Denovo density didn’t output a structure

[Anonymous]

I had a bunch of assembled fragments and I ran the below protocol on them for the fragment assignment and the genration of a consesus trajectory. 

#!/bin/sh



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-mode consensus 

-in::file::silent round1/assembled.*silent 

-consensus_frac 1.0 -energy_cut 0.05 

-mute core



# use the old model as a starting point

cp S_0001.pdb round1_model.pdb

 

Surprisngly, the script did not output any strcutres. This is a few lines from the log in my terminal, did the script ran successfully? If so, where can I find my structure? 

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

denovo_density: Score cut = -69153.8 (14895/297916)

denovo_density: Highest frequency = 201

denovo_density: Residue 72 stdev = 310.654 pose =       138.8251302619481       141.0146517130280       97.72079704151980 count = 201

denovo_density: Residue 73 stdev = 298.539 pose =       139.0025394963242       142.0479014400399       99.17878956951867 count = 402

denovo_density: Residue 74 stdev = 198.407 pose =       138.2260276398613       141.9612660746082       100.3133442320160 count = 402

denovo_density: Residue 75 stdev = 195.247 pose =       136.4008981329717       143.8642440583106       98.70014593941440 count = 402

denovo_density: Residue 76 stdev = 265.268 pose =       137.0841083486396       142.0427318255124       98.23466119770795 count = 402

denovo_density: Residue 77 stdev = 216.811 pose =       137.8472521508295       139.4494956040824       100.0041580324948 count = 402

denovo_density: Residue 78 stdev = 171.075 pose =       136.1212418224289       140.9915995606610       99.87954656096328 count = 402

denovo_density: Residue 79 stdev = 230.329 pose =       135.1649940119765       141.8879337852738       98.20768323378184 count = 402

denovo_density: Residue 80 stdev = 268.447 pose =       136.3753071278023       138.8567393598506       98.98710229309833 count = 402

denovo_density: Residue 81 stdev = 242.922 pose =       135.7620713546463       137.7403121387735       99.92026896253427 count = 201

denovo_density: NO RESIDUES IN CONSENSUS ASSIGNMENT.

cp: cannot stat ‘S_0001.pdb’: No such file or directory

 

[Anonymous]

The script will not produce output if a consensus is not reached among the docked fragments. I could be wrong but I believe the consensus_frac variable controls how high the consensus should be in order to be accepted so you could try and lowering that. You could also try and improving sampling by modifying n_to_search in step1.

[Anonymous]

Thanks, lowering the value works.  

[Anonymous]

hi ,i successfully run the same command above but there are  not any pdb file generated ,it is said:

:~/rosetta/main/source/bin$ ./denovo_density.linuxgccrelease -mode consensus -in::file::silent 1/assembled.*silent -consensus_frac 0.1 -energy_cut 0.05 -mute core -database /home/advanced/rosetta/main/database -out::path::pdb 2

denovo_density: Score cut = -48434.5 (1664/33299)

denovo_density: Highest frequency = 33

denovo_density: Residue 1 stdev = 444.035 pose =       36.80768511812136      -9.672755317262961      -28.75481051347792 count = 5

denovo_density: Residue 2 stdev = 327.581 pose =       36.18176406147701      -8.318007242412317      -27.67295226204978 count = 10

denovo_density: Residue 3 stdev = 245.997 pose =       37.46669934554542      -3.761268353543774      -29.61737313624764 count = 13

denovo_density: Residue 4 stdev = 175.933 pose =       38.32079024213813      -3.603874298030175      -28.39649710594686 count = 13

denovo_density: Residue 5 stdev = 140.483 pose =       36.76042506116890      -1.537790758069795      -27.40058657390887 count = 13

denovo_density: Residue 6 stdev = 145.766 pose =       36.33669995462689      -4.135084400026911      -28.01225036532002 count = 13

denovo_density: Residue 7 stdev = 101.435 pose =       37.69050755777021      -6.299769841098855      -27.55199245768652 count = 13

denovo_density: Residue 8 stdev = 297.62 pose =       37.73189624240533      -7.037116020616319      -18.48579397859394 count = 16

denovo_density: Residue 9 stdev = 227.616 pose =       37.83726279846766      -7.484450249661085      -18.37417805205926 count = 16

denovo_density: Residue 10 stdev = 281.251 pose =       37.76003909823169      -9.390755922516234      -9.682152867070505 count = 16

denovo_density: Residue 11 stdev = 259.759 pose =       39.84774896330482      -11.14110850556514      0.3232098188389048 count = 14

denovo_density: Residue 12 stdev = 621.549 pose =       41.07866542476452      -9.923217890128111      -16.36143065945344 count = 31

denovo_density: Residue 13 stdev = 647.909 pose =       41.30345745152421      -10.07248353025863      -13.03562952323288 count = 36

