 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_2.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_2.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_2.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_2.1aj4.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 1062 atoms, MODEL 1088 atoms, 536 common with TARGET 
           Number of atoms possible to evaluate: 536 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 3.538625 
 
 CA-RMS TARGET<->PARENT(1ncx)	 3.287245 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.396291 
 
 CA-RMS TARGET<->PARENT(1aj4)	 5.635736 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.41           46.3   136   100.0   136     ARMSMC  
     WELL ORDERED  . . . . .    77.41           46.3   136   100.0   136     ARMSMC  
     NO INTER CONTACTS . . .    77.41           46.3   136   100.0   136     ARMSMC  
     SHIFTED CHAIN . . . . .    77.41           46.3   136   100.0   136     ARMSMC  
     ALTERNATIVE PARENT  . .   127.93            0.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    55.21           70.8    72   100.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    77.49           45.6   114   100.0   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    75.28           48.3   116   100.0   116     ARMSMC  
     BURIED  . . . . . . . .    88.72           35.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    76.96           50.0    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    90.14           32.2    59   100.0    59     ARMSSC1 
     WELL ORDERED  . . . . .    90.14           32.2    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .    90.14           32.2    59   100.0    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .    85.52           35.3    51   100.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .    85.60           35.0    40   100.0    40     ARMSSC1 
     SHIFTED CHAIN . . . . .    90.14           32.2    59   100.0    59     ARMSSC1 
     ALTERNATIVE PARENT  . .    56.82            0.0     1   100.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .    82.12           37.5    32   100.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    89.46           30.6    49   100.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    85.04           34.6    52   100.0    52     ARMSSC1 
     BURIED  . . . . . . . .   121.46           14.3     7   100.0     7     ARMSSC1 
     CORE  . . . . . . . . .    93.37           40.0    10   100.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.66           38.3    47   100.0    47     ARMSSC2 
     WELL ORDERED  . . . . .    84.66           38.3    47   100.0    47     ARMSSC2 
     NO INTER CONTACTS . . .    84.66           38.3    47   100.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    63.72           47.2    36   100.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .    80.44           38.7    31   100.0    31     ARMSSC2 
     SHIFTED CHAIN . . . . .    84.66           38.3    47   100.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .    66.90            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    86.62           26.9    26   100.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    85.66           43.2    37   100.0    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    81.21           41.9    43   100.0    43     ARMSSC2 
     BURIED  . . . . . . . .   115.41            0.0     4   100.0     4     ARMSSC2 
     CORE  . . . . . . . . .    80.85           20.0    10   100.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    58.82           42.1    19   100.0    19     ARMSSC3 
     WELL ORDERED  . . . . .    58.82           42.1    19   100.0    19     ARMSSC3 
     NO INTER CONTACTS . . .    58.82           42.1    19   100.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .    59.53           41.2    17   100.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .    54.76           53.3    15   100.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .    58.82           42.1    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    53.46           41.7    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    61.12           30.8    13   100.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    58.58           41.2    17   100.0    17     ARMSSC3 
     BURIED  . . . . . . . .    60.85           50.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    53.50           66.7     6   100.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    96.07           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   122.81            0.0     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    99.42           20.0     5   100.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    96.07           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    77.13            0.0     1   100.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.98464     r(1,2) =   0.03206     r(1,3) =   0.17164 
 r(2,1) =   0.10762     r(2,2) =   0.88552     r(2,3) =   0.45196 
 r(3,1) =  -0.13750     r(3,2) =   0.46349     r(3,3) =  -0.87537 
THE OFFSET VECTOR: 
 v(1) =  -9.89725     v(2) = -34.31404     v(3) = -31.89199 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.60           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.54         69   100.0    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2108                            CRMSCA  
     WELL ORDERED  . . . . .   14.54         69   100.0    69     CRMSCA  
     NO INTER CONTACTS . . .   14.54         69   100.0    69     CRMSCA  
     SHIFTED CHAIN . . . . .   14.54         69   100.0    69     CRMSCA  
     ALTERNATIVE PARENT  . .   14.04          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .   14.28         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   14.55         58   100.0    58     CRMSCA  
     SURFACE . . . . . . . .   14.81         59   100.0    59     CRMSCA  
     BURIED  . . . . . . . .   12.84         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .   14.51         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.61        337   100.0   337     CRMSMC  
     WELL ORDERED  . . . . .   14.61        337   100.0   337     CRMSMC  
     NO INTER CONTACTS . . .   14.61        337   100.0   337     CRMSMC  
     SHIFTED CHAIN . . . . .   14.61        337   100.0   337     CRMSMC  
     ALTERNATIVE PARENT  . .   14.11          5   100.0     5     CRMSMC  
     SECONDARY STRUCTURE . .   14.29        176   100.0   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   14.67        283   100.0   283     CRMSMC  
     SURFACE . . . . . . . .   14.80        290   100.0   290     CRMSMC  
     BURIED  . . . . . . . .   13.37         47   100.0    47     CRMSMC  
     CORE  . . . . . . . . .   14.31         54   100.0    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.93        260    33.1   786     CRMSSC  
     WELL ORDERED  . . . . .   16.93        260    33.1   786     CRMSSC  
     NO INTER CONTACTS . . .   16.93        260    33.1   786     CRMSSC  
     RELIABLE SIDE CHAINS  .   17.01        216    29.1   742     CRMSSC  
