Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 15-Nov-2005 16:53:02 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 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 dref=4.2 Calibration constant for peak list 1: 1.84E+07 Upper limit set for 3503 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 439 12.5% 3.00-3.99 A: 1173 33.5% 4.00-4.99 A: 1324 37.8% 5.00-5.99 A: 567 16.2% 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 dref=4.2 Calibration constant for peak list 2: 8.32E+06 Upper limit set for 1291 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 112 8.7% 3.00-3.99 A: 472 36.6% 4.00-4.99 A: 485 37.6% 5.00-5.99 A: 222 17.2% 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 dref=4.2 Calibration constant for peak list 3: 1.40E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 26 9.3% 3.00-3.99 A: 87 31.0% 4.00-4.99 A: 150 53.4% 5.00-5.99 A: 18 6.4% 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 dref=4.2 Calibration constant for peak list 4: 6.87E+06 Upper limit set for 227 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 4 1.8% 3.00-3.99 A: 83 36.6% 4.00-4.99 A: 139 61.2% 5.00-5.99 A: 1 0.4% 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, 18/139 at lower/upper bound, average 4.17 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3974 upper limits, 3974 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA ASP 37 - QG PRO 38 3.96 4.11 6.06 Number of modified constraints: 2211 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2211 upper limits, 2211 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, 2211 upper limits, 2211 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 136 s, f = 37.3351. Structure annealed in 133 s, f = 31.3253. Structure annealed in 135 s, f = 37.1952. Structure annealed in 137 s, f = 49.3690. Structure annealed in 136 s, f = 32.1514. Structure annealed in 135 s, f = 49.4388. Structure annealed in 138 s, f = 31.7047. Structure annealed in 136 s, f = 30.6428. Structure annealed in 135 s, f = 36.3236. Structure annealed in 132 s, f = 50.2502. Structure annealed in 102 s, f = 39.5845. Structure annealed in 104 s, f = 29.0291. Structure annealed in 133 s, f = 27.9889. Structure annealed in 135 s, f = 35.4170. Structure annealed in 135 s, f = 32.9599. Structure annealed in 133 s, f = 31.1339. Structure annealed in 131 s, f = 32.2043. Structure annealed in 137 s, f = 35.1741. Structure annealed in 134 s, f = 27.7153. Structure annealed in 138 s, f = 30.1521. Structure annealed in 135 s, f = 29.4818. Structure annealed in 135 s, f = 34.3437. Structure annealed in 134 s, f = 29.5743. Structure annealed in 132 s, f = 30.9492. Structure annealed in 135 s, f = 31.0275. Structure annealed in 138 s, f = 28.1451. Structure annealed in 135 s, f = 31.0972. Structure annealed in 135 s, f = 34.7333. Structure annealed in 132 s, f = 30.3996. Structure annealed in 138 s, f = 29.4215. Structure annealed in 134 s, f = 29.2811. Structure annealed in 134 s, f = 29.9770. Structure annealed in 132 s, f = 35.5217. Structure annealed in 137 s, f = 29.0621. Structure annealed in 133 s, f = 33.8560. Structure annealed in 131 s, f = 33.8066. Structure annealed in 135 s, f = 29.7174. Structure annealed in 139 s, f = 30.0773. Structure annealed in 101 s, f = 27.8312. Structure annealed in 99 s, f = 31.2164. Structure annealed in 137 s, f = 27.8502. Structure annealed in 132 s, f = 30.5254. Structure annealed in 137 s, f = 47.2217. Structure annealed in 134 s, f = 27.4617. Structure annealed in 141 s, f = 255.296. Structure annealed in 131 s, f = 40.7619. Structure annealed in 136 s, f = 34.9790. Structure annealed in 134 s, f = 32.1492. Structure annealed in 135 s, f = 30.8528. Structure annealed in 131 s, f = 31.2010. Structure annealed in 135 s, f = 29.1968. Structure