Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 10-Nov-2005 17:37:03 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, 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 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, 222 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: 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 5320 peaks, 227 of 5320 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 ** 5320 of 5320 peaks, 5320 of 5320 assignments selected. - znf42: peaks calibrate ** simple 3906 upper limits added, 9/461 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3906 upper limits, 3906 assignments. - znf42: distance modify Number of modified constraints: 2038 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2038 upper limits, 2038 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, 2038 upper limits, 2038 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 = 23.6415. Structure annealed in 135 s, f = 9.85996. Structure annealed in 132 s, f = 7.68052. Structure annealed in 133 s, f = 10.4833. Structure annealed in 134 s, f = 9.66828. Structure annealed in 136 s, f = 10.0641. Structure annealed in 136 s, f = 9.61355. Structure annealed in 136 s, f = 18.2799. Structure annealed in 131 s, f = 19.1021. Structure annealed in 129 s, f = 10.0137. Structure annealed in 127 s, f = 14.6788. Structure annealed in 112 s, f = 10.9420. Structure annealed in 133 s, f = 22.2935. Structure annealed in 131 s, f = 8.66806. Structure annealed in 130 s, f = 12.7504. Structure annealed in 131 s, f = 9.86273. Structure annealed in 140 s, f = 326.189. Structure annealed in 134 s, f = 10.3416. Structure annealed in 135 s, f = 10.0046. Structure annealed in 135 s, f = 8.16679. Structure annealed in 111 s, f = 8.01601. Structure annealed in 137 s, f = 7.81710. Structure annealed in 133 s, f = 10.6895. Structure annealed in 136 s, f = 8.17076. Structure annealed in 130 s, f = 7.56540. Structure annealed in 131 s, f = 11.9821. Structure annealed in 131 s, f = 10.2524. Structure annealed in 134 s, f = 8.03417. Structure annealed in 133 s, f = 10.5154. Structure annealed in 133 s, f = 9.65980. Structure annealed in 132 s, f = 62.3088. Structure annealed in 129 s, f = 10.1163. Structure annealed in 136 s, f = 11.6724. Structure annealed in 137 s, f = 7.96018. Structure annealed in 136 s, f = 23.6402. Structure annealed in 136 s, f = 9.25725. Structure annealed in 134 s, f = 10.7153. Structure annealed in 135 s, f = 7.38482. Structure annealed in 125 s, f = 12.2049. Structure annealed in 112 s, f = 8.72981. Structure annealed in 117 s, f = 6.78545. Structure annealed in 133 s, f = 7.26770. Structure annealed in 131 s, f = 9.34989. Structure annealed in 136 s, f = 13.2932. Structure annealed in 131 s, f = 9.20730. Structure annealed in 131 s, f = 24.9379. Structure annealed in 132 s, f = 10.3975. Structure annealed in 133 s, f = 13.4578. Structure annealed in 133 s, f = 23.1554. Structure annealed in 130 s, f = 11.0168. Structure annealed in 133 s, f = 8.83136. Structure annealed in 132 s, f = 11.4898. Structure annealed in 131 s, f = 10.9935. Structure annealed in 136 s, f = 9.98540. Structure annealed in 136 s, f = 15.7953. Structure annealed in 135 s, f = 17.0285. Structure annealed in 135 s, f = 9.65361. Structure annealed in 133 s, f = 9.23948. Structure annealed in 135 s, f = 8.14936. Structure annealed in 106 s, f = 14.7796. Structure