Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 16-Dec-2005 07:16:24 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node8.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node6.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)... topology n0 (o)... n1... n2... n3... n4... 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 "at5g39720.seq" read, 173 residues. cyana> cyana> cyana> - CALC: peakcheck peaks=c13no_new,n15no_new,c13ar_new prot=at5g39720 ------------------------------------------------------------ Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=warn Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - peakcheck: shifts missing "H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" Residue missing shifts GLY 1 H QA HIS 2 H HA QB HD2 HE1 HIS 3 H HA QB HD2 HE1 HIS 4 H HA QB HD2 HE1 HIS 5 HA QB HD2 HE1 HIS 6 H HA QB HD2 HE1 HIS 7 H HB2 HD2 HE1 LEU 8 HB2 GLU 9 HG2 CYS 10 HG SER 11 HB2 ASP 13 HB2 SER 14 HB2 GLN 16 HG2 HIS 18 HB2 PHE 21 HZ GLY 24 H QA SER 25 H HA QB PHE 26 HZ MET 35 HB2 HG2 LEU 36 QD1 ARG 38 HD3 PRO 40 HB2 GLU 41 HB2 PHE 50 HZ ARG 52 QG QD PHE 53 HZ ARG 54 HG2 LEU 55 H HA QB HG QQD LYS 56 H HA QB QG QD QE GLY 57 H QA ARG 58 QB QG TYR 60 HB2 QE PRO 61 QB QG QD CYS 62 HG GLU 67 HB2 HG2 LYS 68 HG2 HD2 HE2 LEU 76 QD1 SER 81 QB GLU 83 HG2 GLU 85 HB2 GLU 96 HG2 VAL 103 QG1 ARG 104 HD2 GLU 105 HG2 SER 108 HB2 LYS 110 HD2 HE2 LYS 114 QG HE2 TYR 116 HB2 MET 117 HB2 LYS 121 HG2 HD2 ASP 123 HB2 PRO 124 HG2 HD2 PHE 127 HB2 QE HZ GLU 129 HB2 HG2 TRP 130 HE3 ASN 131 HA PHE 132 QE HZ GLU 134 HB2 TRP 135 HZ3 LYS 136 HA HB2 HG2 QD HE2 ARG 137 HB2 HIS 139 HD2 HE1 LYS 140 HB2 HG2 HD2 HE2 LYS 141 HB2 HG2 HE2 LYS 142 HB2 HG2 QD HE2 PHE 143 QE HZ GLU 145 HB2 LYS 148 HB2 HG2 HD2 HE2 LYS 149 HA QB QG QD QE MET 151 HB2 QE GLU 152 HB2 CYS 153 HB2 HG LYS 154 HB2 HG2 HD2 HE2 LYS 155 HG2 HD2 HE2 LYS 156 HA QB QG QD QE PRO 157 HG2 GLY 161 HA2 ASN 162 HB2 ASP 163 HB2 ASP 164 HA QB ILE 165 H QG1 SER 166 H HA QB HIS 167 H VAL 168 QG1 LEU 169 HG QD1 ARG 170 HA QB QG QD GLU 171 H HG2 ASP 172 HB2 GLN 173 HA QB QG 186 missing chemical shifts, completeness 81.1%. ------------------------------------------------------------ Peak list : c13no_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - peakcheck: read peaks c13no_new format= Peak list "c13no_new.peaks" read, 3501 peaks, 2936 assignments. - peakcheck: atom shift unusual Atom Shift Dev Mean +/- Minimum Maximum HG2 GLU 91 0.205 10.42 2.29 0.20 1.48 2.79 HB2 GLU 94 0.734 5.63 2.03 0.23 0.72 2.90 2 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 2936 0.003 0.003 0.030 0.013 0 0.040 2 2936 -0.003 -0.004 0.030 0.009 0 0.030 3 2936 0.000 -0.020 0.299 0.091 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_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - peakcheck: read peaks n15no_new format= Peak list "n15no_new.peaks" read, 1847 peaks, 1520 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1520 0.005 0.005 0.032 0.013 0 0.040 2 1520 0.000 0.000 0.029 0.005 0 0.030 3 1520 0.001 0.010 0.276 0.055 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_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - peakcheck: read peaks c13ar_new format= Peak list "c13ar_new.peaks" read, 570 peaks, 272 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 272 0.005 0.004 0.029 0.013 0 0.040 2 272 -0.006 -0.006 0.019 0.009 0 0.030 3 272 0.000 0.000 0.120 0.007 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. - CALC: calibration prot=at5g39720 peaks=c13no_new,n15no_new,c13ar_new dref=4.2 - calibration: read prot at5g39720 unknown=warn Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - calibration: read peaks c13no_new format= Peak list "c13no_new.peaks" read, 3501 peaks, 2936 assignments. - calibration: peaks select "** list=1" 3501 of 3501 peaks, 3501 of 3501 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3501 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 1: 1.01E+07 Upper limit set for 3501 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 458 13.1% 3.00-3.99 A: 1165 33.3% 4.00-4.99 A: 1534 43.8% 5.00-5.99 A: 344 9.8% 6.00- A: 0 0.0% All: 3501 100.0% - calibration: read prot at5g39720 unknown=warn append Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - calibration: read peaks n15no_new format= append Peak list "n15no_new.peaks" read, 1847 peaks, 1520 assignments. - calibration: peaks select "** list=2" 1847 of 5348 peaks, 1847 of 5348 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1847 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 2: 5.59E+06 Upper limit set for 1847 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 168 9.1% 3.00-3.99 A: 633 34.3% 4.00-4.99 A: 851 46.1% 5.00-5.99 A: 194 10.5% 6.00- A: 0 0.0% All: 1847 100.0% - calibration: read prot at5g39720 unknown=warn append Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - calibration: read peaks c13ar_new format= append Peak list "c13ar_new.peaks" read, 570 peaks, 272 assignments. - calibration: peaks select "** list=3" 570 of 5918 peaks, 570 of 5918 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 570 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 3: 4.83E+06 Upper limit set for 570 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 56 9.8% 3.00-3.99 A: 176 30.9% 4.00-4.99 A: 313 54.9% 5.00-5.99 A: 25 4.4% 6.00- A: 0 0.0% All: 570 100.0% - calibration: peaks select ** 5918 of 5918 peaks, 5918 of 5918 assignments selected. - CALC: peaks calibrate ** simple 4094 upper limits added, 7/70 at lower/upper bound, average 4.17 A. - CALC: write upl at5g39720-in.upl Distance constraint file "at5g39720-in.upl" written, 4094 upper limits, 4094 assignments. - CALC: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA PHE 147 - QE PHE 147 3.84 3.94 6.76 Number of modified constraints: 2138 - CALC: write upl at5g39720.upl Distance constraint file "at5g39720.upl" written, 2138 upper limits, 2138 assignments. - CALC: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl at5g39720.upl Distance constraint file "at5g39720.upl" read, 2138 upper limits, 2138 assignments. - CALC: read aco at5g39720.aco Angle constraint file "at5g39720.aco" read, 203 constraints for 203 angles. - CALC: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 5671). Structure annealed in 79 