Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 29-Nov-2005 17:50:52 n-1<30725> ssi:boot:base:linear: booting n0 (wolf01) n-1<30725> ssi:boot:base:linear: booting n1 (wolf02) n-1<30725> ssi:boot:base:linear: booting n2 (wolf03) n-1<30725> ssi:boot:base:linear: booting n3 (wolf04) n-1<30725> ssi:boot:base:linear: booting n4 (wolf05) n-1<30725> ssi:boot:base:linear: booting n5 (wolf06) n-1<30725> ssi:boot:base:linear: booting n6 (wolf07) n-1<30725> ssi:boot:base:linear: booting n7 (wolf08) n-1<30725> ssi:boot:base:linear: booting n8 (wolf09) n-1<30725> ssi:boot:base:linear: booting n9 (wolf10) n-1<30725> ssi:boot:base:linear: booting n10 (wolf11) n-1<30725> ssi:boot:base:linear: booting n11 (wolf12) n-1<30725> ssi:boot:base:linear: booting n12 (wolf13) n-1<30725> ssi:boot:base:linear: booting n13 (wolf14) n-1<30725> ssi:boot:base:linear: booting n14 (wolf15) n-1<30725> ssi:boot:base:linear: booting n15 (wolf16) n-1<30725> ssi:boot:base:linear: finished LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. Sequence file "znf42.seq" read, 219 residues. Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 403 identity constraints created. 8836 symmetry constraints created. cyana> cyana> cyana> - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: shifts missing "H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" Residue missing shifts GLY 35 H QA SER 36 H HA QB ASP 37 H CYS 49 HG PHE 50 HZ CYS 69 HG LEU 84 QD2 GLY 335 H QA SER 336 H HA QB ASP 337 H CYS 349 HG PHE 350 HZ CYS 369 HG LEU 384 QD2 20 missing chemical shifts, completeness 98.0%. ------------------------------------------------------------ Peak list : c13no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 2996 assignments. - peakcheck: atom shift unusual Atom Shift Dev Mean +/- Minimum Maximum HG3 ARG 44 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 44 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 48 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 66 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 73 -0.640 4.25 0.72 0.32 -1.03 1.31 HG3 ARG 344 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 344 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 348 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 366 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 373 -0.640 4.25 0.72 0.32 -1.03 1.31 10 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 2996 0.000 0.003 0.460 0.013 1 0.030 2 3343 0.000 0.000 0.291 0.006 1 0.030 3 3343 0.000 0.000 0.297 0.032 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD1 LEU 73 0.281 0.281 0.460 25 HD3 ARG 78 2.772 2.772 0.291 19 2 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1210 2 0.291 HD3 ARG 78 2948 1 0.460 QD1 LEU 73 2 deviations larger than tolerance. ------------------------------------------------------------ Peak list : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1274 peaks, 1111 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1111 0.002 0.002 0.030 0.011 1 0.030 2 1257 0.000 0.000 0.011 0.001 0 0.030 3 1257 0.000 -0.001 0.186 0.009 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD1 LEU 118 0.930 0.902 0.030 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1240 1 -0.030 QD1 LEU 118 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : c13ar Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 222 0.004 0.005 0.030 0.013 0 0.030 2 280 0.000 0.000 0.000 0.000 0 0.030 3 280 0.000 0.000 0.000 0.000 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks 0 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 0 deviations larger than tolerance. ------------------------------------------------------------ Peak list : fc12no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 227 peaks, 147 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 147 0.000 -0.001 0.029 0.016 0 0.030 2 161 0.000 0.000 0.014 0.005 0 0.030 3 161 0.000 -0.005 0.297 0.035 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks 0 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 0 deviations larger than tolerance. - znf42: calibration prot=znf42 peaks=c13no,n15no,c13ar,fc12no constant=3.0E7,1.2 E7,2.0E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 2996 assignments. - calibration: peaks select "** list=1" 3489 of 3489 peaks, 3489 of 