 
####################################################### 
#                                                     # 
#                        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/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.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 845 atoms, MODEL 1766 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 810 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    42.61           81.0   184    91.5   201     ARMSMC  
     WELL ORDERED  . . . . .    42.11           82.0   161   100.0   161     ARMSMC  
     NO INTER CONTACTS . . .    39.01           85.0   100    95.2   105     ARMSMC  
     SHIFTED CHAIN . . . . .    38.76           80.6   124    87.9   141     ARMSMC  
     ALTERNATIVE PARENT  . .    88.98           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    33.78           90.1   121    95.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    47.81           76.4    72    80.9    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    45.16           78.4   134    88.7   151     ARMSMC  
     BURIED  . . . . . . . .    34.84           88.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    38.90           83.9   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    91.77           34.9    83    91.2    91     ARMSSC1 
     WELL ORDERED  . . . . .    92.13           33.3    54   100.0    54     ARMSSC1 
     NO INTER CONTACTS . . .    89.37           42.9    42    93.3    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    90.86           35.5    76    90.5    84     ARMSSC1 
     CHANGED ANGLES  . . . .    97.31           27.6    58    87.9    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    91.55           35.7    56    87.5    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    93.02           50.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    93.04           37.0    54    94.7    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    90.12           35.3    34    81.0    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    90.28           34.4    61    88.4    69     ARMSSC1 
     BURIED  . . . . . . . .    95.77           36.4    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    92.90           34.7    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.91           36.2    58    90.6    64     ARMSSC2 
     WELL ORDERED  . . . . .    87.00           35.7    28   100.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    77.51           51.6    31    93.9    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    84.29           31.8    44    89.8    49     ARMSSC2 
     CHANGED ANGLES  . . . .    84.36           31.7    41    87.2    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    75.99           44.7    38    86.4    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     8.40          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    86.41           37.5    40    95.2    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    75.31           40.9    22    78.6    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    87.36           25.6    43    87.8    49     ARMSSC2 
     BURIED  . . . . . . . .    63.79           66.7    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    85.70           33.3    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.52           34.6    26    83.9    31     ARMSSC3 
     WELL ORDERED  . . . . .    62.09           50.0    10   100.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    90.86           30.8    13    86.7    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.77           40.9    22    84.6    26     ARMSSC3 
     CHANGED ANGLES  . . . .    92.67           26.3    19    79.2    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    87.89           33.3    15    75.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    74.38           42.9    21    91.3    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    91.60           33.3     9    64.3    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    88.21           30.4    23    82.1    28     ARMSSC3 
     BURIED  . . . . . . . .    28.35           66.7     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    78.91           35.3    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.09           22.2     9    75.0    12     ARMSSC4 
     WELL ORDERED  . . . . .    98.47           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    93.17           20.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    98.09           22.2     9    75.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .    94.55           25.0     8    72.7    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    84.37            0.0     3    50.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   109.06           14.3     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    94.61           28.6     7    70.0    10     ARMSSC4 
     BURIED  . . . . . . . .   109.41            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    98.09           22.2     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.06669     r(1,2) =   0.97551     r(1,3) =  -0.20961 
 r(2,1) =  -0.22484     r(2,2) =  -0.18999     r(2,3) =  -0.95570 
 r(3,1) =  -0.97211     r(3,2) =   0.11086     r(3,3) =   0.20666 
THE OFFSET VECTOR: 
 v(1) =  17.73709     v(2) =  65.65639     v(3) =  33.58116 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.13           (Number of atoms:   46) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   20.92         99    96.1   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2113                            CRMSCA  
     WELL ORDERED  . . . . .   20.59         85   100.0    85     CRMSCA  
     NO INTER CONTACTS . . .   15.39         54   100.0    54     CRMSCA  
     SHIFTED CHAIN . . . . .   25.04         69    94.5    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.16          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   22.93         65   100.0    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   31.65         43    91.5    47     CRMSCA  
     SURFACE . . . . . . . .   24.17         74    94.9    78     CRMSCA  
     BURIED  . . . . . . . .    2.06         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    2.07         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   20.97        491    96.1   511     CRMSMC  
     WELL ORDERED  . . . . .   20.54        420   100.0   420     CRMSMC  
     NO INTER CONTACTS . . .   15.26        267   100.0   267     CRMSMC  
     SHIFTED CHAIN . . . . .   25.07        343    94.5   363     CRMSMC  
     ALTERNATIVE PARENT  . .    2.79         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   23.00        324   100.0   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   31.67        214    91.5   234     CRMSMC  
     SURFACE . . . . . . . .   24.22        367    94.8   387     CRMSMC  
