mkdir tmp
mkdir und
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  3lynA/T0125-3lynA-karplus1.a2m \
                -target T0125 -template 3lynA \
                -out T0125-3lynA-karplus1  -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lynA-orig.a2m
Writing a2m file: tmp/3lynA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27966


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp -alignfile tmp/3lynA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lynA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp.mod tmp/3lynA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27966 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lynA-align.mod
tmp/3lynA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27966/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lynA-orig.a2m tmp/3lynA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lynA-align.mod
Running w0.5 tmp/3lynA-orig.a2m tmp/3lynA-align.mod
Running align2model tmp/3lynA-align -i tmp/3lynA-align.mod -db tmp/3lynA-orig.a2m -db tmp/3lynA-pdb.a2m
partial PDB gets fragment 0 through 98 extending end
partial PDB gets fragment 99 through 121 extending start
Debugging on !
Reading sequence file
Reading input structure 
124 residues read 
Measuring phi and psi 
Getting chi values
GLN    0   10
GLU    1   16
GLN    2   13
SER    3    3
VAL    5    2
GLN    6   11
ARG    7   27
MET    9   10
VAL   10    1
ASN   11    4
PHE   12    2
LEU   13    3
ASP   14    4
GLU   15   12
GLU   16   12
MET   17   10
HIS   18    4
LYS   19   26
VAL   21    2
LYS   22   26
ARG   23   27
PHE   24    4
ASP   26    5
MET   27    8
ARG   28   32
TRP   29    6
ASN   30    4
PRO   33    2
PHE   35    3
VAL   36    1
PHE   37    3
LEU   38    3
LYS   40   23
LYS   41   24
GLU   45   13
ARG   46   27
MET   48   10
ARG   49   27
TYR   50    3
CYS   51    2
MET   52   10
ASP   53    4
ARG   56   26
TYR   57    3
SER   58    3
LYS   60   28
ILE   61    3
LEU   62    3
GLN   63   14
LEU   64    2
LYS   65   29
HIS   66    2
LEU   67    5
VAL   69    2
ASN   70    6
LYS   71   30
LYS   72   31
THR   73    2
LEU   74    3
LYS   76   29
MET   77   10
ARG   79   27
PHE   80    2
VAL   81    1
TYR   83    3
ASN   85    5
TYR   86    3
ILE   89    2
ARG   90   27
GLU   91   12
LEU   92    3
TYR   93    2
ASP   95    4
VAL   96    3
PHE   97    2
ARG   98   16
ARG  101   21
LYS  104   30
MET  105   10
THR  106    2
ARG  110   28
TYR  112    4
SER  113    2
SER  114    2
LYS  115   29
ASP  116    6
THR  119    1
PHE  120    2
CYS  122    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue F 25 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 39 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 75 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue F 81 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue V 97 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 16 rotamers of residue R 99 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 21 rotamers of residue R 102 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
ssdist    52    1  123    1      3.2100
ssdist    52    1  123    2      4.7955
ssdist    52    2  123    1      4.1973
ssdist    52    2  123    2      3.8711
Found 0 disulfide bonds.
