 
####################################################### 
#                                                     # 
#                        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 914 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 435 
 
 
 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 . . . . . . . . . .    26.62           87.7   106    52.7   201     ARMSMC  
     WELL ORDERED  . . . . .    27.54           86.6    97    60.2   161     ARMSMC  
     NO INTER CONTACTS . . .    30.67           85.9    71    67.6   105     ARMSMC  
     SHIFTED CHAIN . . . . .    32.87           80.9    47    33.3   141     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    26.46           89.9    69    54.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    33.72            0.0     1     1.1    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    21.87           90.0    60    39.7   151     ARMSMC  
     BURIED  . . . . . . . .    31.77           84.8    46    92.0    50     ARMSMC  
     CORE  . . . . . . . . .    26.55           88.6   105    93.8   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.44           50.0    48    52.7    91     ARMSSC1 
     WELL ORDERED  . . . . .    89.37           45.5    33    61.1    54     ARMSSC1 
     NO INTER CONTACTS . . .    75.73           60.0    30    66.7    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    87.78           46.5    43    51.2    84     ARMSSC1 
     CHANGED ANGLES  . . . .    96.95           40.0    25    37.9    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    74.35           57.1    21    32.8    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    78.62           58.1    31    54.4    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   121.96            0.0     1     2.4    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    87.77           44.4    27    39.1    69     ARMSSC1 
     BURIED  . . . . . . . .    79.96           57.1    21    95.5    22     ARMSSC1 
     CORE  . . . . . . . . .    83.46           51.1    47    95.9    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.94           40.0    35    54.7    64     ARMSSC2 
     WELL ORDERED  . . . . .    80.37           36.8    19    67.9    28     ARMSSC2 
     NO INTER CONTACTS . . .    86.92           42.9    21    63.6    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    75.20           42.3    26    53.1    49     ARMSSC2 
     CHANGED ANGLES  . . . .    85.45           40.0    20    42.6    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    77.04           46.7    15    34.1    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    87.07           41.7    24    57.1    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    81.14            0.0     1     3.6    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    80.95           38.1    21    42.9    49     ARMSSC2 
     BURIED  . . . . . . . .    88.24           42.9    14    93.3    15     ARMSSC2 
     CORE  . . . . . . . . .    84.02           41.2    34    94.4    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.42           23.5    17    54.8    31     ARMSSC3 
     WELL ORDERED  . . . . .    65.96           33.3     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    88.13           11.1     9    60.0    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    88.09           20.0    15    57.7    26     ARMSSC3 
     CHANGED ANGLES  . . . .    91.44           23.1    13    54.2    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    85.13           33.3     6    30.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    74.54           28.6    14    60.9    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   127.29            0.0     1     7.1    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    84.26           28.6    14    50.0    28     ARMSSC3 
     BURIED  . . . . . . . .    85.17            0.0     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    80.99           25.0    16    94.1    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   110.90           11.1     9    75.0    12     ARMSSC4 
     WELL ORDERED  . . . . .   127.49            0.0     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .   104.96            0.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .   110.90           11.1     9    75.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .   104.23           12.5     8    72.7    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    74.13           33.3     3    50.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   118.23            0.0     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 . . . . . . . .   109.17           14.3     7    70.0    10     ARMSSC4 
     BURIED  . . . . . . . .   116.78            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .   110.90           11.1     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.04836     r(1,2) =   0.99181     r(1,3) =  -0.11820 
 r(2,1) =  -0.37330     r(2,2) =  -0.12771     r(2,3) =  -0.91888 
 r(3,1) =  -0.92645     r(3,2) =  -0.00031     r(3,3) =   0.37642 
THE OFFSET VECTOR: 
 v(1) =  16.31210     v(2) =  62.85191     v(3) =  32.80157 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.88           (Number of atoms:   54) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.03         55    53.4   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0188                            CRMSCA  
     WELL ORDERED  . . . . .    1.06         51    60.0    85     CRMSCA  
     NO INTER CONTACTS . . .    0.90         36    66.7    54     CRMSCA  
     SHIFTED CHAIN . . . . .    1.31         25    34.2    73     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.89         35    53.8    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.16          1     2.1    47     CRMSCA  
     SURFACE . . . . . . . .    1.08         31    39.7    78     CRMSCA  
     BURIED  . . . . . . . .    0.97         24    96.0    25     CRMSCA  
     CORE  . . . . . . . . .    0.88         54    96.4    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.10        272    53.2   511     CRMSMC  
     WELL ORDERED  . . . . .    1.11        254    60.5   420     CRMSMC  
     NO INTER CONTACTS . . .    0.98        178    66.7   267     CRMSMC  
     SHIFTED CHAIN . . . . .    1.34        124    34.2   363     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.97        174    53.7   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.98          5     2.1   234     CRMSMC  