     CHANGED ANGLES  . . . .   17.75        158   100.0   158     CRMSSC  
     SECONDARY STRUCTURE . .   16.54        145    33.8   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS   16.90        212    31.8   666     CRMSSC  
     SURFACE . . . . . . . .   17.17        234    34.0   689     CRMSSC  
     BURIED  . . . . . . . .   14.63         26    26.8    97     CRMSSC  
     CORE  . . . . . . . . .   17.07         48    40.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   15.67        536    50.5  1062     CRMSALL 
     WELL ORDERED  . . . . .   15.67        536    50.5  1062     CRMSALL 
     NO INTER CONTACTS . . .   15.67        536    50.5  1062     CRMSALL 
     SHIFTED CHAIN . . . . .   15.67        536    50.5  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   14.62          7    50.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   15.34        289    50.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS   15.68        444    49.4   898     CRMSALL 
     SURFACE . . . . . . . .   15.92        470    50.8   925     CRMSALL 
     BURIED  . . . . . . . .   13.77         66    48.2   137     CRMSALL 
     CORE  . . . . . . . . .   15.62         92    56.1   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    11.26      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2    15.81     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3    14.85     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    11.07     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2    16.09    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3    14.92    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    11.83     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2    16.72    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3    16.42    188    49.0   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.12      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     6.82     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     5.84     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.11     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     6.83    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     5.99    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.06     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     7.43    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     7.58    188    49.0   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.340      0.416       0.246     69   100.0    69     ERRCA  
     WELL ORDERED  . . . . .    8.340      0.416       0.246     69   100.0    69     ERRCA  
     NO INTER CONTACTS . . .    8.340      0.416       0.246     69   100.0    69     ERRCA  
     SHIFTED CHAIN . . . . .    8.340      0.416       0.246     69   100.0    69     ERRCA  
     ALTERNATIVE PARENT  . .    9.045      0.475       0.237      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    8.310      0.425       0.243     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    8.354      0.412       0.237     58   100.0    58     ERRCA  
     SURFACE . . . . . . . .    8.541      0.419       0.241     59   100.0    59     ERRCA  
     BURIED  . . . . . . . .    7.158      0.400       0.273     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    8.268      0.438       0.291     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.353      0.407       0.234    337   100.0   337     ERRMC  
     WELL ORDERED  . . . . .    8.353      0.407       0.234    337   100.0   337     ERRMC  
     NO INTER CONTACTS . . .    8.353      0.407       0.234    337   100.0   337     ERRMC  
     SHIFTED CHAIN . . . . .    8.353      0.407       0.234    337   100.0   337     ERRMC  
     ALTERNATIVE PARENT  . .    9.042      0.472       0.236      5   100.0     5     ERRMC  
     SECONDARY STRUCTURE . .    8.216      0.412       0.232    176   100.0   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    8.435      0.408       0.229    283   100.0   283     ERRMC  
     SURFACE . . . . . . . .    8.486      0.408       0.229    290   100.0   290     ERRMC  
     BURIED  . . . . . . . .    7.534      0.400       0.262     47   100.0    47     ERRMC  
     CORE  . . . . . . . . .    7.924      0.401       0.262     54   100.0    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.490      0.456       0.240    260    33.1   786     ERRSC  
     WELL ORDERED  . . . . .   10.490      0.456       0.240    260    33.1   786     ERRSC  
     NO INTER CONTACTS . . .   10.490      0.456       0.240    260    33.1   786     ERRSC  
     RELIABLE SIDE CHAINS  .   10.626      0.462       0.245    216    29.1   742     ERRSC  
     CHANGED ANGLES  . . . .   11.234      0.473       0.245    158   100.0   158     ERRSC  
     SHIFTED CHAIN . . . . .   10.490      0.456       0.240    260    33.1   786     ERRSC  
     ALTERNATIVE PARENT  . .   11.105      0.525       0.263      3    30.0    10     ERRSC  
     SECONDARY STRUCTURE . .   10.440      0.473       0.253    145    33.8   429     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.676      0.473       0.245    212    31.8   666     ERRSC  
     SURFACE . . . . . . . .   10.711      0.462       0.244    234    34.0   689     ERRSC  
     BURIED  . . . . . . . .    8.506      0.403       0.202     26    26.8    97     ERRSC  
     CORE  . . . . . . . . .    9.670      0.383       0.216     48    40.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.295      0.429       0.238    536    50.5  1062     ERRALL 
     WELL ORDERED  . . . . .    9.295      0.429       0.238    536    50.5  1062     ERRALL 
     NO INTER CONTACTS . . .    9.295      0.429       0.238    536    50.5  1062     ERRALL 
     SHIFTED CHAIN . . . . .    9.295      0.429       0.238    536    50.5  1062     ERRALL 
     ALTERNATIVE PARENT  . .    9.542      0.485       0.243      7    50.0    14     ERRALL 
     SECONDARY STRUCTURE . .    9.209      0.438       0.242    289    50.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.418      0.437       0.237    444    49.4   898     ERRALL 
     SURFACE . . . . . . . .    9.499      0.433       0.237    470    50.8   925     ERRALL 
     BURIED  . . . . . . . .    7.843      0.402       0.245     66    48.2   137     ERRALL 
     CORE  . . . . . . . . .    8.704      0.393       0.242     92    56.1   164     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)         1         5         7        11        30      69      69   DISTCA 
CA  (P)      1.45      7.25     10.14     15.94     43.48              69   DISTCA 
CA  (RMS)    0.77      1.21      1.60      2.82      6.08                   DISTCA 
 
ALL (N)         3        16        38        71       191     536    1062   DISTALL 
ALL (P)      0.28      1.51      3.58      6.69     17.98            1062   DISTALL 
ALL (RMS)    0.77      1.38      2.12      3.17      6.19                   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)          11            11            58          RMSLSI 
CA  (P)       15.94         15.94         84.06          RMSLSI 
CA  (RMS)      1.81         14.51         14.55          RMSLSI 
 
 
 
END of the results output 