3489 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3489 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 327 9.4% 3.00-3.99 A: 768 22.0% 4.00-4.99 A: 1384 39.7% 5.00-5.99 A: 1008 28.9% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1274 peaks, 1111 assignments. - calibration: peaks select "** list=2" 1274 of 4763 peaks, 1274 of 4763 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1274 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1274 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 334 26.2% 4.00-4.99 A: 489 38.4% 5.00-5.99 A: 356 27.9% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - calibration: peaks select "** list=3" 281 of 5044 peaks, 281 of 5044 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal constant=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 21 7.5% 3.00-3.99 A: 57 20.3% 4.00-4.99 A: 161 57.3% 5.00-5.99 A: 42 14.9% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 227 peaks, 147 assignments. - calibration: peaks select "** list=4" 227 of 5271 peaks, 227 of 5271 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 227 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 227 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 1 0.4% 3.00-3.99 A: 50 22.0% 4.00-4.99 A: 157 69.2% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 227 100.0% - calibration: peaks select ** 5271 of 5271 peaks, 5271 of 5271 assignments selected. - znf42: peaks calibrate ** simple 4018 upper limits added, 9/479 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4018 upper limits, 4018 assignments. - znf42: distance modify Number of modified constraints: 2120 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2120 upper limits, 2120 assignments. - znf42: ./init - init: read lib /user/cyana-2.1/lib/cyana.lib Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. - init: read seq znf42.seq Sequence file "znf42.seq" read, 219 residues. - init: molecules define 35..128 335..428 Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 - init: molecule identity 403 identity constraints created. - init: molecule symdist "CA 35..128" "CA 335..428" 8836 symmetry constraints created. - znf42: read upl znf42.upl Distance constraint file "znf42.upl" read, 2120 upper limits, 2120 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 267 constraints for 267 angles. - znf42: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 35671). Structure annealed in 41 s, f = 13.7615. Structure annealed in 40 s, f = 17.5925. Structure annealed in 39 s, f = 12.2980. Structure annealed in 39 s, f = 11.5597. Structure annealed in 39 s, f = 13.6041. Structure annealed in 39 s, f = 17.4426. Structure annealed in 39 s, f = 15.8275. Structure annealed in 40 s, f = 18.2031. Structure annealed in 39 s, f = 18.2851. Structure annealed in 39 s, f = 13.6790. Structure annealed in 40 s, f = 18.4769. Structure annealed in 39 s, f = 14.1337. Structure annealed in 40 s, f = 12.8482. Structure annealed in 39 s, f = 12.5846. Structure annealed in 39 s, f = 14.3369. Structure annealed in 40 s, f = 20.7856. Structure annealed in 39 s, f = 20.5184. Structure annealed in 39 s, f = 11.9040. Structure annealed in 39 s, f = 13.0230. Structure annealed in 39 s, f = 13.4964. Structure annealed in 39 s, f = 14.0709. Structure annealed in 39 s, f = 16.4739. Structure annealed in 39 s, f = 13.3479. Structure annealed in 39 s, f = 11.6433. Structure annealed in 39 s, f = 12.7872. Structure annealed in 39 s, f = 12.4951. Structure annealed in 39 s, f = 14.7122. Structure annealed in 39 s, f = 13.0273. Structure annealed in 39 s, f = 15.0213. Structure annealed in 39 s, f = 27.7605. Structure annealed in 40 s, f = 13.4758. Structure annealed in 39 s, f = 16.9488. Structure annealed in 39 s, f = 16.8642. Structure annealed in 39 s, f = 17.0948. Structure annealed in 39 s, f = 15.6308. Structure annealed in 39 s, f = 17.9326. Structure annealed in 39 s, f = 13.6110. Structure annealed in 39 s, f = 13.6156. Structure annealed in 40 s, f = 12.6303. Structure annealed in 39 s, f = 14.9169. Structure annealed in 39 s, f = 12.6538. Structure annealed in 40 s, f = 18.5154. Structure annealed in 40 s, f = 14.1360. Structure annealed in 39 s, f = 14.8262. Structure annealed in 39 s, f = 15.5125. Structure annealed in 