Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 10-Nov-2005 16:16:38 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= *** WARNING: Assignment of peak 14 not found in chemical shift list. *** WARNING: Assignment of peak 14 not found in chemical shift list. *** WARNING: Assignment of peak 65 not found in chemical shift list. *** WARNING: Assignment of peak 66 not found in chemical shift list. *** WARNING: Assignment of peak 67 not found in chemical shift list. *** WARNING: Assignment of peak 69 not found in chemical shift list. *** WARNING: Assignment of peak 320 not found in chemical shift list. *** WARNING: Assignment of peak 337 not found in chemical shift list. *** WARNING: Assignment of peak 338 not found in chemical shift list. Peak list "c13ar.peaks" read, 281 peaks, 223 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 225 0.004 0.005 0.045 0.013 1 0.030 2 272 0.000 0.000 0.000 0.000 0 0.030 3 272 0.000 0.000 0.000 0.000 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks H GLN 391 7.918 7.946 0.045 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 97 1 0.045 H GLN 391 1 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 0.031 0.016 1 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 HB2 LEU 396 1.544 1.571 0.031 2 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 8352 1 0.031 HB2 LEU 396 1 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 *** WARNING: Assignment of peak 14 not found in chemical shift list. *** WARNING: Assignment of peak 14 not found in chemical shift list. *** WARNING: Assignment of peak 65 not found in chemical shift list. *** WARNING: Assignment of peak 66 not found in chemical shift list. *** WARNING: Assignment of peak 67 not found in chemical shift list. *** WARNING: Assignment of peak 69 not found in chemical shift list. *** WARNING: Assignment of peak 320 not found in chemical shift list. *** WARNING: Assignment of peak 337 not found in chemical shift list. *** WARNING: Assignment of peak 338 not found in chemical shift list. Peak list "c13ar.peaks" read, 281 peaks, 223 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: 22 7.8% 3.00-3.99 A: 60 21.4% 4.00-4.99 A: 166 59.1% 5.00-5.99 A: 33 11.7% 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 3908 upper limits added, 9/457 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3908 upper limits, 3908 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HB2 TRP 72 - HZ3 TRP 72 4.45 4.82 6.44 Upper HB3 TRP 72 - HZ3 TRP 72 4.57 4.82 6.44 Number of modified constraints: 2043 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2043 upper limits, 2043 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, 2043 upper limits, 2043 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 139 s, f = 138.336. Structure annealed in 139 s, f = 165.427. Structure annealed in 141 s, f = 139.865. Structure annealed in 142 s, f = 146.243. Structure annealed in 140 s, f = 144.111. Structure annealed in 141 s, f = 146.283. Structure annealed in 141 s, f = 148.469. Structure annealed in 141 s, f = 138.665. Structure annealed in 140 s, f = 150.089. Structure annealed in 137 s, f = 136.815. Structure annealed in 105 s, f = 406.208. Structure annealed in 106 s, f = 396.271. Structure annealed in 137 s, f = 139.932. Structure annealed in 139 s, f = 140.634. Structure annealed in 134 s, f = 145.273. Structure annealed in 142 s, f = 139.397. Structure annealed in 142 s, f = 150.950. Structure annealed in 140 s, f = 143.273. Structure annealed in 142 s, f = 151.273. Structure annealed in 143 s, f = 144.082. Structure annealed in 138 s, f = 141.057. Structure annealed in 138 s, f = 148.344. Structure annealed in 137 s, f = 148.275. Structure annealed in 133 s, f = 139.214. Structure annealed in 140 s, f = 139.288. Structure annealed in 142 s, f = 261.977. Structure annealed in 137 s, f = 146.225. Structure annealed in 140 s, f = 137.100. Structure annealed in 140 s, f = 139.123. Structure annealed in 144 s, f = 152.538. Structure annealed in 137 s, f = 143.874. Structure annealed in 140 s, f = 143.551. Structure annealed in 141 s, f = 144.339. Structure annealed in 138 s, f = 152.267. Structure annealed in 140 s, f = 147.021. Structure annealed in 145 s, f = 228.552. Structure annealed in 134 s, f = 253.733. Structure annealed in 142 s, f = 146.301. Structure annealed in 104 s, f = 323.254. Structure annealed in 104 s, f = 138.207. Structure annealed in 135 s, f = 