Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 09-Nov-2005 18:18:47 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= *** WARNING: Inconsistent heavy atom assignment for peak 1987. *** WARNING: Inconsistent heavy atom assignment for peak 1988. Peak list "c13no.peaks" read, 3520 peaks, 2897 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 2897 0.000 0.002 0.030 0.010 0 0.030 2 3294 0.000 0.000 0.029 0.003 0 0.030 3 3294 0.000 0.005 7.729 0.194 2 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks CB ALA 43 18.284 18.284 7.729 16 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1987 3 7.729 CB ALA 43 1988 3 7.729 CB ALA 43 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, 177 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 177 0.004 0.004 0.030 0.012 0 0.030 2 238 0.000 0.000 0.000 0.000 0 0.030 3 238 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, 225 peaks, 149 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 149 -0.001 -0.001 0.029 0.016 0 0.030 2 155 0.000 0.000 0.014 0.005 0 0.030 3 155 0.000 -0.005 0.297 0.036 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 1987. *** WARNING: Inconsistent heavy atom assignment for peak 1988. Peak list "c13no.peaks" read, 3520 peaks, 2897 assignments. - calibration: peaks select "** list=1" 3520 of 3520 peaks, 3520 of 3520 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3520 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3520 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.4% 3.00-3.99 A: 774 22.0% 4.00-4.99 A: 1393 39.6% 5.00-5.99 A: 1021 29.0% 6.00- A: 0 0.0% All: 3520 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 4812 peaks, 1292 of 4812 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, 177 assignments. - calibration: peaks select "** list=3" 281 of 5093 peaks, 281 of 5093 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: 22 7.8% 3.00-3.99 A: 57 20.3% 4.00-4.99 A: 168 59.8% 5.00-5.99 A: 34 12.1% 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, 225 peaks, 149 assignments. - calibration: peaks select "** list=4" 225 of 5318 peaks, 225 of 5318 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 225 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 225 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 1 0.4% 3.00-3.99 A: 49 21.8% 4.00-4.99 A: 157 69.8% 5.00-5.99 A: 18 8.0% 6.00- A: 0 0.0% All: 225 100.0% - calibration: peaks select ** 5318 of 5318 peaks, 5318 of 5318 assignments selected. - znf42: peaks calibrate ** simple 3861 upper limits added, 9/457 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3861 upper limits, 3861 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HB3 TRP 72 - HZ3 TRP 72 4.57 4.82 6.44 Number of modified constraints: 2008 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2008 upper limits, 2008 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, 2008 upper limits, 2008 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 131 s, f = 6.14055. Structure annealed in 136 s, f = 13.1943. Structure annealed in 135 s, f = 6.69504. Structure annealed in 133 s, f = 7.28578. Structure annealed in 132 s, f = 8.42924. Structure annealed in 134 s, f = 6.08234. Structure annealed in 136 s, f = 7.35539. Structure annealed in 135 s, f = 9.11853. Structure annealed in 131 s, f = 7.17734. Structure annealed in 127 s, f = 7.06193. Structure annealed in 114 s, f = 6.96702. Structure annealed in 113 s, f = 7.62101. Structure annealed in 133 s, f = 8.15489. Structure annealed in 130 s, f = 6.58024. Structure annealed in 134 s, f = 86.4839. Structure annealed in 132 s, f = 11.8177. Structure annealed in 134 s, f = 6.75971. Structure annealed in 133 s, f = 6.79014. Structure annealed in 134 s, f = 6.68034. Structure annealed in 136 s, f = 12.3874. Structure annealed in 100 s, f = 8.78396. Structure annealed in 132 s, f = 19.4373. Structure annealed in 132 s, f = 7.48102. Structure annealed in 129 s, f = 6.08807. Structure annealed in 136 s, f = 14.2309. Structure annealed in 132 s, f = 11.5416. Structure annealed in 131 s, f = 7.75697. Structure annealed in 131 s, f = 8.40573. Structure annealed in 135 s, f = 10.4804. Structure annealed in 135 s, f = 7.76245. Structure annealed in 129 s, f = 9.00662. Structure annealed in 135 s, f = 8.41445. Structure annealed in 136 s, f = 13.2683. Structure annealed in 131 s, f = 6.61444. Structure annealed in 133 s, f = 9.70012. Structure annealed in 136 s, f = 6.45768. Structure