denovo_density: Residue 14 stdev = 632.102 pose =       40.89423895931746      -5.560267231502219      -19.14711560082702 count = 54

denovo_density: Residue 15 stdev = 543.574 pose =       39.68426651831797      -5.309559150575242      -15.62258324742031 count = 60

denovo_density: Residue 16 stdev = 489.07 pose =       38.71487798051613      -4.730963965149813      -19.34387844761087 count = 79

denovo_density: Residue 17 stdev = 442.451 pose =       40.19060917826332      -5.823122444683725      -22.67814801572376 count = 95

denovo_density: Residue 18 stdev = 396.379 pose =       40.95954681252125      -5.556475933530727      -20.24060638118880 count = 98

denovo_density: Residue 19 stdev = 330.107 pose =       38.38799911219636      -4.577983836477115      -20.62068424787072 count = 96

denovo_density: Residue 20 stdev = 305.609 pose =       36.49682905924783      -5.788216095263162      -24.02130673998060 count = 108

denovo_density: Residue 21 stdev = 303.275 pose =       37.62018910332555      -6.812941060701709      -23.85021841262112 count = 88

denovo_density: Residue 22 stdev = 231.011 pose =       37.79743702093041      -5.608345875389539      -23.33578642366718 count = 83

denovo_density: Residue 23 stdev = 233.345 pose =       35.17901982275345      -7.234770113996247      -22.20706523116795 count = 65

denovo_density: Residue 24 stdev = 200.116 pose =       34.58405387161785      -7.545736928929862      -22.36637752835169 count = 59

denovo_density: Residue 25 stdev = 245.642 pose =       33.57724626680189      -8.782417421191161      -22.50980367453732 count = 40

denovo_density: Residue 26 stdev = 423.241 pose =       28.32807893823258      -10.44993085693588      -21.53864940495866 count = 21

denovo_density: Residue 27 stdev = 471.895 pose =       24.68182791625659      -10.85322313200379      -23.70316511665039 count = 18

denovo_density: Residue 28 stdev = 391.273 pose =       28.54347299904570      -9.440926092858744      -20.43181700386909 count = 15

denovo_density: Residue 32 stdev = 74.9929 pose =       34.31659680234675     -0.8025307456552935      -22.92465843179027 count = 8

denovo_density: Residue 33 stdev = 55.6093 pose =       34.24010346439981      -1.983862063588428      -21.49198715390484 count = 16

denovo_density: Residue 34 stdev = 45.6311 pose =       36.44435543273611      0.2111611637673244      -20.90661480981592 count = 23

denovo_density: Residue 35 stdev = 39.3015 pose =       34.37602804418181       1.316729973906745      -19.72414693494770 count = 29

denovo_density: Residue 36 stdev = 30.6782 pose =       33.96523490381998     -0.4113129112722858      -17.95714786693132 count = 36

denovo_density: Residue 37 stdev = 23.6744 pose =       37.21597163342344      0.2946191209388960      -16.98346790517336 count = 43

denovo_density: Residue 38 stdev = 29.4539 pose =       36.49748230570579       2.734082169512811      -16.19924875724362 count = 43

denovo_density: Residue 39 stdev = 30.5014 pose =       33.71008666769829       1.856062395615786      -14.57542669567338 count = 50

denovo_density: Residue 40 stdev = 33.5015 pose =       35.80205201383087      0.3929503930093106      -13.28960065273823 count = 53

denovo_density: Residue 41 stdev = 22.1575 pose =       38.30366483716993       2.849460032192407      -12.32704382300293 count = 48

denovo_density: Residue 42 stdev = 6.77735 pose =       35.69920365785752       4.963095737248219      -10.50117466310191 count = 43

denovo_density: Residue 43 stdev = 11.013 pose =       34.51891218648429       2.784242550525669      -8.610312214264781 count = 36

denovo_density: Residue 44 stdev = 22.0785 pose =       37.80216322997254       2.443340185620005      -7.722966367356744 count = 30

denovo_density: Residue 45 stdev = 23.8152 pose =       38.15794592177590       5.340978780329730      -6.732898431887472 count = 23

denovo_density: Residue 46 stdev = 23.5285 pose =       34.82422028691401       5.533434338053011      -4.455611666237100 count = 16

denovo_density: Residue 47 stdev = 34.5879 pose =       35.80646075603329       2.738180923228442      -2.994833160131678 count = 16

denovo_density: Residue 48 stdev = 1.40649 pose =       38.49825340080206       4.262911809718951      0.2316301560842768 count = 9

denovo_density: Residue 49 stdev = 0.841569 pose =       36.33604083381596       6.389815001057191       2.111185444459379 count = 6

