Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 08-Nov-2005 21:10:33 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node4.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node3.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node2.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... 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 0.002 0.030 0.010 0 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 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= *** 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, 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, 1292 peaks, 1081 assignments. - calibration: peaks select "** list=2" 1292 of 4791 peaks, 1292 of 4791 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 5072 peaks, 281 of 5072 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 5297 peaks, 225 of 5297 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 ** 5297 of 5297 peaks, 5297 of 5297 assignments selected. - znf42: peaks calibrate ** simple 3830 upper limits added, 9/427 at lower/upper bound, average 4.45 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3830 upper limits, 3830 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: 1986 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 1986 upper limits, 1986 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, 1986 upper limits, 1986 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 133 s, f = 92.6303. Structure annealed in 132 s, f = 6.29950. Structure annealed in 133 s, f = 5.81721. Structure annealed in 132 s, f = 9.58302. Structure annealed in 134 s, f = 7.74938. Structure annealed in 130 s, f = 6.17203. Structure annealed in 134 s, f = 7.41051. Structure annealed in 135 s, f = 5.71348. Structure annealed in 119 s, f = 9.75374. Structure annealed in 113 s, f = 10.8201. Structure annealed in 133 s, f = 6.01464. Structure annealed in 133 s, f = 6.35028. Structure annealed in 110 s, f = 6.43568. Structure annealed in 134 s, f = 6.29696. Structure annealed in 129 s, f = 5.58471. Structure annealed in 128 s, f = 6.78694. Structure annealed in 133 s, f = 5.33402. Structure annealed in 129 s, f = 5.75574. Structure annealed in 128 s, f = 5.76345. Structure annealed in 133 s, f = 14.1752. Structure annealed in 131 s, f = 4.90463. Structure annealed in 132 s, f = 18.2885. Structure annealed in 134 s, f = 10.4470. Structure annealed in 122 s, f = 5.65739. Structure annealed in 109 s, f = 5.27521. Structure annealed in 126 s, f = 8.41026. Structure annealed in 135 s, f = 21.1899. Structure annealed in 130 s, f = 10.2826. Structure annealed in 129 s, f = 6.05796. Structure annealed in 131 s, f = 7.30231. Structure annealed in 136 s, f = 11.1213. Structure annealed in 140 s, f = 171.177. Structure annealed in 133 s, f = 10.1600. Structure annealed in 135 s, f = 7.30034. Structure annealed in 135 s, f = 8.71223. Structure annealed in 108 s, f = 11.9365. Structure annealed in 128 s, f = 6.75428. Structure annealed in 133 s, f = 6.60904. Structure annealed in 132 s, f = 4.92707. Structure annealed in 132 s, f = 7.04063. Structure annealed in 127 s, f = 6.46264. Structure annealed in 132 s, f = 16.7258. Structure annealed in 135 s, f = 105.486. Structure annealed in 130 s, f = 5.63125. Structure annealed in 145 s, f = 193.093. Structure annealed in 132 s, f = 5.09626. Structure annealed in 93 s, f = 11.6089. Structure annealed in 99 s, f = 11.2033. Structure annealed in 128 s, f = 7.34716. Structure annealed in 132 s, f = 9.65492. Structure annealed in 138 s, f = 361.101. Structure annealed in 134 s, f = 7.87740. Structure annealed in 134 s, f = 7.59770. Structure annealed in 133 