 
####################################################### 
#                                                     # 
#                        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 919 atoms, 844 common with TARGET 
           Number of atoms possible to evaluate: 393 
 
 
 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 . . . . . . . . . .    47.41           77.5    80    39.8   201     ARMSMC  
     WELL ORDERED  . . . . .    44.32           82.5    63    39.1   161     ARMSMC  
     NO INTER CONTACTS . . .    61.88           73.7    19    18.1   105     ARMSMC  
     SHIFTED CHAIN . . . . .    48.10           76.6    77    54.6   141     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    32.29           88.4    43    33.9   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    39.45           81.5    65    73.0    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    42.02           80.0    75    49.7   151     ARMSMC  
     BURIED  . . . . . . . .    97.31           40.0     5    10.0    50     ARMSMC  
     CORE  . . . . . . . . .    72.41           60.0    15    13.4   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.21           29.7    37    40.7    91     ARMSSC1 
     WELL ORDERED  . . . . .    76.87           33.3    21    38.9    54     ARMSSC1 
     NO INTER CONTACTS . . .    83.63           25.0     8    17.8    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    84.00           27.3    33    39.3    84     ARMSSC1 
     CHANGED ANGLES  . . . .    85.38           28.1    32    48.5    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    83.12           28.6    35    54.7    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    84.76           31.6    19    33.3    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    88.38           27.6    29    69.0    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    83.61           29.4    34    49.3    69     ARMSSC1 
     BURIED  . . . . . . . .    45.90           33.3     3    13.6    22     ARMSSC1 
     CORE  . . . . . . . . .    46.75           37.5     8    16.3    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.13           43.5    23    35.9    64     ARMSSC2 
     WELL ORDERED  . . . . .    44.49           62.5     8    28.6    28     ARMSSC2 
     NO INTER CONTACTS . . .    70.99           14.3     7    21.2    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    59.58           50.0    16    32.7    49     ARMSSC2 
     CHANGED ANGLES  . . . .    72.09           50.0    20    42.6    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.13           43.5    23    52.3    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    42.18           61.5    13    31.0    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    64.23           52.6    19    67.9    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    72.95           47.6    21    42.9    49     ARMSSC2 
     BURIED  . . . . . . . .    62.89            0.0     2    13.3    15     ARMSSC2 
     CORE  . . . . . . . . .   101.59            0.0     4    11.1    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.62           25.0     8    25.8    31     ARMSSC3 
     WELL ORDERED  . . . . .    61.22           25.0     4    40.0    10     ARMSSC3 
     NO INTER CONTACTS . . .   114.94            0.0     2    13.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.62           25.0     8    30.8    26     ARMSSC3 
     CHANGED ANGLES  . . . .    90.12           20.0     5    20.8    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    77.62           25.0     8    40.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    89.96           20.0     5    21.7    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    77.62           25.0     8    57.1    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    77.62           25.0     8    28.6    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 . . . . . . . . . .   101.49            0.0     1     8.3    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  .   101.49            0.0     1     8.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .   101.49            0.0     1     9.1    11     ARMSSC4 
     SHIFTED CHAIN . . . . .   101.49            0.0     1    16.7     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   101.49            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   101.49            0.0     1    10.0    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) =   0.85550     r(1,2) =  -0.51377     r(1,3) =   0.06452 
 r(2,1) =   0.32823     r(2,2) =   0.63444     r(2,3) =   0.69982 
 r(3,1) =  -0.40048     r(3,2) =  -0.57752     r(3,3) =   0.71140 
THE OFFSET VECTOR: 
 v(1) =   1.72473     v(2) =  37.01384     v(3) =  30.36212 
 