Residue clashes:
keepclash    10   48     12.1621
keepclash    13   17     27.1076
keepclash    13   82     18.5391
keepclash    16   84    107.3519
keepclash    19   23     11.4927
keepclash    24   93     16.3826
keepclash    39  104     10.0321
keepclash    42  113     12.7585
keepclash    49  121     34.2515
keepclash    49  122     24.5114
keepclash    58   62     11.8867
keepclash    62   78     18.8660
keepclash    63   70     17.1752
keepclash    81   85    134.1439
keepclash    94   98     99.5765
turnclash     42   18   46    0     70.4462
turnclash     42   19  110    0     33.6116
Cluster     1 =  10  48
Cluster     2 =  13  17  82
Cluster     3 =  16  84
Cluster     4 =  19  23
Cluster     5 =  24  93
Cluster     6 =  39 104
Cluster     7 =  42  46  49 110 113 121 122
Cluster     8 =  58  62  63  70  78
Cluster     9 =  81  85
Cluster    10 =  94  98
29 clashing residues after turn 
Residue clashes:
10-48
13-17
13-82
16-84
19-23
24-93
39-104
42-113
42-46
42-110
49-121
49-122
49-46
58-62
62-78
63-70
63-78
81-85
94-98
cluster 1 has 2 members and 0.000e+00 combinations:
 48  10 
Energy     15.8346
Searching cluster 10
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 15.834639: keeping 
Solved cluster 1: residual clashing  0.34
cluster 2 has 3 members and 5.000e+00 combinations:
 82  13  17 
Energy     49.2487
Searching cluster 13
Combinations for 3 members in cluster 2 OK: 5.000e+00 - Sending to search
25.300039 < 49.248661: keeping 
18.539112 < 29.499090: keeping 
Solved cluster 2: residual clashing 22.90
cluster 3 has 2 members and 2.000e+00 combinations:
 84  16 
Energy    110.6187
Searching cluster 16
Combinations for 2 members in cluster 3 OK: 2.000e+00 - Sending to search
95.422852 < 110.618668: keeping 
Solved cluster 3: residual clashing 99.08
cluster 4 has 2 members and 7.200e+01 combinations:
 19  23 
Energy     11.4927
Searching cluster 19
Combinations for 2 members in cluster 4 OK: 7.200e+01 - Sending to search
0.000000 < 11.492699: keeping 
Solved cluster 4: residual clashing  0.01
cluster 5 has 2 members and 1.200e+01 combinations:
 93  24 
Energy     17.6941
Searching cluster 24
Combinations for 2 members in cluster 5 OK: 1.200e+01 - Sending to search
10.000000 < 17.694063: keeping 
0.000000 < 11.801806: keeping 
Solved cluster 5: residual clashing  1.96
cluster 6 has 2 members and 0.000e+00 combinations:
 104  39 
Energy     26.5148
Searching cluster 39
Combinations for 2 members in cluster 6 OK: 0.000e+00 - Sending to search
10.607635 < 26.514778: keeping 
Solved cluster 6: residual clashing 21.86
cluster 7 has 7 members and 0.000e+00 combinations:
 110  46  122  121  113  42  49 
Energy     76.6007
Searching cluster 42
Combinations for 7 members in cluster 7 OK: 0.000e+00 - Sending to search
46.422337 < 76.600670: keeping 
12.758527 < 50.671638: keeping 
2.934880 < 17.505014: keeping 
0.000000 < 7.861828: keeping 
Solved cluster 7: residual clashing  5.60
cluster 8 has 5 members and 8.000e+01 combinations:
 63  58  70  62  78 
Energy     49.4935
Searching cluster 58
Combinations for 5 members in cluster 8 OK: 8.000e+01 - Sending to search
29.616022 < 49.493477: keeping 
24.653889 < 29.953959: keeping 
17.729336 < 27.515882: keeping 
10.554165 < 19.363644: keeping 
3.059417 < 14.011037: keeping 
Solved cluster 8: residual clashing 10.25
cluster 9 has 2 members and 0.000e+00 combinations:
 85  81 
Energy    164.9517
Searching cluster 81
Combinations for 2 members in cluster 9 OK: 0.000e+00 - Sending to search
2.407387 < 164.951721: keeping 
Solved cluster 9: residual clashing 12.85
cluster 10 has 2 members and 1.000e+00 combinations:
 94  98 
Energy    101.2719
Searching cluster 94
Combinations for 2 members in cluster 10 OK: 1.000e+00 - Sending to search
Solved cluster 10: residual clashing 101.27
Still clashes at these sidechain pairs:
ires=   13 irot=    1 jres=   82 jrot=    1      18.5391
ires=   16 irot=    9 jres=   84 jrot=    2      95.4229
ires=   39 irot=    2 jres=  104 jrot=    1      10.6076
ires=   94 irot=    1 jres=   98 jrot=    2      99.5765
Residual clashes =  257.47961
Printing 
make: *** No rule to make target ` ', needed by `indexes'.  Stop.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make: [und/T0125-3lynA-karplus2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make: [und/T0125-3lynA-karplus2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  3lynA/T0125-3lynA-karplus2.a2m \
                -target T0125 -template 3lynA \
                -out T0125-3lynA-karplus2  -outdir und
Couldn't open file 3lynA/T0125-3lynA-karplus2.a2m or 3lynA/T0125-3lynA-karplus2.a2m.gz for input
Can't open A2M file 3lynA/T0125-3lynA-karplus2.a2m for input
/projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file.
