 
####################################################### 
#                                                     # 
#                        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: 780 
 
 
 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 . . . . . . . . . .    31.99           89.3   206    88.8   232     ARMSMC  
     WELL ORDERED  . . . . .    31.99           89.3   206    88.8   232     ARMSMC  
     NO INTER CONTACTS . . .    34.96           88.6   114    97.4   117     ARMSMC  
     SHIFTED CHAIN . . . . .    38.38           87.0   108    90.8   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    14.15           93.2   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    95.19           50.0     2    40.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    39.80           86.0   121    83.4   145     ARMSMC  
     BURIED  . . . . . . . .    15.01           94.1    85    97.7    87     ARMSMC  
     CORE  . . . . . . . . .    30.74           89.7   204    89.9   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    63.22           71.4    84    88.4    95     ARMSSC1 
     WELL ORDERED  . . . . .    63.22           71.4    84    88.4    95     ARMSSC1 
     NO INTER CONTACTS . . .    52.88           78.7    47    97.9    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .    64.06           70.5    78    88.6    88     ARMSSC1 
     CHANGED ANGLES  . . . .    92.09           40.5    37    84.1    44     ARMSSC1 
     SHIFTED CHAIN . . . . .    68.85           69.0    42    89.4    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    63.90           71.2    52   100.0    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 . . . . . . . .    69.45           64.4    45    81.8    55     ARMSSC1 
     BURIED  . . . . . . . .    55.17           79.5    39    97.5    40     ARMSSC1 
     CORE  . . . . . . . . .    63.22           71.4    84    90.3    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.38           61.3    62    88.6    70     ARMSSC2 
     WELL ORDERED  . . . . .    65.70           62.5    56    87.5    64     ARMSSC2 
     NO INTER CONTACTS . . .    56.90           67.6    37    97.4    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .    55.69           64.3    42    85.7    49     ARMSSC2 
     CHANGED ANGLES  . . . .    80.62           40.5    37    82.2    45     ARMSSC2 
     SHIFTED CHAIN . . . . .    68.46           54.5    33    86.8    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    66.28           62.5    40   100.0    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 . . . . . . . .    63.39           60.6    33    82.5    40     ARMSSC2 
     BURIED  . . . . . . . .    65.50           62.1    29    96.7    30     ARMSSC2 
     CORE  . . . . . . . . .    64.38           61.3    62    91.2    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    93.94           30.0    20    87.0    23     ARMSSC3 
     WELL ORDERED  . . . . .   101.19           23.1    13    81.2    16     ARMSSC3 
     NO INTER CONTACTS . . .    89.72           25.0    12    92.3    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .    83.13           33.3    18    90.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    99.00           22.2    18    85.7    21     ARMSSC3 
     SHIFTED CHAIN . . . . .   104.75            9.1    11    91.7    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    92.22           25.0    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 . . . . . . . .    84.66           33.3    15    83.3    18     ARMSSC3 
     BURIED  . . . . . . . .   117.45           20.0     5   100.0     5     ARMSSC3 
     CORE  . . . . . . . . .    93.94           30.0    20    87.0    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.41           30.0    10    90.9    11     ARMSSC4 
     WELL ORDERED  . . . . .    97.41           16.7     6    85.7     7     ARMSSC4 
     NO INTER CONTACTS . . .    72.01           28.6     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    77.41           30.0    10    90.9    11     ARMSSC4 
     CHANGED ANGLES  . . . .    77.41           30.0    10    90.9    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    79.30           40.0     5    83.3     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    74.57           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 . . . . . . . .    66.37           37.5     8    88.9     9     ARMSSC4 
     BURIED  . . . . . . . .   111.09            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    77.41           30.0    10    90.9    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.93382     r(1,2) =  -0.26466     r(1,3) =   0.24071 
 r(2,1) =  -0.33133     r(2,2) =  -0.89357     r(2,3) =   0.30291 
 r(3,1) =   0.13493     r(3,2) =  -0.36262     r(3,3) =  -0.92212 
THE OFFSET VECTOR: 
 v(1) =  12.67258     v(2) =   3.39890     v(3) =  41.97624 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.13           (Number of atoms:  101) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.25        104    88.9   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0120                            CRMSCA  
     WELL ORDERED  . . . . .    1.25        104    88.9   117     CRMSCA  
     NO INTER CONTACTS . . .    1.19         58    98.3    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.59         54    90.0    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.18         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.11          1    33.3     3     CRMSCA  
     SURFACE . . . . . . . .    1.36         61    83.6    73     CRMSCA  
     BURIED  . . . . . . . .    1.08         43    97.7    44     CRMSCA  
     CORE  . . . . . . . . .    1.19        103    90.4   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.29        513    89.1   576     CRMSMC  
     WELL ORDERED  . . . . .    1.29        513    89.1   576     CRMSMC  
     NO INTER CONTACTS . . .    1.22        285    98.3   290     CRMSMC  
     SHIFTED CHAIN . . . . .    1.63        264    90.1   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.19        295   100.0   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.23          4    28.6    14     CRMSMC  