annealed in 137 s, f = 28.8407. Structure annealed in 133 s, f = 28.9400. Structure annealed in 138 s, f = 34.2114. Structure annealed in 136 s, f = 27.0525. Structure annealed in 138 s, f = 34.5617. Structure annealed in 136 s, f = 33.0568. Structure annealed in 138 s, f = 47.1704. Structure annealed in 135 s, f = 26.8985. Structure annealed in 139 s, f = 500.667. Structure annealed in 134 s, f = 36.3048. Structure annealed in 136 s, f = 30.6389. Structure annealed in 136 s, f = 263.590. Structure annealed in 136 s, f = 32.4628. Structure annealed in 137 s, f = 35.7314. Structure annealed in 136 s, f = 26.0209. Structure annealed in 136 s, f = 28.7648. Structure annealed in 130 s, f = 31.8261. Structure annealed in 102 s, f = 28.6906. Structure annealed in 130 s, f = 37.7484. Structure annealed in 98 s, f = 29.7296. Structure annealed in 134 s, f = 31.7514. Structure annealed in 138 s, f = 144.907. Structure annealed in 137 s, f = 27.8850. Structure annealed in 138 s, f = 34.6920. Structure annealed in 135 s, f = 49.6389. Structure annealed in 139 s, f = 34.1921. Structure annealed in 135 s, f = 35.3360. Structure annealed in 133 s, f = 29.8015. Structure annealed in 136 s, f = 126.195. Structure annealed in 137 s, f = 29.0048. Structure annealed in 137 s, f = 33.6670. Structure annealed in 132 s, f = 28.1749. Structure annealed in 143 s, f = 451.834. Structure annealed in 141 s, f = 384.406. Structure annealed in 133 s, f = 35.5121. Structure annealed in 137 s, f = 28.4809. Structure annealed in 133 s, f = 177.822. Structure annealed in 138 s, f = 247.733. Structure annealed in 139 s, f = 30.4209. Structure annealed in 139 s, f = 30.0578. Structure annealed in 131 s, f = 31.2040. Structure annealed in 140 s, f = 421.187. Structure annealed in 131 s, f = 32.0877. Structure annealed in 135 s, f = 33.3369. Structure annealed in 135 s, f = 29.3917. Structure annealed in 100 s, f = 29.0955. Structure annealed in 101 s, f = 36.8988. Structure annealed in 97 s, f = 27.3833. Structure annealed in 100 s, f = 31.4542. 100 structures finished in 817 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 26.02 106 0.0447 1.00 12 27.7 0.32 6 1.3855 6.81 2 26.90 113 0.0459 1.02 13 27.4 0.31 7 1.4612 8.45 3 27.05 113 0.0465 0.98 14 26.8 0.36 4 1.3488 6.02 4 27.38 110 0.0464 1.03 14 26.7 0.34 7 1.4627 8.20 5 27.46 103 0.0456 1.02 14 27.0 0.36 7 1.3560 7.03 6 27.72 119 0.0480 0.99 11 26.7 0.37 6 1.4230 8.06 7 27.83 109 0.0465 1.00 14 27.8 0.47 7 1.4762 10.08 8 27.85 116 0.0463 1.02 13 27.1 0.35 3 1.3085 6.14 9 27.89 122 0.0463 0.99 20 28.9 0.38 7 1.4902 6.75 10 27.99 116 0.0468 1.03 15 27.6 0.34 6 1.3449 6.31 11 28.15 112 0.0460 1.01 12 28.9 0.33 7 1.4145 6.36 12 28.18 106 0.0447 0.92 18 31.2 0.38 10 1.6591 8.26 13 28.48 105 0.0460 0.93 20 30.4 0.34 9 1.5875 10.04 14 28.69 122 0.0485 0.96 17 27.5 0.34 5 1.3780 7.13 15 28.76 119 0.0467 1.00 19 29.4 0.36 6 1.3500 6.60 16 28.84 109 0.0458 0.92 19 29.5 0.47 8 1.5058 8.73 17 28.94 107 0.0465 0.98 17 31.8 0.34 7 1.5482 9.02 18 29.00 117 0.0470 0.98 19 31.5 0.43 4 1.2792 5.71 19 29.03 113 0.0460 0.87 27 32.1 0.41 9 1.6836 12.42 20 29.06 118 0.0466 1.00 15 30.9 0.44 6 1.3900 6.16 Ave 28.06 113 0.0463 0.98 16 28.8 0.37 7 1.4426 7.71 +/- 0.80 6 0.0009 0.04 4 1.8 0.05 2 0.1086 1.68 Min 26.02 103 0.0447 0.87 11 26.7 0.31 3 1.2792 5.71 Max 29.06 122 0.0485 1.03 27 32.1 0.47 10 1.6836 12.42 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 12 0 0 2 133 19 0 0 3 138 14 0 0 4 142 10 0 0 5 144 8 0 0 6 135 17 0 0 7 136 14 2 0 8 137 15 0 0 9 139 13 0 0 10 140 12 0 0 11 139 13 0 0 12 132 18 2 0 13 135 17 0 0 14 136 16 0 0 15 138 14 0 0 16 135 17 0 0 17 140 12 0 0 18 137 15 0 0 19 134 18 0 0 20 140 12 0 0 all 90.5% 9.4% 0.1% 0.0% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 15-Nov-2005 17:08:46