 
####################################################### 
#                                                     # 
#                        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) 
 
# WARNING! TARGET 884 atoms, MODEL 575 atoms, 575 common with TARGET 
           Number of atoms possible to evaluate: 556 
 
 
 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 . . . . . . . . . .    32.67           93.2   220    94.8   232     ARMSMC  
     WELL ORDERED  . . . . .    32.67           93.2   220    94.8   232     ARMSMC  
     NO INTER CONTACTS . . .    39.03           91.4   116    99.1   117     ARMSMC  
     SHIFTED CHAIN . . . . .    28.86           96.3   108    90.8   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    20.75           94.8   115    97.5   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    40.48           91.0   134    92.4   145     ARMSMC  
     BURIED  . . . . . . . .    13.28           96.5    86    98.9    87     ARMSMC  
     CORE  . . . . . . . . .    32.67           93.2   220    96.9   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    47.41           75.9    29    30.5    95     ARMSSC1 
     WELL ORDERED  . . . . .    47.41           75.9    29    30.5    95     ARMSSC1 
     NO INTER CONTACTS . . .    27.04           85.0    20    41.7    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .    50.02           73.1    26    29.5    88     ARMSSC1 
     CHANGED ANGLES  . . . .    99.35           16.7     6    13.6    44     ARMSSC1 
     SHIFTED CHAIN . . . . .    60.79           60.0    15    31.9    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    54.47           71.4    14    26.9    52     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    64.51           61.5    13    23.6    55     ARMSSC1 
     BURIED  . . . . . . . .    26.34           87.5    16    40.0    40     ARMSSC1 
     CORE  . . . . . . . . .    47.41           75.9    29    31.2    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    59.87           78.9    19    27.1    70     ARMSSC2 
     WELL ORDERED  . . . . .    61.47           77.8    18    28.1    64     ARMSSC2 
     NO INTER CONTACTS . . .    69.29           71.4    14    36.8    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .    42.29           85.7    14    28.6    49     ARMSSC2 
     CHANGED ANGLES  . . . .    91.07           50.0     4     8.9    45     ARMSSC2 
     SHIFTED CHAIN . . . . .    49.24           80.0    10    26.3    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    47.00           85.7     7    17.5    40     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    28.02           88.9     9    22.5    40     ARMSSC2 
     BURIED  . . . . . . . .    78.12           70.0    10    33.3    30     ARMSSC2 
     CORE  . . . . . . . . .    59.87           78.9    19    27.9    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.39           40.0     5    21.7    23     ARMSSC3 
     WELL ORDERED  . . . . .    86.56           50.0     4    25.0    16     ARMSSC3 
     NO INTER CONTACTS . . .    85.61           33.3     3    23.1    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .    81.39           40.0     5    25.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    99.93           33.3     3    14.3    21     ARMSSC3 
     SHIFTED CHAIN . . . . .    99.93           33.3     3    25.0    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .   105.45            0.0     1     8.3    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 . . . . . . . .    84.48            0.0     2    11.1    18     ARMSSC3 
     BURIED  . . . . . . . .    79.27           66.7     3    60.0     5     ARMSSC3 
     CORE  . . . . . . . . .    81.39           40.0     5    21.7    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.06            0.0     3    27.3    11     ARMSSC4 
     WELL ORDERED  . . . . .    70.06            0.0     3    42.9     7     ARMSSC4 
     NO INTER CONTACTS . . .    68.13            0.0     2    28.6     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    70.06            0.0     3    27.3    11     ARMSSC4 
     CHANGED ANGLES  . . . .    70.06            0.0     3    27.3    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    70.06            0.0     3    50.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    73.77            0.0     1    16.7     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 . . . . . . . .    73.77            0.0     1    11.1     9     ARMSSC4 
     BURIED  . . . . . . . .    68.13            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    70.06            0.0     3    27.3    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.11538     r(1,2) =  -0.36872     r(1,3) =  -0.92235 
 r(2,1) =   0.68917     r(2,2) =   0.69842     r(2,3) =  -0.19299 
 r(3,1) =   0.71535     r(3,2) =  -0.61339     r(3,3) =   0.33470 
THE OFFSET VECTOR: 
 v(1) =  12.33899     v(2) =  -2.08797     v(3) =  84.50099 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.18           (Number of atoms:  114) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.21        115    98.3   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0106                            CRMSCA  
     WELL ORDERED  . . . . .    1.21        115    98.3   117     CRMSCA  
     NO INTER CONTACTS . . .    1.23         59   100.0    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.51         58    96.7    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.06         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.12          1    33.3     3     CRMSCA  
     SURFACE . . . . . . . .    1.29         71    97.3    73     CRMSCA  
     BURIED  . . . . . . . .    1.08         44   100.0    44     CRMSCA  
     CORE  . . . . . . . . .    1.18        114   100.0   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.24        483    83.9   576     CRMSMC  
     WELL ORDERED  . . . . .    1.24        483    83.9   576     CRMSMC  
     NO INTER CONTACTS . . .    1.28        257    88.6   290     CRMSMC  
