 
####################################################### 
#                                                     # 
#                        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 926 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 420 
 
 
 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 . . . . . . . . . .    27.98           92.3   104    51.7   201     ARMSMC  
     WELL ORDERED  . . . . .    29.15           94.3    88    54.7   161     ARMSMC  
     NO INTER CONTACTS . . .    31.27           92.2    77    73.3   105     ARMSMC  
     SHIFTED CHAIN . . . . .    38.32           87.8    49    34.8   141     ARMSMC  
     ALTERNATIVE PARENT  . .    24.68           75.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    23.86           97.3    73    57.5   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.42           66.7    12    13.5    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    33.93           88.9    63    41.7   151     ARMSMC  
     BURIED  . . . . . . . .    14.72           97.6    41    82.0    50     ARMSMC  
     CORE  . . . . . . . . .    14.17           95.7    92    82.1   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.17           54.3    46    50.5    91     ARMSSC1 
     WELL ORDERED  . . . . .    57.78           63.3    30    55.6    54     ARMSSC1 
     NO INTER CONTACTS . . .    75.27           51.5    33    73.3    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    73.51           51.2    43    51.2    84     ARMSSC1 
     CHANGED ANGLES  . . . .    85.90           38.5    26    39.4    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.71           47.6    21    32.8    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    37.03            0.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    74.19           57.6    33    57.9    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    94.63           16.7     6    14.3    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    73.68           50.0    28    40.6    69     ARMSSC1 
     BURIED  . . . . . . . .    67.08           61.1    18    81.8    22     ARMSSC1 
     CORE  . . . . . . . . .    66.95           60.0    40    81.6    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    58.89           51.4    35    54.7    64     ARMSSC2 
     WELL ORDERED  . . . . .    62.31           50.0    20    71.4    28     ARMSSC2 
     NO INTER CONTACTS . . .    50.11           60.9    23    69.7    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    61.97           44.4    27    55.1    49     ARMSSC2 
     CHANGED ANGLES  . . . .    70.50           38.1    21    44.7    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    46.56           46.7    15    34.1    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    53.72            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    56.93           57.7    26    61.9    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    37.34           50.0     4    14.3    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    64.26           43.5    23    46.9    49     ARMSSC2 
     BURIED  . . . . . . . .    46.89           66.7    12    80.0    15     ARMSSC2 
     CORE  . . . . . . . . .    61.12           51.6    31    86.1    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.70           22.2    18    58.1    31     ARMSSC3 
     WELL ORDERED  . . . . .    74.70           16.7     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    79.43           27.3    11    73.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    72.60           28.6    14    53.8    26     ARMSSC3 
     CHANGED ANGLES  . . . .    90.35           21.4    14    58.3    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    89.95           28.6     7    35.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    76.73           26.7    15    65.2    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   110.65            0.0     1     7.1    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    83.10           26.7    15    53.6    28     ARMSSC3 
     BURIED  . . . . . . . .    74.32            0.0     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    79.67           23.5    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    89.53           33.3     9    75.0    12     ARMSSC4 
     WELL ORDERED  . . . . .   110.73           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    60.76           60.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    89.53           33.3     9    75.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .    94.70           25.0     8    72.7    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    80.06            0.0     3    50.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    84.37           42.9     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 . . . . . . . .   101.02           14.3     7    70.0    10     ARMSSC4 
     BURIED  . . . . . . . .    18.84          100.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    89.53           33.3     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.14215     r(1,2) =   0.84855     r(1,3) =  -0.50967 
 r(2,1) =   0.41935     r(2,2) =  -0.51803     r(2,3) =  -0.74551 
 r(3,1) =  -0.89663     r(3,2) =  -0.10776     r(3,3) =  -0.42948 
THE OFFSET VECTOR: 
 v(1) =  15.69931     v(2) =  51.47940     v(3) =  42.05486 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.01           (Number of atoms:   48) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.55         53    51.5   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0293                            CRMSCA  
     WELL ORDERED  . . . . .    1.49         46    54.1    85     CRMSCA  
     NO INTER CONTACTS . . .    1.72         39    72.2    54     CRMSCA  
     SHIFTED CHAIN . . . . .    2.10         25    34.2    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.68          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    1.43         37    56.9    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.53          6    12.8    47     CRMSCA  
     SURFACE . . . . . . . .    1.76         32    41.0    78     CRMSCA  
     BURIED  . . . . . . . .    1.16         21    84.0    25     CRMSCA  
     CORE  . . . . . . . . .    1.06         47    83.9    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.62        262    51.3   511     CRMSMC  
     WELL ORDERED  . . . . .    1.54        230    54.8   420     CRMSMC  
     NO INTER CONTACTS . . .    1.77        193    72.3   267     CRMSMC  
     SHIFTED CHAIN . . . . .    2.18        124    34.2   363     CRMSMC  
     ALTERNATIVE PARENT  . .    2.90         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    1.42        184    56.8   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.68         30    12.8   234     CRMSMC  
     SURFACE . . . . . . . .    1.85        158    40.8   387     CRMSMC  
