Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 23-Nov-2005 17:03:14 n-1<10756> ssi:boot:base:linear: booting n0 (wolf01) n-1<10756> ssi:boot:base:linear: booting n1 (wolf02) n-1<10756> ssi:boot:base:linear: booting n2 (wolf03) n-1<10756> ssi:boot:base:linear: booting n3 (wolf04) n-1<10756> ssi:boot:base:linear: booting n4 (wolf05) n-1<10756> ssi:boot:base:linear: booting n5 (wolf06) n-1<10756> ssi:boot:base:linear: booting n6 (wolf07) n-1<10756> ssi:boot:base:linear: booting n7 (wolf08) n-1<10756> ssi:boot:base:linear: booting n8 (wolf09) n-1<10756> ssi:boot:base:linear: booting n9 (wolf10) n-1<10756> ssi:boot:base:linear: booting n10 (wolf11) n-1<10756> ssi:boot:base:linear: booting n11 (wolf12) n-1<10756> ssi:boot:base:linear: booting n12 (wolf13) n-1<10756> 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, 3503 peaks, 2971 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 2971 0.000 0.002 0.030 0.009 0 0.030 2 3321 0.000 0.000 0.029 0.003 0 0.030 3 3321 0.000 0.000 0.297 0.031 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 : 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, 1291 peaks, 1090 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1090 0.002 0.002 0.030 0.011 0 0.030 2 1225 0.000 0.000 0.011 0.001 0 0.030 3 1225 0.000 0.000 0.234 0.016 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 : 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, 3503 peaks, 2971 assignments. - calibration: peaks select "** list=1" 3503 of 3503 peaks, 3503 of 3503 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3503 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3503 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 326 9.3% 3.00-3.99 A: 771 22.0% 4.00-4.99 A: 1391 39.7% 5.00-5.99 A: 1013 28.9% 6.00- A: 0 0.0% All: 3503 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, 1291 peaks, 1090 assignments. - calibration: peaks select "** list=2" 1291 of 4794 peaks, 1291 of 4794 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1291 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1291 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.2% 3.00-3.99 A: 340 26.3% 4.00-4.99 A: 500 38.7% 5.00-5.99 A: 356 27.6% 6.00- A: 0 0.0% All: 1291 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 5075 peaks, 281 of 5075 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 5302 peaks, 227 of 5302 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 ** 5302 of 5302 peaks, 5302 of 5302 assignments selected. - znf42: peaks calibrate ** simple 3974 upper limits added, 9/469 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3974 upper limits, 3974 assignments. - znf42: distance modify Number of modified constraints: 2083 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2083 upper limits, 2083 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, 2083 upper limits, 2083 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 40 s, f = 10.0020. Structure annealed in 39 s, f = 13.2622. Structure annealed in 40 s, f = 59.8795. Structure annealed in 39 s, f = 12.3265. Structure annealed in 40 s, f = 9.94692. Structure annealed in 42 s, f = 341.425. Structure annealed in 40 s, f = 11.7942. Structure annealed in 39 s, f = 11.2485. Structure annealed in 39 s, f = 13.5599. Structure annealed in 39 s, f = 7.51998. Structure annealed in 39 s, f = 11.7412. Structure annealed in 40 s, f = 24.9596. Structure annealed in 40 s, f = 10.2842. Structure annealed in 39 s, f = 9.85615. Structure annealed in 40 s, f = 189.918. Structure annealed in 39 s, f = 8.22235. Structure annealed in 40 s, f = 25.9298. Structure annealed in 42 s, f = 201.208. Structure annealed in 39 s, f = 14.8750. Structure annealed in 39 s, f = 16.7091. Structure annealed in 39 s, f = 8.96718. Structure annealed in 39 s, f = 13.6456. Structure annealed in 39 s, f = 10.1892. Structure annealed in 39 s, f = 10.1143. Structure annealed in 40 s, f = 9.28002. Structure annealed in 39 s, f = 12.6768. Structure annealed in 39 s, f = 10.8904. Structure annealed in 39 s, f = 9.41730. Structure annealed in 39 s, f = 14.5952. Structure annealed in 39 s, f = 11.5637. Structure annealed in 39 s, f = 20.4527. Structure annealed in 39 s, f = 8.32761. Structure annealed