 
####################################################### 
#                                                     # 
#                        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 483 atoms, 483 common with TARGET 
           Number of atoms possible to evaluate: 456 
 
 
 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 . . . . . . . . . .    31.00           92.9   224    96.6   232     ARMSMC  
     WELL ORDERED  . . . . .    31.00           92.9   224    96.6   232     ARMSMC  
     NO INTER CONTACTS . . .    33.64           92.1   114    97.4   117     ARMSMC  
     SHIFTED CHAIN . . . . .    38.90           89.4   113    95.0   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    10.68           96.5   114    96.6   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS   126.48            0.0     2    40.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    37.70           90.6   138    95.2   145     ARMSMC  
     BURIED  . . . . . . . .    14.89           96.5    86    98.9    87     ARMSMC  
     CORE  . . . . . . . . .    28.73           93.7   222    97.8   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) =   0.96244     r(1,2) =  -0.02804     r(1,3) =   0.27005 
 r(2,1) =  -0.23523     r(2,2) =   0.41057     r(2,3) =   0.88096 
 r(3,1) =  -0.13558     r(3,2) =  -0.91140     r(3,3) =   0.38855 
THE OFFSET VECTOR: 
 v(1) = -19.37041     v(2) = -42.71342     v(3) =  69.66803 
 
 Number of iteration 22                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.05           (Number of atoms:  110) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.30        114    97.4   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0114                            CRMSCA  
     WELL ORDERED  . . . . .    1.30        114    97.4   117     CRMSCA  
     NO INTER CONTACTS . . .    1.31         58    98.3    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.69         57    95.0    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.35         58    98.3    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.21          1    33.3     3     CRMSCA  
     SURFACE . . . . . . . .    1.44         70    95.9    73     CRMSCA  
     BURIED  . . . . . . . .    1.03         44   100.0    44     CRMSCA  
     CORE  . . . . . . . . .    1.27        113    99.1   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.31        456    79.2   576     CRMSMC  
     WELL ORDERED  . . . . .    1.31        456    79.2   576     CRMSMC  
     NO INTER CONTACTS . . .    1.29        232    80.0   290     CRMSMC  
     SHIFTED CHAIN . . . . .    1.69        228    77.8   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.29        232    78.6   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.80          4    28.6    14     CRMSMC  
     SURFACE . . . . . . . .    1.43        280    78.7   356     CRMSMC  
     BURIED  . . . . . . . .    1.08        176    80.0   220     CRMSMC  
     CORE  . . . . . . . . .    1.26        452    80.4   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 . . . . . . . . . .    1.31        456    51.6   884     CRMSALL 
     WELL ORDERED  . . . . .    1.31        456    53.2   857     CRMSALL 
     NO INTER CONTACTS . . .    1.29        232    52.7   440     CRMSALL 
     SHIFTED CHAIN . . . . .    1.69        228    50.8   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.29        232    49.0   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.80          4    17.4    23     CRMSALL 
     SURFACE . . . . . . . .    1.43        280    51.9   539     CRMSALL 
     BURIED  . . . . . . . .    1.08        176    51.0   345     CRMSALL 
     CORE  . . . . . . . . .    1.26        452    52.5   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 . . . . . . . . . .    2.949      0.599       0.661    114    97.4   117     ERRCA  
     WELL ORDERED  . . . . .    2.949      0.599       0.661    114    97.4   117     ERRCA  
     NO INTER CONTACTS . . .    2.938      0.591       0.659     58    98.3    59     ERRCA  
     SHIFTED CHAIN . . . . .    2.565      0.481       0.567     57    95.0    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    3.019      0.622       0.678     58    98.3    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.791      0.110       0.070      1    33.3     3     ERRCA  
     SURFACE . . . . . . . .    2.880      0.579       0.640     70    95.9    73     ERRCA  
     BURIED  . . . . . . . .    3.058      0.631       0.694     44   100.0    44     ERRCA  
     CORE  . . . . . . . . .    2.968      0.603       0.666    113    99.1   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.926      0.595       0.657    456    79.2   576     ERRMC  
     WELL ORDERED  . . . . .    2.926      0.595       0.657    456    79.2   576     ERRMC  
     NO INTER CONTACTS . . .    2.923      0.590       0.656    232    80.0   290     ERRMC  
     SHIFTED CHAIN . . . . .    2.544      0.479       0.564    228    77.8   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    2.988      0.615       0.674    232    78.6   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.135      0.156       0.142      4    28.6    14     ERRMC  
     SURFACE . . . . . . . .    2.858      0.576       0.637    280    78.7   356     ERRMC  
     BURIED  . . . . . . . .    3.034      0.625       0.688    176    80.0   220     ERRMC  
     CORE  . . . . . . . . .    2.942      0.598       0.661    452    80.4   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 . . . . . . . . . .    2.926      0.595       0.657    456    51.6   884     ERRALL 
     WELL ORDERED  . . . . .    2.926      0.595       0.657    456    53.2   857     ERRALL 
     NO INTER CONTACTS . . .    2.923      0.590       0.656    232    52.7   440     ERRALL 
     SHIFTED CHAIN . . . . .    2.544      0.479       0.564    228    50.8   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    2.988      0.615       0.674    232    49.0   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.135      0.156       0.142      4    17.4    23     ERRALL 
     SURFACE . . . . . . . .    2.858      0.576       0.637    280    51.9   539     ERRALL 
     BURIED  . . . . . . . .    3.034      0.625       0.688    176    51.0   345     ERRALL 
     CORE  . . . . . . . . .    2.942      0.598       0.661    452    52.5   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)        57       109       111       113       114     114     117   DISTCA 
CA  (P)     48.72     93.16     94.87     96.58     97.44             117   DISTCA 
CA  (RMS)    0.70      1.04      1.08      1.20      1.30                   DISTCA 
 
ALL (N)       227       434       443       454       456     456     884   DISTALL 
ALL (P)     25.68     49.10     50.11     51.36     51.58             884   DISTALL 
ALL (RMS)    0.70      1.05      1.10      1.26      1.31                   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           113             1          RMSLSI 
CA  (P)       97.44         96.58          0.85          RMSLSI 
CA  (RMS)      1.09          1.27          3.21          RMSLSI 
 
 
 
END of the results output 