 Number of iteration 26                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   9.01           (Number of atoms:   46) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.01         46    44.7   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1958                            CRMSCA  
     WELL ORDERED  . . . . .    8.91         37    43.5    85     CRMSCA  
     NO INTER CONTACTS . . .    9.60         12    22.2    54     CRMSCA  
     SHIFTED CHAIN . . . . .    8.45         44    60.3    73     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    6.75         27    41.5    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    7.53         38    80.9    47     CRMSCA  
     SURFACE . . . . . . . .    8.50         43    55.1    78     CRMSCA  
     BURIED  . . . . . . . .   14.45          3    12.0    25     CRMSCA  
     CORE  . . . . . . . . .   14.06          8    14.3    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.00        228    44.6   511     CRMSMC  
     WELL ORDERED  . . . . .    8.79        180    42.9   420     CRMSMC  
     NO INTER CONTACTS . . .    9.48         59    22.1   267     CRMSMC  
     SHIFTED CHAIN . . . . .    8.43        218    60.1   363     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    6.66        134    41.4   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    7.53        188    80.3   234     CRMSMC  
     SURFACE . . . . . . . .    8.48        213    55.0   387     CRMSMC  
     BURIED  . . . . . . . .   14.51         15    12.1   124     CRMSMC  
     CORE  . . . . . . . . .   13.97         40    14.4   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   11.12        210    48.5   433     CRMSSC  
     WELL ORDERED  . . . . .    9.92        114    46.0   248     CRMSSC  
     NO INTER CONTACTS . . .   11.53         58    27.6   210     CRMSSC  
     RELIABLE SIDE CHAINS  .   11.05        180    48.5   371     CRMSSC  
     CHANGED ANGLES  . . . .   10.90        154    54.8   281     CRMSSC  
     SECONDARY STRUCTURE . .   10.26        142    47.8   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.46        181    85.0   213     CRMSSC  
     SURFACE . . . . . . . .   10.85        199    57.8   344     CRMSSC  
     BURIED  . . . . . . . .   15.19         11    12.4    89     CRMSSC  
     CORE  . . . . . . . . .   14.56         29    13.2   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.08        393    46.5   845     CRMSALL 
     WELL ORDERED  . . . . .    9.16        260    43.8   593     CRMSALL 
     NO INTER CONTACTS . . .   10.46        106    24.9   426     CRMSALL 
     SHIFTED CHAIN . . . . .    9.68        379    63.1   601     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    8.78        249    44.7   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.13        332    82.8   401     CRMSALL 
     SURFACE . . . . . . . .    9.71        370    56.4   656     CRMSALL 
     BURIED  . . . . . . . .   14.82         23    12.2   189     CRMSALL 
     CORE  . . . . . . . . .   14.17         61    13.7   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     7.53     38    95.0    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     7.53    188    94.5   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     9.13    332    95.4   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     6.10     38    95.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     6.06    188    94.5   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     7.84    332    95.4   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 . . . . . . . . . .    6.961      0.705       0.352     46    44.7   103     ERRCA  
     WELL ORDERED  . . . . .    6.745      0.689       0.345     37    43.5    85     ERRCA  
     NO INTER CONTACTS . . .    7.406      0.720       0.360     12    22.2    54     ERRCA  
     SHIFTED CHAIN . . . . .    6.539      0.697       0.348     44    60.3    73     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     2     ERRCA  
     SECONDARY STRUCTURE . .    5.078      0.651       0.326     27    41.5    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.716      0.672       0.336     38    80.9    47     ERRCA  
     SURFACE . . . . . . . .    6.520      0.694       0.347     43    55.1    78     ERRCA  
     BURIED  . . . . . . . .   13.281      0.867       0.433      3    12.0    25     ERRCA  
     CORE  . . . . . . . . .   12.874      0.862       0.431      8    14.3    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.920      0.704       0.352    228    44.6   511     ERRMC  
     WELL ORDERED  . . . . .    6.586      0.686       0.343    180    42.9   420     ERRMC  
     NO INTER CONTACTS . . .    7.202      0.701       0.350     59    22.1   267     ERRMC  
     SHIFTED CHAIN . . . . .    6.492      0.695       0.348    218    60.1   363     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    10     ERRMC  
     SECONDARY STRUCTURE . .    4.983      0.651       0.326    134    41.4   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.686      0.671       0.336    188    80.3   234     ERRMC  
     SURFACE . . . . . . . .    6.476      0.693       0.346    213    55.0   387     ERRMC  
     BURIED  . . . . . . . .   13.225      0.864       0.432     15    12.1   124     ERRMC  
     CORE  . . . . . . . . .   12.721      0.860       0.430     40    14.4   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.019      0.762       0.381    210    48.5   433     ERRSC  
     WELL ORDERED  . . . . .    7.550      0.709       0.355    114    46.0   248     ERRSC  
     NO INTER CONTACTS . . .    9.185      0.759       0.380     58    27.6   210     ERRSC  
     RELIABLE SIDE CHAINS  .    8.981      0.762       0.381    180    48.5   371     ERRSC  
     CHANGED ANGLES  . . . .    8.846      0.761       0.380    154    54.8   281     ERRSC  
     SHIFTED CHAIN . . . . .    8.770      0.758       0.379    204    66.0   309     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     6     ERRSC  
     SECONDARY STRUCTURE . .    8.178      0.744       0.372    142    47.8   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    8.397      0.748       0.374    181    85.0   213     ERRSC  
     SURFACE . . . . . . . .    8.738      0.756       0.378    199    57.8   344     ERRSC  
     BURIED  . . . . . . . .   14.107      0.875       0.437     11    12.4    89     ERRSC  
     CORE  . . . . . . . . .   12.899      0.849       0.425     29    13.2   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.917      0.731       0.366    393    46.5   845     ERRALL 
     WELL ORDERED  . . . . .    6.861      0.691       0.346    260    43.8   593     ERRALL 
     NO INTER CONTACTS . . .    8.103      0.727       0.364    106    24.9   426     ERRALL 
     SHIFTED CHAIN . . . . .    7.593      0.725       0.363    379    63.1   601     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    14     ERRALL 
     SECONDARY STRUCTURE . .    6.663      0.698       0.349    249    44.7   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    7.035      0.708       0.354    332    82.8   401     ERRALL 
     SURFACE . . . . . . . .    7.564      0.723       0.361    370    56.4   656     ERRALL 
     BURIED  . . . . . . . .   13.601      0.868       0.434     23    12.2   189     ERRALL 
     CORE  . . . . . . . . .   12.723      0.854       0.427     61    13.7   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)         0         2         6        12        30      46     103   DISTCA 
CA  (P)      0.00      1.94      5.83     11.65     29.13             103   DISTCA 
CA  (RMS)    0.00      1.40      2.02      3.24      5.76                   DISTCA 
 
ALL (N)         4        13        39        99       231     393     845   DISTALL 
ALL (P)      0.47      1.54      4.62     11.72     27.34             845   DISTALL 
ALL (RMS)    0.85      1.35      2.20      3.43      6.03                   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             8            38          RMSLSI 
CA  (P)       54.37          7.77         36.89          RMSLSI 
CA  (RMS)      1.04         14.06          7.53          RMSLSI 
 
 
 
END of the results output 
