 
####################################################### 
#                                                     # 
#                        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: 541 
 
 
 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 . . . . . . . . . .    42.07           80.6   134    66.7   201     ARMSMC  
     WELL ORDERED  . . . . .    37.30           84.5   110    68.3   161     ARMSMC  
     NO INTER CONTACTS . . .    33.92           84.9    86    81.9   105     ARMSMC  
     SHIFTED CHAIN . . . . .    54.68           66.2    74    52.5   141     ARMSMC  
     ALTERNATIVE PARENT  . .    64.68           75.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    26.84           90.5    74    58.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.87           59.1    22    24.7    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    44.90           81.0    84    55.6   151     ARMSMC  
     BURIED  . . . . . . . .    36.85           80.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    32.79           84.8   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.13           47.5    61    67.0    91     ARMSSC1 
     WELL ORDERED  . . . . .    77.23           52.6    38    70.4    54     ARMSSC1 
     NO INTER CONTACTS . . .    88.45           48.6    37    82.2    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    85.61           46.4    56    66.7    84     ARMSSC1 
     CHANGED ANGLES  . . . .    98.50           33.3    36    54.5    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    94.64           41.2    34    53.1    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    10.66          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    84.81           45.5    33    57.9    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    93.46           41.7    12    28.6    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    85.03           46.2    39    56.5    69     ARMSSC1 
     BURIED  . . . . . . . .    85.31           50.0    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    82.96           49.0    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.03           53.3    45    70.3    64     ARMSSC2 
     WELL ORDERED  . . . . .    59.46           61.9    21    75.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    76.79           53.8    26    78.8    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    64.11           57.6    33    67.3    49     ARMSSC2 
     CHANGED ANGLES  . . . .    79.66           42.9    28    59.6    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    84.17           48.0    25    56.8    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    24.73          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    66.63           57.7    26    61.9    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    91.89           44.4     9    32.1    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.62           43.3    30    61.2    49     ARMSSC2 
     BURIED  . . . . . . . .    52.64           73.3    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    64.77           55.6    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.59           18.2    22    71.0    31     ARMSSC3 
     WELL ORDERED  . . . . .    57.80           33.3     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    84.88           18.2    11    73.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    76.06           22.2    18    69.2    26     ARMSSC3 
     CHANGED ANGLES  . . . .    86.61           22.2    18    75.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    93.68           18.2    11    55.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    75.77           20.0    15    65.2    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   110.29            0.0     5    35.7    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    81.94           21.1    19    67.9    28     ARMSSC3 
     BURIED  . . . . . . . .    86.56            0.0     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    72.45           23.5    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.47           50.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .   121.72           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    85.55           60.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    96.47           50.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .    82.39           55.6     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    66.34           50.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    97.66           57.1     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   117.71            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    87.26           50.0     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .   126.80           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    93.81           55.6     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.81070     r(1,2) =  -0.09619     r(1,3) =  -0.57751 
 r(2,1) =  -0.00442     r(2,2) =  -0.98538     r(2,3) =   0.17033 
 r(3,1) =  -0.58545     r(3,2) =   0.14064     r(3,3) =   0.79842 
THE OFFSET VECTOR: 
 v(1) =  14.29685     v(2) =  48.29436     v(3) =  48.38939 
 