denovo_density: Residue 50 stdev = 4.54751e-13 pose =       34.60547128212541       3.246743908274810       3.794062423749053 count = 3

denovo_density: Residue 62 stdev = 346.122 pose =       34.76065738634593      -10.86834575927829       6.424717170657607 count = 5

denovo_density: Residue 63 stdev = 274.408 pose =       33.40889487277713      -10.94940881062382       8.244989095413615 count = 10

denovo_density: Residue 64 stdev = 240.709 pose =       31.91882453328899      -8.095171356780147       8.083235290853983 count = 15

denovo_density: Residue 65 stdev = 264.723 pose =       32.40909316193753      -8.717004476795482       5.971226420059321 count = 20

denovo_density: Residue 66 stdev = 222.249 pose =       31.84761527408181      -12.06401541575279       5.975379486621923 count = 25

denovo_density: Residue 67 stdev = 159.955 pose =       29.95705400985043      -11.23877568589758       7.354426115078342 count = 25

denovo_density: Residue 68 stdev = 156.5 pose =       28.96442812570277      -8.317798727076992       6.041832204578911 count = 25

denovo_density: Residue 69 stdev = 167.297 pose =       29.23583523599030      -10.33276952954848       4.193129238865165 count = 25

denovo_density: Residue 70 stdev = 115.348 pose =       28.17440220721186      -12.85038045930913       5.216663492580517 count = 25

denovo_density: Residue 71 stdev = 84.4678 pose =       26.46832549859078      -10.34814467892285       5.679047558319285 count = 20

denovo_density: Residue 72 stdev = 95.0066 pose =       25.99944965172165      -9.295160097273323       3.553646828560014 count = 15

denovo_density: Residue 73 stdev = 90.3409 pose =       26.60186109226407      -12.09389501530496       2.451361412442278 count = 10

denovo_density: Residue 74 stdev = 49.2723 pose =       24.77116122264509      -13.52794807268751       3.398844037976930 count = 5

denovo_density: Residue 75 stdev = 1.13687e-13 pose =      0.9718786748410773      -18.91211836475870      -42.78187110335905 count = 14

denovo_density: Residue 76 stdev = 22.4275 pose =      0.6812344193890936      -16.64725551719397      -38.92427535505281 count = 31

denovo_density: Residue 77 stdev = 14.1645 pose =       2.842714771223234      -15.45822388512068      -36.84513248836171 count = 31

denovo_density: Residue 78 stdev = 17.5677 pose =       4.208843905363947      -17.19630653775062      -33.93298685424816 count = 31

denovo_density: Residue 79 stdev = 7.99351 pose =       4.545686493257059      -16.19733757544745      -30.70759915733769 count = 31

denovo_density: Residue 80 stdev = 1.89362 pose =       2.642159403650831      -13.57092923688997      -31.65392913269614 count = 31

denovo_density: Residue 81 stdev = 0.390308 pose =       1.602558043914240      -12.09095059778613      -29.12521648957674 count = 31

denovo_density: Residue 82 stdev = 3.62057 pose =     -0.3791886261844489      -9.554875992627238      -29.40505906272461 count = 31

denovo_density: Residue 83 stdev = 11.4712 pose =       1.071272322790170      -6.985891658105610      -30.33779246939136 count = 31

denovo_density: Residue 84 stdev = 38.1022 pose =       1.450429305194017      -6.756429343797292      -28.95839397986095 count = 17

denovo_density: Residue 95 stdev = 259.303 pose =       40.60984445760401      -3.237640261200362      -33.91792288427801 count = 8

denovo_density: Residue 96 stdev = 291.417 pose =       37.53347927444303      -4.354101182373325      -25.35476324822188 count = 11

denovo_density: Residue 97 stdev = 118.834 pose =       37.17493730229874      -6.951730711249335      -24.52593267837814 count = 44

denovo_density: Residue 98 stdev = 97.1188 pose =       39.26552089464315      -8.997250755268997      -24.21694342460653 count = 77

denovo_density: Residue 99 stdev = 79.8521 pose =       40.43829030267917      -7.909261383235649      -21.77049676723853 count = 108

denovo_density: Residue 100 stdev = 59.578 pose =       37.71263480824130      -8.820527064755003      -19.71025769093961 count = 133

denovo_density: Residue 101 stdev = 48.7068 pose =       37.17292579820005      -12.44368490175619      -20.56380028199208 count = 158

denovo_density: Residue 102 stdev = 43.7884 pose =       40.02337066393183      -13.57286313951752      -18.71257447070896 count = 183

denovo_density: Residue 103 stdev = 37.608 pose =       39.01076924590660      -12.27271015152684      -15.46838764357533 count = 208

denovo_density: Residue 104 stdev = 26.3219 pose =       36.17526224290535      -14.71678880010164      -15.01931723540329 count = 225

