 
####################################################### 
#                                                     # 
#                        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 506 atoms, 506 common with TARGET 
           Number of atoms possible to evaluate: 420 
 
 
 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 . . . . . . . . . .    79.71           49.5   202    87.1   232     ARMSMC  
     WELL ORDERED  . . . . .    79.71           49.5   202    87.1   232     ARMSMC  
     NO INTER CONTACTS . . .    73.56           58.0   100    85.5   117     ARMSMC  
     SHIFTED CHAIN . . . . .    78.74           53.7    95    79.8   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    62.30           66.1   109    92.4   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    57.39           20.0     5   100.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    82.99           47.5   122    84.1   145     ARMSMC  
     BURIED  . . . . . . . .    74.44           52.5    80    92.0    87     ARMSMC  
     CORE  . . . . . . . . .    80.20           50.3   197    86.8   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    95     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    95     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    88     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    44     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    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 . . . . . . . .     0.00            0.0     0     0.0    55     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    40     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    70     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    64     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    49     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    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 . . . . . . . .     0.00            0.0     0     0.0    40     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    30     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    21     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    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 . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     5     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    11     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     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 . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.71040     r(1,2) =   0.05148     r(1,3) =   0.70191 
 r(2,1) =  -0.62264     r(2,2) =  -0.41895     r(2,3) =   0.66091 
 r(3,1) =   0.32809     r(3,2) =  -0.90655     r(3,3) =  -0.26557 
THE OFFSET VECTOR: 
 v(1) = -31.88303     v(2) =  20.73319     v(3) =  40.71936 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.97           (Number of atoms:   16) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   17.61        105    89.7   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1677                            CRMSCA  
     WELL ORDERED  . . . . .   17.61        105    89.7   117     CRMSCA  
     NO INTER CONTACTS . . .   16.11         52    88.1    59     CRMSCA  
     SHIFTED CHAIN . . . . .   16.03         51    85.0    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .   13.97         56    94.9    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   20.12          3   100.0     3     CRMSCA  
     SURFACE . . . . . . . .   18.45         63    86.3    73     CRMSCA  
     BURIED  . . . . . . . .   16.28         42    95.5    44     CRMSCA  
     CORE  . . . . . . . . .   17.53        102    89.5   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   17.65        420    72.9   576     CRMSMC  
     WELL ORDERED  . . . . .   17.65        420    72.9   576     CRMSMC  
     NO INTER CONTACTS . . .   16.09        208    71.7   290     CRMSMC  
     SHIFTED CHAIN . . . . .   16.04        204    69.6   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .   14.16        224    75.9   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   20.06         12    85.7    14     CRMSMC  
     SURFACE . . . . . . . .   18.47        252    70.8   356     CRMSMC  
     BURIED  . . . . . . . .   16.35        168    76.4   220     CRMSMC  
     CORE  . . . . . . . . .   17.58        408    72.6   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   416     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   389     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   350     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   205     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    11     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   247     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   169     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   17.65        420    47.5   884     CRMSALL 
     WELL ORDERED  . . . . .   17.65        420    49.0   857     CRMSALL 
     NO INTER CONTACTS . . .   16.09        208    47.3   440     CRMSALL 
     SHIFTED CHAIN . . . . .   16.04        204    45.4   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .   14.16        224    47.4   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS   20.06         12    52.2    23     CRMSALL 
     SURFACE . . . . . . . .   18.47        252    46.8   539     CRMSALL 
     BURIED  . . . . . . . .   16.35        168    48.7   345     CRMSALL 
     CORE  . . . . . . . . .   17.58        408    47.4   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 . . . . . . . . . .   15.097      1.000       0.500    105    89.7   117     ERRCA  
     WELL ORDERED  . . . . .   15.097      1.000       0.500    105    89.7   117     ERRCA  
     NO INTER CONTACTS . . .   13.867      1.000       0.500     52    88.1    59     ERRCA  
     SHIFTED CHAIN . . . . .   13.255      1.000       0.500     51    85.0    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .   11.195      1.000       0.500     56    94.9    59     ERRCA  
     LARGE SHIFTS/INSERTIONS   18.685      1.000       0.500      3   100.0     3     ERRCA  
     SURFACE . . . . . . . .   16.068      1.000       0.500     63    86.3    73     ERRCA  
     BURIED  . . . . . . . .   13.641      1.000       0.500     42    95.5    44     ERRCA  
     CORE  . . . . . . . . .   14.992      1.000       0.500    102    89.5   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   15.104      1.000       0.500    420    72.9   576     ERRMC  
     WELL ORDERED  . . . . .   15.104      1.000       0.500    420    72.9   576     ERRMC  
     NO INTER CONTACTS . . .   13.817      1.000       0.500    208    71.7   290     ERRMC  
     SHIFTED CHAIN . . . . .   13.200      1.000       0.500    204    69.6   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .   11.289      1.000       0.500    224    75.9   295     ERRMC  
     LARGE SHIFTS/INSERTIONS   18.712      1.000       0.500     12    85.7    14     ERRMC  
     SURFACE . . . . . . . .   16.021      1.000       0.500    252    70.8   356     ERRMC  
     BURIED  . . . . . . . .   13.727      1.000       0.500    168    76.4   220     ERRMC  
     CORE  . . . . . . . . .   14.998      1.000       0.500    408    72.6   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   416     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   389     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   204     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   350     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   205     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    11     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   247     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   169     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   15.104      1.000       0.500    420    47.5   884     ERRALL 
     WELL ORDERED  . . . . .   15.104      1.000       0.500    420    49.0   857     ERRALL 
     NO INTER CONTACTS . . .   13.817      1.000       0.500    208    47.3   440     ERRALL 
     SHIFTED CHAIN . . . . .   13.200      1.000       0.500    204    45.4   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .   11.289      1.000       0.500    224    47.4   473     ERRALL 
     LARGE SHIFTS/INSERTIONS   18.712      1.000       0.500     12    52.2    23     ERRALL 
     SURFACE . . . . . . . .   16.021      1.000       0.500    252    46.8   539     ERRALL 
     BURIED  . . . . . . . .   13.727      1.000       0.500    168    48.7   345     ERRALL 
     CORE  . . . . . . . . .   14.998      1.000       0.500    408    47.4   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)        14        15        16        17        31     105     117   DISTCA 
CA  (P)     11.97     12.82     13.68     14.53     26.50             117   DISTCA 
CA  (RMS)    0.65      0.80      0.97      1.43      5.20                   DISTCA 
 
ALL (N)        54        57        60        72       124     420     884   DISTALL 
ALL (P)      6.11      6.45      6.79      8.14     14.03             884   DISTALL 
ALL (RMS)    0.58      0.66      0.82      1.96      5.18                   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           102             3          RMSLSI 
CA  (P)       97.44         87.18          2.56          RMSLSI 
CA  (RMS)      1.09         17.53         20.12          RMSLSI 
 
 
 
END of the results output 
