 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    70.52           50.7   136   100.0   136     ARMSMC  
     WELL ORDERED  . . . . .    70.52           50.7   136   100.0   136     ARMSMC  
     NO INTER CONTACTS . . .    70.52           50.7   136   100.0   136     ARMSMC  
     SHIFTED CHAIN . . . . .    70.52           50.7   136   100.0   136     ARMSMC  
     ALTERNATIVE PARENT  . .   164.78            0.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    57.46           70.8    72   100.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.67           47.4   114   100.0   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    70.59           50.0   116   100.0   116     ARMSMC  
     BURIED  . . . . . . . .    70.09           55.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    58.11           68.2    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.15           30.5    59   100.0    59     ARMSSC1 
     WELL ORDERED  . . . . .    85.15           30.5    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .    85.15           30.5    59   100.0    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .    86.29           27.5    51   100.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .    85.42           35.0    40   100.0    40     ARMSSC1 
     SHIFTED CHAIN . . . . .    85.15           30.5    59   100.0    59     ARMSSC1 
     ALTERNATIVE PARENT  . .    28.21          100.0     1   100.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .    89.35           25.0    32   100.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    82.17           34.7    49   100.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    83.24           30.8    52   100.0    52     ARMSSC1 
     BURIED  . . . . . . . .    98.18           28.6     7   100.0     7     ARMSSC1 
     CORE  . . . . . . . . .    98.46           10.0    10   100.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.00           36.2    47   100.0    47     ARMSSC2 
     WELL ORDERED  . . . . .    73.00           36.2    47   100.0    47     ARMSSC2 
     NO INTER CONTACTS . . .    73.00           36.2    47   100.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    76.11           38.9    36   100.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .    80.47           29.0    31   100.0    31     ARMSSC2 
     SHIFTED CHAIN . . . . .    73.00           36.2    47   100.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .    31.95            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    82.21           42.3    26   100.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    71.79           35.1    37   100.0    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    70.78           34.9    43   100.0    43     ARMSSC2 
     BURIED  . . . . . . . .    93.58           50.0     4   100.0     4     ARMSSC2 
     CORE  . . . . . . . . .    77.30           40.0    10   100.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.94            5.3    19   100.0    19     ARMSSC3 
     WELL ORDERED  . . . . .    77.94            5.3    19   100.0    19     ARMSSC3 
     NO INTER CONTACTS . . .    77.94            5.3    19   100.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .    79.76            5.9    17   100.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .    78.46            6.7    15   100.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .    77.94            5.3    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    71.26            8.3    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    80.93            7.7    13   100.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    78.94            5.9    17   100.0    17     ARMSSC3 
     BURIED  . . . . . . . .    68.83            0.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    71.03            0.0     6   100.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    92.33           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    83.60           33.3     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    95.50           20.0     5   100.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    92.33           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    74.47            0.0     1   100.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.76566     r(1,2) =   0.45068     r(1,3) =   0.45897 
 r(2,1) =   0.41788     r(2,2) =  -0.89095     r(2,3) =   0.17773 
 r(3,1) =   0.48902     r(3,2) =   0.05571     r(3,3) =  -0.87049 
THE OFFSET VECTOR: 
 v(1) = -84.15076     v(2) =  26.50795     v(3) =  19.89326 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.57           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   11.81         69   100.0    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1712                            CRMSCA  
     WELL ORDERED  . . . . .   11.81         69   100.0    69     CRMSCA  
     NO INTER CONTACTS . . .   11.81         69   100.0    69     CRMSCA  
     SHIFTED CHAIN . . . . .   11.81         69   100.0    69     CRMSCA  
     ALTERNATIVE PARENT  . .   18.23          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .   10.15         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.39         58   100.0    58     CRMSCA  
     SURFACE . . . . . . . .   12.21         59   100.0    59     CRMSCA  
     BURIED  . . . . . . . .    9.10         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .   13.84         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   11.78        337   100.0   337     CRMSMC  
     WELL ORDERED  . . . . .   11.78        337   100.0   337     CRMSMC  
     NO INTER CONTACTS . . .   11.78        337   100.0   337     CRMSMC  
     SHIFTED CHAIN . . . . .   11.78        337   100.0   337     CRMSMC  
     ALTERNATIVE PARENT  . .   17.96          5   100.0     5     CRMSMC  
     SECONDARY STRUCTURE . .   10.13        176   100.0   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.37        283   100.0   283     CRMSMC  
     SURFACE . . . . . . . .   12.22        290   100.0   290     CRMSMC  
     BURIED  . . . . . . . .    8.59         47   100.0    47     CRMSMC  
     CORE  . . . . . . . . .   13.76         54   100.0    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.22        260    33.1   786     CRMSSC  
     WELL ORDERED  . . . . .   13.22        260    33.1   786     CRMSSC  
     NO INTER CONTACTS . . .   13.22        260    33.1   786     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.62        216    29.1   742     CRMSSC  
     CHANGED ANGLES  . . . .   13.41        158   100.0   158     CRMSSC  
     SECONDARY STRUCTURE . .   11.24        145    33.8   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS   12.61        212    31.8   666     CRMSSC  