denovo_density: Residue 105 stdev = 27.2792 pose =       38.26309576687865      -17.59399300101655      -14.36568458438436 count = 222

denovo_density: Residue 106 stdev = 22.8874 pose =       39.57500047539013      -16.45538386296323      -11.20349576075993 count = 189

denovo_density: Residue 107 stdev = 13.8117 pose =       36.61519936275693      -15.87971038431779      -9.136978406971384 count = 156

denovo_density: Residue 108 stdev = 0.410832 pose =       35.15131405481686      -19.67816345440474      -8.910822981142838 count = 125

denovo_density: Residue 109 stdev = 0.833916 pose =       37.85934178909422      -21.10032464762097      -7.223771498959459 count = 100

denovo_density: Residue 110 stdev = 0.36773 pose =       37.55535834294529      -19.09182453674358      -4.580595393373492 count = 75

denovo_density: Residue 111 stdev = 0.0832464 pose =       33.96017399497765      -19.79993211132745      -4.290635702349078 count = 50

denovo_density: Residue 112 stdev = 3.64599e-13 pose =       32.58693595535723      -22.56654196674583      -6.138971741934304 count = 25

denovo_density: Residue 115 stdev = 343.658 pose =       31.42452953731755      -17.66137328363327      -19.63439688308086 count = 3

denovo_density: Residue 116 stdev = 392.706 pose =       30.80812408168673      -17.02823315912821      -20.86913829153369 count = 3

denovo_density: Residue 117 stdev = 352.167 pose =       32.55362608619757      -15.63828127224471      -22.93212748900211 count = 3

denovo_density: Residue 118 stdev = 343.989 pose =       33.95156782716864      -16.24230517045530      -24.11701721045387 count = 3

denovo_density: Residue 119 stdev = 192.313 pose =       27.49543259566611      -8.579070293469940       3.060149916565163 count = 22

denovo_density: Residue 120 stdev = 140.974 pose =       30.15716569918451      -4.955199537070248       7.089809061847812 count = 37

denovo_density: Residue 121 stdev = 112.853 pose =       30.68179024892820      -1.941301517889795       7.176082629268270 count = 57

denovo_density: Residue 122 stdev = 75.1071 pose =       33.00782536803013      -1.999109312615773       8.005645411395948 count = 77

denovo_density: Residue 123 stdev = 60.5022 pose =       33.24133273670081      -3.208100639183829       6.059402669562590 count = 97

denovo_density: Residue 124 stdev = 53.4401 pose =       33.04647720986666     -0.6194775428846250       6.005944892491951 count = 113

denovo_density: Residue 125 stdev = 50.3491 pose =       35.28185711043637      0.5125231138724964       6.308914895690374 count = 119

denovo_density: Residue 126 stdev = 45.5056 pose =       36.17725648112416      -1.066234698068468       5.377111005760556 count = 134

denovo_density: Residue 127 stdev = 56.1013 pose =       35.26005651829303     -0.8860715613627940       2.986668658795076 count = 149

denovo_density: Residue 128 stdev = 67.2223 pose =       35.76547027302712       2.448461002669979       2.185728926874967 count = 145

denovo_density: Residue 129 stdev = 72.3322 pose =       38.02965524614256       2.206284914853294       1.942249130031949 count = 130

denovo_density: Residue 130 stdev = 88.9875 pose =       37.56453327348759      0.4741335884614355     -0.2060545677494494 count = 125

denovo_density: Residue 131 stdev = 99.2939 pose =       35.78841566281018       1.927467331164249      -2.682274180658455 count = 120

denovo_density: Residue 132 stdev = 93.0092 pose =       36.30573809168015       4.368539337695918      -4.710823545462165 count = 114

denovo_density: Residue 133 stdev = 96.5165 pose =       37.69318918820406       2.492905946492304      -6.907296041583671 count = 95

denovo_density: Residue 134 stdev = 58.2694 pose =       34.63464365128128       1.678439403424332      -9.120212466759885 count = 89

denovo_density: Residue 135 stdev = 53.8756 pose =       33.50502374997876       3.859353284721116      -10.74164609772083 count = 89

denovo_density: Residue 136 stdev = 60.0605 pose =       36.09445758243618       2.884976530672025      -12.19026808793426 count = 74

denovo_density: Residue 137 stdev = 64.3982 pose =       35.07278483691424     -0.3553992581929601      -12.36772510878196 count = 75

denovo_density: Residue 138 stdev = 60.7565 pose =       31.92233693619624      0.7219409211498102      -13.74897360749132 count = 75

denovo_density: Residue 139 stdev = 73.7694 pose =       33.31483194451867       2.392972588512302      -15.14218676720841 count = 63

denovo_density: Residue 140 stdev = 115.852 pose =       34.26670873600496      -1.273869563975507      -15.71004086632903 count = 52

