 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0060.inter 
CONANA-PAIR            ../CONANA/T0060.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0060.1gif_A.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0060.1fim.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
           TARGET 884 atoms, MODEL 884 atoms, 884 common with TARGET 
           Number of atoms possible to evaluate: 884 
 
 
 CA-RMS TARGET<->PARENT(1gif-A)	 1.091738 
 
 CA-RMS TARGET<->PARENT(1fim)	 1.538250 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    35.05           90.1   232   100.0   232     ARMSMC  
     WELL ORDERED  . . . . .    35.05           90.1   232   100.0   232     ARMSMC  
     NO INTER CONTACTS . . .    29.83           93.2   117   100.0   117     ARMSMC  
     SHIFTED CHAIN . . . . .    40.37           87.4   119   100.0   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    21.70           94.9   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS   126.80           20.0     5   100.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    42.73           86.2   145   100.0   145     ARMSMC  
     BURIED  . . . . . . . .    15.26           96.6    87   100.0    87     ARMSMC  
     CORE  . . . . . . . . .    30.02           91.6   227   100.0   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.09           64.2    95   100.0    95     ARMSSC1 
     WELL ORDERED  . . . . .    68.09           64.2    95   100.0    95     ARMSSC1 
     NO INTER CONTACTS . . .    60.65           68.8    48   100.0    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .    68.43           63.6    88   100.0    88     ARMSSC1 
     CHANGED ANGLES  . . . .    90.51           36.4    44   100.0    44     ARMSSC1 
     SHIFTED CHAIN . . . . .    75.66           57.4    47   100.0    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    69.20           61.5    52   100.0    52     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   115.08            0.0     2   100.0     2     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    70.93           58.2    55   100.0    55     ARMSSC1 
     BURIED  . . . . . . . .    63.99           72.5    40   100.0    40     ARMSSC1 
     CORE  . . . . . . . . .    66.72           65.6    93   100.0    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.80           58.6    70   100.0    70     ARMSSC2 
     WELL ORDERED  . . . . .    62.93           60.9    64   100.0    64     ARMSSC2 
     NO INTER CONTACTS . . .    60.46           52.6    38   100.0    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .    56.03           57.1    49   100.0    49     ARMSSC2 
     CHANGED ANGLES  . . . .    71.47           53.3    45   100.0    45     ARMSSC2 
     SHIFTED CHAIN . . . . .    63.87           52.6    38   100.0    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    61.29           60.0    40   100.0    40     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    56.98           50.0     2   100.0     2     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    62.09           52.5    40   100.0    40     ARMSSC2 
     BURIED  . . . . . . . .    61.40           66.7    30   100.0    30     ARMSSC2 
     CORE  . . . . . . . . .    61.93           58.8    68   100.0    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.36           34.8    23   100.0    23     ARMSSC3 
     WELL ORDERED  . . . . .    79.53           31.2    16   100.0    16     ARMSSC3 
     NO INTER CONTACTS . . .    84.16           30.8    13   100.0    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .    82.29           35.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    78.37           33.3    21   100.0    21     ARMSSC3 
     SHIFTED CHAIN . . . . .    62.37           41.7    12   100.0    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    75.07           33.3    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    77.62           38.9    18   100.0    18     ARMSSC3 
     BURIED  . . . . . . . .    85.36           20.0     5   100.0     5     ARMSSC3 
     CORE  . . . . . . . . .    79.36           34.8    23   100.0    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    60.38           45.5    11   100.0    11     ARMSSC4 
     WELL ORDERED  . . . . .    72.14           42.9     7   100.0     7     ARMSSC4 
     NO INTER CONTACTS . . .    56.51           42.9     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    60.38           45.5    11   100.0    11     ARMSSC4 
     CHANGED ANGLES  . . . .    60.38           45.5    11   100.0    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    54.30           66.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    71.46           33.3     6   100.0     6     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    60.44           44.4     9   100.0     9     ARMSSC4 
     BURIED  . . . . . . . .    60.11           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    60.38           45.5    11   100.0    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.66919     r(1,2) =   0.42054     r(1,3) =   0.61264 
 r(2,1) =  -0.71166     r(2,2) =  -0.12543     r(2,3) =  -0.69124 
 r(3,1) =  -0.21385     r(3,2) =  -0.89856     r(3,3) =   0.38322 
THE OFFSET VECTOR: 
 v(1) = -28.95264     v(2) =  36.07519     v(3) =  70.17345 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.17           (Number of atoms:  112) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.50        117   100.0   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0128                            CRMSCA  
     WELL ORDERED  . . . . .    1.50        117   100.0   117     CRMSCA  
     NO INTER CONTACTS . . .    1.26         59   100.0    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.95         60   100.0    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.34         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.88          3   100.0     3     CRMSCA  
     SURFACE . . . . . . . .    1.68         73   100.0    73     CRMSCA  
     BURIED  . . . . . . . .    1.13         44   100.0    44     CRMSCA  
     CORE  . . . . . . . . .    1.38        114   100.0   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.55        576   100.0   576     CRMSMC  
     WELL ORDERED  . . . . .    1.55        576   100.0   576     CRMSMC  
