
#######################################################
#                                                     #
#                        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:    51       6_C - 56_C        2.13     2.13
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.56     2.16
  LCS_AVERAGE:     98.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       7_C - 52_C        0.97     2.27
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.86     2.24
  LCS_AVERAGE:     84.62

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   49   51      0    3    3    3    5    6    7    7    9   25   35   41   46   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     46   50   51      3    5   12   33   45   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   50   51      3   21   44   44   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   50   51     18   41   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   50   51     18   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   50   51     26   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   50   51     12   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   50   51     22   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   50   51      8   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   50   51     20   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   50   51     21   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   50   51     26   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   50   51     29   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   50   51     24   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   50   51     22   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   50   51      3   42   44   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   50   51      3   10   40   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   50   51      4   29   41   45   46   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     12   50   51      3    4    6   16   33   47   48   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     12   50   51      3    8   16   30   42   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     12   50   51      3    4   16   25   42   47   49   50   50   50   50   50   50   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  94.21  (  84.62   98.00  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     29     42     44     45     46     47     49     50     50     50     50     50     50     51     51     51     51     51     51     51 
GDT PERCENT_AT  56.86  82.35  86.27  88.24  90.20  92.16  96.08  98.04  98.04  98.04  98.04  98.04  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.52   0.65   0.78   0.86   1.22   1.42   1.56   1.56   1.56   1.56   1.56   1.56   2.13   2.13   2.13   2.13   2.13   2.13   2.13
GDT RMS_ALL_AT   2.39   2.31   2.32   2.25   2.24   2.21   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.13   2.13   2.13   2.13   2.13   2.13   2.13