     BURIED  . . . . . . . .    1.18        104    83.9   124     CRMSMC  
     CORE  . . . . . . . . .    1.10        232    83.8   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.98        208    48.0   433     CRMSSC  
     WELL ORDERED  . . . . .    2.61        128    51.6   248     CRMSSC  
     NO INTER CONTACTS . . .    3.31        141    67.1   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.93        178    48.0   371     CRMSSC  
     CHANGED ANGLES  . . . .    3.55        116    41.3   281     CRMSSC  
     SECONDARY STRUCTURE . .    3.02        153    51.5   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.82         21     9.9   213     CRMSSC  
     SURFACE . . . . . . . .    3.15        134    39.0   344     CRMSSC  
     BURIED  . . . . . . . .    2.66         74    83.1    89     CRMSSC  
     CORE  . . . . . . . . .    2.47        187    85.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.36        420    49.7   845     CRMSALL 
     WELL ORDERED  . . . . .    1.99        319    53.8   593     CRMSALL 
     NO INTER CONTACTS . . .    2.57        297    69.7   426     CRMSALL 
     SHIFTED CHAIN . . . . .    2.96        190    31.6   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.09         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    2.33        301    54.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.71         45    11.2   401     CRMSALL 
     SURFACE . . . . . . . .    2.56        262    39.9   656     CRMSALL 
     BURIED  . . . . . . . .    1.97        158    83.6   189     CRMSALL 
     CORE  . . . . . . . . .    1.89        375    84.5   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.53      6   100.0     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     3.68     30   100.0    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     4.71     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     0.00      0     0.0   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.14      6   100.0     6      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.58     30   100.0    30      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.62     45   100.0    45      40-TNPSIQ-45   
 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 . . . . . . . . . .    0.613      0.248       0.210     53    51.5   103     ERRCA  
     WELL ORDERED  . . . . .    0.570      0.240       0.211     46    54.1    85     ERRCA  
     NO INTER CONTACTS . . .    0.676      0.238       0.182     39    72.2    54     ERRCA  
     SHIFTED CHAIN . . . . .    0.934      0.277       0.181     25    34.2    73     ERRCA  
     ALTERNATIVE PARENT  . .    1.625      0.437       0.218      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.486      0.200       0.174     37    56.9    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.246      0.487       0.244      6    12.8    47     ERRCA  
     SURFACE . . . . . . . .    0.718      0.263       0.216     32    41.0    78     ERRCA  
     BURIED  . . . . . . . .    0.454      0.224       0.200     21    84.0    25     ERRCA  
     CORE  . . . . . . . . .    0.405      0.217       0.206     47    83.9    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.657      0.261       0.227    262    51.3   511     ERRMC  
     WELL ORDERED  . . . . .    0.601      0.252       0.227    230    54.8   420     ERRMC  
     NO INTER CONTACTS . . .    0.724      0.260       0.214    193    72.3   267     ERRMC  
     SHIFTED CHAIN . . . . .    0.996      0.295       0.204    124    34.2   363     ERRMC  
     ALTERNATIVE PARENT  . .    1.842      0.465       0.233     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.513      0.224       0.205    184    56.8   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.366      0.490       0.245     30    12.8   234     ERRMC  
     SURFACE . . . . . . . .    0.763      0.268       0.220    158    40.8   387     ERRMC  
     BURIED  . . . . . . . .    0.495      0.250       0.238    104    83.9   124     ERRMC  
     CORE  . . . . . . . . .    0.436      0.231       0.224    232    83.8   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.485      0.344       0.194    208    48.0   433     ERRSC  
     WELL ORDERED  . . . . .    1.206      0.305       0.184    128    51.6   248     ERRSC  
     NO INTER CONTACTS . . .    1.705      0.360       0.197    141    67.1   210     ERRSC  
     RELIABLE SIDE CHAINS  .    1.416      0.332       0.190    178    48.0   371     ERRSC  
     CHANGED ANGLES  . . . .    1.961      0.401       0.206    116    41.3   281     ERRSC  
     SHIFTED CHAIN . . . . .    2.095      0.416       0.219     90    29.1   309     ERRSC  
     ALTERNATIVE PARENT  . .    2.416      0.540       0.270      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    1.463      0.332       0.183    153    51.5   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.154      0.619       0.309     21     9.9   213     ERRSC  
     SURFACE . . . . . . . .    1.607      0.363       0.203    134    39.0   344     ERRSC  
     BURIED  . . . . . . . .    1.265      0.309       0.177     74    83.1    89     ERRSC  
     CORE  . . . . . . . . .    1.185      0.313       0.181    187    85.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.055      0.305       0.217    420    49.7   845     ERRALL 
     WELL ORDERED  . . . . .    0.826      0.275       0.215    319    53.8   593     ERRALL 
     NO INTER CONTACTS . . .    1.172      0.311       0.213    297    69.7   426     ERRALL 
     SHIFTED CHAIN . . . . .    1.482      0.351       0.215    190    31.6   601     ERRALL 
     ALTERNATIVE PARENT  . .    2.017      0.487       0.243     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    0.987      0.283       0.202    301    54.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.107      0.540       0.270     45    11.2   401     ERRALL 
     SURFACE . . . . . . . .    1.180      0.318       0.215    262    39.9   656     ERRALL 
     BURIED  . . . . . . . .    0.847      0.284       0.221    158    83.6   189     ERRALL 
     CORE  . . . . . . . . .    0.808      0.277       0.211    375    84.5   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)        32        44        49        52        53      53     103   DISTCA 
CA  (P)     31.07     42.72     47.57     50.49     51.46             103   DISTCA 
CA  (RMS)    0.65      0.83      1.08      1.33      1.55                   DISTCA 
 
ALL (N)       178       289       359       401       418     420     845   DISTALL 
ALL (P)     21.07     34.20     42.49     47.46     49.47             845   DISTALL 
ALL (RMS)    0.66      1.00      1.43      1.86      2.23                   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            47             6          RMSLSI 
CA  (P)       54.37         45.63          5.83          RMSLSI 
CA  (RMS)      1.04          1.06          3.53          RMSLSI 
 
 
 
END of the results output 