     SURFACE . . . . . . . .    1.15        153    39.5   387     CRMSMC  
     BURIED  . . . . . . . .    1.03        119    96.0   124     CRMSMC  
     CORE  . . . . . . . . .    0.96        267    96.4   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.89        215    49.7   433     CRMSSC  
     WELL ORDERED  . . . . .    2.55        142    57.3   248     CRMSSC  
     NO INTER CONTACTS . . .    2.70        130    61.9   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.89        181    48.8   371     CRMSSC  
     CHANGED ANGLES  . . . .    3.54        113    40.2   281     CRMSSC  
     SECONDARY STRUCTURE . .    2.78        144    48.5   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    4.85          4     1.9   213     CRMSSC  
     SURFACE . . . . . . . .    3.10        129    37.5   344     CRMSSC  
     BURIED  . . . . . . . .    2.54         86    96.6    89     CRMSSC  
     CORE  . . . . . . . . .    2.84        211    95.9   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.16        435    51.5   845     CRMSALL 
     WELL ORDERED  . . . . .    1.82        351    59.2   593     CRMSALL 
     NO INTER CONTACTS . . .    1.97        274    64.3   426     CRMSALL 
     SHIFTED CHAIN . . . . .    2.23        191    31.8   601     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    2.07        284    51.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.48          8     2.0   401     CRMSALL 
     SURFACE . . . . . . . .    2.35        253    38.6   656     CRMSALL 
     BURIED  . . . . . . . .    1.87        182    96.3   189     CRMSALL 
     CORE  . . . . . . . . .    2.10        427    96.2   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     6      40-TNPSIQ-45   
 CA  LOOP  2     0.00      0     0.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    30      40-TNPSIQ-45   
 MC  LOOP  2     0.00      0     0.0   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    45      40-TNPSIQ-45   
 ALL LOOP  2     0.00      0     0.0   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 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 . . . . . . . . . .    0.410      0.262       0.143     55    53.4   103     ERRCA  
     WELL ORDERED  . . . . .    0.417      0.256       0.141     51    60.0    85     ERRCA  
     NO INTER CONTACTS . . .    0.372      0.272       0.149     36    66.7    54     ERRCA  
     SHIFTED CHAIN . . . . .    0.644      0.367       0.185     25    34.2    73     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.336      0.239       0.123     35    53.8    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.566      0.751       0.376      1     2.1    47     ERRCA  
     SURFACE . . . . . . . .    0.407      0.255       0.144     31    39.7    78     ERRCA  
     BURIED  . . . . . . . .    0.414      0.271       0.142     24    96.0    25     ERRCA  
     CORE  . . . . . . . . .    0.352      0.253       0.139     54    96.4    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.457      0.287       0.165    272    53.2   511     ERRMC  
     WELL ORDERED  . . . . .    0.454      0.277       0.160    254    60.5   420     ERRMC  
     NO INTER CONTACTS . . .    0.414      0.285       0.158    178    66.7   267     ERRMC  
     SHIFTED CHAIN . . . . .    0.657      0.374       0.200    124    34.2   363     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.381      0.257       0.138    174    53.7   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.340      0.734       0.367      5     2.1   234     ERRMC  
     SURFACE . . . . . . . .    0.478      0.297       0.180    153    39.5   387     ERRMC  
     BURIED  . . . . . . . .    0.429      0.274       0.145    119    96.0   124     ERRMC  
     CORE  . . . . . . . . .    0.403      0.278       0.161    267    96.4   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.812      0.530       0.270    215    49.7   433     ERRSC  
     WELL ORDERED  . . . . .    1.570      0.493       0.252    142    57.3   248     ERRSC  
     NO INTER CONTACTS . . .    1.581      0.501       0.259    130    61.9   210     ERRSC  
     RELIABLE SIDE CHAINS  .    1.775      0.520       0.266    181    48.8   371     ERRSC  
     CHANGED ANGLES  . . . .    2.480      0.620       0.310    113    40.2   281     ERRSC  
     SHIFTED CHAIN . . . . .    1.958      0.579       0.290     91    29.4   309     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     6     ERRSC  
     SECONDARY STRUCTURE . .    1.657      0.507       0.258    144    48.5   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.164      0.772       0.386      4     1.9   213     ERRSC  
     SURFACE . . . . . . . .    1.999      0.567       0.289    129    37.5   344     ERRSC  
     BURIED  . . . . . . . .    1.531      0.476       0.242     86    96.6    89     ERRSC  
     CORE  . . . . . . . . .    1.768      0.526       0.268    211    95.9   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.106      0.401       0.215    435    51.5   845     ERRALL 
     WELL ORDERED  . . . . .    0.882      0.358       0.196    351    59.2   593     ERRALL 
     NO INTER CONTACTS . . .    0.943      0.378       0.200    274    64.3   426     ERRALL 
     SHIFTED CHAIN . . . . .    1.250      0.466       0.242    191    31.8   601     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    14     ERRALL 
     SECONDARY STRUCTURE . .    1.004      0.375       0.194    284    51.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.799      0.755       0.378      8     2.0   401     ERRALL 
     SURFACE . . . . . . . .    1.239      0.428       0.234    253    38.6   656     ERRALL 
     BURIED  . . . . . . . .    0.921      0.362       0.188    182    96.3   189     ERRALL 
     CORE  . . . . . . . . .    1.055      0.394       0.212    427    96.2   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)        43        54        54        55        55      55     103   DISTCA 
CA  (P)     41.75     52.43     52.43     53.40     53.40             103   DISTCA 
CA  (RMS)    0.67      0.88      0.88      1.03      1.03                   DISTCA 
 
ALL (N)       223       329       373       416       434     435     845   DISTALL 
ALL (P)     26.39     38.93     44.14     49.23     51.36             845   DISTALL 
ALL (RMS)    0.66      0.98      1.26      1.73      2.11                   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            54             1          RMSLSI 
CA  (P)       54.37         52.43          0.97          RMSLSI 
CA  (RMS)      1.04          0.88          4.16          RMSLSI 
 
 
 
END of the results output 