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed.
make: *** [und/T0125-3lynA-karplus2.index] Error 1
indexmake: No such file or directory
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make: [und/T0125-3lynA-karplus2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make: [und/T0125-3lynA-karplus2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  3lynA/T0125-3lynA-karplus2.a2m \
                -target T0125 -template 3lynA \
                -out T0125-3lynA-karplus2  -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lynA-orig.a2m
Writing a2m file: tmp/3lynA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31144


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp -alignfile tmp/3lynA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lynA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp.mod tmp/3lynA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31144 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lynA-align.mod
tmp/3lynA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31144/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lynA-orig.a2m tmp/3lynA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lynA-align.mod
Running w0.5 tmp/3lynA-orig.a2m tmp/3lynA-align.mod
Running align2model tmp/3lynA-align -i tmp/3lynA-align.mod -db tmp/3lynA-orig.a2m -db tmp/3lynA-pdb.a2m
partial PDB gets fragment 0 through 29 extending end
partial PDB gets fragment 30 through 98 extending start extending end
partial PDB gets fragment 99 through 121 extending start
Debugging on !
Reading sequence file
Reading input structure 
126 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    2
VAL    1    3
SER    2    2
ARG    3   27
GLN    4   11
GLN    6   12
SER    7    3
TYR    8    2
VAL    9    1
GLN   10   12
ARG   11   27
MET   13   10
VAL   14    1
ASN   15    4
LEU   17    3
ASP   18    4
GLU   19   12
GLU   20   12
MET   21   10
HIS   22    4
LYS   23   26
VAL   25    3
LYS   26   24
ARG   27   22
PHE   28    4
ASN   32    4
PRO   35    2
PHE   37    3
VAL   38    1
PHE   39    3
LEU   40    3
LYS   42   23
LYS   43   24
GLU   47   13
ARG   48   27
MET   50   10
ARG   51   27
TYR   52    3
CYS   53    2
MET   54   10
ASP   55    4
ARG   58   26
TYR   59    3
SER   60    3
LYS   62   28
ILE   63    3
LEU   64    3
GLN   65   14
LEU   66    2
LYS   67   29
HIS   68    2
LEU   69    5
VAL   71    2
ASN   72    6
LYS   73   30
LYS   74   31
THR   75    2
LEU   76    3
LYS   78   29
MET   79   10
ARG   81   27
PHE   82    2
VAL   83    1
TYR   85    3
ASN   87    5
TYR   88    3
ILE   91    2
ARG   92   27
GLU   93   12
LEU   94    3
TYR   95    2
ASP   97    4
VAL   98    3
PHE   99    2
ARG  100   16
ARG  103   21
LYS  106   30
MET  107   10
THR  108    2
ARG  112   28
TYR  114    4
SER  115    2
SER  116    2
LYS  117   29
ASP  118    6
THR  121    1
PHE  122    2
CYS  124    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 15 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue N 16 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue F 29 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue N 33 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 41 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 77 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue F 83 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue V 99 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 16 rotamers of residue R 101 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 21 rotamers of residue R 104 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
ssdist    54    1  125    1      3.2100
ssdist    54    1  125    2      4.7955
ssdist    54    2  125    1      4.1973
ssdist    54    2  125    2      3.8711
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   74     15.7168
keepclash     5   77     14.5723
keepclash    12   82     13.5946
keepclash    16   86     15.7043
keepclash    25   29     79.5941
keepclash    28   95     53.8626
keepclash    41  106     10.0321
keepclash    44  115     12.7585
keepclash    51  123     34.2515
keepclash    51  124     24.5114
keepclash    60   64     11.8867
keepclash    64   80     18.8660
keepclash    65   72     17.1752
keepclash    83   87    134.1439
keepclash    96  100     99.5765
turnclash     28    4   24    7     78.9538
turnclash     28   21   98    0     30.0000
turnclash     44   18   48    0     70.4462
turnclash     44   19  112    0     33.6116
Cluster     1 =   4  74
Cluster     2 =   5  77
Cluster     3 =  12  16  82  86
Cluster     4 =  24  28  95  98
Cluster     5 =  25  29
Cluster     6 =  41 106
Cluster     7 =  44  48  51 112 115 123 124
Cluster     8 =  60  64  65  72  80
Cluster     9 =  83  87
Cluster    10 =  96 100
32 clashing residues after turn 
Residue clashes:
4-74
5-77
12-82
16-86
25-29
