Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 08-Nov-2005 16:23:01 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-node9.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node8.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n6 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n7 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n8 (cesg-node4.biochem.wisc.edu - 2 CPUs)... Executing hboot on n9 (cesg-node3.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, 3499 peaks, 2860 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 2860 0.000 0.003 0.592 0.015 1 0.030 2 3254 0.000 0.000 0.029 0.003 0 0.030 3 3254 0.000 0.000 0.297 0.037 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, 1294 peaks, 1056 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1056 0.002 0.003 1.158 0.042 2 0.030 2 1216 0.000 -0.001 1.137 0.033 1 0.030 3 1216 0.000 -0.003 3.640 0.106 1 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HB3 TRP 72 2.763 2.765 0.627 4 HB3 LEU 73 0.972 0.968 1.158 3 N GLN 101 120.823 120.823 3.640 12 H GLN 101 8.498 8.498 1.137 17 4 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 237 2 -1.137 H GLN 101 237 3 -3.640 N GLN 101 751 1 -0.627 HB3 TRP 72 1419 1 1.158 HB3 LEU 73 4 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, 3499 peaks, 2860 assignments. - calibration: peaks select "** list=1" 3499 of 3499 peaks, 3499 of 3499 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3499 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3499 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.4% 3.00-3.99 A: 774 22.1% 4.00-4.99 A: 1397 39.9% 5.00-5.99 A: 996 28.5% 6.00- A: 0 0.0% All: 3499 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, 1294 peaks, 1056 assignments. - calibration: peaks select "** list=2" 1294 of 4793 peaks, 1294 of 4793 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1294 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1294 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.2% 3.00-3.99 A: 341 26.4% 4.00-4.99 A: 498 38.5% 5.00-5.99 A: 360 27.8% 6.00- A: 0 0.0% All: 1294 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 5074 peaks, 281 of 5074 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 5299 peaks, 225 of 5299 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 ** 5299 of 5299 peaks, 5299 of 5299 assignments selected. - znf42: peaks calibrate ** simple 3805 upper limits added, 9/426 at lower/upper bound, average 4.45 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3805 upper limits, 3805 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: 1979 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 1979 upper limits, 1979 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, 1979 upper limits, 1979 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 268 constraints for 268 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 = 6.97991. Structure annealed in 134 s, f = 14.4428. Structure annealed in 134 s, f = 8.76310. Structure annealed in 132 s, f = 6.90195. Structure annealed in 139 s, f = 355.032. Structure annealed in 135 s, f = 7.11901. Structure annealed in 128 s, f = 7.60270. Structure annealed in 132 s, f = 9.96150. Structure annealed in 98 s, f = 10.9472. Structure annealed in 97 s, f = 8.70102. Structure annealed in 130 s, f = 8.78119. Structure annealed in 131 s, f = 11.6436. Structure annealed in 134 s, f = 10.1899. Structure annealed in 132 s, f = 8.86013. Structure annealed in 133 s, f = 11.9520. Structure annealed in 132 s, f = 7.43013. Structure annealed in 134 s, f = 12.2541. Structure annealed in 133 s, f = 6.12725. Structure annealed in 120 s, f = 7.98621. Structure annealed in 102 s, f = 10.7983. Structure annealed in 108 s, f = 10.6049. Structure annealed in 134 s, f = 8.43964. Structure annealed in 133 s, f = 7.95161. Structure annealed in 131 s, f = 9.50495. Structure annealed in 134 s, f = 6.65445. Structure annealed in 133 s, f = 8.33425. Structure annealed in 133 s, f = 7.21913. Structure annealed in 134 s, f = 9.58148. Structure annealed in 127 s, f = 7.55123. Structure annealed in 133 s, f = 11.9617. Structure annealed in 131 s, f = 8.88302. Structure annealed in 130 s, f = 8.39791. Structure annealed in 130 s, f = 11.5931. Structure annealed in 131 s, f = 8.20765. Structure annealed in 133 s, f = 8.91439. Structure annealed in 131 s, f = 6.61642. Structure annealed in 