annealed in 135 s, f = 11.8933. Structure annealed in 135 s, f = 9.21305. Structure annealed in 133 s, f = 9.14804. Structure annealed in 107 s, f = 12.5060. Structure annealed in 128 s, f = 6.73022. Structure annealed in 130 s, f = 5.84618. Structure annealed in 135 s, f = 6.96538. Structure annealed in 136 s, f = 200.425. Structure annealed in 129 s, f = 9.74430. Structure annealed in 128 s, f = 7.50633. Structure annealed in 127 s, f = 9.71475. Structure annealed in 132 s, f = 5.31330. Structure annealed in 131 s, f = 10.6600. Structure annealed in 132 s, f = 8.06115. Structure annealed in 135 s, f = 8.73000. Structure annealed in 138 s, f = 362.771. Structure annealed in 133 s, f = 13.2879. Structure annealed in 136 s, f = 8.50376. Structure annealed in 134 s, f = 8.96903. Structure annealed in 135 s, f = 7.08778. Structure annealed in 133 s, f = 6.23604. Structure annealed in 134 s, f = 5.92172. Structure annealed in 114 s, f = 11.6190. Structure annealed in 110 s, f = 11.7609. Structure annealed in 130 s, f = 12.5946. Structure annealed in 129 s, f = 7.67982. Structure annealed in 129 s, f = 5.76475. Structure annealed in 129 s, f = 7.19328. Structure annealed in 131 s, f = 7.39981. Structure annealed in 135 s, f = 11.4868. Structure annealed in 129 s, f = 6.71164. Structure annealed in 137 s, f = 11.4539. Structure annealed in 128 s, f = 7.86077. Structure annealed in 131 s, f = 6.87620. Structure annealed in 135 s, f = 8.11764. Structure annealed in 133 s, f = 7.46326. Structure annealed in 132 s, f = 8.86309. Structure annealed in 132 s, f = 13.2832. Structure annealed in 135 s, f = 6.67543. Structure annealed in 128 s, f = 7.08622. Structure annealed in 133 s, f = 7.13296. Structure annealed in 137 s, f = 5.53634. Structure annealed in 94 s, f = 8.32725. Structure annealed in 129 s, f = 10.3779. Structure annealed in 132 s, f = 8.43348. Structure annealed in 129 s, f = 7.81628. Structure annealed in 134 s, f = 13.4108. Structure annealed in 129 s, f = 7.74519. Structure annealed in 128 s, f = 11.3615. Structure annealed in 129 s, f = 380.460. Structure annealed in 129 s, f = 8.57261. Structure annealed in 133 s, f = 371.899. Structure annealed in 132 s, f = 7.32566. Structure annealed in 133 s, f = 12.1150. Structure annealed in 140 s, f = 199.888. Structure annealed in 128 s, f = 10.8102. Structure annealed in 134 s, f = 6.43073. Structure annealed in 134 s, f = 12.1014. Structure annealed in 130 s, f = 7.53996. Structure annealed in 135 s, f = 6.84439. Structure annealed in 132 s, f = 7.93474. Structure annealed in 94 s, f = 8.72667. Structure annealed in 100 s, f = 11.5739. Structure annealed in 95 s, f = 13.4091. 100 structures finished in 820 s (8 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 5.31 12 0.0163 0.52 5 12.7 0.23 1 0.8478 5.78 2 5.54 10 0.0172 0.51 2 12.9 0.22 0 0.8296 4.67 3 5.76 13 0.0172 0.46 3 12.5 0.23 1 0.8145 6.13 4 5.85 14 0.0176 0.51 2 13.7 0.21 1 0.8325 5.81 5 5.92 9 0.0158 0.58 2 12.7 0.23 1 0.8472 6.48 6 6.08 11 0.0168 0.48 5 12.7 0.30 1 0.8270 5.65 7 6.09 12 0.0181 0.50 7 12.9 0.25 1 0.8179 5.68 8 6.14 12 0.0174 0.51 3 12.6 0.22 1 0.8355 5.94 9 6.24 16 0.0201 0.68 4 12.9 0.28 1 0.8540 5.96 10 6.43 11 0.0165 0.52 4 13.0 0.23 1 0.8257 5.87 11 6.46 15 0.0201 0.63 4 13.7 0.28 1 0.8425 5.70 12 6.58 19 0.0190 0.47 5 15.1 0.26 2 0.8746 5.99 13 6.61 14 0.0176 0.49 4 13.6 0.24 0 0.7943 4.81 14 6.68 13 0.0181 0.54 3 12.8 0.22 1 0.8085 6.00 15 6.68 12 0.0178 0.51 2 12.2 0.22 1 0.9055 5.08 16 6.70 13 0.0191 0.71 6 12.2 0.29 0 0.7457 4.41 17 6.71 12 0.0171 0.53 2 13.3 0.23 0 0.8879 4.71 18 6.73 17 0.0194 0.51 3 13.8 0.23 1 0.7930 5.08 19 6.76 14 0.0187 0.51 4 12.3 0.23 0 0.8307 4.92 20 6.79 10 0.0175 0.54 2 12.5 0.23 0 0.7768 4.34 Ave 6.30 13 0.0179 0.54 4 13.0 0.24 1 0.8296 5.45 +/- 0.43 2 0.0012 0.06 1 0.7 0.02 1 0.0360 0.62 Min 5.31 9 0.0158 0.46 2 12.2 0.21 0 0.7457 4.34 Max 6.79 19 0.0201 0.71 7 15.1 0.30 2 0.9055 6.48 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 ------ --- --- --- --- 1 140 10 2 0 2 134 14 2 2 (ASP 37, ASP 337) 3 136 14 2 0 4 138 13 1 0 5 138 14 0 0 6 139 13 0 0 7 137 13 0 2 (ASP 37, ASP 337) 8 134 14 2 2 (ASP 37, ASP 337) 9 139 13 0 0 10 136 14 2 0 11 139 11 2 0 12 133 17 2 0 13 133 19 0 0 14 138 12 2 0 15 142 10 0 0 16 138 10 2 2 (ASP 37, ASP 337) 17 144 8 0 0 18 139 13 0 0 19 139 13 0 0 20 134 16 2 0 all 90.5% 8.6% 0.7% 0.3% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 09-Nov-2005 18:34:32