denovo_density: Residue 141 stdev = 145.845 pose =       30.58613051433135      -4.220980398420299      -15.67900614010735 count = 38

denovo_density: Residue 142 stdev = 142.475 pose =       29.14813672767716      -1.795549165562991      -17.01242416950791 count = 38

denovo_density: Residue 143 stdev = 158.767 pose =       31.28479075054555      -1.226325779072253      -18.94071628901962 count = 38

denovo_density: Residue 144 stdev = 210.406 pose =       28.95184964535965      -5.902399969795821      -18.64893707745954 count = 23

denovo_density: Residue 145 stdev = 202.141 pose =       26.26528618184695      -5.733228298283279      -18.81012772750058 count = 23

denovo_density: Residue 146 stdev = 326.355 pose =       20.90675286646457      -10.12565798755242      -9.484415345610126 count = 7

denovo_density: Residue 147 stdev = 295.756 pose =       19.18392196934280      -11.25232419615006      -11.56056116512917 count = 7

denovo_density: Residue 148 stdev = 297.757 pose =       15.43063546259415      -13.54106973476451      -12.72461388866210 count = 4

denovo_density: Residue 157 stdev = 287.55 pose =       18.09727395071544      -8.711013004950351      -5.718918563795453 count = 9

denovo_density: Residue 158 stdev = 272.989 pose =       20.20422265927822      -6.066769508495446      -4.811483038770837 count = 17

denovo_density: Residue 159 stdev = 431.769 pose =       24.07904820519049      -6.554869168307699      -10.43116307144317 count = 28

denovo_density: Residue 160 stdev = 411.895 pose =       25.59696434305953      -7.093291277939798      -13.47118003822336 count = 39

denovo_density: Residue 161 stdev = 367.92 pose =       26.30225460231063      -4.251559369541939      -14.98677107507616 count = 48

denovo_density: Residue 162 stdev = 382.917 pose =       25.98511839504176      -3.570591871144015      -14.00497177551155 count = 48

denovo_density: Residue 163 stdev = 392.195 pose =       25.11474512487754      -5.922496778613771      -12.85558476973458 count = 53

denovo_density: Residue 164 stdev = 324.464 pose =       26.32492835185928      -5.271035720338207      -13.00673335289678 count = 53

denovo_density: Residue 165 stdev = 285.966 pose =       26.16737073629278      -2.546525622040219      -12.24746013899415 count = 53

denovo_density: Residue 166 stdev = 331.76 pose =       26.41660907797685      -3.592693860952119      -12.85379063690759 count = 44

denovo_density: Residue 167 stdev = 336.634 pose =       28.02257529968781      -5.557376311378410      -14.43324429805528 count = 36

denovo_density: Residue 168 stdev = 271.285 pose =       27.56774380637908      -3.922513086749721      -13.71918111683045 count = 25

denovo_density: Residue 169 stdev = 271.691 pose =       25.25939787475463      -3.666978670774315      -10.96150452974057 count = 14

denovo_density: Residue 170 stdev = 102.915 pose =       16.32248433440141      -2.879748577456192       1.569963673704563 count = 5

denovo_density: Residue 171 stdev = 113.601 pose =       19.07255637612341      -2.995566374529249      0.5126313831910435 count = 5

denovo_density: Residue 185 stdev = 72.1731 pose =      -2.843821156139759      -14.79759190959300      -21.75157515618679 count = 3

denovo_density: Residue 186 stdev = 38.375 pose =      -2.066427915521105      -14.71674264122191      -21.20574746587474 count = 6

denovo_density: Residue 187 stdev = 37.8601 pose =      -1.481568806988215      -12.86535006757619      -22.30733695064674 count = 9

denovo_density: Residue 188 stdev = 50.7767 pose =      -3.287571741342338      -13.13650479711734      -20.28460100478404 count = 12

denovo_density: Residue 189 stdev = 22.1548 pose =      -3.421783757313746      -14.61696664000995      -18.83894969025630 count = 15

denovo_density: Residue 190 stdev = 9.64071 pose =      -1.167522365499670      -13.12646150252284      -20.49808485559324 count = 15

denovo_density: Residue 191 stdev = 31.263 pose =      -1.052223282337487      -11.57022747832937      -20.62598654917561 count = 15

denovo_density: Residue 192 stdev = 38.0295 pose =      -2.813255989787103      -13.20573745802559      -18.10326446652608 count = 15

denovo_density: Residue 193 stdev = 18.2321 pose =      -1.780916657210335      -13.84574173689912      -17.85282700892843 count = 15

denovo_density: Residue 194 stdev = 27.3223 pose =      0.2763858315208133      -11.97335152458853      -19.45227009116009 count = 12