28-95
28-24
28-98
41-106
44-115
44-48
44-112
51-123
51-124
51-48
60-64
64-80
65-72
65-80
82-86
83-87
96-100
cluster 1 has 2 members and 3.840e+02 combinations:
 74  4 
Energy     15.7168
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.840e+02 - Sending to search
0.743478 < 15.716831: keeping 
0.000000 < 2.027011: keeping 
Solved cluster 1: residual clashing  0.52
cluster 2 has 2 members and 2.400e+01 combinations:
 77  5 
Energy     33.8630
Searching cluster 5
Combinations for 2 members in cluster 2 OK: 2.400e+01 - Sending to search
14.454842 < 33.862953: keeping 
Solved cluster 2: residual clashing 33.80
cluster 3 has 4 members and 2.000e+02 combinations:
 86  16  12  82 
Energy     41.8139
Searching cluster 12
Combinations for 4 members in cluster 3 OK: 2.000e+02 - Sending to search
15.704327 < 41.813908: keeping 
Solved cluster 3: residual clashing 28.55
cluster 4 has 4 members and 8.550e+02 combinations:
 98  24  95  28 
Energy     55.1865
Searching cluster 24
Combinations for 4 members in cluster 4 OK: 8.550e+02 - Sending to search
3.485192 < 55.186470: keeping 
0.000000 < 5.243447: keeping 
Solved cluster 4: residual clashing  1.83
cluster 5 has 2 members and 0.000e+00 combinations:
 25  29 
Energy    292.7284
Searching cluster 25
Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search
21.725395 < 292.728394: keeping 
0.000000 < 38.959991: keeping 
Solved cluster 5: residual clashing  6.88
cluster 6 has 2 members and 0.000e+00 combinations:
 106  41 
Energy     26.5148
Searching cluster 41
Combinations for 2 members in cluster 6 OK: 0.000e+00 - Sending to search
10.607635 < 26.514778: keeping 
Solved cluster 6: residual clashing 21.86
cluster 7 has 7 members and 0.000e+00 combinations:
 112  48  124  123  115  44  51 
Energy     76.6007
Searching cluster 44
Combinations for 7 members in cluster 7 OK: 0.000e+00 - Sending to search
46.422337 < 76.600670: keeping 
12.758527 < 50.671638: keeping 
2.934880 < 17.505014: keeping 
0.000000 < 7.861828: keeping 
Solved cluster 7: residual clashing  5.60
cluster 8 has 5 members and 8.000e+01 combinations:
 65  60  72  64  80 
Energy     49.4935
Searching cluster 60
Combinations for 5 members in cluster 8 OK: 8.000e+01 - Sending to search
29.616022 < 49.493477: keeping 
24.653889 < 29.953959: keeping 
17.729336 < 27.515882: keeping 
10.554165 < 19.363644: keeping 
3.059417 < 14.011037: keeping 
Solved cluster 8: residual clashing 10.25
cluster 9 has 2 members and 0.000e+00 combinations:
 87  83 
Energy    164.9517
Searching cluster 83
Combinations for 2 members in cluster 9 OK: 0.000e+00 - Sending to search
2.407387 < 164.951721: keeping 
Solved cluster 9: residual clashing 12.85
cluster 10 has 2 members and 1.000e+00 combinations:
 96  100 
Energy    101.2719
Searching cluster 96
Combinations for 2 members in cluster 10 OK: 1.000e+00 - Sending to search
Solved cluster 10: residual clashing 101.27
Still clashes at these sidechain pairs:
ires=    5 irot=    2 jres=   77 jrot=    1      14.4548
ires=   16 irot=    1 jres=   86 jrot=    2      15.7043
ires=   29 irot=    3 jres=   39 jrot=    1      30.0000
ires=   41 irot=    2 jres=  106 jrot=    1      10.6076
ires=   96 irot=    1 jres=  100 jrot=    2      99.5765
Residual clashes =  197.87094
Printing 
make: *** No rule to make target ` ', needed by `indexes'.  Stop.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make: [und/T0125-3lynA-karplus3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make: [und/T0125-3lynA-karplus3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  3lynA/T0125-3lynA-karplus3.a2m \
                -target T0125 -template 3lynA \
                -out T0125-3lynA-karplus3  -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lynA-orig.a2m
Writing a2m file: tmp/3lynA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25345


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp -alignfile tmp/3lynA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lynA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp.mod tmp/3lynA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25345 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lynA-align.mod
tmp/3lynA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25345/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lynA-orig.a2m tmp/3lynA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lynA-align.mod
Running w0.5 tmp/3lynA-orig.a2m tmp/3lynA-align.mod
Running align2model tmp/3lynA-align -i tmp/3lynA-align.mod -db tmp/3lynA-orig.a2m -db tmp/3lynA-pdb.a2m
partial PDB gets fragment 0 through 29 extending end
partial PDB gets fragment 30 through 85 extending start extending end
partial PDB gets fragment 86 through 100 extending start extending end
partial PDB gets fragment 101 through 121 extending start
Debugging on !
