 
####################################################### 
#                                                     # 
#                        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 836 atoms, 284 common with TARGET 
           Number of atoms possible to evaluate: 268 
 
 
 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 . . . . . . . . . .    53.85           60.8   130    95.6   136     ARMSMC  
     WELL ORDERED  . . . . .    53.85           60.8   130    95.6   136     ARMSMC  
     NO INTER CONTACTS . . .    53.85           60.8   130    95.6   136     ARMSMC  
     SHIFTED CHAIN . . . . .    53.85           60.8   130    95.6   136     ARMSMC  
     ALTERNATIVE PARENT  . .   174.17            0.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    38.18           75.4    69    95.8    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    57.58           57.4   108    94.7   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    53.16           61.8   110    94.8   116     ARMSMC  
     BURIED  . . . . . . . .    57.47           55.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    29.31           77.3    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    40     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    52     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    31     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    43     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     4     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.44938     r(1,2) =   0.88892     r(1,3) =  -0.08873 
 r(2,1) =  -0.60480     r(2,2) =   0.22963     r(2,3) =  -0.76255 
 r(3,1) =  -0.65747     r(3,2) =   0.39634     r(3,3) =   0.64082 
THE OFFSET VECTOR: 
 v(1) = -33.71867     v(2) =  38.34704     v(3) = -68.05952 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.89           (Number of atoms:   25) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.90         67    97.1    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1030                            CRMSCA  
     WELL ORDERED  . . . . .    6.90         67    97.1    69     CRMSCA  
     NO INTER CONTACTS . . .    6.90         67    97.1    69     CRMSCA  
     SHIFTED CHAIN . . . . .    6.90         67    97.1    69     CRMSCA  
     ALTERNATIVE PARENT  . .   14.11          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .    6.83         35    97.2    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    7.08         56    96.6    58     CRMSCA  
     SURFACE . . . . . . . .    7.21         57    96.6    59     CRMSCA  
     BURIED  . . . . . . . .    4.72         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .    5.92         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.75        268    79.5   337     CRMSMC  
     WELL ORDERED  . . . . .    6.75        268    79.5   337     CRMSMC  
     NO INTER CONTACTS . . .    6.75        268    79.5   337     CRMSMC  
     SHIFTED CHAIN . . . . .    6.75        268    79.5   337     CRMSMC  
     ALTERNATIVE PARENT  . .   13.90          4    80.0     5     CRMSMC  
     SECONDARY STRUCTURE . .    6.65        140    79.5   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.91        224    79.2   283     CRMSMC  
     SURFACE . . . . . . . .    7.08        228    78.6   290     CRMSMC  
     BURIED  . . . . . . . .    4.44         40    85.1    47     CRMSMC  
     CORE  . . . . . . . . .    5.89         44    81.5    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   786     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   786     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   786     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   742     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   158     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   666     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   689     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    97     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.75        268    25.2  1062     CRMSALL 
     WELL ORDERED  . . . . .    6.75        268    25.2  1062     CRMSALL 
     NO INTER CONTACTS . . .    6.75        268    25.2  1062     CRMSALL 
     SHIFTED CHAIN . . . . .    6.75        268    25.2  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   13.90          4    28.6    14     CRMSALL 
     SECONDARY STRUCTURE . .    6.65        140    24.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.91        224    24.9   898     CRMSALL 
     SURFACE . . . . . . . .    7.08        228    24.6   925     CRMSALL 
     BURIED  . . . . . . . .    4.44         40    29.2   137     CRMSALL 
     CORE  . . . . . . . . .    5.89         44    26.8   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    14.76      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     3.18     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     4.38     22    91.7    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    14.39     36    81.8    44      72-PGDPEEFVK-80   
 MC  LOOP  2     3.06     92    82.9   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     4.36     88    74.6   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    14.39     36    26.7   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.06     92    26.8   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     4.36     88    22.9   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.08      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     3.06     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     3.87     22    91.7    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.15     36    81.8    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.96     92    82.9   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     3.84     88    74.6   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.15     36    26.7   135      72-PGDPEEFVK-80   
 ALL LOOP  2     2.96     92    26.8   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     3.84     88    22.9   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 . . . . . . . . . .    5.298      1.000       0.500     67    97.1    69     ERRCA  
     WELL ORDERED  . . . . .    5.298      1.000       0.500     67    97.1    69     ERRCA  
     NO INTER CONTACTS . . .    5.298      1.000       0.500     67    97.1    69     ERRCA  
     SHIFTED CHAIN . . . . .    5.298      1.000       0.500     67    97.1    69     ERRCA  
     ALTERNATIVE PARENT  . .   14.109      1.000       0.500      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    4.831      1.000       0.500     35    97.2    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.325      1.000       0.500     56    96.6    58     ERRCA  
     SURFACE . . . . . . . .    5.547      1.000       0.500     57    96.6    59     ERRCA  
     BURIED  . . . . . . . .    3.884      1.000       0.500     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    5.166      1.000       0.500     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.223      1.000       0.500    268    79.5   337     ERRMC  
     WELL ORDERED  . . . . .    5.223      1.000       0.500    268    79.5   337     ERRMC  
     NO INTER CONTACTS . . .    5.223      1.000       0.500    268    79.5   337     ERRMC  
     SHIFTED CHAIN . . . . .    5.223      1.000       0.500    268    79.5   337     ERRMC  
     ALTERNATIVE PARENT  . .   13.863      1.000       0.500      4    80.0     5     ERRMC  
     SECONDARY STRUCTURE . .    4.761      1.000       0.500    140    79.5   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.245      1.000       0.500    224    79.2   283     ERRMC  
     SURFACE . . . . . . . .    5.504      1.000       0.500    228    78.6   290     ERRMC  
     BURIED  . . . . . . . .    3.627      1.000       0.500     40    85.1    47     ERRMC  
     CORE  . . . . . . . . .    5.116      1.000       0.500     44    81.5    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   742     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   158     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   786     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    10     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   666     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   689     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    97     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.223      1.000       0.500    268    25.2  1062     ERRALL 
     WELL ORDERED  . . . . .    5.223      1.000       0.500    268    25.2  1062     ERRALL 
     NO INTER CONTACTS . . .    5.223      1.000       0.500    268    25.2  1062     ERRALL 
     SHIFTED CHAIN . . . . .    5.223      1.000       0.500    268    25.2  1062     ERRALL 
     ALTERNATIVE PARENT  . .   13.863      1.000       0.500      4    28.6    14     ERRALL 
     SECONDARY STRUCTURE . .    4.761      1.000       0.500    140    24.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.245      1.000       0.500    224    24.9   898     ERRALL 
     SURFACE . . . . . . . .    5.504      1.000       0.500    228    24.6   925     ERRALL 
     BURIED  . . . . . . . .    3.627      1.000       0.500     40    29.2   137     ERRALL 
     CORE  . . . . . . . . .    5.116      1.000       0.500     44    26.8   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        14        29        41        56      67      69   DISTCA 
CA  (P)      2.90     20.29     42.03     59.42     81.16              69   DISTCA 
CA  (RMS)    0.76      1.54      2.02      2.61      4.26                   DISTCA 
 
ALL (N)         7        55       115       171       227     268    1062   DISTALL 
ALL (P)      0.66      5.18     10.83     16.10     21.37            1062   DISTALL 
ALL (RMS)    0.74      1.55      2.07      2.74      4.31                   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            56          RMSLSI 
CA  (P)       15.94         15.94         81.16          RMSLSI 
CA  (RMS)      1.81          5.92          7.08          RMSLSI 
 
 
 
END of the results output 