39 s, f = 13.9290. Structure annealed in 40 s, f = 16.4311. Structure annealed in 40 s, f = 127.855. Structure annealed in 41 s, f = 333.194. Structure annealed in 39 s, f = 13.5669. Structure annealed in 40 s, f = 16.1967. Structure annealed in 42 s, f = 185.163. Structure annealed in 40 s, f = 20.2563. Structure annealed in 40 s, f = 17.2172. Structure annealed in 39 s, f = 18.6755. Structure annealed in 39 s, f = 11.7761. Structure annealed in 39 s, f = 17.0521. Structure annealed in 39 s, f = 14.2872. Structure annealed in 39 s, f = 15.8826. Structure annealed in 39 s, f = 13.9919. Structure annealed in 39 s, f = 14.2198. Structure annealed in 39 s, f = 18.4778. Structure annealed in 39 s, f = 17.5565. Structure annealed in 41 s, f = 375.163. Structure annealed in 39 s, f = 12.6353. Structure annealed in 39 s, f = 17.4501. Structure annealed in 39 s, f = 13.3511. Structure annealed in 39 s, f = 16.2904. Structure annealed in 39 s, f = 11.2510. Structure annealed in 41 s, f = 306.796. Structure annealed in 40 s, f = 17.7890. Structure annealed in 39 s, f = 13.8832. Structure annealed in 40 s, f = 13.2235. Structure annealed in 39 s, f = 11.1998. Structure annealed in 39 s, f = 14.1458. Structure annealed in 39 s, f = 13.4851. Structure annealed in 39 s, f = 17.6684. Structure annealed in 39 s, f = 11.8463. Structure annealed in 39 s, f = 19.4259. Structure annealed in 39 s, f = 14.1481. Structure annealed in 40 s, f = 11.7126. Structure annealed in 39 s, f = 14.7059. Structure annealed in 40 s, f = 15.3797. Structure annealed in 39 s, f = 11.8121. Structure annealed in 39 s, f = 16.5243. Structure annealed in 40 s, f = 13.9161. Structure annealed in 39 s, f = 13.4658. Structure annealed in 39 s, f = 16.4204. Structure annealed in 40 s, f = 12.2268. Structure annealed in 41 s, f = 180.015. Structure annealed in 40 s, f = 17.6484. Structure annealed in 39 s, f = 20.1272. Structure annealed in 40 s, f = 33.2034. Structure annealed in 39 s, f = 15.7302. Structure annealed in 39 s, f = 21.7029. Structure annealed in 40 s, f = 12.7985. Structure annealed in 38 s, f = 16.2917. Structure annealed in 39 s, f = 14.7810. Structure annealed in 38 s, f = 12.5204. Structure annealed in 38 s, f = 13.0822. 100 structures finished in 183 s (1 s/structure). - znf42: overview znf42.ovw structures=20 pdb Structural statistics: str target upper limits van der Waals torsion angles function # rms max # sum max # rms max 1 11.20 35 0.0282 1.00 10 16.4 0.25 1 0.8517 5.61 2 11.25 34 0.0285 0.99 8 16.6 0.29 0 0.8622 4.05 3 11.56 32 0.0279 0.98 6 15.8 0.25 1 0.9206 5.79 4 11.64 39 0.0296 0.99 9 16.8 0.28 2 0.9100 5.53 5 11.71 34 0.0281 0.99 12 16.3 0.30 0 0.8078 4.52 6 11.78 35 0.0282 1.00 9 17.7 0.35 1 0.9073 5.79 7 11.81 40 0.0293 0.99 13 18.7 0.30 1 0.8866 5.71 8 11.85 33 0.0278 1.00 9 18.4 0.26 2 0.9559 6.02 9 11.90 34 0.0286 0.99 9 16.0 0.27 0 0.8820 4.93 10 12.23 35 0.0307 1.03 6 17.0 0.23 1 0.8076 7.16 11 12.30 35 0.0285 1.00 8 17.4 0.26 0 0.7862 4.59 12 12.50 34 0.0291 0.99 11 17.0 0.30 2 0.9217 6.02 13 12.52 35 0.0292 0.99 8 17.4 0.30 2 0.8834 5.62 14 12.58 36 0.0284 0.99 12 17.8 0.28 0 0.8567 4.44 15 12.63 38 0.0285 0.99 13 17.1 0.26 2 0.9473 5.79 16 12.64 39 0.0301 1.00 9 16.4 0.24 0 0.9009 4.87 17 12.65 39 0.0301 1.00 8 18.5 0.24 2 0.9614 5.62 18 12.79 40 0.0304 0.99 9 17.0 0.28 0 0.8734 4.72 19 12.80 38 0.0301 0.99 9 16.6 0.23 0 0.8421 4.45 20 12.85 43 0.0314 1.00 10 16.6 0.30 0 0.8221 4.39 Ave 12.16 36 0.0291 1.00 9 17.1 0.27 1 0.8793 5.28 +/- 0.52 3 0.0010 0.01 2 0.8 0.03 1 0.0491 0.75 Min 11.20 32 0.0278 0.98 6 15.8 0.23 0 0.7862 4.05 Max 12.85 43 0.0314 1.03 13 18.7 0.35 2 0.9614 7.16 Cut 0.20 0.20 5.00 Overview file "znf42.ovw" written. PDB coordinate file "znf42.pdb" written, 20 conformers. - znf42: ramaplot znf42.rama nobackground label Struct fav add gen dis ------ --- --- --- --- 1 132 18 2 0 2 134 14 4 0 3 136 16 0 0 4 143 9 0 0 5 138 14 0 0 6 141 11 0 0 7 138 14 0 0 8 137 15 0 0 9 133 19 0 0 10 137 13 0 2 (ASP 37, ASP 337) 11 139 13 0 0 12 134 17 1 0 13 137 14 1 0 14 132 18 2 0 15 143 9 0 0 16 138 12 2 0 17 140 12 0 0 18 134 16 2 0 19 134 18 0 0 20 141 11 0 0 all 90.2% 9.3% 0.5% 0.1% Postscript file "znf42.rama" written. cyana> LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 29-Nov-2005 17:54:31