denovo_density: Residue 195 stdev = 62.1539 pose =     -0.3992392565451307      -11.38295254339955      -18.56955819927413 count = 9

denovo_density: Residue 196 stdev = 64.5548 pose =      -1.654310070427938      -13.05977041506451      -16.48577006383657 count = 6

denovo_density: Residue 197 stdev = 55.5649 pose =      0.4199413800426447      -12.67173915465033      -17.46838832343715 count = 3

denovo_density: Residue 206 stdev = 357.976 pose =       42.48872037068929      -7.574480106486072       2.359346773953981 count = 6

denovo_density: Residue 207 stdev = 229.973 pose =       35.34721249728276      -6.700093150444188       8.273881586722249 count = 23

denovo_density: Residue 208 stdev = 149.022 pose =       36.91826773101103      -5.720616704317122       10.74232422433899 count = 35

denovo_density: Residue 209 stdev = 98.8433 pose =       36.83523120260390      -6.003101489362687       10.69085879889369 count = 59

denovo_density: Residue 210 stdev = 119.348 pose =       35.96182771944807      -6.681493428156512       9.170782592904192 count = 80

denovo_density: Residue 211 stdev = 128.886 pose =       34.33750306140927      -5.670611088287734       7.665611174973412 count = 102

denovo_density: Residue 212 stdev = 142.507 pose =       34.05127901078064      -3.546707805711328       5.960741849397129 count = 120

denovo_density: Residue 213 stdev = 154.361 pose =       34.95065686774109      -4.159291598549489       4.741426563208555 count = 136

denovo_density: Residue 214 stdev = 156.353 pose =       34.45946465330539      -4.262411207297800       2.806037762592258 count = 151

denovo_density: Residue 215 stdev = 149.22 pose =       33.69165856863265      -1.814949456903786       1.824943865785119 count = 156

denovo_density: Residue 216 stdev = 171.245 pose =       35.33656892863025      -1.490061605284195       1.365183637385398 count = 139

denovo_density: Residue 217 stdev = 169.626 pose =       36.17656860638139      -2.010159591714512     -0.4817483850041628 count = 127

denovo_density: Residue 218 stdev = 183.641 pose =       35.29589607774958     -0.6158028009863166      -3.117569496335201 count = 106

denovo_density: Residue 219 stdev = 215.217 pose =       36.77190671768168       1.278561263503521      -3.689254217756787 count = 88

denovo_density: Residue 220 stdev = 223.163 pose =       39.53396555305972       1.321865762146618      -3.673261569421570 count = 69

denovo_density: Residue 221 stdev = 223.328 pose =       39.61716402810685      0.4546228318538991      -3.903909264711846 count = 54

denovo_density: Residue 222 stdev = 237.298 pose =       38.86318175640233      0.6352367617194696      -2.139278742205319 count = 38

denovo_density: Residue 223 stdev = 116.369 pose =       36.52185052183383     -0.6016986740634771      0.4289342188681933 count = 28

denovo_density: Residue 224 stdev = 111.911 pose =       36.21387633327272      -4.361172925990873       1.748544437464383 count = 22

denovo_density: Residue 225 stdev = 95.1511 pose =       34.85405309757628      -4.730574903033586     -0.1802903948273868 count = 22

denovo_density: Residue 226 stdev = 117.996 pose =       32.49027749688384      -4.390381889482213      -4.146947812748968 count = 27

denovo_density: Residue 227 stdev = 133.467 pose =       33.93140640189756      -3.209438511036448      -8.060326993747900 count = 24

denovo_density: Residue 228 stdev = 92.0134 pose =       35.16859362911151      -3.240237108163333      -11.22109622306105 count = 21

denovo_density: Residue 229 stdev = 57.5255 pose =       33.78777371033150      -2.733915806610596      -13.94332962991242 count = 18

denovo_density: Residue 230 stdev = 0.063296 pose =       32.60136413003200       1.759299190454982      -19.30060785043005 count = 15

denovo_density: Residue 231 stdev = 0.128429 pose =       35.71147884029298       2.134692403906560      -21.42166856282604 count = 15

denovo_density: Residue 232 stdev = 0.0301881 pose =       35.49566281909470      -1.683342240616209      -22.25595498298713 count = 10

denovo_density: Residue 233 stdev = 2.22045e-16 pose =       31.74982421256735      -1.344452905106321      -23.56377792881884 count = 5

denovo_density: Residue 234 stdev = 0 pose =       33.10864981381032       1.018257115796482      -26.21321533985436 count = 5

denovo_density: Residue 246 stdev = 8.66646e-14 pose =       15.52846725666281      -2.304586033561200      -6.034705260230937 count = 24

denovo_density: Residue 247 stdev = 9.92855e-14 pose =       13.23132544321178      -4.871358730197754      -7.640979494050637 count = 24