s, f = 20.1317. Structure annealed in 77 s, f = 15.5837. Structure annealed in 73 s, f = 16.2154. Structure annealed in 75 s, f = 16.6616. Structure annealed in 76 s, f = 17.0828. Structure annealed in 77 s, f = 16.8489. Structure annealed in 77 s, f = 17.8255. Structure annealed in 77 s, f = 17.3972. Structure annealed in 78 s, f = 16.5971. Structure annealed in 72 s, f = 16.0148. Structure annealed in 68 s, f = 20.4058. Structure annealed in 75 s, f = 14.8507. Structure annealed in 75 s, f = 19.6274. Structure annealed in 75 s, f = 19.3932. Structure annealed in 75 s, f = 16.7946. Structure annealed in 77 s, f = 60.0059. Structure annealed in 80 s, f = 47.9360. Structure annealed in 75 s, f = 15.6607. Structure annealed in 77 s, f = 16.9201. Structure annealed in 74 s, f = 15.1818. Structure annealed in 73 s, f = 18.8197. Structure annealed in 89 s, f = 1298.66. Structure annealed in 76 s, f = 13.7304. Structure annealed in 76 s, f = 16.7448. Structure annealed in 75 s, f = 16.0503. Structure annealed in 75 s, f = 20.3798. Structure annealed in 77 s, f = 17.1214. Structure annealed in 78 s, f = 41.4298. Structure annealed in 79 s, f = 16.7792. Structure annealed in 73 s, f = 15.0773. Structure annealed in 77 s, f = 17.0591. Structure annealed in 75 s, f = 18.0891. Structure annealed in 75 s, f = 16.1268. Structure annealed in 76 s, f = 17.4821. Structure annealed in 75 s, f = 34.0529. Structure annealed in 73 s, f = 19.0863. Structure annealed in 77 s, f = 20.7575. Structure annealed in 78 s, f = 17.0317. Structure annealed in 74 s, f = 26.0215. Structure annealed in 74 s, f = 14.7294. Structure annealed in 76 s, f = 22.7603. Structure annealed in 76 s, f = 28.7558. Structure annealed in 76 s, f = 18.6508. Structure annealed in 75 s, f = 45.1677. Structure annealed in 77 s, f = 14.6141. Structure annealed in 75 s, f = 29.7424. Structure annealed in 74 s, f = 16.9869. Structure annealed in 77 s, f = 59.0143. Structure annealed in 74 s, f = 14.5543. Structure annealed in 73 s, f = 14.9818. Structure annealed in 73 s, f = 25.9242. Structure annealed in 75 s, f = 15.2176. Structure annealed in 70 s, f = 18.4409. Structure annealed in 76 s, f = 18.6549. Structure annealed in 78 s, f = 18.1602. Structure annealed in 76 s, f = 29.1709. Structure annealed in 73 s, f = 19.3745. Structure annealed in 77 s, f = 15.8207. Structure annealed in 73 s, f = 20.0282. Structure annealed in 77 s, f = 33.1884. Structure annealed in 76 s, f = 50.9026. Structure annealed in 74 s, f = 14.3704. Structure annealed in 75 s, f = 17.2018. Structure annealed in 78 s, f = 49.9771. Structure annealed in 76 s, f = 26.2624. Structure annealed in 73 s, f = 29.6537. Structure annealed in 77 s, f = 14.5442. Structure annealed in 75 s, f = 15.1560. Structure annealed in 78 s, f = 18.8796. Structure annealed in 74 s, f = 16.4555. Structure annealed in 74 s, f = 18.7569. Structure annealed in 75 s, f = 16.6312. Structure annealed in 75 s, f = 18.2009. Structure annealed in 74 s, f = 14.4091. Structure annealed in 76 s, f = 16.7637. Structure annealed in 78 s, f = 18.0344. Structure annealed in 74 s, f = 