Reading sequence file
Reading input structure 
128 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    2
VAL    1    3
SER    2    2
ARG    3   27
GLN    4   11
GLN    6   12
SER    7    3
TYR    8    2
VAL    9    1
GLN   10   12
ARG   11   27
MET   13   10
VAL   14    1
ASN   15    4
LEU   17    3
ASP   18    4
GLU   19   12
GLU   20   12
MET   21   10
HIS   22    4
LYS   23   26
VAL   25    3
LYS   26   24
ARG   27   22
PHE   28    4
ASN   32    4
PRO   35    2
PHE   37    3
VAL   38    1
PHE   39    3
LEU   40    3
LYS   42   23
LYS   43   24
GLU   47   13
ARG   48   27
MET   50   10
ARG   51   27
TYR   52    3
CYS   53    2
MET   54   10
ASP   55    4
ARG   58   26
TYR   59    3
SER   60    3
LYS   62   28
ILE   63    3
LEU   64    3
GLN   65   14
LEU   66    2
LYS   67   29
HIS   68    2
LEU   69    5
VAL   71    2
ASN   72    6
LYS   73   30
LYS   74   31
THR   75    2
LEU   76    3
LYS   78   29
MET   79   10
ARG   81   27
PHE   82    2
VAL   83    1
TYR   85    3
ASN   87    5
VAL   90    1
ILE   91    4
ARG   92   27
GLU   93   12
LEU   94    3
ASP   97    4
VAL   98    1
PHE   99    3
ARG  100   32
ASP  101    4
VAL  102    2
GLN  103   11
LYS  108   30
MET  109   10
THR  110    2
ARG  114   28
TYR  116    4
SER  117    2
SER  118    2
LYS  119   29
ASP  120    6
THR  123    1
PHE  124    2
CYS  126    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 15 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue N 16 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue F 29 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 4 rotamers of residue N 33 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 41 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 77 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue F 83 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 5 rotamers of residue N 88 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 1 rotamers of residue V 91 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
ssdist    54    1  127    1      3.2100
ssdist    54    1  127    2      4.7955
ssdist    54    2  127    1      4.1973
ssdist    54    2  127    2      3.8711
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   74     15.7168
keepclash     5   77     14.5723
keepclash    12   82     13.5946
keepclash    16   86     15.7043
keepclash    20   92     12.7354
keepclash    24   93     16.8945
keepclash    25   29     79.5941
keepclash    41  108     10.0321
keepclash    44  117     12.7585
keepclash    51  125     34.2515
keepclash    51  126     24.5114
keepclash    60   64     11.8867
keepclash    64   80     18.8660
keepclash    65   72     17.1752
keepclash    83   87    134.1439
keepclash    92   96     26.8608
turnclash     44   18   48    0     70.4462
turnclash     44   19  114    0     33.6116
Cluster     1 =   4  74
Cluster     2 =   5  77
Cluster     3 =  12  16  82  86
Cluster     4 =  20  24  92  93  96
Cluster     5 =  25  29
Cluster     6 =  41 108
Cluster     7 =  44  48  51 114 117 125 126
Cluster     8 =  60  64  65  72  80
Cluster     9 =  83  87
31 clashing residues after turn 
Residue clashes:
4-74
5-77
12-82
16-86
20-92
20-93
24-93
24-96
25-29
41-108
44-117
44-48
44-114
51-125
51-126
51-48
60-64
64-80
65-72
65-80
82-86
83-87
92-96
cluster 1 has 2 members and 3.840e+02 combinations:
 74  4 
Energy     15.7168
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.840e+02 - Sending to search
0.743478 < 15.716831: keeping 
0.000000 < 2.027011: keeping 