annealed in 130 s, f = 13.8813. Structure annealed in 131 s, f = 6.56440. Structure annealed in 133 s, f = 14.3378. Structure annealed in 138 s, f = 290.084. Structure annealed in 131 s, f = 13.1747. Structure annealed in 135 s, f = 11.1452. Structure annealed in 134 s, f = 13.2241. Structure annealed in 136 s, f = 8.04499. Structure annealed in 132 s, f = 11.9202. Structure annealed in 135 s, f = 11.5021. Structure annealed in 136 s, f = 11.5812. Structure annealed in 135 s, f = 11.4160. Structure annealed in 136 s, f = 16.3969. Structure annealed in 133 s, f = 8.12288. Structure annealed in 131 s, f = 10.8539. Structure annealed in 137 s, f = 8.36240. Structure annealed in 135 s, f = 8.47110. Structure annealed in 143 s, f = 288.861. Structure annealed in 96 s, f = 17.4706. Structure annealed in 100 s, f = 10.2893. Structure annealed in 130 s, f = 8.94996. Structure annealed in 131 s, f = 8.06290. Structure annealed in 133 s, f = 9.39946. Structure annealed in 130 s, f = 12.5988. Structure annealed in 134 s, f = 9.86050. Structure annealed in 130 s, f = 8.17558. Structure annealed in 135 s, f = 7.21576. Structure annealed in 134 s, f = 10.6235. Structure annealed in 134 s, f = 10.5137. Structure annealed in 126 s, f = 12.7097. Structure annealed in 134 s, f = 11.0898. Structure annealed in 131 s, f = 10.0350. Structure annealed in 136 s, f = 379.638. Structure annealed in 137 s, f = 8.61678. Structure annealed in 135 s, f = 29.0823. Structure annealed in 132 s, f = 12.4306. Structure annealed in 136 s, f = 13.6153. Structure annealed in 133 s, f = 13.7425. Structure annealed in 131 s, f = 8.67335. Structure annealed in 130 s, f = 19.8807. 100 structures finished in 797 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 6.56 22 0.0205 0.53 3 12.1 0.27 1 0.7418 5.11 2 6.79 20 0.0203 0.58 5 13.1 0.28 1 0.7394 5.11 3 7.22 19 0.0211 0.53 6 13.7 0.27 0 0.7473 4.59 4 7.27 18 0.0212 0.70 3 14.9 0.28 0 0.9682 4.59 5 7.38 20 0.0224 0.66 3 13.0 0.29 1 1.0119 6.04 6 7.57 18 0.0209 0.72 4 14.6 0.31 1 0.8785 5.27 7 7.68 24 0.0221 0.55 4 14.3 0.27 1 0.8541 5.26 8 7.82 28 0.0236 0.64 3 14.2 0.30 1 1.0011 7.83 9 7.96 20 0.0225 0.68 4 13.9 0.28 0 0.7571 4.46 10 8.02 22 0.0212 0.66 4 13.3 0.30 0 0.6798 4.30 11 8.03 23 0.0218 0.65 10 13.9 0.27 0 0.7358 4.76 12 8.05 23 0.0220 0.63 6 14.2 0.27 1 0.9488 6.12 13 8.06 28 0.0221 0.51 3 15.3 0.26 2 0.8758 5.86 14 8.12 20 0.0204 0.58 7 14.2 0.27 1 0.7968 5.13 15 8.15 21 0.0215 0.62 9 16.2 0.27 0 0.8430 4.96 16 8.17 22 0.0220 0.75 9 14.8 0.34 0 0.7280 4.10 17 8.17 14 0.0194 0.67 8 15.0 0.29 0 0.8488 4.89 18 8.18 19 0.0225 0.77 5 14.8 0.28 0 0.7714 4.30 19 8.36 33 0.0233 0.66 3 13.9 0.27 1 0.8073 6.20 20 8.47 24 0.0230 0.65 4 15.4 0.27 1 0.8853 5.17 Ave 7.80 22 0.0217 0.64 5 14.2 0.28 1 0.8310 5.20 +/- 0.50 4 0.0011 0.07 2 0.9 0.02 1 0.0947 0.85 Min 6.56 14 0.0194 0.51 3 12.1 0.26 0 0.6798 4.10 Max 8.47 33 0.0236 0.77 10 16.2 0.34 2 1.0119 7.83 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 ------ --- --- --- --- 1 139 13 0 0 2 138 14 0 0 3 135 14 3 0 4 134 16 2 0 5 139 11 2 0 6 140 12 0 0 7 134 18 0 0 8 140 12 0 0 9 133 17 0 2 (ASP 37, ASP 337) 10 139 13 0 0 11 139 13 0 0 12 135 15 0 2 (GLU 125, GLU 425) 13 135 15 2 0 14 137 15 0 0 15 141 11 0 0 16 140 12 0 0 17 136 14 2 0 18 136 16 0 0 19 136 14 2 0 20 139 13 0 0 all 90.3% 9.1% 0.4% 0.1% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 10-Nov-2005 17:52:26