17.8320. Structure annealed in 75 s, f = 15.2359. Structure annealed in 77 s, f = 49.4041. Structure annealed in 74 s, f = 14.7012. Structure annealed in 76 s, f = 14.7826. Structure annealed in 76 s, f = 26.9903. Structure annealed in 73 s, f = 25.5917. Structure annealed in 76 s, f = 15.1849. Structure annealed in 76 s, f = 17.3130. Structure annealed in 77 s, f = 28.7093. Structure annealed in 77 s, f = 18.1918. Structure annealed in 76 s, f = 19.5484. Structure annealed in 76 s, f = 27.8735. Structure annealed in 75 s, f = 18.9042. Structure annealed in 75 s, f = 17.5265. Structure annealed in 74 s, f = 16.8809. Structure annealed in 77 s, f = 15.4459. Structure annealed in 78 s, f = 16.6249. Structure annealed in 72 s, f = 16.7591. Structure annealed in 73 s, f = 16.0918. Structure annealed in 74 s, f = 27.6416. Structure annealed in 75 s, f = 16.0434. Structure annealed in 71 s, f = 16.9842. Structure annealed in 71 s, f = 16.0390. 100 structures finished in 770 s (7 s/structure). - CALC: overview at5g39720.ovw structures=20 pdb Structural statistics: str target upper limits van der Waals torsion angles function # rms max # sum max # rms max 1 13.73 65 0.0340 0.49 9 18.6 0.39 12 2.5023 12.04 2 14.37 63 0.0348 0.49 12 20.3 0.30 14 2.5458 14.05 3 14.41 68 0.0349 0.49 11 19.8 0.36 12 2.4617 15.00 4 14.54 68 0.0352 0.49 9 19.3 0.33 11 2.5813 13.77 5 14.55 62 0.0350 0.50 10 20.3 0.30 15 2.5687 13.58 6 14.61 64 0.0359 0.49 11 19.9 0.30 15 2.4561 13.44 7 14.70 64 0.0361 0.48 7 20.1 0.29 11 2.4554 12.03 8 14.73 65 0.0359 0.49 9 20.2 0.30 11 2.5123 12.01 9 14.78 66 0.0353 0.49 8 21.5 0.29 13 2.5577 13.77 10 14.85 66 0.0350 0.51 11 21.0 0.32 13 2.5335 12.84 11 14.98 57 0.0362 0.92 9 19.1 0.38 15 2.5784 10.95 12 15.08 59 0.0367 0.60 11 19.0 0.30 14 2.5103 13.70 13 15.16 65 0.0366 0.90 9 19.4 0.30 15 2.6386 13.34 14 15.18 67 0.0357 0.49 13 20.4 0.34 12 2.5239 12.56 15 15.18 64 0.0362 0.50 10 20.3 0.32 16 2.6276 13.97 16 15.22 70 0.0364 0.60 12 20.7 0.30 12 2.4436 14.04 17 15.24 71 0.0368 0.51 10 19.6 0.30 14 2.6314 13.03 18 15.45 68 0.0372 0.82 11 20.3 0.29 12 2.5007 13.24 19 15.58 63 0.0368 0.49 11 21.3 0.31 16 2.5632 14.59 20 15.66 68 0.0369 0.81 14 19.9 0.44 14 2.6178 13.82 Ave 14.90 65 0.0359 0.58 10 20.0 0.32 13 2.5405 13.29 +/- 0.45 3 0.0008 0.15 2 0.7 0.04 2 0.0597 0.96 Min 13.73 57 0.0340 0.48 7 18.6 0.29 11 2.4436 10.95 Max 15.66 71 0.0372 0.92 14 21.5 0.44 16 2.6386 15.00 Cut 0.20 0.20 5.00 Overview file "at5g39720.ovw" written. PDB coordinate file "at5g39720.pdb" written, 20 conformers. - CALC: ramaplot at5g39720.rama nobackground label Struct fav add gen dis ------ --- --- --- --- 1 112 33 6 2 (HIS 5, ASP 13) 2 112 36 4 1 (HIS 2) 3 114 36 3 0 4 115 34 4 0 5 113 34 6 0 6 113 34 6 0 7 111 38 3 1 (LYS 156) 8 112 34 5 2 (LYS 155, LYS 156) 9 114 35 2 2 (ASP 13, LYS 155) 10 108 40 5 0 11 113 35 5 0 12 115 32 5 1 (ASP 163) 13 114 36 3 0 14 118 31 4 0 15 112 36 5 0 16 110 39 2 2 (HIS 2, PHE 127) 17 109 39 5 0 18 111 40 2 0 19 116 36 1 0 20 111 38 3 1 (HIS 5) all 73.6% 23.4% 2.6% 0.4% Postscript file "at5g39720.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 16-Dec-2005 07:30:35