Solved cluster 1: residual clashing  0.52
cluster 2 has 2 members and 2.400e+01 combinations:
 77  5 
Energy     33.8630
Searching cluster 5
Combinations for 2 members in cluster 2 OK: 2.400e+01 - Sending to search
14.454842 < 33.862953: keeping 
Solved cluster 2: residual clashing 33.80
cluster 3 has 4 members and 2.000e+02 combinations:
 86  16  12  82 
Energy     41.8139
Searching cluster 12
Combinations for 4 members in cluster 3 OK: 2.000e+02 - Sending to search
15.704327 < 41.813908: keeping 
Solved cluster 3: residual clashing 28.55
cluster 4 has 5 members and 0.000e+00 combinations:
 96  92  20  24  93 
Energy     64.3543
Searching cluster 20
Combinations for 5 members in cluster 4 OK: 0.000e+00 - Sending to search
56.490715 < 64.354279: keeping 
54.936111 < 64.354271: keeping 
42.237843 < 63.306648: keeping 
39.596222 < 48.711987: keeping 
32.219685 < 45.444954: keeping 
29.578066 < 39.290894: keeping 
26.860817 < 36.023865: keeping 
Solved cluster 4: residual clashing 33.47
cluster 5 has 2 members and 0.000e+00 combinations:
 25  29 
Energy    292.7284
Searching cluster 25
Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search
21.725395 < 292.728394: keeping 
0.000000 < 38.959991: keeping 
Solved cluster 5: residual clashing  6.88
cluster 6 has 2 members and 0.000e+00 combinations:
 108  41 
Energy     41.9132
Searching cluster 41
Combinations for 2 members in cluster 6 OK: 0.000e+00 - Sending to search
10.607635 < 41.913181: keeping 
Solved cluster 6: residual clashing 38.71
cluster 7 has 7 members and 0.000e+00 combinations:
 114  48  126  125  117  44  51 
Energy     76.6007
Searching cluster 44
Combinations for 7 members in cluster 7 OK: 0.000e+00 - Sending to search
46.422337 < 76.600670: keeping 
12.758527 < 50.671638: keeping 
2.934880 < 17.505014: keeping 
0.000000 < 7.861828: keeping 
Solved cluster 7: residual clashing  5.60
cluster 8 has 5 members and 8.000e+01 combinations:
 65  60  72  64  80 
Energy     49.4935
Searching cluster 60
Combinations for 5 members in cluster 8 OK: 8.000e+01 - Sending to search
29.616022 < 49.493477: keeping 
24.653889 < 29.953959: keeping 
17.729336 < 27.515882: keeping 
10.554165 < 19.363644: keeping 
3.059417 < 14.011037: keeping 
Solved cluster 8: residual clashing 10.25
cluster 9 has 2 members and 0.000e+00 combinations:
 87  83 
Energy    164.9517
Searching cluster 83
Combinations for 2 members in cluster 9 OK: 0.000e+00 - Sending to search
2.407387 < 164.951721: keeping 
Solved cluster 9: residual clashing 12.85
Still clashes at these sidechain pairs:
ires=    5 irot=    2 jres=   77 jrot=    1      14.4548
ires=   16 irot=    1 jres=   86 jrot=    2      15.7043
ires=   29 irot=    3 jres=   39 jrot=    1      30.0000
ires=   41 irot=    2 jres=  108 jrot=    1      10.6076
ires=   92 irot=    2 jres=   96 jrot=    1      26.8608
Residual clashes =  146.66504
Printing 
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make: [und/T0125-2lisA-karplus1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make: [und/T0125-2lisA-karplus1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  2lisA/T0125-2lisA-karplus1.a2m \
                -target T0125 -template 2lisA \
                -out T0125-2lisA-karplus1  -outdir und
Couldn't open file 2lisA/T0125-2lisA-karplus1.a2m or 2lisA/T0125-2lisA-karplus1.a2m.gz for input
Can't open A2M file 2lisA/T0125-2lisA-karplus1.a2m for input
/projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file.
