Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 11-Nov-2005 17:44:32 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node4.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node3.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node2.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... done ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/s/src/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, 1292 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, 1292 peaks, 1090 assignments. - calibration: peaks select "** list=2" 1292 of 4795 peaks, 1292 of 4795 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1292 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1292 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: 357 27.6% 6.00- A: 0 0.0% All: 1292 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 5076 peaks, 281 of 5076 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 5303 peaks, 227 of 5303 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 ** 5303 of 5303 peaks, 5303 of 5303 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 /s/src/cyana-2.1/lib/cyana.lib Library file "/s/src/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 134 s, f = 8.77890. Structure annealed in 132 s, f = 11.9470. Structure annealed in 133 s, f = 12.8958. Structure annealed in 133 s, f = 10.8891. Structure annealed in 136 s, f = 12.5126. Structure annealed in 135 s, f = 11.9325. Structure annealed in 138 s, f = 9.04930. Structure annealed in 139 s, f = 12.7136. Structure annealed in 113 s, f = 70.7526. Structure annealed in 125 s, f = 13.0003. Structure annealed in 130 s, f = 13.2975. Structure annealed in 132 s, f = 10.2586. Structure annealed in 108 s, f = 18.4591. Structure annealed in 131 s, f = 16.0729. Structure annealed in 135 s, f = 6.88038. Structure annealed in 131 s, f = 9.04086. Structure annealed in 133 s, f = 16.7890. Structure annealed in 131 s, f = 11.5334. Structure annealed in 132 s, f = 9.68782. Structure annealed in 127 s, f = 19.9301. Structure annealed in 138 s, f = 8.72777. Structure annealed in 136 s, f = 30.9106. Structure annealed in 139 s, f = 14.9721. Structure annealed in 121 s, f = 12.0524. Structure annealed in 114 s, f = 10.9535. Structure annealed in 132 s, f = 9.43388. Structure annealed in 128 s, f = 13.1990. Structure annealed in 131 s, f = 12.8448. Structure annealed in 131 s, f = 14.0085. Structure annealed in 133 s, f = 10.3567. Structure annealed in 132 s, f = 8.69129. Structure annealed in 135 s, f = 16.0553. Structure annealed in 136 s, f = 12.7030. Structure annealed in 135 s, f = 10.0622. Structure annealed in 139 s, f = 8.36058. Structure annealed in 110 s, f = 11.6540. Structure annealed in 127 s, f = 11.2098. Structure annealed in 132 s, f = 9.16714. Structure annealed in 132 s, f = 13.3497. Structure annealed in 131 s, f = 10.4778. Structure annealed in 134 s, f = 13.2375. Structure annealed in 132 s, f = 14.5775. Structure annealed in 131 s, f = 9.08292. Structure annealed in 135 s, f = 10.4424. Structure annealed in 137 s, f = 21.4459. Structure annealed in 137 s, f = 13.9104. Structure annealed in 123 s, f = 180.097. Structure annealed in 112 s, f = 10.4826. Structure annealed in 129 s, f = 18.3091. Structure annealed in 133 s, f = 75.3863. Structure annealed in 133 s, f = 10.8086. Structure annealed in 131 s, f = 8.45432. Structure annealed in 130 s, f = 8.71836. Structure annealed in 136 s, f = 14.2711. Structure annealed in 133 s, f = 15.8738. Structure annealed in 135 s, f = 8.46771. Structure annealed in 136 s, f = 9.16254. Structure