denovo_density: Residue 248 stdev = 2.93309e-13 pose =       15.53347737471973      -5.691908454275575      -10.54885170216861 count = 24

denovo_density: Residue 249 stdev = 10.5551 pose =       16.00148796349822      -8.528930102795409      -7.687948477860920 count = 50

denovo_density: Residue 250 stdev = 9.4837 pose =       13.46959333717926      -10.72861991332541      -8.972583880148669 count = 75

denovo_density: Residue 251 stdev = 34.4971 pose =       12.65207310336102      -13.06107957992220      -8.440987345125521 count = 106

denovo_density: Residue 252 stdev = 64.5109 pose =       11.55896312237923      -13.44746240065320      -9.515244367063772 count = 137

denovo_density: Residue 253 stdev = 91.3675 pose =       9.398606660083471      -14.43331775508369      -9.175371998407815 count = 168

denovo_density: Residue 254 stdev = 121.576 pose =       8.368583432281506      -12.39586138182437      -10.65417776754808 count = 199

denovo_density: Residue 255 stdev = 114.813 pose =       10.35433909840983      -13.60394259212075      -13.24669974270393 count = 201

denovo_density: Residue 256 stdev = 111.825 pose =       9.731916154124933      -16.55931941191732      -12.94448618781079 count = 231

denovo_density: Residue 257 stdev = 138.6 pose =       6.722239988068385      -15.75357308026701      -12.68979991341682 count = 260

denovo_density: Residue 258 stdev = 180.486 pose =       7.866621684885674      -13.54494122234268      -14.67440314638534 count = 239

denovo_density: Residue 259 stdev = 185.748 pose =       10.48743659346422      -14.95999022117090      -15.74997217105956 count = 219

denovo_density: Residue 260 stdev = 204.245 pose =       8.513007133703548      -16.56614820543075      -15.21010036453690 count = 188

denovo_density: Residue 261 stdev = 254.002 pose =       6.764750174969675      -14.85463065989639      -16.06103259786857 count = 157

denovo_density: Residue 262 stdev = 273.002 pose =       9.296806051851357      -13.87005464386239      -18.12148404313337 count = 130

denovo_density: Residue 263 stdev = 284.604 pose =       11.24391667291078      -14.98848256350877      -17.97793453404217 count = 104

denovo_density: Residue 264 stdev = 404.367 pose =       12.16546609047970      -12.75491771338289      -15.98741478960865 count = 78

denovo_density: Residue 265 stdev = 500.904 pose =       18.94540729416632      -7.327417705634052      -12.88112373505114 count = 52

denovo_density: Residue 266 stdev = 4.40026 pose =       37.47021856003517       2.393772619317399      -2.099507050715945 count = 23

denovo_density: Residue 267 stdev = 31.0282 pose =       33.79909292613058       3.297217748351341      -4.063137658443605 count = 24

denovo_density: Residue 268 stdev = 78.516 pose =       34.56880757877087       4.227254425428226      -5.856679203119313 count = 25

denovo_density: Residue 269 stdev = 338.785 pose =       28.25200482253967      -1.243841137660536      -10.44725806083795 count = 37

denovo_density: Residue 270 stdev = 357.774 pose =       21.21489747980188      -3.389447360399801      -13.32103058042002 count = 44

denovo_density: Residue 271 stdev = 417.54 pose =       17.10339423923173      -2.986476113907116      -14.79318745198136 count = 52

denovo_density: Residue 272 stdev = 460.74 pose =       16.99030437910206      -5.137112977022918      -15.48701804822980 count = 47

denovo_density: Residue 273 stdev = 379.369 pose =       15.12121816359148      -6.704778833093286      -17.12901539706946 count = 53

denovo_density: Residue 274 stdev = 295.173 pose =       8.534401914850967      -6.183158355866668      -17.87937275237090 count = 63

denovo_density: Residue 275 stdev = 313.184 pose =       7.286159634659954      -6.753341041874487      -16.54789103696717 count = 78

denovo_density: Residue 276 stdev = 232.639 pose =       5.451365839202523      -8.205270750259468      -16.38770890639042 count = 89

denovo_density: Residue 277 stdev = 146.535 pose =       3.384034436424693      -7.334971880864890      -15.93940997238963 count = 101

denovo_density: Residue 278 stdev = 112.455 pose =       1.500327996615266      -7.485735799028724      -13.85834419833445 count = 101

denovo_density: Residue 279 stdev = 116.581 pose =       3.243149128823120      -7.960157390511722      -12.76989864423401 count = 106

denovo_density: Residue 280 stdev = 108.821 pose =       4.201028591350884      -6.579395138484826      -12.20723122539305 count = 104

denovo_density: Residue 281 stdev = 151.482 pose =       4.410099435186138      -5.789334916368933      -11.46745285495028 count = 118

