.101     0    0.195   0.902    16.015    0.000    0.060
LGA    Y    28_C      Y    28_C    17.009     0    0.676   1.229    19.131    0.000    0.000
LGA    N    29_C      N    29_C    19.368     0    0.154   0.196    21.859    0.000    0.000
LGA    V    30_C      V    30_C    18.328     0    0.642   0.909    18.918    0.000    0.000
LGA    N    31_C      N    31_C    17.566     0    0.288   1.025    22.343    0.000    0.000
LGA    Q    32_C      Q    32_C    10.395     0    0.492   1.065    13.085    0.714    0.370
LGA    P    33_C      P    33_C     8.275     0    0.044   0.417    10.160   11.190    6.803
LGA    R    34_C      R    34_C     5.034     0    0.128   0.553    10.004   24.048   13.377
LGA    H    35_C      H    35_C     2.738     0    0.049   0.239     3.822   50.119   59.190
LGA    F    36_C      F    36_C     3.295     0    0.130   1.275     8.381   61.190   32.727
LGA    C    37_C      C    37_C     1.677     0    0.351   0.515     3.039   79.643   70.952
LGA    K    38_C      K    38_C     1.340     0    0.154   0.861     7.141   72.976   50.053
LGA    A    39_C      A    39_C     3.348     0    0.103   0.125     4.266   53.571   50.286
LGA    C    40_C      C    40_C     1.281     0    0.241   0.828     1.961   79.286   78.571
LGA    Q    41_C      Q    41_C     1.946     0    0.423   1.366     7.419   72.857   49.153
LGA    R    42_C      R    42_C     5.916     0    0.574   1.315    15.718   18.333    7.576
LGA    Y    43_C      Y    43_C    11.060     0    0.598   1.479    18.346    0.714    0.238
LGA    W    44_C      W    44_C    11.840     0    0.576   0.819    16.519    0.000    0.000
LGA    T    45_C      T    45_C    15.435     0    0.598   1.042    18.547    0.000    0.000
LGA    S    46_C      S    46_C    21.690     0    0.177   0.617    24.228    0.000    0.000
LGA    G    47_C      G    47_C    25.065     0    0.287   0.287    25.065    0.000    0.000
LGA    G    48_C      G    48_C    19.788     0    0.663   0.663    21.187    0.000    0.000
LGA    T    49_C      T    49_C    19.446     0    0.040   1.124    23.229    0.000    0.000
LGA    M    50_C      M    50_C    15.077     0    0.025   1.429    17.437    0.000    0.000
LGA    R    51_C      R    51_C    15.711     0    0.100   1.220    27.231    0.000    0.000
LGA    S    52_C      S    52_C    14.224     0    0.054   0.715    17.460    0.000    0.000
LGA    V    53_C      V    53_C    15.640     0    0.203   1.229    17.751    0.000    0.000
LGA    P    54_C      P    54_C    16.897     0    0.194   0.271    19.907    0.000    0.000
LGA    I    55_C      I    55_C    15.060     0    0.134   1.609    16.944    0.000    0.357
LGA    G    56_C      G    56_C    18.950     0    0.060   0.060    20.400    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):     6.396          6.403                  7.366           29.678   24.026

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     20    2.10    43.137    37.469     0.910

LGA_LOCAL      RMSD:   2.099  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.386  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.396  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.426276 * X  +   0.133152 * Y  +   0.894740 * Z  + -58.569607
  Y_new =  -0.872923 * X  +  -0.319978 * Y  +  -0.368265 * Z  +  10.006884
  Z_new =   0.237262 * X  +  -0.938022 * Y  +   0.252630 * Z  +  -1.207027 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.025066 -0.239546 -1.307716   [DEG: -116.0277  -13.7250  -74.9266 ]
ZXZ:  1.180340  1.315398  2.893850   [DEG:   67.6285   75.3668  165.8054 ]
 
# END of job
