 
####################################################### 
#                                                     # 
#                        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 678 atoms, 609 common with TARGET 
           Number of atoms possible to evaluate: 244 
 
 
 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 . . . . . . . . . .    22.79           84.7   118    58.7   201     ARMSMC  
     WELL ORDERED  . . . . .    21.92           89.2   102    63.4   161     ARMSMC  
     NO INTER CONTACTS . . .    22.87           82.5    80    76.2   105     ARMSMC  
     SHIFTED CHAIN . . . . .    26.22           79.3    58    41.1   141     ARMSMC  
     ALTERNATIVE PARENT  . .    26.55           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    16.67           94.2    69    54.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    20.58           75.0     8     9.0    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    22.35           82.9    70    46.4   151     ARMSMC  
     BURIED  . . . . . . . .    23.40           87.5    48    96.0    50     ARMSMC  
     CORE  . . . . . . . . .    22.94           85.5   110    98.2   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) =   0.64249     r(1,2) =   0.20869     r(1,3) =  -0.73733 
 r(2,1) =  -0.32931     r(2,2) =  -0.79363     r(2,3) =  -0.51158 
 r(3,1) =  -0.69192     r(3,2) =   0.57149     r(3,3) =  -0.44118 
THE OFFSET VECTOR: 
 v(1) = -27.12000     v(2) = 101.34912     v(3) =  75.38786 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.03           (Number of atoms:   57) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.37         61    59.2   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0224                            CRMSCA  
     WELL ORDERED  . . . . .    1.21         54    63.5    85     CRMSCA  
     NO INTER CONTACTS . . .    1.31         41    75.9    54     CRMSCA  
     SHIFTED CHAIN . . . . .    1.73         31    42.5    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.77          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.97         35    53.8    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.37          5    10.6    47     CRMSCA  
     SURFACE . . . . . . . .    1.58         36    46.2    78     CRMSCA  
     BURIED  . . . . . . . .    0.97         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    1.01         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.40        244    47.7   511     CRMSMC  
     WELL ORDERED  . . . . .    1.28        222    52.9   420     CRMSMC  
     NO INTER CONTACTS . . .    1.33        164    61.4   267     CRMSMC  
     SHIFTED CHAIN . . . . .    1.76        124    34.2   363     CRMSMC  
     ALTERNATIVE PARENT  . .    3.11          8    80.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.96        140    43.2   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.43         20     8.5   234     CRMSMC  
     SURFACE . . . . . . . .    1.60        144    37.2   387     CRMSMC  
     BURIED  . . . . . . . .    1.05        100    80.6   124     CRMSMC  
     CORE  . . . . . . . . .    1.05        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 . . . . . . . . . .    1.40        244    28.9   845     CRMSALL 
     WELL ORDERED  . . . . .    1.28        222    37.4   593     CRMSALL 
     NO INTER CONTACTS . . .    1.33        164    38.5   426     CRMSALL 
     SHIFTED CHAIN . . . . .    1.76        124    20.6   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.11          8    57.1    14     CRMSALL 
     SECONDARY STRUCTURE . .    0.96        140    25.1   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.43         20     5.0   401     CRMSALL 
     SURFACE . . . . . . . .    1.60        144    22.0   656     CRMSALL 
     BURIED  . . . . . . . .    1.05        100    52.9   189     CRMSALL 
     CORE  . . . . . . . . .    1.05        224    50.5   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.92      4    66.7     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     3.05     16    53.3    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     3.05     16    35.6    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     0.32      4    66.7     6      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.68     16    53.3    30      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.68     16    35.6    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 . . . . . . . . . .    1.112      1.000       0.500     61    59.2   103     ERRCA  
     WELL ORDERED  . . . . .    1.001      1.000       0.500     54    63.5    85     ERRCA  
     NO INTER CONTACTS . . .    1.085      1.000       0.500     41    75.9    54     ERRCA  
     SHIFTED CHAIN . . . . .    1.437      1.000       0.500     31    42.5    73     ERRCA  
     ALTERNATIVE PARENT  . .    2.674      1.000       0.500      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.914      1.000       0.500     35    53.8    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.238      1.000       0.500      5    10.6    47     ERRCA  
     SURFACE . . . . . . . .    1.274      1.000       0.500     36    46.2    78     ERRCA  
     BURIED  . . . . . . . .    0.878      1.000       0.500     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    0.922      1.000       0.500     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.139      1.000       0.500    244    47.7   511     ERRMC  
     WELL ORDERED  . . . . .    1.049      1.000       0.500    222    52.9   420     ERRMC  
     NO INTER CONTACTS . . .    1.096      1.000       0.500    164    61.4   267     ERRMC  
     SHIFTED CHAIN . . . . .    1.437      1.000       0.500    124    34.2   363     ERRMC  
     ALTERNATIVE PARENT  . .    3.026      1.000       0.500      8    80.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.898      1.000       0.500    140    43.2   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.293      1.000       0.500     20     8.5   234     ERRMC  
     SURFACE . . . . . . . .    1.305      1.000       0.500    144    37.2   387     ERRMC  
     BURIED  . . . . . . . .    0.901      1.000       0.500    100    80.6   124     ERRMC  
     CORE  . . . . . . . . .    0.947      1.000       0.500    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 . . . . . . . . . .    1.139      1.000       0.500    244    28.9   845     ERRALL 
     WELL ORDERED  . . . . .    1.049      1.000       0.500    222    37.4   593     ERRALL 
     NO INTER CONTACTS . . .    1.096      1.000       0.500    164    38.5   426     ERRALL 
     SHIFTED CHAIN . . . . .    1.437      1.000       0.500    124    20.6   601     ERRALL 
     ALTERNATIVE PARENT  . .    3.026      1.000       0.500      8    57.1    14     ERRALL 
     SECONDARY STRUCTURE . .    0.898      1.000       0.500    140    25.1   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.293      1.000       0.500     20     5.0   401     ERRALL 
     SURFACE . . . . . . . .    1.305      1.000       0.500    144    22.0   656     ERRALL 
     BURIED  . . . . . . . .    0.901      1.000       0.500    100    52.9   189     ERRALL 
     CORE  . . . . . . . . .    0.947      1.000       0.500    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)        40        56        58        61        61      61     103   DISTCA 
CA  (P)     38.83     54.37     56.31     59.22     59.22             103   DISTCA 
CA  (RMS)    0.74      1.00      1.09      1.37      1.37                   DISTCA 
 
ALL (N)       146       220       230       243       244     244     845   DISTALL 
ALL (P)     17.28     26.04     27.22     28.76     28.88             845   DISTALL 
ALL (RMS)    0.72      0.99      1.09      1.35      1.40                   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             5          RMSLSI 
CA  (P)       54.37         54.37          4.85          RMSLSI 
CA  (RMS)      1.04          1.01          3.37          RMSLSI 
 
 
 
END of the results output 