denovo_density: Residue 282 stdev = 142.375 pose =       4.928164787170008      -6.486020105291940      -9.952499288746594 count = 126

denovo_density: Residue 283 stdev = 142.556 pose =       7.196754666170003      -6.149431788848222      -10.32350038571248 count = 128

denovo_density: Residue 284 stdev = 174.85 pose =       8.194184763780170      -4.384954249782373      -10.37072336319150 count = 118

denovo_density: Residue 285 stdev = 225.433 pose =       8.207017658327731      -4.441407902553674      -9.258163902147018 count = 105

denovo_density: Residue 286 stdev = 206.427 pose =       9.683717550075759      -5.933314907891563      -9.705781631596468 count = 90

denovo_density: Residue 287 stdev = 197.448 pose =       11.55065794583554      -4.776483667349549      -10.66204369997307 count = 78

denovo_density: Residue 288 stdev = 241.92 pose =       11.00188470429154      -3.699832287185844      -10.01888555719169 count = 72

denovo_density: Residue 289 stdev = 214.681 pose =       9.851211415372227      -4.926562680837888      -8.084867682961747 count = 62

denovo_density: Residue 290 stdev = 162.469 pose =       10.05501621585224      -6.446126566428891      -8.973156899379688 count = 52

denovo_density: Residue 291 stdev = 195.264 pose =       10.50568409784983      -6.053390828701849      -9.720210847852686 count = 42

denovo_density: Residue 292 stdev = 153.671 pose =       5.174507345170498      -8.234801889163043      -11.23061432670035 count = 30

denovo_density: Residue 293 stdev = 45.9963 pose =       5.241879132889536      -9.477623416739039      -12.83461898401162 count = 33

denovo_density: Residue 294 stdev = 26.4402 pose =       5.385556047113492      -9.144123819365568      -12.01014383138078 count = 37

denovo_density: Residue 295 stdev = 30.5095 pose =       2.949308875948620      -10.18281266345754      -9.951640205423210 count = 42

denovo_density: Residue 296 stdev = 19.8316 pose =       3.837090257780638      -10.88667730674443      -10.34679923753766 count = 51

denovo_density: Residue 297 stdev = 33.0958 pose =       6.672838085642721      -10.54434007527862      -11.72545149879269 count = 54

denovo_density: Residue 298 stdev = 71.3197 pose =       6.026956985311462      -11.03917136794360      -10.41977320069000 count = 59

denovo_density: Residue 299 stdev = 82.7845 pose =       4.398629502099338      -12.41171843393346      -9.717755553006567 count = 60

denovo_density: Residue 300 stdev = 100.435 pose =       6.303916436007131      -11.59697862828387      -10.94074220599498 count = 56

denovo_density: Residue 301 stdev = 137.522 pose =       9.342466832970899      -12.30741170805767      -11.97546815492160 count = 55

denovo_density: Residue 302 stdev = 182.111 pose =       9.196716772427651      -13.36604815000879      -10.55474281183184 count = 50

denovo_density: Residue 303 stdev = 252.336 pose =       11.31752008822112      -13.55091645001995      -10.15167837989690 count = 46

denovo_density: Residue 304 stdev = 261.689 pose =       14.88703826514386      -14.04366221280359      -12.19405415742778 count = 41

denovo_density: Residue 305 stdev = 267.807 pose =       17.37664060283849      -14.67538569607354      -12.58251077525894 count = 35

denovo_density: Residue 306 stdev = 342.955 pose =       21.21098069994829      -15.44736111923003      -12.86831561285723 count = 29

denovo_density: Residue 307 stdev = 325.835 pose =       24.63388563117788      -16.17209512842318      -13.05729194139350 count = 24

denovo_density: Residue 308 stdev = 223.299 pose =       27.42059019689697      -15.37035550466450      -12.45929634202712 count = 19

denovo_density: Residue 309 stdev = 235.544 pose =       28.17480226082639      -12.54768075810226      -13.22539980909942 count = 19

denovo_density: Residue 310 stdev = 280.939 pose =       28.96050028047171      -14.60183384590075      -15.97384070950462 count = 16

denovo_density: Residue 311 stdev = 300.899 pose =       27.17239943984605      -15.26380590049355      -17.28616966786014 count = 13

denovo_density: Residue 312 stdev = 306.537 pose =       24.03670663144681      -14.60968976502160      -18.88841858008721 count = 9

denovo_density: Residue 313 stdev = 328.372 pose =       26.51644324707496      -13.01726710255644      -19.77081261443125 count = 6

denovo_density: Residue 314 stdev = 352.775 pose =       27.30734400904931      -14.67535933581858      -22.06674745527733 count = 3

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv

basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt

Is there anying goes wrong?Thanks

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