 
####################################################### 
#                                                     # 
#                        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: 501 
 
 
 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 . . . . . . . . . .    26.89           91.8   122    60.7   201     ARMSMC  
     WELL ORDERED  . . . . .    27.42           92.3   104    64.6   161     ARMSMC  
     NO INTER CONTACTS . . .    17.11           92.5    80    76.2   105     ARMSMC  
     SHIFTED CHAIN . . . . .    36.62           83.9    62    44.0   141     ARMSMC  
     ALTERNATIVE PARENT  . .    14.95          100.0     3    75.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    12.60           98.6    71    55.9   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    63.23           80.0    10    11.2    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    25.96           94.5    73    48.3   151     ARMSMC  
     BURIED  . . . . . . . .    28.22           87.8    49    98.0    50     ARMSMC  
     CORE  . . . . . . . . .    20.75           92.9   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.93           50.0    56    61.5    91     ARMSSC1 
     WELL ORDERED  . . . . .    69.82           61.1    36    66.7    54     ARMSSC1 
     NO INTER CONTACTS . . .    83.95           45.7    35    77.8    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    82.30           47.1    51    60.7    84     ARMSSC1 
     CHANGED ANGLES  . . . .   105.27           12.5    32    48.5    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    80.81           48.3    29    45.3    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    93.95           50.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    81.03           50.0    32    56.1    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   102.21           28.6     7    16.7    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    75.96           52.9    34    49.3    69     ARMSSC1 
     BURIED  . . . . . . . .    85.71           45.5    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    76.22           53.1    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    66.68           52.4    42    65.6    64     ARMSSC2 
     WELL ORDERED  . . . . .    53.16           66.7    21    75.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    59.54           60.0    25    75.8    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    71.77           48.4    31    63.3    49     ARMSSC2 
     CHANGED ANGLES  . . . .    85.66           20.0    25    53.2    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    71.08           50.0    22    50.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     6.46          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    61.94           60.0    25    59.5    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    52.77           50.0     6    21.4    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    75.72           37.0    27    55.1    49     ARMSSC2 
     BURIED  . . . . . . . .    46.14           80.0    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    68.73           52.8    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.59           38.1    21    67.7    31     ARMSSC3 
     WELL ORDERED  . . . . .    34.03           66.7     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .   100.06           27.3    11    73.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    87.08           35.3    17    65.4    26     ARMSSC3 
     CHANGED ANGLES  . . . .    95.72           23.5    17    70.8    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    88.81           40.0    10    50.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    81.51           40.0    15    65.2    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    81.36           50.0     4    28.6    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    84.63           38.9    18    64.3    28     ARMSSC3 
     BURIED  . . . . . . . .    97.53           33.3     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    87.78           35.3    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    91.40           30.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .    90.24           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    90.54           40.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    91.40           30.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .    96.11           22.2     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    86.59           25.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    89.63           28.6     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   119.93            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    85.22           25.0     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .   112.81           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    87.66           33.3     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.13399     r(1,2) =   0.97592     r(1,3) =  -0.17215 
 r(2,1) =  -0.23581     r(2,2) =  -0.13732     r(2,3) =  -0.96205 
 r(3,1) =  -0.96252     r(3,2) =   0.16950     r(3,3) =   0.21173 
THE OFFSET VECTOR: 
 v(1) =  18.12333     v(2) =  64.88833     v(3) =  33.13974 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.02           (Number of atoms:   57) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.56         63    61.2   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0247                            CRMSCA  
     WELL ORDERED  . . . . .    1.25         55    64.7    85     CRMSCA  
     NO INTER CONTACTS . . .    1.35         41    75.9    54     CRMSCA  
     SHIFTED CHAIN . . . . .    2.08         33    45.2    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.93          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    1.02         36    55.4    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.86          7    14.9    47     CRMSCA  
     SURFACE . . . . . . . .    1.82         38    48.7    78     CRMSCA  
     BURIED  . . . . . . . .    1.03         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    0.93         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.65        312    61.1   511     CRMSMC  
     WELL ORDERED  . . . . .    1.24        272    64.8   420     CRMSMC  
     NO INTER CONTACTS . . .    1.36        203    76.0   267     CRMSMC  
     SHIFTED CHAIN . . . . .    2.19        164    45.2   363     CRMSMC  
     ALTERNATIVE PARENT  . .    3.18         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    1.01        179    55.2   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.11         35    15.0   234     CRMSMC  
     SURFACE . . . . . . . .    1.93        188    48.6   387     CRMSMC  