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed.
make: *** [und/T0125-2lisA-karplus1.index] Error 1
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make: [und/2lisA-T0125-karplus1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make: [und/2lisA-T0125-karplus1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
                -a2m  2lisA/2lisA-T0125-karplus1.a2m \
                -target T0125 -template 2lisA \
                -out 2lisA-T0125-karplus1  -outdir und
Skipped atom 427, because occupancy 0.49 <= existing 0.510001
Skipped atom 429, because occupancy 0.49 <= existing 0.510001
Skipped atom 431, because occupancy 0.49 <= existing 0.510001
Skipped atom 433, because occupancy 0.49 <= existing 0.510001
Skipped atom 435, because occupancy 0.49 <= existing 0.510001
Skipped atom 437, because occupancy 0.49 <= existing 0.510001
Skipped atom 439, because occupancy 0.49 <= existing 0.510001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2lisA-orig.a2m
Writing a2m file: tmp/2lisA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2858


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp -alignfile tmp/2lisA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2lisA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp.mod tmp/2lisA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2858 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2lisA-align.mod
tmp/2lisA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2858/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2lisA-orig.a2m tmp/2lisA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2lisA-align.mod
Running w0.5 tmp/2lisA-orig.a2m tmp/2lisA-align.mod
Running align2model tmp/2lisA-align -i tmp/2lisA-align.mod -db tmp/2lisA-orig.a2m -db tmp/2lisA-pdb.a2m
partial PDB gets fragment 3 through 38 extending start extending end
partial PDB gets fragment 39 through 93 extending start extending end
partial PDB gets fragment 94 through 105 extending start extending end
partial PDB gets fragment 106 through 128 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
134 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
ASP    2    6
ASP    3    6
VAL    4    3
VAL    5    3
VAL    6    3
SER    7    3
ARG    8   32
GLN    9   11
GLN   11   13
SER   12    3
TYR   13    2
VAL   14    2
GLN   15   11
ARG   16   29
MET   18   10
VAL   19    1
ASN   20    4
LEU   22    3
ASP   23    4
GLU   24   12
GLU   25   12
MET   26   10
HIS   27    4
LYS   28   26
VAL   30    3
LYS   31   25
ARG   32   24
PHE   33    4
ASP   35    5
MET   36   12
PRO   40    2
PHE   42    3
VAL   43    1
PHE   44    3
LEU   45    3
LYS   47   25
LYS   48   24
GLU   52   14
ARG   53   26
MET   55   10
ARG   56   30
TYR   57    3
CYS   58    2
MET   59   10
ASP   60    4
ARG   63   26
TYR   64    2
SER   65    3
LYS   66   30
ILE   68    4
LEU   69    3
GLN   70   14
LEU   71    2
LYS   72   30
HIS   73    2
LEU   74    4
PRO   75    2
VAL   76    2
ASN   77    5
LYS   78   26
LYS   79   30
THR   80    2
LEU   81    3
LYS   83   28
MET   84   10
ARG   86   27
PHE   87    2
VAL   88    1
TYR   90    3
ASN   92    4
TYR   93    3
ARG   96   32
GLU   97   15
LEU   98    3
TYR   99    3
VAL  102    1
PHE  103    3
ARG  104   26
VAL  106    2
GLN  107    8
ARG  110   19
MET  114   12
THR  115    2
ARG  119   28
LYS  120   26
TYR  121    3
SER  122    2
SER  123    2
LYS  124   31
ASP  125    5
THR  128    1
PHE  129    3
CYS  131    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue N 21 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 12 rotamers of residue M 37 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 41 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 46 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 82 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue F 88 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue Y 94 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 32 rotamers of residue R 97 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue V 107 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 8 rotamers of residue Q 108 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 19 rotamers of residue R 111 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
ssdist    59    1  132    1      3.5322
ssdist    59    1  132    2      2.8896
ssdist    59    2  132    1      4.2643
ssdist    59    2  132    2      2.1671
disulfide 1 found   A   59    2   A  132    2      2.1671   163.13  -114.66   162.75
Found 1 disulfide bonds.
