 
####################################################### 
#                                                     # 
#                        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 444 atoms, 412 common with TARGET 
           Number of atoms possible to evaluate: 412 
 
 
 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 . . . . . . . . . .    77.02           46.9   194    96.5   201     ARMSMC  
     WELL ORDERED  . . . . .    76.30           48.4   161   100.0   161     ARMSMC  
     NO INTER CONTACTS . . .    79.95           45.0   100    95.2   105     ARMSMC  
     SHIFTED CHAIN . . . . .    82.37           40.3   134    95.0   141     ARMSMC  
     ALTERNATIVE PARENT  . .   100.42            0.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    60.84           61.2   121    95.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    73.74           47.6    82    92.1    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    78.92           45.8   144    95.4   151     ARMSMC  
     BURIED  . . . . . . . .    71.27           50.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    79.34           46.4   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    91     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    54     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    84     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    66     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    69     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    22     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    64     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    28     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    49     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    49     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    31     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    10     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    26     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    12     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     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 . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.72906     r(1,2) =   0.41695     r(1,3) =  -0.54280 
 r(2,1) =  -0.35872     r(2,2) =  -0.90816     r(2,3) =  -0.21578 
 r(3,1) =  -0.58292     r(3,2) =   0.03740     r(3,3) =   0.81167 
THE OFFSET VECTOR: 
 v(1) =  16.17412     v(2) =  42.80363     v(3) =  49.35396 
 