annealed in 139 s, f = 21.4320. Structure annealed in 104 s, f = 9.34667. Structure annealed in 129 s, f = 10.7329. Structure annealed in 97 s, f = 9.95652. Structure annealed in 132 s, f = 9.58469. Structure annealed in 131 s, f = 16.4263. Structure annealed in 132 s, f = 10.2586. Structure annealed in 132 s, f = 12.3851. Structure annealed in 139 s, f = 12.2543. Structure annealed in 138 s, f = 17.9762. Structure annealed in 134 s, f = 9.44496. Structure annealed in 132 s, f = 11.9918. Structure annealed in 139 s, f = 11.4506. Structure annealed in 128 s, f = 18.9896. Structure annealed in 130 s, f = 22.0001. Structure annealed in 134 s, f = 8.48539. Structure annealed in 137 s, f = 12.9220. Structure annealed in 130 s, f = 9.46303. Structure annealed in 151 s, f = 24.1923. Structure annealed in 153 s, f = 7.79763. Structure annealed in 134 s, f = 8.50200. Structure annealed in 95 s, f = 11.5838. Structure annealed in 133 s, f = 15.3310. Structure annealed in 139 s, f = 12.8239. Structure annealed in 98 s, f = 12.7243. Structure annealed in 130 s, f = 16.5491. Structure annealed in 133 s, f = 13.2870. Structure annealed in 132 s, f = 13.5638. Structure annealed in 127 s, f = 12.5153. Structure annealed in 134 s, f = 7.97013. Structure annealed in 136 s, f = 10.5901. Structure annealed in 134 s, f = 12.3214. Structure annealed in 158 s, f = 8.96536. Structure annealed in 157 s, f = 14.5551. Structure annealed in 131 s, f = 10.2399. Structure annealed in 99 s, f = 10.3997. Structure annealed in 127 s, f = 9.43712. Structure annealed in 99 s, f = 11.1981. Structure annealed in 134 s, f = 10.8587. Structure annealed in 132 s, f = 11.0091. Structure annealed in 125 s, f = 10.9520. Structure annealed in 132 s, f = 88.4623. Structure annealed in 129 s, f = 11.0031. 100 structures finished in 1232 s (12 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 6.88 26 0.0205 0.56 5 13.9 0.23 0 0.8245 3.94 2 7.80 23 0.0231 0.63 6 14.4 0.25 0 0.8746 4.93 3 7.97 22 0.0221 0.69 8 14.5 0.29 2 0.8673 5.38 4 8.36 28 0.0223 0.57 5 14.1 0.27 0 0.8547 4.08 5 8.45 23 0.0217 0.58 8 15.4 0.28 0 0.7765 4.86 6 8.47 31 0.0240 0.73 4 14.9 0.27 0 0.8104 4.44 7 8.49 29 0.0226 0.59 4 14.4 0.22 0 0.8159 4.23 8 8.50 32 0.0244 0.76 1 14.7 0.22 1 0.8252 5.95 9 8.69 31 0.0232 0.70 6 16.0 0.37 0 0.9430 4.15 10 8.72 28 0.0227 0.67 8 16.6 0.34 1 0.9426 6.34 11 8.73 26 0.0225 0.64 4 15.7 0.29 0 0.8612 4.05 12 8.78 23 0.0226 0.83 5 15.7 0.33 1 0.8938 5.31 13 8.97 21 0.0250 1.18 4 14.4 0.25 1 0.7865 5.63 14 9.04 25 0.0223 0.61 8 16.5 0.27 3 1.0277 6.04 15 9.05 22 0.0225 0.56 9 16.5 0.32 0 0.9568 4.26 16 9.08 22 0.0218 0.60 7 14.9 0.34 2 0.8733 6.21 17 9.16 23 0.0221 0.69 8 16.1 0.33 0 0.8834 4.69 18 9.17 28 0.0234 0.57 7 16.8 0.25 0 0.8797 4.69 19 9.35 24 0.0240 0.69 5 15.2 0.22 0 0.9797 4.91 20 9.43 24 0.0229 0.72 6 14.9 0.33 2 0.8852 5.63 Ave 8.65 26 0.0228 0.68 6 15.3 0.28 1 0.8781 4.99 +/- 0.58 3 0.0010 0.14 2 0.9 0.05 1 0.0638 0.76 Min 6.88 21 0.0205 0.56 1 13.9 0.22 0 0.7765 3.94 Max 9.43 32 0.0250 1.18 9 16.8 0.37 3 1.0277 6.34 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 ------ --- --- --- --- 1 137 15 0 0 2 139 13 0 0 3 142 10 0 0 4 137 13 2 0 5 134 18 0 0 6 140 12 0 0 7 139 13 0 0 8 139 12 1 0 9 136 14 2 0 10 138 12 2 0 11 137 15 0 0 12 135 17 0 0 13 140 10 0 2 (SER 36, SER 336) 14 134 16 0 2 (ARG 124, ARG 424) 15 136 14 2 0 16 134 14 2 2 (SER 36, SER 336) 17 137 13 0 2 (ARG 124, ARG 424) 18 137 15 0 0 19 139 13 0 0 20 137 15 0 0 all 90.4% 9.0% 0.4% 0.3% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 11-Nov-2005 18:06:39