in 39 s, f = 13.0432. Structure annealed in 39 s, f = 9.25839. Structure annealed in 39 s, f = 16.5308. Structure annealed in 39 s, f = 12.5678. Structure annealed in 39 s, f = 9.05555. Structure annealed in 39 s, f = 14.0533. Structure annealed in 39 s, f = 13.8414. Structure annealed in 40 s, f = 15.2138. Structure annealed in 41 s, f = 322.229. Structure annealed in 39 s, f = 12.6330. Structure annealed in 39 s, f = 20.5265. Structure annealed in 39 s, f = 10.9460. Structure annealed in 39 s, f = 9.39489. Structure annealed in 40 s, f = 12.7111. Structure annealed in 39 s, f = 10.9225. Structure annealed in 39 s, f = 18.8683. Structure annealed in 39 s, f = 10.6105. Structure annealed in 39 s, f = 11.0567. Structure annealed in 39 s, f = 11.0460. Structure annealed in 39 s, f = 10.6553. Structure annealed in 39 s, f = 26.3398. Structure annealed in 39 s, f = 10.4907. Structure annealed in 39 s, f = 11.0762. Structure annealed in 39 s, f = 13.8900. Structure annealed in 40 s, f = 24.2093. Structure annealed in 39 s, f = 10.4826. Structure annealed in 39 s, f = 9.93128. Structure annealed in 40 s, f = 10.0279. Structure annealed in 39 s, f = 14.0655. Structure annealed in 39 s, f = 12.0320. Structure annealed in 39 s, f = 9.79485. Structure annealed in 40 s, f = 11.0071. Structure annealed in 39 s, f = 17.0516. Structure annealed in 39 s, f = 14.0996. Structure annealed in 39 s, f = 10.5944. Structure annealed in 40 s, f = 11.6291. Structure annealed in 39 s, f = 8.93557. Structure annealed in 40 s, f = 11.8958. Structure annealed in 40 s, f = 14.3970. Structure annealed in 39 s, f = 13.9769. Structure annealed in 39 s, f = 10.9407. Structure annealed in 40 s, f = 30.0533. Structure annealed in 39 s, f = 10.7348. Structure annealed in 39 s, f = 8.94925. Structure annealed in 39 s, f = 9.08131. Structure annealed in 39 s, f = 12.2638. Structure annealed in 39 s, f = 8.99097. Structure annealed in 41 s, f = 178.927. Structure annealed in 39 s, f = 11.4351. Structure annealed in 39 s, f = 10.3861. Structure annealed in 39 s, f = 12.7472. Structure annealed in 39 s, f = 9.17556. Structure annealed in 39 s, f = 27.5181. Structure annealed in 40 s, f = 12.0178. Structure annealed in 39 s, f = 20.9054. Structure annealed in 39 s, f = 10.5450. Structure annealed in 39 s, f = 9.86326. Structure annealed in 39 s, f = 9.73999. Structure annealed in 39 s, f = 9.69388. Structure annealed in 40 s, f = 10.3402. Structure annealed in 40 s, f = 8.58830. Structure annealed in 39 s, f = 29.1334. Structure annealed in 39 s, f = 14.0784. Structure annealed in 39 s, f = 13.7935. Structure annealed in 39 s, f = 9.95280. Structure annealed in 40 s, f = 120.654. Structure annealed in 40 s, f = 13.4763. Structure annealed in 39 s, f = 48.2690. 100 structures finished in 165 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 7.52 24 0.0222 0.61 5 14.2 0.28 0 0.8683 4.44 2 8.22 29 0.0224 0.58 8 15.9 0.25 1 0.8662 5.26 3 8.33 28 0.0230 0.72 8 15.4 0.35 0 0.8410 4.90 4 8.59 27 0.0238 0.58 7 15.2 0.24 0 0.9007 4.93 5 8.94 25 0.0222 0.58 6 15.4 0.28 0 0.8821 4.98 6 8.95 21 0.0215 0.59 8 16.0 0.24 0 0.8990 4.32 7 8.97 26 0.0225 0.66 5 15.8 0.24 2 0.8557 5.64 8 8.99 23 0.0226 0.75 5 16.9 0.30 0 0.9211 4.97 9 9.06 23 0.0247 0.88 6 16.3 0.31 1 0.8305 5.00 10 9.08 27 0.0229 0.71 10 16.6 0.29 2 0.9070 6.01 11 9.18 32 0.0246 0.68 6 16.7 0.23 3 1.0570 6.90 12 9.26 34 0.0240 0.63 9 17.5 0.33 2 1.0746 6.12 13 9.28 25 0.0223 0.69 9 16.7 0.31 2 0.9696 5.38 14 9.40 28 0.0238 0.73 6 14.7 0.26 2 0.8626 6.91 15 9.42 28 0.0228 0.61 7 15.6 0.26 0 0.7906 4.14 16 9.69 26 0.0235 0.60 8 16.7 0.45 2 1.1013 8.07 17 9.74 31 0.0232 0.64 6 16.9 0.26 0 0.9110 4.47 18 9.80 24 0.0244 0.92 8 16.0 0.34 1 0.8481 5.16 19 9.86 23 0.0231 0.66 5 14.5 0.30 0 0.8159 4.06 20 9.86 33 0.0250 0.55 6 16.5 0.23 0 1.0099 4.84 Ave 9.11 27 0.0232 0.67 7 16.0 0.29 1 0.9106 5.33 +/- 0.59 3 0.0009 0.10 1 0.9 0.05 1 0.0857 1.00 Min 7.52 21 0.0215 0.55 5 14.2 0.23 0 0.7906 4.06 Max 9.86 34 0.0250 0.92 10 17.5 0.45 3 1.1013 8.07 Cut 0.20 0.20 5.00 Overview file "znf42.ovw" written. PDB coordinate file "znf42.pdb" written, 20 conformers. cyana> LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 23-Nov-2005 17:06:29