 Number of iteration 26                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.16           (Number of atoms:   58) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.34         68    66.0   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0492                            CRMSCA  
     WELL ORDERED  . . . . .    2.52         57    67.1    85     CRMSCA  
     NO INTER CONTACTS . . .    2.33         43    79.6    54     CRMSCA  
     SHIFTED CHAIN . . . . .    4.37         38    52.1    73     CRMSCA  
     ALTERNATIVE PARENT  . .    3.99          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    1.83         37    56.9    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.64         12    25.5    47     CRMSCA  
     SURFACE . . . . . . . .    3.68         43    55.1    78     CRMSCA  
     BURIED  . . . . . . . .    2.68         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    2.03         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.36        337    65.9   511     CRMSMC  
     WELL ORDERED  . . . . .    2.41        282    67.1   420     CRMSMC  
     NO INTER CONTACTS . . .    2.30        213    79.8   267     CRMSMC  
     SHIFTED CHAIN . . . . .    4.37        189    52.1   363     CRMSMC  
     ALTERNATIVE PARENT  . .    4.23         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    1.64        184    56.8   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.68         60    25.6   234     CRMSMC  
     SURFACE . . . . . . . .    3.73        213    55.0   387     CRMSMC  
     BURIED  . . . . . . . .    2.60        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    2.01        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.44        269    62.1   433     CRMSSC  
     WELL ORDERED  . . . . .    3.44        156    62.9   248     CRMSSC  
     NO INTER CONTACTS . . .    3.46        156    74.3   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.40        223    60.1   371     CRMSSC  
     CHANGED ANGLES  . . . .    5.29        151    53.7   281     CRMSSC  
     SECONDARY STRUCTURE . .    2.67        153    51.5   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.00         49    23.0   213     CRMSSC  
     SURFACE . . . . . . . .    4.89        180    52.3   344     CRMSSC  
     BURIED  . . . . . . . .    3.36         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    3.13        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.91        541    64.0   845     CRMSALL 
     WELL ORDERED  . . . . .    2.86        388    65.4   593     CRMSALL 
     NO INTER CONTACTS . . .    2.91        328    77.0   426     CRMSALL 
     SHIFTED CHAIN . . . . .    5.00        297    49.4   601     CRMSALL 
     ALTERNATIVE PARENT  . .    5.00         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    2.26        301    54.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.30         97    24.2   401     CRMSALL 
     SURFACE . . . . . . . .    4.31        352    53.7   656     CRMSALL 
     BURIED  . . . . . . . .    3.02        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    2.64        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.58      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     8.70      5    12.5    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.69     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     8.90     25    12.6   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.52     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     8.94     44    12.6   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.13      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     0.70      5    12.5    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.33     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     1.60     25    12.6   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.81     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     3.35     44    12.6   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 . . . . . . . . . .    7.046      0.693       0.711     68    66.0   103     ERRCA  
     WELL ORDERED  . . . . .    7.484      0.744       0.764     57    67.1    85     ERRCA  
     NO INTER CONTACTS . . .    7.503      0.748       0.767     43    79.6    54     ERRCA  
     SHIFTED CHAIN . . . . .    6.313      0.610       0.627     38    52.1    73     ERRCA  
     ALTERNATIVE PARENT  . .    5.491      0.473       0.492      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    7.743      0.774       0.795     37    56.9    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.333      0.384       0.387     12    25.5    47     ERRCA  
     SURFACE . . . . . . . .    6.853      0.666       0.685     43    55.1    78     ERRCA  
     BURIED  . . . . . . . .    7.380      0.739       0.757     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    7.628      0.759       0.781     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.058      0.693       0.712    337    65.9   511     ERRMC  
     WELL ORDERED  . . . . .    7.525      0.748       0.768    282    67.1   420     ERRMC  
     NO INTER CONTACTS . . .    7.539      0.750       0.771    213    79.8   267     ERRMC  
     SHIFTED CHAIN . . . . .    6.349      0.612       0.630    189    52.1   363     ERRMC  
     ALTERNATIVE PARENT  . .    5.501      0.491       0.530     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    7.799      0.779       0.798    184    56.8   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.335      0.386       0.390     60    25.6   234     ERRMC  
     SURFACE . . . . . . . .    6.825      0.663       0.682    213    55.0   387     ERRMC  
     BURIED  . . . . . . . .    7.458      0.745       0.763    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    7.648      0.760       0.782    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.016      0.546       0.581    269    62.1   433     ERRSC  
     WELL ORDERED  . . . . .    6.712      0.628       0.663    156    62.9   248     ERRSC  
     NO INTER CONTACTS . . .    6.391      0.594       0.635    156    74.3   210     ERRSC  
     RELIABLE SIDE CHAINS  .    6.190      0.565       0.599    223    60.1   371     ERRSC  
     CHANGED ANGLES  . . . .    5.206      0.448       0.483    151    53.7   281     ERRSC  
     SHIFTED CHAIN . . . . .    5.134      0.446       0.475    145    46.9   309     ERRSC  
     ALTERNATIVE PARENT  . .    3.706      0.331       0.353      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    6.805      0.633       0.680    153    51.5   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.574      0.267       0.264     49    23.0   213     ERRSC  
     SURFACE . . . . . . . .    5.753      0.512       0.546    180    52.3   344     ERRSC  
     BURIED  . . . . . . . .    6.547      0.614       0.654     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    6.559      0.608       0.652    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.544      0.621       0.648    541    64.0   845     ERRALL 
     WELL ORDERED  . . . . .    7.207      0.701       0.727    388    65.4   593     ERRALL 
     NO INTER CONTACTS . . .    7.001      0.677       0.707    328    77.0   426     ERRALL 
     SHIFTED CHAIN . . . . .    5.754      0.533       0.555    297    49.4   601     ERRALL 
     ALTERNATIVE PARENT  . .    4.951      0.442       0.478     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    7.280      0.704       0.737    301    54.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.951      0.328       0.330     97    24.2   401     ERRALL 
     SURFACE . . . . . . . .    6.294      0.589       0.615    352    53.7   656     ERRALL 
     BURIED  . . . . . . . .    7.010      0.682       0.710    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    7.111      0.685       0.718    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)        26        56        58        59        66      68     103   DISTCA 
CA  (P)     25.24     54.37     56.31     57.28     64.08             103   DISTCA 
CA  (RMS)    0.73      1.08      1.16      1.23      2.78                   DISTCA 
 
ALL (N)       156       359       408       448       526     541     845   DISTALL 
ALL (P)     18.46     42.49     48.28     53.02     62.25             845   DISTALL 
ALL (RMS)    0.75      1.19      1.40      1.75      3.36                   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            12          RMSLSI 
CA  (P)       54.37         54.37         11.65          RMSLSI 
CA  (RMS)      1.04          2.03          6.64          RMSLSI 
 
 
 
END of the results output 