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C    10.805     2    0.127   0.149    12.825    1.429    0.816
LGA    T     7_C      T     7_C     4.493     0    0.658   0.534     6.560   35.952   36.531
LGA    K     8_C      K     8_C     2.695     4    0.169   0.187     3.253   61.190   35.291
LGA    I     9_C      I     9_C     1.338     0    0.053   0.728     3.575   77.143   74.583
LGA    L    10_C      L    10_C     1.045     0    0.034   0.184     2.301   85.952   81.607
LGA    P    11_C      P    11_C     0.572     0    0.021   0.051     0.882   90.476   90.476
LGA    C    12_C      C    12_C     0.678     0    0.015   0.084     1.048   90.476   88.968
LGA    P    13_C      P    13_C     1.081     0    0.028   0.270     1.994   83.690   81.497
LGA    R    14_C      R    14_C     1.359     0    0.079   0.960     4.219   79.286   72.814
LGA    C    15_C      C    15_C     1.165     0    0.033   0.174     1.281   81.429   81.429
LGA    N    16_C      N    16_C     0.816     0    0.107   0.198     1.513   90.476   86.012
LGA    S    17_C      S    17_C     0.845     0    0.037   0.123     0.954   90.476   90.476
LGA    M    18_C      M    18_C     0.449     0    0.032   0.616     1.575   92.857   90.655
LGA    E    19_C      E    19_C     0.753     4    0.023   0.029     0.811   90.476   50.265
LGA    T    20_C      T    20_C     0.729     0    0.046   0.103     0.955   90.476   90.476
LGA    K    21_C      K    21_C     0.632     0    0.020   0.524     1.504   90.476   87.513
LGA    F    22_C      F    22_C     0.595     0    0.020   0.042     0.637   90.476   90.476
LGA    C    23_C      C    23_C     0.602     0    0.083   0.090     0.878   90.476   90.476
LGA    Y    24_C      Y    24_C     0.532     0    0.021   0.028     1.602   95.238   86.825
LGA    Y    25_C      Y    25_C     0.271     0    0.062   0.091     0.743  100.000   96.825
LGA    N    26_C      N    26_C     0.624     0    0.076   0.334     1.823   90.476   84.940
LGA    N    27_C      N    27_C     1.085     0    0.016   0.109     1.893   88.214   81.607
LGA    Y    28_C      Y    28_C     0.952     0    0.038   0.070     2.836   90.476   75.437
LGA    N    29_C      N    29_C     0.372     0    0.049   0.192     0.927  100.000   97.619
LGA    V    30_C      V    30_C     0.677     0    0.016   1.153     3.352   90.476   82.177
LGA    N    31_C      N    31_C     0.649     0    0.043   0.390     1.112   90.476   91.726
LGA    Q    32_C      Q    32_C     0.402     0    0.015   0.798     3.698   95.238   82.116
LGA    P    33_C      P    33_C     0.699     0    0.049   0.066     0.879   90.476   90.476
LGA    R    34_C      R    34_C     0.784     0    0.054   0.875     3.622   90.476   76.753
LGA    H    35_C      H    35_C     0.625     0    0.061   0.202     1.046   90.476   89.571
LGA    F    36_C      F    36_C     1.187     0    0.028   0.115     1.829   81.429   79.091
LGA    C    37_C      C    37_C     1.114     0    0.053   0.131     1.481   81.429   82.937
LGA    K    38_C      K    38_C     0.907     0    0.011   0.477     1.846   88.214   85.503
LGA    A    39_C      A    39_C     0.924     0    0.084   0.086     1.035   88.214   88.667
LGA    C    40_C      C    40_C     1.533     0    0.024   0.032     1.724   75.000   74.286
LGA    Q    41_C      Q    41_C     1.708     0    0.035   0.831     3.249   72.857   69.418
LGA    R    42_C      R    42_C     1.596     0    0.056   1.342     8.244   72.857   48.615
LGA    Y    43_C      Y    43_C     1.148     0    0.034   0.106     1.275   81.429   81.429
LGA    W    44_C      W    44_C     0.958     0    0.030   0.167     1.128   90.476   88.537
LGA    T    45_C      T    45_C     0.632     0    0.043   0.142     0.857   90.476   90.476
LGA    S    46_C      S    46_C     0.534     0    0.027   0.031     0.629   90.476   90.476
LGA    G    47_C      G    47_C     0.570     0    0.053   0.053     0.817   90.476   90.476
LGA    G    48_C      G    48_C     0.709     0    0.058   0.058     0.709   92.857   92.857
LGA    T    49_C      T    49_C     0.441     0    0.075   0.104     0.723   95.238   97.279
LGA    M    50_C      M    50_C     0.407     0    0.046   0.725     4.341   95.238   76.131
LGA    R    51_C      R    51_C     1.252     0    0.024   0.262     5.869   88.214   58.095
LGA    S    52_C      S    52_C     1.682     0    0.065   0.135     2.850   79.286   73.175
LGA    V    53_C      V    53_C     1.622     0    0.090   1.111     3.307   70.952   67.483
LGA    P    54_C      P    54_C     4.607     0    0.131   0.330     5.760   38.810   35.918
LGA    I    55_C      I    55_C     3.809     0    0.100   1.355     5.201   38.690   36.726
LGA    G    56_C      G    56_C     4.275     0    0.689   0.689     4.785   35.833   35.833

# 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):     2.134          2.106                  2.198           81.641   76.467

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     50    1.56    92.157    94.418     3.007

LGA_LOCAL      RMSD:   1.563  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.164  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.134  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.651805 * X  +  -0.266784 * Y  +  -0.709913 * Z  + -30.107540
  Y_new =   0.268064 * X  +   0.956703 * Y  +  -0.113405 * Z  +  -6.545334
  Z_new =   0.709430 * X  +  -0.116384 * Y  +   0.695099 * Z  +   6.893938 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.390179 -0.788690 -0.165896   [DEG:   22.3556  -45.1886   -9.5051 ]
ZXZ: -1.412389  0.802238  1.733401   [DEG:  -80.9239   45.9649   99.3165 ]
 
# END of job
