Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 15-Nov-2005 16:16:49 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node13.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node12.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node11.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node10.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node9.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node8.biochem.wisc.edu - 2 CPUs)... Executing hboot on n6 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n7 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n8 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n9 (cesg-node4.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... n6... n7... n8... n9... 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, 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 /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 130 s, f = 13.0145. Structure annealed in 133 s, f = 13.8811. Structure annealed in 130 s, f = 10.4030. Structure annealed in 133 s, f = 11.9622. Structure annealed in 134 s, f = 64.6065. Structure annealed in 132 s, f = 12.9537. Structure annealed in 137 s, f = 47.3596. Structure annealed in 131 s, f = 18.5469. Structure annealed in 131 s, f = 9.37430. Structure annealed in 138 s, f = 395.126. Structure annealed in 125 s, f = 8.89256. Structure annealed in 110 s, f = 8.59678. Structure annealed in 133 s, f = 9.75939. Structure annealed in 124 s, f = 9.03987. Structure annealed in 132 s, f = 24.4631. Structure annealed in 130 s, f = 9.52508. Structure annealed in 131 s, f = 13.4942. Structure annealed in 136 s, f = 11.7788. Structure annealed in 131 s, f = 9.94932. Structure annealed in 134 s, f = 12.0361. Structure annealed in 111 s, f = 9.18044. Structure annealed in 130 s, f = 11.5075. Structure annealed in 131 s, f = 10.3231. Structure annealed in 131 s, f = 10.7333. Structure annealed in 133 s, f = 11.7397. Structure annealed in 129 s, f = 10.4091. Structure annealed in 134 s, f = 8.76950. Structure annealed in 129 s, f = 24.8153. Structure annealed in 133 s, f = 23.2936. Structure annealed in 131 s, f = 10.0336. Structure annealed in 135 s, f = 15.4500. Structure annealed in 132 s, f = 12.0864. Structure annealed in 130 s, f = 10.2660. Structure annealed in 131 s, f = 11.8247. Structure annealed in 139 s, f = 332.331. Structure annealed in 132 s, f = 10.4845. Structure annealed in 129 s, f = 10.3282. Structure annealed in 136 s, f = 12.6282. Structure annealed in 135 s, f = 14.6937. Structure annealed in 119 s, f = 15.6890. Structure annealed in 106 s, f = 14.3616. Structure annealed in 129 s, f = 12.6040. Structure annealed in 135 s, f = 20.5763. Structure annealed in 133 s, f = 8.70991. Structure annealed in 132 s, f = 9.23464. Structure annealed in 131 s, f = 13.2506. Structure annealed in 132 s, f = 14.9690. Structure annealed in 131 s, f = 13.2889. Structure annealed in 130 s, f = 9.68113. Structure annealed in 133 s, f = 14.5673. Structure annealed in 135 s, f = 15.5961. Structure annealed in 129 s, f = 22.7126. Structure annealed in 134 s, f = 16.8139. Structure annealed in 131 s, f = 9.58832. Structure annealed in 129 s, f = 16.5729. Structure annealed in 134 s, f = 10.8979. Structure annealed in 134 s, f = 22.7603. Structure annealed in 137 s, f = 14.9705. Structure annealed in 137 s, f = 10.2741. Structure annealed in 108 s, f = 9.63412. Structure annealed in 129 s, f = 13.2601. Structure annealed in 139 s, f = 327.002. Structure annealed in 131 s, f = 13.2842. Structure annealed in 134 s, f = 11.3213. Structure annealed in 128 s, f = 11.4152. Structure annealed in 132 s, f = 14.4787. Structure annealed in 132 s, f = 14.4535. Structure annealed in 133 s, f = 12.6575. Structure annealed in 128 s, f = 9.38282. Structure annealed in 133 s, f = 9.13325. Structure annealed in 137 s, f = 209.371. Structure annealed in 137 s, f = 25.5584. Structure annealed in 125 s, f = 15.3416. Structure annealed in 134 s, f = 12.1329. Structure annealed in 129 s, f = 9.78487. Structure annealed in 132 s, f = 9.60126. Structure annealed in 135 s, f = 12.5939. Structure annealed in 133 s, f = 9.41887. Structure annealed in 125 s, f = 8.43824. Structure annealed in 113 s, f = 30.8741. Structure annealed in 130 s, f = 9.89978. Structure annealed in 132 s, f = 10.9931. Structure annealed in 133 s, f = 9.96506. Structure annealed in 130 s, f = 23.1895. Structure annealed in 132 s, f = 11.2441. Structure annealed in 136 s, f = 337.108. Structure annealed in 128 s, f = 19.3131. Structure annealed in 133 s, f = 10.1388. Structure annealed in 133 s, f = 23.8872. Structure annealed in 131 s, f = 12.0009. Structure annealed in 132 s, f = 13.5157. Structure annealed in 134 s, f = 11.1901. Structure annealed in 132 s, f = 10.9718. Structure annealed in 129 s, f = 26.0309. Structure annealed in 128 s, f = 11.7265. Structure annealed in 139 s, f = 316.720. Structure annealed in 131 s, f = 12.8343. Structure annealed in 129 s, f = 9.36261. Structure annealed in 105 s, f = 11.7605. Structure annealed in 104 s, f = 11.6394. 100 structures finished in 758 s (7 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 8.44 31 0.0241 0.71 7 14.2 0.26 0 0.8275 4.73 2 8.60 27 0.0230 0.76 6 14.6 0.35 0 0.8640 4.02 3 8.71 26 0.0243 0.70 3 15.0 0.23 0 0.8401 4.55 4 8.77 20 0.0228 0.76 7 15.3 0.30 0 0.7839 3.62 5 8.89 24 0.0232 0.72 4 14.6 0.31 0 0.8784 4.67 6 9.04 25 0.0214 0.60 7 15.8 0.24 1 1.0141 5.67 7 9.13 25 0.0246 0.70 6 15.4 0.31 1 0.9862 5.06 8 9.18 22 0.0227 0.64 7 16.6 0.29 2 1.0045 5.89 9 9.23 27 0.0240 0.67 9 16.5 0.25 0 1.0030 4.70 10 9.36 26 0.0228 0.75 4 15.3 0.23 1 0.8424 5.55 11 9.37 31 0.0232 0.69 5 16.5 0.31 2 1.0037 5.44 12 9.38 26 0.0230 0.62 6 15.9 0.22 1 1.0415 5.34 13 9.42 23 0.0232 0.60 5 15.0 0.23 2 1.0270 6.94 14 9.53 28 0.0234 0.62 7 17.1 0.23 1 0.8745 5.02 15 9.59 25 0.0229 0.73 6 16.6 0.33 2 0.9766 5.55 16 9.60 31 0.0230 0.53 6 17.2 0.23 2 1.0908 5.81 17 9.63 24 0.0228 0.75 8 15.7 0.27 0 0.8071 3.83 18 9.68 28 0.0253 0.74 6 17.0 0.27 0 0.9273 4.90 19 9.76 29 0.0242 0.60 7 17.2 0.24 0 0.9210 4.46 20 9.78 26 0.0222 0.56 7 17.4 0.30 2 1.0557 6.55 Ave 9.26 26 0.0233 0.67 6 16.0 0.27 1 0.9385 5.12 +/- 0.39 3 0.0009 0.07 1 1.0 0.04 1 0.0905 0.83 Min 8.44 20 0.0214 0.53 3 14.2 0.22 0 0.7839 3.62 Max 9.78 31 0.0253 0.76 9 17.4 0.35 2 1.0908 6.94 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 ------ --- --- --- --- 1 139 13 0 0 2 139 13 0 0 3 136 16 0 0 4 133 17 2 0 5 139 13 0 0 6 141 11 0 0 7 135 15 2 0 8 139 13 0 0 9 134 17 1 0 10 136 14 2 0 11 136 16 0 0 12 132 18 2 0 13 136 16 0 0 14 137 15 0 0 15 136 14 2 0 16 138 12 2 0 17 137 15 0 0 18 136 16 0 0 19 137 15 0 0 20 137 15 0 0 all 89.9% 9.7% 0.4% 0.0% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 15-Nov-2005 16:31:30