Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 09-Nov-2005 14:07:56 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node12.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node11.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node10.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node4.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node3.biochem.wisc.edu - 2 CPUs)... Executing hboot on n6 (cesg-node2.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... n6... 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, 3518 peaks, 2883 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 2883 0.000 0.003 0.592 0.015 1 0.030 2 3279 0.000 0.000 0.029 0.003 0 0.030 3 3279 0.000 0.000 0.297 0.035 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks H ALA 43 7.858 7.864 0.592 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1579 1 0.592 H ALA 43 1 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= *** WARNING: Inconsistent heavy atom assignment for peak 1382. 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= Peak list "c13no.peaks" read, 3518 peaks, 2883 assignments. - calibration: peaks select "** list=1" 3518 of 3518 peaks, 3518 of 3518 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3518 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3518 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: 1398 39.7% 5.00-5.99 A: 1014 28.8% 6.00- A: 0 0.0% All: 3518 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append *** WARNING: Inconsistent heavy atom assignment for peak 1382. Peak list "n15no.peaks" read, 1292 peaks, 1081 assignments. - calibration: peaks select "** list=2" 1292 of 4810 peaks, 1292 of 4810 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 5091 peaks, 281 of 5091 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 5316 peaks, 225 of 5316 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 ** 5316 of 5316 peaks, 5316 of 5316 assignments selected. - znf42: peaks calibrate ** simple 3848 upper limits added, 9/443 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3848 upper limits, 3848 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: 1998 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 1998 upper limits, 1998 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, 1998 upper limits, 1998 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 132 s, f = 6.64993. Structure annealed in 130 s, f = 9.06994. Structure annealed in 136 s, f = 12.7821. Structure annealed in 131 s, f = 5.44755. Structure annealed in 137 s, f = 6.28453. Structure annealed in 130 s, f = 7.76187. Structure annealed in 131 s, f = 7.72207. Structure annealed in 132 s, f = 8.32908. Structure annealed in 130 s, f = 9.55100. Structure annealed in 131 s, f = 8.50965. Structure annealed in 94 s, f = 6.07203. Structure annealed in 98 s, f = 43.2670. Structure annealed in 130 s, f = 17.6538. Structure annealed in 129 s, f = 7.39300. Structure annealed in 131 s, f = 6.16203. Structure annealed in 133 s, f = 6.10616. Structure annealed in 137 s, f = 343.686. Structure annealed in 130 s, f = 5.46438. Structure annealed in 127 s, f = 8.02711. Structure annealed in 135 s, f = 10.4744. Structure annealed in 131 s, f = 17.8000. Structure annealed in 130 s, f = 5.09307. Structure annealed in 126 s, f = 5.57676. Structure annealed in 133 s, f = 7.17650. Structure annealed in 136 s, f = 18.5597. Structure annealed in 139 s, f = 84.1561. Structure annealed in 95 s, f = 6.00483. Structure annealed in 97 s, f = 7.52500. Structure annealed in 129 s, f = 5.46638. Structure annealed in 125 s, f = 7.65302. Structure annealed in 130 s, f = 6.48207. Structure annealed in 132 s, f = 8.05381. Structure annealed in 134 s, f = 7.27142. Structure annealed in 127 s, f = 7.77390. Structure annealed in 128 s, f = 9.48366. Structure annealed in 130 s, f = 5.50185. Structure annealed in 136 s, f = 5.99433. Structure annealed in 140 s, f = 167.484. Structure annealed in 134 s, f = 11.5812. Structure annealed in 135 s, f = 5.85795. Structure annealed in 93 s, f = 7.37221. Structure annealed in 126 s, f = 5.24881. Structure