     BURIED  . . . . . . . .    2.17        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    2.16        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   22.34        414    95.6   433     CRMSSC  
     WELL ORDERED  . . . . .   21.71        248   100.0   248     CRMSSC  
     NO INTER CONTACTS . . .   17.23        210   100.0   210     CRMSSC  
     RELIABLE SIDE CHAINS  .   22.91        356    96.0   371     CRMSSC  
     CHANGED ANGLES  . . . .   24.81        266    94.7   281     CRMSSC  
     SECONDARY STRUCTURE . .   24.81        297   100.0   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS   32.34        194    91.1   213     CRMSSC  
     SURFACE . . . . . . . .   25.12        325    94.5   344     CRMSSC  
     BURIED  . . . . . . . .    4.21         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    4.13        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   21.68        810    95.9   845     CRMSALL 
     WELL ORDERED  . . . . .   21.02        593   100.0   593     CRMSALL 
     NO INTER CONTACTS . . .   16.29        426   100.0   426     CRMSALL 
     SHIFTED CHAIN . . . . .   25.87        566    94.2   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.41         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   23.96        557   100.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS   32.05        366    91.3   401     CRMSALL 
     SURFACE . . . . . . . .   24.69        621    94.7   656     CRMSALL 
     BURIED  . . . . . . . .    3.19        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    3.20        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.76      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2    34.57     36    90.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.02     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2    34.60    179    89.9   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.96     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2    34.63    313    89.9   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.89      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     6.02     36    90.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.26     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     6.01    179    89.9   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.32     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     7.00    313    89.9   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.103      0.610       0.470     99    96.1   103     ERRCA  
     WELL ORDERED  . . . . .   12.752      0.614       0.482     85   100.0    85     ERRCA  
     NO INTER CONTACTS . . .    8.671      0.558       0.484     54   100.0    54     ERRCA  
     SHIFTED CHAIN . . . . .   17.131      0.595       0.389     69    94.5    73     ERRCA  
     ALTERNATIVE PARENT  . .    2.921      0.293       0.325      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .   15.478      0.676       0.520     65   100.0    65     ERRCA  
     LARGE SHIFTS/INSERTIONS   25.967      0.717       0.385     43    91.5    47     ERRCA  
     SURFACE . . . . . . . .   16.506      0.652       0.456     74    94.9    78     ERRCA  
     BURIED  . . . . . . . .    3.032      0.487       0.509     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    3.226      0.529       0.535     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.174      0.615       0.474    491    96.1   511     ERRMC  
     WELL ORDERED  . . . . .   12.768      0.621       0.488    420   100.0   420     ERRMC  
     NO INTER CONTACTS . . .    8.657      0.568       0.491    267   100.0   267     ERRMC  
     SHIFTED CHAIN . . . . .   17.225      0.611       0.405    343    94.5   363     ERRMC  
     ALTERNATIVE PARENT  . .    2.904      0.313       0.321     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .   15.534      0.677       0.519    324   100.0   324     ERRMC  
     LARGE SHIFTS/INSERTIONS   26.005      0.724       0.391    214    91.5   234     ERRMC  
     SURFACE . . . . . . . .   16.552      0.649       0.456    367    94.8   387     ERRMC  
     BURIED  . . . . . . . .    3.178      0.514       0.528    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    3.262      0.531       0.538    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.250      0.558       0.394    414    95.6   433     ERRSC  
     WELL ORDERED  . . . . .   13.845      0.578       0.419    248   100.0   248     ERRSC  
     NO INTER CONTACTS . . .   10.062      0.517       0.409    210   100.0   210     ERRSC  
     RELIABLE SIDE CHAINS  .   14.807      0.570       0.406    356    96.0   371     ERRSC  
     CHANGED ANGLES  . . . .   16.678      0.559       0.364    266    94.7   281     ERRSC  
     SHIFTED CHAIN . . . . .   18.800      0.601       0.362    290    93.9   309     ERRSC  
     ALTERNATIVE PARENT  . .    2.939      0.338       0.271      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .   16.950      0.609       0.429    297   100.0   297     ERRSC  
     LARGE SHIFTS/INSERTIONS   26.745      0.733       0.389    194    91.1   213     ERRSC  
     SURFACE . . . . . . . .   17.264      0.598       0.390    325    94.5   344     ERRSC  
     BURIED  . . . . . . . .    3.243      0.413       0.409     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    3.231      0.404       0.399    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.715      0.587       0.436    810    95.9   845     ERRALL 
     WELL ORDERED  . . . . .   13.194      0.605       0.463    593   100.0   593     ERRALL 
     NO INTER CONTACTS . . .    9.373      0.545       0.454    426   100.0   426     ERRALL 
     SHIFTED CHAIN . . . . .   18.043      0.607       0.385    566    94.2   601     ERRALL 
     ALTERNATIVE PARENT  . .    2.860      0.314       0.294     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .   16.280      0.645       0.475    557   100.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS   26.424      0.728       0.389    366    91.3   401     ERRALL 
     SURFACE . . . . . . . .   16.911      0.623       0.422    621    94.7   656     ERRALL 
     BURIED  . . . . . . . .    3.215      0.472       0.480    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    3.239      0.472       0.474    444   100.0   444     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)        29        42        50        63        64      99     103   DISTCA 
CA  (P)     28.16     40.78     48.54     61.17     62.14             103   DISTCA 
CA  (RMS)    0.68      0.93      1.34      2.12      2.20                   DISTCA 
 
ALL (N)       159       263       340       445       505     810     845   DISTALL 
ALL (P)     18.82     31.12     40.24     52.66     59.76             845   DISTALL 
ALL (RMS)    0.70      1.08      1.53      2.31      3.26                   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)          56            56            43          RMSLSI 
CA  (P)       54.37         54.37         41.75          RMSLSI 
CA  (RMS)      1.04          2.07         31.65          RMSLSI 
 
 
 
END of the results output 
