Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 11-Nov-2005 13:14:03 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node11.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= *** WARNING: Inconsistent heavy atom assignment for peak 1409. Peak list "c13no.peaks" read, 3503 peaks, 2974 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 2974 0.000 0.002 0.030 0.009 0 0.030 2 3321 0.000 0.000 0.293 0.006 1 0.030 3 3321 0.000 0.002 7.725 0.138 1 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks CB GLU 99 28.966 28.966 7.725 6 QB GLU 99 2.045 2.045 0.293 9 2 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1409 2 0.293 QB GLU 99 1409 3 7.725 CB GLU 99 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, 1292 peaks, 1081 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1081 0.002 0.002 0.030 0.011 0 0.030 2 1222 0.000 0.000 0.011 0.001 0 0.030 3 1222 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= *** WARNING: Inconsistent heavy atom assignment for peak 1409. Peak list "c13no.peaks" read, 3503 peaks, 2974 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, 1081 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: 499 38.6% 5.00-5.99 A: 358 27.7% 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 3969 upper limits added, 10/470 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3969 upper limits, 3969 assignments. - znf42: distance modify Number of modified constraints: 2084 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2084 upper limits, 2084 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, 2084 upper limits, 2084 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 135 s, f = 20.1146. Structure annealed in 135 s, f = 17.7026. Structure annealed in 133 s, f = 18.1261. Structure annealed in 134 s, f = 25.3393. Structure annealed in 135 s, f = 18.6864. Structure annealed in 130 s, f = 19.5199. Structure annealed in 137 s, f = 21.4213. Structure annealed in 136 s, f = 22.6862. Structure annealed in 99 s, f = 20.0888. Structure annealed in 99 s, f = 17.1143. Structure annealed in 132 s, f = 22.7806. Structure annealed in 130 s, f = 17.2449. Structure annealed in 131 s, f = 15.9163. Structure annealed in 133 s, f = 20.8405. Structure annealed in 131 s, f = 20.6959. Structure annealed in 132 s, f = 21.4556. Structure annealed in 137 s, f = 186.727. Structure annealed in 135 s, f = 25.0771. Structure annealed in 134 s, f = 21.2438. Structure annealed in 134 s, f = 18.4800. Structure annealed in 138 s, f = 36.1082. Structure annealed in 137 s, f = 30.7617. Structure annealed in 99 s, f = 20.5788. Structure annealed in 95 s, f = 31.0034. Structure annealed in 128 s, f = 28.7117. Structure annealed in 130 s, f = 43.5809. Structure annealed in 134 s, f = 17.6616. Structure annealed in 139 s, f = 400.355. Structure annealed in 126 s, f = 17.4379. Structure annealed in 132 s, f = 17.4151. Structure annealed in 136 s, f = 24.5248. Structure annealed in 133 s, f = 22.0532. Structure annealed in 145 s, f = 204.450. Structure annealed in 133 s, f = 18.5773. Structure annealed in 131 s, f = 15.7661. Structure annealed in 99 s, f = 19.2532. Structure annealed in 125 s, f = 19.0247. Structure annealed in 98 s, f = 21.3403. Structure annealed in 129 s, f = 23.2576. Structure annealed in 135 s, f = 17.6557. Structure annealed in 136 s, f = 18.8224. Structure annealed in 133 s, f = 126.463. Structure annealed in 132 s, f = 24.5145. Structure annealed in 135 s, f = 20.3831. Structure annealed in 133 s, f = 18.9266. Structure annealed in 137 s, f = 21.6196. Structure annealed in 128 s, f = 18.6721. Structure annealed in 128 s, f = 65.6931. Structure annealed in 130 s, f = 21.8919. Structure annealed in 133 s, f = 33.7719. Structure annealed in 131 s, f = 22.3857. Structure annealed in 136 s, f = 101.231. Structure annealed in 137 s, f = 23.7496. Structure annealed in 136 s, f = 17.6441. Structure annealed in 135 s, f = 25.0742. Structure annealed in 135 s, f = 22.3872. Structure annealed in 95 s, f = 35.9043. Structure annealed in 98 s, f = 33.9807. Structure annealed in 130 s, f = 17.8457. Structure annealed in 132 s, f = 29.6404. Structure annealed in 135 s, f = 28.9953. Structure annealed in 132 s, f = 16.8509. Structure annealed in 140 s, f = 22.3561. Structure annealed in 138 s, f = 21.4060. Structure annealed in 134 s, f = 24.4005. Structure annealed in 141 s, f = 357.180. Structure annealed in 134 s, f = 18.9743. Structure annealed in 136 s, f = 18.3854. Structure annealed in 129 s, f = 16.6591. Structure annealed in 131 s, f = 28.0187. Structure annealed in 99 s, f = 19.3187. Structure annealed in 99 s, f = 20.8374. Structure annealed in 134 s, f = 18.2873. Structure annealed in 136 s, f = 20.0837. Structure annealed in 129 s, f = 21.3078. Structure annealed in 153 s, f = 19.9291. Structure annealed in 135 s, f = 24.0231. Structure annealed in 153 s, f = 17.7625. Structure annealed in 137 s, f = 27.8254. Structure annealed in 134 s, f = 19.0895. Structure annealed in 131 s, f = 54.7696. Structure annealed in 132 s, f = 20.2310. Structure annealed in 135 s, f = 18.2551. Structure annealed in 135 s, f = 22.1050. Structure annealed in 135 s, f = 18.9706. Structure annealed in 133 s, f = 21.8325. Structure annealed in 137 s, f = 17.9057. Structure annealed in 132 s, f = 24.8956. Structure annealed in 159 s, f = 18.4537. Structure annealed in 156 s, f = 20.2000. Structure annealed in 92 s, f = 20.7170. Structure annealed in 99 s, f = 23.3862. Structure annealed in 131 s, f = 17.8118. Structure annealed in 129 s, f = 34.1394. Structure annealed in 136 s, f = 63.4288. Structure annealed in 134 s, f = 18.2702. Structure annealed in 131 s, f = 19.1982. Structure annealed in 129 s, f = 33.0478. Structure annealed in 138 s, f = 19.3024. Structure annealed in 130 s, f = 19.6278. 100 structures finished in 1238 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 15.77 38 0.0337 1.17 11 19.4 0.30 5 1.5004 13.91 2 15.92 41 0.0331 0.82 9 21.2 0.31 5 1.7039 17.02 3 16.66 44 0.0348 1.20 9 20.4 0.34 5 1.4206 10.64 4 16.85 50 0.0346 0.89 10 22.2 0.31 4 1.6467 15.92 5 17.11 48 0.0365 1.19 10 18.1 0.30 7 1.4587 9.55 6 17.25 38 0.0354 1.27 9 20.3 0.32 6 1.4885 11.84 7 17.42 52 0.0350 0.89 9 22.4 0.34 7 1.6469 13.31 8 17.44 49 0.0340 0.82 10 21.9 0.48 3 1.5424 14.61 9 17.64 46 0.0356 1.21 11 21.3 0.29 5 1.5240 11.50 10 17.66 56 0.0348 0.88 9 23.0 0.29 5 1.6031 13.80 11 17.66 54 0.0346 0.92 7 20.8 0.30 3 1.6265 16.07 12 17.70 44 0.0365 1.17 9 19.5 0.28 5 1.4296 10.12 13 17.76 41 0.0357 1.44 10 21.8 0.42 6 1.5592 11.03 14 17.81 44 0.0362 1.23 10 19.2 0.30 5 1.4746 10.12 15 17.85 46 0.0360 1.24 15 21.1 0.33 8 1.6037 12.37 16 17.91 42 0.0357 1.28 16 21.6 0.42 5 1.6414 11.24 17 18.13 40 0.0363 1.25 9 22.8 0.44 6 1.6144 11.51 18 18.26 42 0.0358 1.26 14 21.9 0.33 7 1.7281 13.18 19 18.27 50 0.0349 0.82 13 22.1 0.48 3 1.5018 13.48 20 18.29 47 0.0356 1.24 13 22.8 0.32 6 1.5531 11.57 Ave 17.47 46 0.0353 1.11 11 21.2 0.34 5 1.5634 12.64 +/- 0.69 5 0.0009 0.19 2 1.3 0.06 1 0.0864 2.07 Min 15.77 38 0.0331 0.82 7 18.1 0.28 3 1.4206 9.55 Max 18.29 56 0.0365 1.44 16 23.0 0.48 8 1.7281 17.02 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 ------ --- --- --- --- 1 138 14 0 0 2 136 16 0 0 3 139 12 1 0 4 138 14 0 0 5 141 9 2 0 6 139 13 0 0 7 135 16 1 0 8 138 14 0 0 9 131 21 0 0 10 132 19 1 0 11 138 13 1 0 12 138 14 0 0 13 138 12 2 0 14 136 15 1 0 15 138 14 0 0 16 136 14 0 2 (SER 36, SER 336) 17 138 14 0 0 18 139 12 1 0 19 136 14 2 0 20 142 10 0 0 all 90.3% 9.2% 0.4% 0.1% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 11-Nov-2005 13:36:17