     NO INTER CONTACTS . . .    1.29        290   100.0   290     CRMSMC  
     SHIFTED CHAIN . . . . .    2.01        293   100.0   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.36        295   100.0   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.13         14   100.0    14     CRMSMC  
     SURFACE . . . . . . . .    1.75        356   100.0   356     CRMSMC  
     BURIED  . . . . . . . .    1.15        220   100.0   220     CRMSMC  
     CORE  . . . . . . . . .    1.42        562   100.0   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.56        416   100.0   416     CRMSSC  
     WELL ORDERED  . . . . .    2.57        389   100.0   389     CRMSSC  
     NO INTER CONTACTS . . .    2.17        204   100.0   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.44        350   100.0   350     CRMSSC  
     CHANGED ANGLES  . . . .    3.27        205   100.0   205     CRMSSC  
     SECONDARY STRUCTURE . .    2.34        237   100.0   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.25         11   100.0    11     CRMSSC  
     SURFACE . . . . . . . .    2.97        247   100.0   247     CRMSSC  
     BURIED  . . . . . . . .    1.82        169   100.0   169     CRMSSC  
     CORE  . . . . . . . . .    2.45        405   100.0   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.07        884   100.0   884     CRMSALL 
     WELL ORDERED  . . . . .    2.05        857   100.0   857     CRMSALL 
     NO INTER CONTACTS . . .    1.75        440   100.0   440     CRMSALL 
     SHIFTED CHAIN . . . . .    2.36        449   100.0   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.89        473   100.0   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.64         23   100.0    23     CRMSALL 
     SURFACE . . . . . . . .    2.36        539   100.0   539     CRMSALL 
     BURIED  . . . . . . . .    1.51        345   100.0   345     CRMSALL 
     CORE  . . . . . . . . .    1.95        861   100.0   861     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.533      0.219       0.178    117   100.0   117     ERRCA  
     WELL ORDERED  . . . . .    0.533      0.219       0.178    117   100.0   117     ERRCA  
     NO INTER CONTACTS . . .    0.413      0.191       0.149     59   100.0    59     ERRCA  
     SHIFTED CHAIN . . . . .    0.705      0.210       0.105     60   100.0    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    0.497      0.232       0.214     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.523      0.505       0.253      3   100.0     3     ERRCA  
     SURFACE . . . . . . . .    0.591      0.211       0.154     73   100.0    73     ERRCA  
     BURIED  . . . . . . . .    0.436      0.233       0.218     44   100.0    44     ERRCA  
     CORE  . . . . . . . . .    0.481      0.212       0.176    114   100.0   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.550      0.220       0.173    576   100.0   576     ERRMC  
     WELL ORDERED  . . . . .    0.550      0.220       0.173    576   100.0   576     ERRMC  
     NO INTER CONTACTS . . .    0.427      0.194       0.148    290   100.0   290     ERRMC  
     SHIFTED CHAIN . . . . .    0.731      0.212       0.106    293   100.0   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    0.493      0.228       0.200    295   100.0   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.759      0.530       0.265     14   100.0    14     ERRMC  
     SURFACE . . . . . . . .    0.621      0.214       0.152    356   100.0   356     ERRMC  
     BURIED  . . . . . . . .    0.434      0.229       0.207    220   100.0   220     ERRMC  
     CORE  . . . . . . . . .    0.494      0.212       0.171    562   100.0   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.124      0.292       0.180    416   100.0   416     ERRSC  
     WELL ORDERED  . . . . .    1.108      0.286       0.178    389   100.0   389     ERRSC  
     NO INTER CONTACTS . . .    0.947      0.275       0.162    204   100.0   204     ERRSC  
     RELIABLE SIDE CHAINS  .    1.036      0.281       0.176    350   100.0   350     ERRSC  
     CHANGED ANGLES  . . . .    1.682      0.359       0.190    205   100.0   205     ERRSC  
     SHIFTED CHAIN . . . . .    1.285      0.304       0.156    209   100.0   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.043      0.294       0.190    237   100.0   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.440      0.516       0.258     11   100.0    11     ERRSC  
     SURFACE . . . . . . . .    1.370      0.309       0.174    247   100.0   247     ERRSC  
     BURIED  . . . . . . . .    0.763      0.268       0.189    169   100.0   169     ERRSC  
     CORE  . . . . . . . . .    1.061      0.286       0.178    405   100.0   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.810      0.253       0.176    884   100.0   884     ERRALL 
     WELL ORDERED  . . . . .    0.793      0.249       0.176    857   100.0   857     ERRALL 
     NO INTER CONTACTS . . .    0.664      0.231       0.154    440   100.0   440     ERRALL 
     SHIFTED CHAIN . . . . .    0.968      0.251       0.128    449   100.0   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    0.758      0.259       0.195    473   100.0   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.042      0.523       0.262     23   100.0    23     ERRALL 
     SURFACE . . . . . . . .    0.949      0.256       0.163    539   100.0   539     ERRALL 
     BURIED  . . . . . . . .    0.594      0.247       0.198    345   100.0   345     ERRALL 
     CORE  . . . . . . . . .    0.751      0.246       0.174    861   100.0   861     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)        54       106       113       114       117     117     117   DISTCA 
CA  (P)     46.15     90.60     96.58     97.44    100.00             117   DISTCA 
CA  (RMS)    0.69      1.09      1.20      1.22      1.50                   DISTCA 
 
ALL (N)       342       721       800       846       883     884     884   DISTALL 
ALL (P)     38.69     81.56     90.50     95.70     99.89             884   DISTALL 
ALL (RMS)    0.71      1.15      1.33      1.56      2.04                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)         114           114             3          RMSLSI 
CA  (P)       97.44         97.44          2.56          RMSLSI 
CA  (RMS)      1.09          1.38          3.88          RMSLSI 
 
 
 
END of the results output 