     SHIFTED CHAIN . . . . .    1.49        239    81.6   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.07        249    84.4   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.12          1     7.1    14     CRMSMC  
     SURFACE . . . . . . . .    1.31        289    81.2   356     CRMSMC  
     BURIED  . . . . . . . .    1.11        194    88.2   220     CRMSMC  
     CORE  . . . . . . . . .    1.23        482    85.8   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    1.36        105    25.2   416     CRMSSC  
     WELL ORDERED  . . . . .    1.36        101    26.0   389     CRMSSC  
     NO INTER CONTACTS . . .    1.40         70    34.3   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    1.32         89    25.4   350     CRMSSC  
     CHANGED ANGLES  . . . .    1.73         23    11.2   205     CRMSSC  
     SECONDARY STRUCTURE . .    1.31         50    21.1   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    11     CRMSSC  
     SURFACE . . . . . . . .    1.46         45    18.2   247     CRMSSC  
     BURIED  . . . . . . . .    1.28         60    35.5   169     CRMSSC  
     CORE  . . . . . . . . .    1.36        105    25.9   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.26        556    62.9   884     CRMSALL 
     WELL ORDERED  . . . . .    1.26        552    64.4   857     CRMSALL 
     NO INTER CONTACTS . . .    1.31        306    69.5   440     CRMSALL 
     SHIFTED CHAIN . . . . .    1.51        278    61.9   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.13        283    59.8   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.12          1     4.3    23     CRMSALL 
     SURFACE . . . . . . . .    1.33        320    59.4   539     CRMSALL 
     BURIED  . . . . . . . .    1.16        236    68.4   345     CRMSALL 
     CORE  . . . . . . . . .    1.26        555    64.5   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 . . . . . . . . . .    1.236      0.380       0.439    115    98.3   117     ERRCA  
     WELL ORDERED  . . . . .    1.236      0.380       0.439    115    98.3   117     ERRCA  
     NO INTER CONTACTS . . .    1.091      0.347       0.398     59   100.0    59     ERRCA  
     SHIFTED CHAIN . . . . .    0.904      0.235       0.268     58    96.7    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.410      0.444       0.514     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.883      0.124       0.083      1    33.3     3     ERRCA  
     SURFACE . . . . . . . .    1.267      0.365       0.424     71    97.3    73     ERRCA  
     BURIED  . . . . . . . .    1.187      0.405       0.464     44   100.0    44     ERRCA  
     CORE  . . . . . . . . .    1.239      0.383       0.442    114   100.0   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.195      0.373       0.427    483    83.9   576     ERRMC  
     WELL ORDERED  . . . . .    1.195      0.373       0.427    483    83.9   576     ERRMC  
     NO INTER CONTACTS . . .    1.058      0.336       0.381    257    88.6   290     ERRMC  
     SHIFTED CHAIN . . . . .    0.861      0.231       0.261    239    81.6   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.356      0.431       0.495    249    84.4   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    0.883      0.124       0.083      1     7.1    14     ERRMC  
     SURFACE . . . . . . . .    1.219      0.358       0.412    289    81.2   356     ERRMC  
     BURIED  . . . . . . . .    1.159      0.396       0.450    194    88.2   220     ERRMC  
     CORE  . . . . . . . . .    1.196      0.374       0.428    482    85.8   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.764      0.281       0.305    105    25.2   416     ERRSC  
     WELL ORDERED  . . . . .    0.765      0.281       0.306    101    26.0   389     ERRSC  
     NO INTER CONTACTS . . .    0.670      0.236       0.245     70    34.3   204     ERRSC  
     RELIABLE SIDE CHAINS  .    0.756      0.280       0.307     89    25.4   350     ERRSC  
     CHANGED ANGLES  . . . .    0.615      0.186       0.171     23    11.2   205     ERRSC  
     SHIFTED CHAIN . . . . .    0.555      0.178       0.172     55    26.3   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    0.899      0.329       0.375     50    21.1   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    11     ERRSC  
     SURFACE . . . . . . . .    0.650      0.227       0.252     45    18.2   247     ERRSC  
     BURIED  . . . . . . . .    0.849      0.322       0.344     60    35.5   169     ERRSC  
     CORE  . . . . . . . . .    0.764      0.281       0.305    105    25.9   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.134      0.359       0.407    556    62.9   884     ERRALL 
     WELL ORDERED  . . . . .    1.137      0.359       0.408    552    64.4   857     ERRALL 
     NO INTER CONTACTS . . .    0.989      0.316       0.353    306    69.5   440     ERRALL 
     SHIFTED CHAIN . . . . .    0.818      0.223       0.248    278    61.9   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.296      0.416       0.477    283    59.8   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    0.883      0.124       0.083      1     4.3    23     ERRALL 
     SURFACE . . . . . . . .    1.162      0.344       0.395    320    59.4   539     ERRALL 
     BURIED  . . . . . . . .    1.095      0.378       0.424    236    68.4   345     ERRALL 
     CORE  . . . . . . . . .    1.134      0.359       0.408    555    64.5   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)        48       111       114       115       115     115     117   DISTCA 
CA  (P)     41.03     94.87     97.44     98.29     98.29             117   DISTCA 
CA  (RMS)    0.68      1.14      1.18      1.21      1.21                   DISTCA 
 
ALL (N)       235       528       548       556       556     556     884   DISTALL 
ALL (P)     26.58     59.73     61.99     62.90     62.90             884   DISTALL 
ALL (RMS)    0.69      1.14      1.20      1.26      1.26                   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             1          RMSLSI 
CA  (P)       97.44         97.44          0.85          RMSLSI 
CA  (RMS)      1.09          1.18          3.12          RMSLSI 
 
 
 
END of the results output 