 Number of iteration 31                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.36           (Number of atoms:   18) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   16.80        103   100.0   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1631                            CRMSCA  
     WELL ORDERED  . . . . .   16.91         85   100.0    85     CRMSCA  
     NO INTER CONTACTS . . .   13.07         54   100.0    54     CRMSCA  
     SHIFTED CHAIN . . . . .   19.71         73   100.0    73     CRMSCA  
     ALTERNATIVE PARENT  . .    8.88          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   17.40         65   100.0    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   23.92         47   100.0    47     CRMSCA  
     SURFACE . . . . . . . .   18.90         78   100.0    78     CRMSCA  
     BURIED  . . . . . . . .    6.98         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    6.24         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   16.75        412    80.6   511     CRMSMC  
     WELL ORDERED  . . . . .   16.64        345    82.1   420     CRMSMC  
     NO INTER CONTACTS . . .   13.05        216    80.9   267     CRMSMC  
     SHIFTED CHAIN . . . . .   19.68        292    80.4   363     CRMSMC  
     ALTERNATIVE PARENT  . .    8.68          8    80.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   17.41        260    80.2   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   23.92        188    80.3   234     CRMSMC  
     SURFACE . . . . . . . .   18.88        312    80.6   387     CRMSMC  
     BURIED  . . . . . . . .    6.67        100    80.6   124     CRMSMC  
     CORE  . . . . . . . . .    6.00        224    80.9   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   433     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   248     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   371     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   281     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   213     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   344     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    89     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   16.75        412    48.8   845     CRMSALL 
     WELL ORDERED  . . . . .   16.64        345    58.2   593     CRMSALL 
     NO INTER CONTACTS . . .   13.05        216    50.7   426     CRMSALL 
     SHIFTED CHAIN . . . . .   19.68        292    48.6   601     CRMSALL 
     ALTERNATIVE PARENT  . .    8.68          8    57.1    14     CRMSALL 
     SECONDARY STRUCTURE . .   17.41        260    46.7   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS   23.92        188    46.9   401     CRMSALL 
     SURFACE . . . . . . . .   18.88        312    47.6   656     CRMSALL 
     BURIED  . . . . . . . .    6.67        100    52.9   189     CRMSALL 
     CORE  . . . . . . . . .    6.00        224    50.5   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     8.64      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2    25.70     40   100.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     8.20     24    80.0    30      40-TNPSIQ-45   
 MC  LOOP  2    25.72    160    80.4   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     8.20     24    53.3    45      40-TNPSIQ-45   
 ALL LOOP  2    25.72    160    46.0   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.97      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     8.72     40   100.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.80     24    80.0    30      40-TNPSIQ-45   
 MC  LOOP  2     8.61    160    80.4   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.80     24    53.3    45      40-TNPSIQ-45   
 ALL LOOP  2     8.61    160    46.0   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 . . . . . . . . . .    9.154      0.432       0.286    103   100.0   103     ERRCA  
     WELL ORDERED  . . . . .    9.305      0.447       0.304     85   100.0    85     ERRCA  
     NO INTER CONTACTS . . .    6.231      0.362       0.258     54   100.0    54     ERRCA  
     SHIFTED CHAIN . . . . .   11.768      0.448       0.245     73   100.0    73     ERRCA  
     ALTERNATIVE PARENT  . .    3.864      0.278       0.139      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .   10.310      0.487       0.331     65   100.0    65     ERRCA  
     LARGE SHIFTS/INSERTIONS   16.593      0.551       0.275     47   100.0    47     ERRCA  
     SURFACE . . . . . . . .   11.096      0.472       0.294     78   100.0    78     ERRCA  
     BURIED  . . . . . . . .    3.096      0.309       0.261     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    2.911      0.333       0.294     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.106      0.432       0.288    412    80.6   511     ERRMC  
     WELL ORDERED  . . . . .    9.102      0.444       0.306    345    82.1   420     ERRMC  
     NO INTER CONTACTS . . .    6.229      0.366       0.262    216    80.9   267     ERRMC  
     SHIFTED CHAIN . . . . .   11.674      0.442       0.242    292    80.4   363     ERRMC  
     ALTERNATIVE PARENT  . .    3.595      0.258       0.129      8    80.0    10     ERRMC  
     SECONDARY STRUCTURE . .   10.324      0.492       0.337    260    80.2   324     ERRMC  
     LARGE SHIFTS/INSERTIONS   16.534      0.546       0.273    188    80.3   234     ERRMC  
     SURFACE . . . . . . . .   11.054      0.470       0.294    312    80.6   387     ERRMC  
     BURIED  . . . . . . . .    3.030      0.315       0.268    100    80.6   124     ERRMC  
     CORE  . . . . . . . . .    2.872      0.337       0.300    224    80.9   277     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   433     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   248     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   210     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   371     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   281     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   309     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     6     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   213     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   344     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    89     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.106      0.432       0.288    412    48.8   845     ERRALL 
     WELL ORDERED  . . . . .    9.102      0.444       0.306    345    58.2   593     ERRALL 
     NO INTER CONTACTS . . .    6.229      0.366       0.262    216    50.7   426     ERRALL 
     SHIFTED CHAIN . . . . .   11.674      0.442       0.242    292    48.6   601     ERRALL 
     ALTERNATIVE PARENT  . .    3.595      0.258       0.129      8    57.1    14     ERRALL 
     SECONDARY STRUCTURE . .   10.324      0.492       0.337    260    46.7   557     ERRALL 
     LARGE SHIFTS/INSERTIONS   16.534      0.546       0.273    188    46.9   401     ERRALL 
     SURFACE . . . . . . . .   11.054      0.470       0.294    312    47.6   656     ERRALL 
     BURIED  . . . . . . . .    3.030      0.315       0.268    100    52.9   189     ERRALL 
     CORE  . . . . . . . . .    2.872      0.337       0.300    224    50.5   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)        11        13        18        24        61     103     103   DISTCA 
CA  (P)     10.68     12.62     17.48     23.30     59.22             103   DISTCA 
CA  (RMS)    0.65      0.87      1.36      2.32      6.01                   DISTCA 
 
ALL (N)        42        59        76       113       255     412     845   DISTALL 
ALL (P)      4.97      6.98      8.99     13.37     30.18             845   DISTALL 
ALL (RMS)    0.61      0.98      1.45      2.58      5.96                   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            47          RMSLSI 
CA  (P)       54.37         54.37         45.63          RMSLSI 
CA  (RMS)      1.04          6.24         23.92          RMSLSI 
 
 
 
END of the results output 