s, f = 5.80714. Structure annealed in 135 s, f = 6.70510. Structure annealed in 131 s, f = 9.22139. Structure annealed in 137 s, f = 4.87696. Structure annealed in 133 s, f = 5.50215. Structure annealed in 126 s, f = 7.97268. Structure annealed in 90 s, f = 6.55115. Structure annealed in 133 s, f = 10.8123. Structure annealed in 131 s, f = 4.83092. Structure annealed in 127 s, f = 5.60606. Structure annealed in 129 s, f = 5.34625. Structure annealed in 135 s, f = 6.57848. Structure annealed in 136 s, f = 7.87097. Structure annealed in 135 s, f = 5.21306. Structure annealed in 97 s, f = 7.29224. Structure annealed in 133 s, f = 6.33878. Structure annealed in 131 s, f = 5.86772. Structure annealed in 137 s, f = 7.61487. Structure annealed in 134 s, f = 4.04147. Structure annealed in 131 s, f = 9.48950. Structure annealed in 129 s, f = 11.6553. Structure annealed in 134 s, f = 7.19304. Structure annealed in 145 s, f = 12.5627. Structure annealed in 133 s, f = 6.99993. Structure annealed in 133 s, f = 6.77825. Structure annealed in 135 s, f = 7.73079. Structure annealed in 136 s, f = 5.93826. Structure annealed in 99 s, f = 178.577. Structure annealed in 93 s, f = 6.29955. Structure annealed in 153 s, f = 7.37661. Structure annealed in 129 s, f = 6.71854. Structure annealed in 129 s, f = 6.82744. Structure annealed in 132 s, f = 5.92193. Structure annealed in 130 s, f = 7.16043. Structure annealed in 133 s, f = 8.44862. Structure annealed in 134 s, f = 10.4163. Structure annealed in 132 s, f = 7.42552. Structure annealed in 153 s, f = 4.76310. Structure annealed in 133 s, f = 11.0830. Structure annealed in 91 s, f = 7.42528. Structure annealed in 95 s, f = 5.44562. Structure annealed in 132 s, f = 6.75902. Structure annealed in 101 s, f = 7.87148. Structure annealed in 128 s, f = 5.03689. Structure annealed in 135 s, f = 5.79509. Structure annealed in 110 s, f = 6.47903. Structure annealed in 129 s, f = 9.56718. 100 structures finished in 1230 s (12 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 4.04 11 0.0150 0.53 1 11.2 0.22 0 0.6154 3.92 2 4.76 9 0.0152 0.47 3 10.7 0.23 0 0.6091 4.86 3 4.83 7 0.0158 0.50 2 11.3 0.22 0 0.6918 4.38 4 4.88 8 0.0149 0.52 3 11.6 0.21 0 0.6869 4.67 5 4.90 12 0.0163 0.51 2 11.8 0.22 0 0.7290 4.61 6 4.93 10 0.0151 0.51 1 11.7 0.21 0 0.7334 4.24 7 5.04 11 0.0165 0.48 1 11.9 0.23 0 0.6698 4.53 8 5.10 9 0.0141 0.50 1 11.1 0.22 0 0.6956 4.18 9 5.21 14 0.0162 0.50 3 12.2 0.22 0 0.6476 4.22 10 5.28 9 0.0147 0.51 1 11.6 0.21 1 0.7025 5.16 11 5.33 10 0.0156 0.51 1 12.0 0.23 0 0.6380 4.44 12 5.35 7 0.0150 0.49 2 12.5 0.23 1 0.7244 5.06 13 5.45 7 0.0153 0.48 3 13.6 0.23 0 0.7933 4.66 14 5.50 10 0.0180 0.71 2 11.8 0.23 0 0.6622 4.54 15 5.58 11 0.0166 0.49 1 11.3 0.22 1 0.6517 5.09 16 5.61 9 0.0165 0.48 3 13.1 0.23 1 0.7186 5.15 17 5.63 10 0.0153 0.51 3 11.6 0.25 0 0.7201 4.90 18 5.66 11 0.0182 0.64 2 10.7 0.22 0 0.6774 4.37 19 5.71 10 0.0164 0.51 4 12.8 0.23 2 0.7594 5.96 20 5.76 13 0.0175 0.66 2 11.7 0.22 0 0.6991 4.14 Ave 5.23 10 0.0159 0.53 2 11.8 0.22 0 0.6913 4.65 +/- 0.41 2 0.0011 0.06 1 0.7 0.01 1 0.0455 0.46 Min 4.04 7 0.0141 0.47 1 10.7 0.21 0 0.6091 3.92 Max 5.76 14 0.0182 0.71 4 13.6 0.25 2 0.7933 5.96 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 ------ --- --- --- --- 1 136 14 2 0 2 138 12 2 0 3 143 9 0 0 4 138 14 0 0 5 139 13 0 0 6 141 11 0 0 7 138 14 0 0 8 138 14 0 0 9 137 15 0 0 10 137 13 2 0 11 135 15 2 0 12 139 13 0 0 13 136 16 0 0 14 133 17 2 0 15 137 15 0 0 16 135 17 0 0 17 138 12 2 0 18 139 13 0 0 19 136 16 0 0 20 133 16 1 2 (GLU 125, GLU 425) all 90.3% 9.2% 0.4% 0.1% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 08-Nov-2005 21:32:39