     BURIED  . . . . . . . .    1.10        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    0.97        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.88        249    57.5   433     CRMSSC  
     WELL ORDERED  . . . . .    2.20        152    61.3   248     CRMSSC  
     NO INTER CONTACTS . . .    2.76        150    71.4   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.76        207    55.8   371     CRMSSC  
     CHANGED ANGLES  . . . .    3.65        137    48.8   281     CRMSSC  
     SECONDARY STRUCTURE . .    2.47        149    50.2   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    4.74         29    13.6   213     CRMSSC  
     SURFACE . . . . . . . .    3.17        160    46.5   344     CRMSSC  
     BURIED  . . . . . . . .    2.27         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    2.54        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.34        501    59.3   845     CRMSALL 
     WELL ORDERED  . . . . .    1.68        376    63.4   593     CRMSALL 
     NO INTER CONTACTS . . .    2.13        314    73.7   426     CRMSALL 
     SHIFTED CHAIN . . . . .    2.82        257    42.8   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.62         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    1.89        293    52.6   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.48         57    14.2   401     CRMSALL 
     SURFACE . . . . . . . .    2.65        312    47.6   656     CRMSALL 
     BURIED  . . . . . . . .    1.73        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    1.90        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.21      4    66.7     6      40-TNPSIQ-45   
 CA  LOOP  2     4.96      2     5.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.22     20    66.7    30      40-TNPSIQ-45   
 MC  LOOP  2     5.62     10     5.0   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.08     31    68.9    45      40-TNPSIQ-45   
 ALL LOOP  2     4.93     18     5.2   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.09      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     2.17     20    66.7    30      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.87     31    68.9    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 . . . . . . . . . .    0.624      0.251       0.219     63    61.2   103     ERRCA  
     WELL ORDERED  . . . . .    0.493      0.235       0.220     55    64.7    85     ERRCA  
     NO INTER CONTACTS . . .    0.505      0.216       0.183     41    75.9    54     ERRCA  
     SHIFTED CHAIN . . . . .    0.794      0.211       0.113     33    45.2    73     ERRCA  
     ALTERNATIVE PARENT  . .    1.840      0.461       0.230      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.353      0.188       0.179     36    55.4    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.722      0.557       0.278      7    14.9    47     ERRCA  
     SURFACE . . . . . . . .    0.801      0.289       0.247     38    48.7    78     ERRCA  
     BURIED  . . . . . . . .    0.355      0.193       0.177     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    0.361      0.213       0.212     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.648      0.252       0.217    312    61.1   511     ERRMC  
     WELL ORDERED  . . . . .    0.480      0.231       0.216    272    64.8   420     ERRMC  
     NO INTER CONTACTS . . .    0.511      0.218       0.184    203    76.0   267     ERRMC  
     SHIFTED CHAIN . . . . .    0.852      0.223       0.127    164    45.2   363     ERRMC  
     ALTERNATIVE PARENT  . .    2.110      0.500       0.250     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.361      0.194       0.188    179    55.2   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.829      0.555       0.278     35    15.0   234     ERRMC  
     SURFACE . . . . . . . .    0.819      0.287       0.239    188    48.6   387     ERRMC  
     BURIED  . . . . . . . .    0.388      0.198       0.184    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    0.372      0.213       0.210    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.521      0.381       0.246    249    57.5   433     ERRSC  
     WELL ORDERED  . . . . .    1.051      0.333       0.246    152    61.3   248     ERRSC  
     NO INTER CONTACTS . . .    1.424      0.366       0.236    150    71.4   210     ERRSC  
     RELIABLE SIDE CHAINS  .    1.427      0.367       0.237    207    55.8   371     ERRSC  
     CHANGED ANGLES  . . . .    2.286      0.482       0.266    137    48.8   281     ERRSC  
     SHIFTED CHAIN . . . . .    1.880      0.390       0.205    125    40.5   309     ERRSC  
     ALTERNATIVE PARENT  . .    3.010      0.579       0.290      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    1.194      0.327       0.206    149    50.2   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.491      0.604       0.302     29    13.6   213     ERRSC  
     SURFACE . . . . . . . .    1.760      0.408       0.252    160    46.5   344     ERRSC  
     BURIED  . . . . . . . .    1.092      0.332       0.236     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    1.262      0.351       0.239    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.077      0.314       0.232    501    59.3   845     ERRALL 
     WELL ORDERED  . . . . .    0.704      0.272       0.230    376    63.4   593     ERRALL 
     NO INTER CONTACTS . . .    0.936      0.285       0.207    314    73.7   426     ERRALL 
     SHIFTED CHAIN . . . . .    1.341      0.300       0.164    257    42.8   601     ERRALL 
     ALTERNATIVE PARENT  . .    2.459      0.529       0.265     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    0.779      0.260       0.198    293    52.6   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.187      0.579       0.290     57    14.2   401     ERRALL 
     SURFACE . . . . . . . .    1.305      0.349       0.247    312    47.6   656     ERRALL 
     BURIED  . . . . . . . .    0.701      0.257       0.208    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    0.806      0.280       0.224    444   100.0   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)        38        55        57        62        63      63     103   DISTCA 
CA  (P)     36.89     53.40     55.34     60.19     61.17             103   DISTCA 
CA  (RMS)    0.64      0.88      0.96      1.38      1.56                   DISTCA 
 
ALL (N)       237       355       409       474       501     501     845   DISTALL 
ALL (P)     28.05     42.01     48.40     56.09     59.29             845   DISTALL 
ALL (RMS)    0.66      0.96      1.26      1.86      2.34                   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             7          RMSLSI 
CA  (P)       54.37         54.37          6.80          RMSLSI 
CA  (RMS)      1.04          0.93          3.86          RMSLSI 
 
 
 
END of the results output 