132 s, f = 8.02088. Structure annealed in 97 s, f = 13.3416. Structure annealed in 99 s, f = 8.32311. Structure annealed in 124 s, f = 15.4138. Structure annealed in 102 s, f = 9.11539. Structure annealed in 128 s, f = 6.81183. Structure annealed in 128 s, f = 8.28800. Structure annealed in 131 s, f = 8.96156. Structure annealed in 133 s, f = 8.52169. Structure annealed in 133 s, f = 6.56014. Structure annealed in 132 s, f = 6.67460. Structure annealed in 132 s, f = 10.2931. Structure annealed in 134 s, f = 10.7071. Structure annealed in 129 s, f = 8.53700. Structure annealed in 134 s, f = 6.91667. Structure annealed in 134 s, f = 8.12930. Structure annealed in 130 s, f = 7.67291. Structure annealed in 131 s, f = 13.6052. Structure annealed in 130 s, f = 6.47321. Structure annealed in 130 s, f = 9.10375. Structure annealed in 134 s, f = 6.97293. Structure annealed in 105 s, f = 6.36473. Structure annealed in 130 s, f = 8.07787. Structure annealed in 96 s, f = 7.27777. Structure annealed in 134 s, f = 47.4875. Structure annealed in 98 s, f = 6.56818. Structure annealed in 134 s, f = 8.14829. Structure annealed in 134 s, f = 10.1472. Structure annealed in 130 s, f = 8.27937. Structure annealed in 129 s, f = 8.68369. Structure annealed in 133 s, f = 18.7134. Structure annealed in 131 s, f = 7.66823. Structure annealed in 134 s, f = 11.7123. Structure annealed in 133 s, f = 12.3761. Structure annealed in 129 s, f = 11.3612. Structure annealed in 143 s, f = 362.729. Structure annealed in 132 s, f = 8.48474. Structure annealed in 131 s, f = 9.30577. Structure annealed in 133 s, f = 7.09322. Structure annealed in 134 s, f = 28.7628. Structure annealed in 107 s, f = 8.29332. Structure annealed in 124 s, f = 7.31772. Structure annealed in 131 s, f = 8.36983. Structure annealed in 130 s, f = 7.57675. Structure annealed in 131 s, f = 7.29284. Structure annealed in 132 s, f = 6.97541. Structure annealed in 127 s, f = 11.6829. Structure annealed in 131 s, f = 6.54944. Structure annealed in 131 s, f = 6.19393. Structure annealed in 132 s, f = 8.89454. Structure annealed in 132 s, f = 7.48633. Structure annealed in 132 s, f = 7.79347. Structure annealed in 132 s, f = 7.92298. Structure annealed in 132 s, f = 8.76007. Structure annealed in 131 s, f = 8.49883. Structure annealed in 130 s, f = 11.9606. Structure annealed in 132 s, f = 13.7113. Structure annealed in 127 s, f = 8.40407. Structure annealed in 110 s, f = 10.3639. Structure annealed in 97 s, f = 7.49088. Structure annealed in 99 s, f = 10.4749. Structure annealed in 130 s, f = 7.61131. Structure annealed in 128 s, f = 11.9766. Structure annealed in 101 s, f = 141.427. 100 structures finished in 794 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 6.13 11 0.0187 0.88 4 11.9 0.22 1 0.8399 6.77 2 6.19 9 0.0181 0.88 2 11.3 0.22 2 0.8511 6.49 3 6.37 18 0.0196 0.70 2 12.7 0.23 1 0.8307 7.57 4 6.47 18 0.0205 0.70 2 12.9 0.23 1 0.8154 7.50 5 6.55 8 0.0191 0.91 3 11.9 0.27 1 0.8095 7.03 6 6.56 19 0.0201 0.72 1 11.9 0.21 2 0.8924 6.42 7 6.57 19 0.0206 0.71 2 11.9 0.22 1 0.8675 7.45 8 6.62 12 0.0196 0.91 2 12.9 0.22 1 0.8362 6.78 9 6.65 9 0.0187 0.90 2 12.7 0.22 1 0.9309 7.56 10 6.67 9 0.0187 0.88 4 13.1 0.22 1 0.8844 6.73 11 6.81 12 0.0194 0.90 3 12.1 0.21 2 0.8879 6.42 12 6.90 12 0.0202 0.89 5 13.3 0.23 3 0.8934 6.26 13 6.92 13 0.0194 0.88 3 13.9 0.23 1 0.9166 7.24 14 6.97 12 0.0200 0.86 1 13.5 0.21 2 0.8528 6.83 15 6.98 21 0.0215 0.72 2 14.0 0.23 1 0.8861 7.18 16 6.98 11 0.0185 0.92 3 12.8 0.21 2 0.8492 6.36 17 7.09 22 0.0219 0.65 4 13.7 0.25 2 0.9093 6.78 18 7.12 12 0.0197 0.88 3 13.4 0.24 1 0.8602 6.68 19 7.22 15 0.0197 0.83 2 13.1 0.22 1 0.9600 8.14 20 7.28 9 0.0190 0.88 2 12.7 0.23 1 0.8724 7.03 Ave 6.75 14 0.0197 0.83 3 12.8 0.23 1 0.8723 6.96 +/- 0.32 4 0.0009 0.09 1 0.7 0.01 1 0.0379 0.48 Min 6.13 8 0.0181 0.65 1 11.3 0.21 1 0.8095 6.26 Max 7.28 22 0.0219 0.92 5 14.0 0.27 3 0.9600 8.14 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 ------ --- --- --- --- 1 141 9 2 0 2 136 16 0 0 3 137 13 2 0 4 138 14 0 0 5 138 14 0 0 6 142 10 0 0 7 132 18 0 2 (ASP 37, ASP 337) 8 135 16 1 0 9 135 17 0 0 10 133 15 4 0 11 135 15 2 0 12 137 15 0 0 13 135 15 0 2 (ARG 124, ARG 424) 14 139 11 2 0 15 140 12 0 0 16 133 19 0 0 17 139 13 0 0 18 139 13 0 0 19 138 14 0 0 20 136 14 2 0 all 90.1% 9.3% 0.5% 0.1% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 08-Nov-2005 16:38:17