     SURFACE . . . . . . . .    1.39        298    83.7   356     CRMSMC  
     BURIED  . . . . . . . .    1.13        215    97.7   220     CRMSMC  
     CORE  . . . . . . . . .    1.24        509    90.6   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    1.98        364    87.5   416     CRMSSC  
     WELL ORDERED  . . . . .    1.96        337    86.6   389     CRMSSC  
     NO INTER CONTACTS . . .    1.87        200    98.0   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    1.81        304    86.9   350     CRMSSC  
     CHANGED ANGLES  . . . .    2.59        169    82.4   205     CRMSSC  
     SECONDARY STRUCTURE . .    2.06        237   100.0   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    11     CRMSSC  
     SURFACE . . . . . . . .    2.20        199    80.6   247     CRMSSC  
     BURIED  . . . . . . . .    1.67        165    97.6   169     CRMSSC  
     CORE  . . . . . . . . .    1.98        364    89.9   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.64        780    88.2   884     CRMSALL 
     WELL ORDERED  . . . . .    1.62        753    87.9   857     CRMSALL 
     NO INTER CONTACTS . . .    1.55        432    98.2   440     CRMSALL 
     SHIFTED CHAIN . . . . .    1.95        401    89.3   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.67        473   100.0   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.23          4    17.4    23     CRMSALL 
     SURFACE . . . . . . . .    1.79        443    82.2   539     CRMSALL 
     BURIED  . . . . . . . .    1.42        337    97.7   345     CRMSALL 
     CORE  . . . . . . . . .    1.62        776    90.1   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 . . . . . . . . . .    0.874      0.607       0.307    104    88.9   117     ERRCA  
     WELL ORDERED  . . . . .    0.874      0.607       0.307    104    88.9   117     ERRCA  
     NO INTER CONTACTS . . .    0.883      0.634       0.324     58    98.3    59     ERRCA  
     SHIFTED CHAIN . . . . .    1.259      0.723       0.361     54    90.0    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    0.819      0.591       0.302     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.855      0.885       0.443      1    33.3     3     ERRCA  
     SURFACE . . . . . . . .    0.957      0.625       0.313     61    83.6    73     ERRCA  
     BURIED  . . . . . . . .    0.757      0.581       0.300     43    97.7    44     ERRCA  
     CORE  . . . . . . . . .    0.845      0.604       0.306    103    90.4   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.778      0.499       0.261    513    89.1   576     ERRMC  
     WELL ORDERED  . . . . .    0.778      0.499       0.261    513    89.1   576     ERRMC  
     NO INTER CONTACTS . . .    0.764      0.507       0.262    285    98.3   290     ERRMC  
     SHIFTED CHAIN . . . . .    1.133      0.595       0.297    264    90.1   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    0.717      0.483       0.253    295   100.0   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.669      0.794       0.397      4    28.6    14     ERRMC  
     SURFACE . . . . . . . .    0.851      0.511       0.263    298    83.7   356     ERRMC  
     BURIED  . . . . . . . .    0.676      0.483       0.258    215    97.7   220     ERRMC  
     CORE  . . . . . . . . .    0.755      0.497       0.260    509    90.6   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.406      0.792       0.402    364    87.5   416     ERRSC  
     WELL ORDERED  . . . . .    1.402      0.811       0.410    337    86.6   389     ERRSC  
     NO INTER CONTACTS . . .    1.389      0.805       0.405    200    98.0   204     ERRSC  
     RELIABLE SIDE CHAINS  .    1.284      0.780       0.395    304    86.9   350     ERRSC  
     CHANGED ANGLES  . . . .    1.904      0.749       0.378    169    82.4   205     ERRSC  
     SHIFTED CHAIN . . . . .    1.705      0.807       0.406    185    88.5   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.463      0.817       0.413    237   100.0   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    11     ERRSC  
     SURFACE . . . . . . . .    1.533      0.755       0.380    199    80.6   247     ERRSC  
     BURIED  . . . . . . . .    1.252      0.837       0.427    165    97.6   169     ERRSC  
     CORE  . . . . . . . . .    1.406      0.792       0.402    364    89.9   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.033      0.588       0.304    780    88.2   884     ERRALL 
     WELL ORDERED  . . . . .    1.017      0.590       0.304    753    87.9   857     ERRALL 
     NO INTER CONTACTS . . .    1.015      0.597       0.305    432    98.2   440     ERRALL 
     SHIFTED CHAIN . . . . .    1.351      0.653       0.328    401    89.3   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.049      0.603       0.311    473   100.0   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.669      0.794       0.397      4    17.4    23     ERRALL 
     SURFACE . . . . . . . .    1.116      0.576       0.294    443    82.2   539     ERRALL 
     BURIED  . . . . . . . .    0.924      0.605       0.318    337    97.7   345     ERRALL 
     CORE  . . . . . . . . .    1.019      0.587       0.304    776    90.1   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)        50        99       102       104       104     104     117   DISTCA 
CA  (P)     42.74     84.62     87.18     88.89     88.89             117   DISTCA 
CA  (RMS)    0.68      1.09      1.15      1.25      1.25                   DISTCA 
 
ALL (N)       325       669       730       773       780     780     884   DISTALL 
ALL (P)     36.76     75.68     82.58     87.44     88.24             884   DISTALL 
ALL (RMS)    0.69      1.12      1.29      1.53      1.64                   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           103             1          RMSLSI 
CA  (P)       97.44         88.03          0.85          RMSLSI 
CA  (RMS)      1.09          1.19          4.11          RMSLSI 
 
 
 
END of the results output 