145.898. Structure annealed in 136 s, f = 136.538. Structure annealed in 136 s, f = 259.656. Structure annealed in 140 s, f = 144.091. Structure annealed in 138 s, f = 147.904. Structure annealed in 140 s, f = 368.130. Structure annealed in 140 s, f = 151.533. Structure annealed in 138 s, f = 146.350. Structure annealed in 138 s, f = 134.642. Structure annealed in 138 s, f = 145.481. Structure annealed in 142 s, f = 142.171. Structure annealed in 140 s, f = 142.215. Structure annealed in 134 s, f = 247.016. Structure annealed in 135 s, f = 142.504. Structure annealed in 142 s, f = 146.317. Structure annealed in 138 s, f = 166.510. Structure annealed in 139 s, f = 157.893. Structure annealed in 144 s, f = 155.567. Structure annealed in 139 s, f = 150.917. Structure annealed in 134 s, f = 140.549. Structure annealed in 137 s, f = 146.453. Structure annealed in 139 s, f = 144.742. Structure annealed in 141 s, f = 258.293. Structure annealed in 137 s, f = 142.702. Structure annealed in 140 s, f = 151.067. Structure annealed in 139 s, f = 145.398. Structure annealed in 142 s, f = 223.956. Structure annealed in 139 s, f = 145.721. Structure annealed in 101 s, f = 133.524. Structure annealed in 103 s, f = 139.767. Structure annealed in 140 s, f = 226.568. Structure annealed in 140 s, f = 172.013. Structure annealed in 139 s, f = 140.534. Structure annealed in 142 s, f = 146.680. Structure annealed in 140 s, f = 253.280. Structure annealed in 139 s, f = 153.158. Structure annealed in 137 s, f = 138.639. Structure annealed in 145 s, f = 245.076. Structure annealed in 134 s, f = 139.680. Structure annealed in 141 s, f = 142.083. Structure annealed in 135 s, f = 227.296. Structure annealed in 141 s, f = 147.825. Structure annealed in 138 s, f = 139.187. Structure annealed in 135 s, f = 138.358. Structure annealed in 139 s, f = 137.859. Structure annealed in 139 s, f = 145.940. Structure annealed in 142 s, f = 141.008. Structure annealed in 137 s, f = 155.178. Structure annealed in 140 s, f = 158.501. Structure annealed in 136 s, f = 144.759. Structure annealed in 137 s, f = 138.280. Structure annealed in 138 s, f = 141.338. Structure annealed in 138 s, f = 137.537. Structure annealed in 141 s, f = 146.458. Structure annealed in 141 s, f = 145.394. Structure annealed in 140 s, f = 146.167. Structure annealed in 94 s, f = 137.965. Structure annealed in 103 s, f = 138.257. Structure annealed in 121 s, f = 251.855. Structure annealed in 108 s, f = 142.324. 100 structures finished in 828 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 1 133.52 110 0.1136 8.00 68 66.8 0.52 29 3.5490 25.52 2 134.64 111 0.1140 7.88 85 67.1 0.50 27 3.5340 27.93 3 136.54 113 0.1144 8.02 82 71.3 0.54 38 3.8259 27.64 4 136.82 119 0.1083 7.15 101 80.7 0.45 43 4.5695 27.11 5 137.10 119 0.1115 7.78 83 70.9 0.49 42 4.0012 27.79 6 137.54 116 0.1141 7.89 75 70.4 0.57 33 3.7781 29.04 7 137.86 123 0.1138 7.93 83 70.1 0.49 31 3.4752 26.02 8 137.97 120 0.1120 7.79 89 71.2 0.47 34 3.7905 27.38 9 138.21 118 0.1145 8.15 83 72.1 0.57 29 3.5757 27.34 10 138.26 121 0.1117 7.70 106 76.4 0.52 32 3.8741 28.70 11 138.28 111 0.1147 8.00 78 70.9 0.52 28 3.6952 27.66 12 138.34 117 0.1119 7.76 105 79.8 0.59 35 4.0125 25.96 13 138.36 121 0.1121 7.81 83 77.5 0.47 36 4.1658 29.93 14 138.64 113 0.1149 8.12 70 69.3 0.55 33 3.7225 23.89 15 138.66 125 0.1119 7.56 105 81.8 0.50 38 4.2377 26.22 16 139.12 119 0.1136 7.86 78 69.3 0.50 30 3.8927 30.97 17 139.19 108 0.1136 7.87 81 70.5 0.49 32 4.0919 29.20 18 139.21 132 0.1125 7.68 81 75.2 0.50 34 4.2171 30.30 19 139.29 116 0.1127 7.68 91 76.0 0.50 42 4.1644 27.88 20 139.40 121 0.1127 7.81 93 77.2 0.53 36 4.0763 27.83 Ave 137.85 118 0.1129 7.82 86 73.2 0.51 34 3.9125 27.72 +/- 1.49 6 0.0015 0.21 11 4.4 0.04 5 0.2775 1.67 Min 133.52 108 0.1083 7.15 68 66.8 0.45 27 3.4752 23.89 Max 139.40 132 0.1149 8.15 106 81.8 0.59 43 4.5695 30.97 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 ------ --- --- --- --- 1 134 18 0 0 2 130 21 1 0 3 137 15 0 0 4 135 16 0 1 (LEU 373) 5 134 15 1 2 (GLU 125, GLU 425) 6 130 21 1 0 7 132 17 3 0 8 128 24 0 0 9 130 18 4 0 10 133 11 8 0 11 131 21 0 0 12 131 18 1 2 (ARG 123, ARG 423) 13 130 17 1 4 (ARG 123, GLU 125, ARG 423, GLU 425) 14 133 17 2 0 15 135 17 0 0 16 133 18 1 0 17 130 22 0 0 18 131 21 0 0 19 135 17 0 0 20 133 17 1 1 (LEU 373) all 87.0% 11.9% 0.8% 0.3% Postscript file "znf42.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 10-Nov-2005 16:32:31