annealed in 134 s, f = 5.91618. Structure annealed in 94 s, f = 13.1658. Structure annealed in 133 s, f = 10.4926. Structure annealed in 136 s, f = 472.609. Structure annealed in 129 s, f = 6.28178. Structure annealed in 131 s, f = 21.2027. Structure annealed in 130 s, f = 5.94787. Structure annealed in 133 s, f = 11.3246. Structure annealed in 136 s, f = 10.5568. Structure annealed in 141 s, f = 350.635. Structure annealed in 134 s, f = 7.89350. Structure annealed in 135 s, f = 5.74925. Structure annealed in 129 s, f = 7.86168. Structure annealed in 131 s, f = 6.37673. Structure annealed in 128 s, f = 5.82322. Structure annealed in 132 s, f = 6.15355. Structure annealed in 132 s, f = 12.5620. Structure annealed in 127 s, f = 7.94447. Structure annealed in 133 s, f = 6.08424. Structure annealed in 129 s, f = 7.61740. Structure annealed in 135 s, f = 5.86721. Structure annealed in 133 s, f = 9.26883. Structure annealed in 139 s, f = 7.81039. Structure annealed in 131 s, f = 7.42333. Structure annealed in 99 s, f = 9.03341. Structure annealed in 95 s, f = 6.06699. Structure annealed in 125 s, f = 5.84656. Structure annealed in 128 s, f = 7.88081. Structure annealed in 133 s, f = 6.85316. Structure annealed in 129 s, f = 6.24349. Structure annealed in 129 s, f = 6.31980. Structure annealed in 132 s, f = 6.83447. Structure annealed in 131 s, f = 101.468. Structure annealed in 134 s, f = 9.44336. Structure annealed in 136 s, f = 14.2388. Structure annealed in 135 s, f = 5.80500. Structure annealed in 135 s, f = 8.71330. Structure annealed in 133 s, f = 8.79457. Structure annealed in 128 s, f = 10.8526. Structure annealed in 98 s, f = 7.08489. Structure annealed in 98 s, f = 5.44382. Structure annealed in 128 s, f = 5.51703. Structure annealed in 128 s, f = 8.16487. Structure annealed in 131 s, f = 7.87221. Structure annealed in 125 s, f = 5.89851. Structure annealed in 133 s, f = 6.04021. Structure annealed in 135 s, f = 8.62610. Structure annealed in 133 s, f = 5.68925. Structure annealed in 133 s, f = 6.88382. Structure annealed in 134 s, f = 6.32651. Structure annealed in 131 s, f = 12.4885. Structure annealed in 128 s, f = 6.21711. Structure annealed in 109 s, f = 5.95215. Structure annealed in 129 s, f = 9.06666. Structure annealed in 98 s, f = 5.99455. Structure annealed in 128 s, f = 12.3486. Structure annealed in 131 s, f = 7.97783. Structure annealed in 129 s, f = 8.10574. 100 structures finished in 1059 s (10 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 5.09 8 0.0152 0.51 3 11.4 0.24 0 0.6604 3.99 2 5.25 11 0.0162 0.52 2 12.7 0.22 0 0.6774 4.90 3 5.44 11 0.0152 0.52 4 12.2 0.25 0 0.7030 4.83 4 5.45 12 0.0161 0.54 1 10.7 0.22 0 0.6389 3.82 5 5.46 14 0.0163 0.52 3 12.1 0.25 0 0.6398 4.38 6 5.47 16 0.0169 0.49 3 12.6 0.22 0 0.7286 4.55 7 5.50 13 0.0170 0.55 3 12.2 0.22 0 0.7197 4.99 8 5.52 12 0.0166 0.49 2 12.2 0.22 0 0.6666 4.60 9 5.58 11 0.0174 0.47 2 11.7 0.23 1 0.6752 5.08 10 5.69 14 0.0178 0.48 2 13.1 0.23 1 0.7528 5.31 11 5.75 13 0.0186 0.61 3 12.5 0.22 0 0.7104 4.45 12 5.81 16 0.0174 0.53 1 12.8 0.22 0 0.7272 4.54 13 5.82 14 0.0178 0.57 2 12.5 0.24 1 0.9066 6.51 14 5.85 11 0.0156 0.49 2 11.8 0.23 0 0.6672 4.75 15 5.86 19 0.0182 0.48 5 13.6 0.30 1 0.7384 5.20 16 5.87 10 0.0169 0.63 4 13.4 0.22 0 0.7339 4.13 17 5.90 13 0.0174 0.63 5 12.9 0.26 1 0.7911 5.01 18 5.92 12 0.0183 0.55 5 12.8 0.25 1 0.7337 5.16 19 5.95 13 0.0183 0.70 2 9.9 0.21 1 0.6097 5.19 20 5.95 11 0.0169 0.59 4 12.7 0.24 0 0.6808 3.89 Ave 5.66 13 0.0170 0.54 3 12.3 0.23 0 0.7081 4.77 +/- 0.24 2 0.0010 0.06 1 0.9 0.02 0 0.0629 0.60 Min 5.09 8 0.0152 0.47 1 9.9 0.21 0 0.6097 3.82 Max 5.95 19 0.0186 0.70 5 13.6 0.30 1 0.9066 6.51 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 12 2 0 2 136 16 0 0 3 140 12 0 0 4 136 16 0 0 5 135 17 0 0 6 139 13 0 0 7 141 11 0 0 8 135 16 1 0 9 135 17 0 0 10 135 17 0 0 11 140 10 2 0 12 135 17 0 0 13 134 18 0 0 14 138 14 0 0 15 139 11 0 2 (SER 36, SER 336) 16 141 11 0 0 17 135 17 0 0 18 138 14 0 0 19 141 11 0 0 20 132 17 3 0 all 90.2% 9.4% 0.3% 0.1% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 09-Nov-2005 14:27:18