     SURFACE . . . . . . . .   13.79        234    34.0   689     CRMSSC  
     BURIED  . . . . . . . .    5.99         26    26.8    97     CRMSSC  
     CORE  . . . . . . . . .   15.65         48    40.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   12.45        536    50.5  1062     CRMSALL 
     WELL ORDERED  . . . . .   12.45        536    50.5  1062     CRMSALL 
     NO INTER CONTACTS . . .   12.45        536    50.5  1062     CRMSALL 
     SHIFTED CHAIN . . . . .   12.45        536    50.5  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   18.30          7    50.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   10.67        289    50.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS   11.94        444    49.4   898     CRMSALL 
     SURFACE . . . . . . . .   12.97        470    50.8   925     CRMSALL 
     BURIED  . . . . . . . .    7.91         66    48.2   137     CRMSALL 
     CORE  . . . . . . . . .   14.70         92    56.1   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    18.83      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     9.55     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     7.94     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    18.85     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     9.44    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     7.98    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    19.13     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     9.59    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     9.08    188    49.0   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.02      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     6.73     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     6.14     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.20     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     6.90    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     6.29    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.58     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     8.20    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     7.52    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 . . . . . . . . . .    5.430      0.302       0.253     69   100.0    69     ERRCA  
     WELL ORDERED  . . . . .    5.430      0.302       0.253     69   100.0    69     ERRCA  
     NO INTER CONTACTS . . .    5.430      0.302       0.253     69   100.0    69     ERRCA  
     SHIFTED CHAIN . . . . .    5.430      0.302       0.253     69   100.0    69     ERRCA  
     ALTERNATIVE PARENT  . .    9.227      0.339       0.169      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    4.846      0.298       0.276     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.053      0.285       0.241     58   100.0    58     ERRCA  
     SURFACE . . . . . . . .    5.656      0.304       0.248     59   100.0    59     ERRCA  
     BURIED  . . . . . . . .    4.097      0.289       0.279     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    7.420      0.392       0.314     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.436      0.297       0.257    337   100.0   337     ERRMC  
     WELL ORDERED  . . . . .    5.436      0.297       0.257    337   100.0   337     ERRMC  
     NO INTER CONTACTS . . .    5.436      0.297       0.257    337   100.0   337     ERRMC  
     SHIFTED CHAIN . . . . .    5.436      0.297       0.257    337   100.0   337     ERRMC  
     ALTERNATIVE PARENT  . .    8.945      0.331       0.166      5   100.0     5     ERRMC  
     SECONDARY STRUCTURE . .    4.903      0.300       0.288    176   100.0   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.071      0.281       0.246    283   100.0   283     ERRMC  
     SURFACE . . . . . . . .    5.676      0.301       0.253    290   100.0   290     ERRMC  
     BURIED  . . . . . . . .    3.954      0.273       0.284     47   100.0    47     ERRMC  
     CORE  . . . . . . . . .    7.349      0.383       0.318     54   100.0    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.625      0.267       0.210    260    33.1   786     ERRSC  
     WELL ORDERED  . . . . .    5.625      0.267       0.210    260    33.1   786     ERRSC  
     NO INTER CONTACTS . . .    5.625      0.267       0.210    260    33.1   786     ERRSC  
     RELIABLE SIDE CHAINS  .    5.951      0.279       0.219    216    29.1   742     ERRSC  
     CHANGED ANGLES  . . . .    5.745      0.267       0.211    158   100.0   158     ERRSC  
     SHIFTED CHAIN . . . . .    5.625      0.267       0.210    260    33.1   786     ERRSC  
     ALTERNATIVE PARENT  . .    9.846      0.353       0.177      3    30.0    10     ERRSC  
     SECONDARY STRUCTURE . .    4.745      0.265       0.237    145    33.8   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.177      0.252       0.198    212    31.8   666     ERRSC  
     SURFACE . . . . . . . .    5.801      0.261       0.194    234    34.0   689     ERRSC  
     BURIED  . . . . . . . .    4.044      0.320       0.353     26    26.8    97     ERRSC  
     CORE  . . . . . . . . .    7.602      0.335       0.262     48    40.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.536      0.284       0.237    536    50.5  1062     ERRALL 
     WELL ORDERED  . . . . .    5.536      0.284       0.237    536    50.5  1062     ERRALL 
     NO INTER CONTACTS . . .    5.536      0.284       0.237    536    50.5  1062     ERRALL 
     SHIFTED CHAIN . . . . .    5.536      0.284       0.237    536    50.5  1062     ERRALL 
     ALTERNATIVE PARENT  . .    9.279      0.339       0.170      7    50.0    14     ERRALL 
     SECONDARY STRUCTURE . .    4.858      0.285       0.265    289    50.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.132      0.269       0.225    444    49.4   898     ERRALL 
     SURFACE . . . . . . . .    5.747      0.283       0.227    470    50.8   925     ERRALL 
     BURIED  . . . . . . . .    4.032      0.292       0.308     66    48.2   137     ERRALL 
     CORE  . . . . . . . . .    7.485      0.361       0.293     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)         2         7         9        16        42      69      69   DISTCA 
CA  (P)      2.90     10.14     13.04     23.19     60.87              69   DISTCA 
CA  (RMS)    0.73      1.31      1.57      2.97      5.97                   DISTCA 
 
ALL (N)         4        24        47       129       302     536    1062   DISTALL 
ALL (P)      0.38      2.26      4.43     12.15     28.44            1062   DISTALL 
ALL (RMS)    0.84      1.54      2.04      3.47      6.02                   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         13.84         11.39          RMSLSI 
 
 
 
END of the results output 