Residue clashes:
keepclash     9   79     20.7762
keepclash    17   87     18.2878
keepclash    22   97     33.4328
keepclash    33  105     11.0607
keepclash    37   43     79.8296
keepclash    46  113     10.8754
keepclash    56  130     44.5728
keepclash    56  131     29.2696
keepclash    69   85     22.8009
keepclash    88   92     26.8148
keepclash   100  104    136.6003
keepclash   107  111     15.2382
turnclash     33    4   29    9     68.4799
Cluster     1 =   9  79
Cluster     2 =  17  87
Cluster     3 =  22  97 100 104 107 111
Cluster     4 =  29  33  37  43 105
Cluster     5 =  46 113
Cluster     6 =  56 130 131
Cluster     7 =  69  85
Cluster     8 =  88  92
24 clashing residues after turn 
Residue clashes:
9-79
17-87
22-97
33-37
33-105
33-29
37-43
37-105
43-105
46-113
56-130
56-131
69-85
88-92
97-100
100-104
104-111
105-29
107-111
cluster 1 has 2 members and 4.500e+02 combinations:
 79  9 
Energy     22.0285
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 4.500e+02 - Sending to search
0.932775 < 22.028460: keeping 
0.000000 < 3.468528: keeping 
Solved cluster 1: residual clashing  0.01
cluster 2 has 2 members and 7.200e+01 combinations:
 17  87 
Energy     19.5714
Searching cluster 17
Combinations for 2 members in cluster 2 OK: 7.200e+01 - Sending to search
0.000000 < 19.571375: keeping 
Solved cluster 2: residual clashing  1.61
cluster 3 has 6 members and 0.000e+00 combinations:
 22  107  104  100  97  111 
Energy    268.8965
Searching cluster 22
Combinations for 6 members in cluster 3 OK: 0.000e+00 - Sending to search
176.904968 < 268.896545: keeping 
179.949722 < 262.691833: keeping 
171.583389 < 257.612427: keeping 
151.838486 < 251.407715: keeping 
143.472153 < 218.956757: keeping 
143.472153 < 212.752045: keeping 
143.472153 < 210.705780: keeping 
151.838486 < 205.873413: keeping 
143.472153 < 188.505341: keeping 
143.472153 < 182.300644: keeping 
48.670990 < 179.188416: keeping 
40.304661 < 132.559662: keeping 
43.349411 < 126.354950: keeping 
34.983082 < 121.275551: keeping 
15.238178 < 115.070847: keeping 
6.871848 < 82.619888: keeping 
6.871848 < 76.415192: keeping 
6.871848 < 74.368919: keeping 
15.238178 < 69.536545: keeping 
6.871848 < 52.168484: keeping 
6.871848 < 45.963779: keeping 
10.000000 < 42.851563: keeping 
Solved cluster 3: residual clashing 42.07
cluster 4 has 5 members and 6.156e+04 combinations:
 29  43  37  33  105 
Energy    112.6597
Searching cluster 29
Combinations for 5 members in cluster 4 OK: 6.156e+04 - Sending to search
83.653954 < 112.659714: keeping 
79.829559 < 97.343498: keeping 
69.809364 < 93.758217: keeping 
58.748699 < 86.852234: keeping 
54.924309 < 71.536018: keeping 
35.826225 < 67.950737: keeping 
24.765560 < 53.177616: keeping 
20.941168 < 37.861401: keeping 
19.994366 < 34.276119: keeping 
3.824392 < 33.638046: keeping 
0.000000 < 21.598070: keeping 
0.000000 < 18.012787: keeping 
0.000000 < 14.480703: keeping 
Solved cluster 4: residual clashing 13.58
cluster 5 has 2 members and 0.000e+00 combinations:
 113  46 
Energy     24.4542
Searching cluster 46
Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search
Solved cluster 5: residual clashing 24.45
cluster 6 has 3 members and 0.000e+00 combinations:
 131  130  56 
Energy     73.8424
Searching cluster 56
Combinations for 3 members in cluster 6 OK: 0.000e+00 - Sending to search
49.868702 < 73.842407: keeping 
0.000000 < 49.898113: keeping 
Solved cluster 6: residual clashing  1.01
cluster 7 has 2 members and 8.000e+00 combinations:
 69  85 
Energy     22.8009
Searching cluster 69
Combinations for 2 members in cluster 7 OK: 8.000e+00 - Sending to search
0.000000 < 22.800941: keeping 
Solved cluster 7: residual clashing  0.34
cluster 8 has 2 members and 0.000e+00 combinations:
 92  88 
Energy     51.4174
Searching cluster 88
Combinations for 2 members in cluster 8 OK: 0.000e+00 - Sending to search
0.000000 < 51.417400: keeping 
Solved cluster 8: residual clashing 11.97
Still clashes at these sidechain pairs:
ires=   46 irot=    1 jres=  113 jrot=    1      10.8754
Residual clashes =   81.06648
Printing