Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 14-Jun-2005 18:34:51 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 2.0 (intel-lam) Copyright (c) 2002-04 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/s/src/cyana-2.0/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 cyana> cyana> cyana> - NOEASSIGN: noeassign peaks=n15no,c13no,c13ar,fc12no prot=znf42 keep=KEEP ======================= Check ======================== - noeassign: peakcheck peaks=n15no,c13no,c13ar,fc12no format= prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1976 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 : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1976 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1293 peaks, 99 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 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 QD2 LEU 373 -0.640 4.25 0.72 0.32 -1.03 1.31 8 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 99 0.000 0.000 0.008 0.001 0 0.030 2 1287 0.000 0.000 0.002 0.000 0 0.030 3 1287 0.000 0.000 0.006 0.001 0 0.300 - 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 : c13no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1976 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3513 peaks, 1018 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1018 0.000 0.000 0.015 0.001 0 0.030 2 3513 0.000 0.000 0.005 0.000 0 0.030 3 3513 0.000 0.000 0.222 0.014 0 0.300 - 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, 1976 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 17 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 17 0.000 0.000 0.001 0.000 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 0.300 - 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, 1976 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 332 peaks, 156 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 156 0.000 -0.001 0.029 0.008 0 0.030 2 330 0.000 0.000 0.010 0.003 0 0.030 3 330 0.000 0.000 0.000 0.000 0 0.300 - 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. - noeassign: cisprocheck CB CG CB-CG Ptrans Pcis Result PRO 38: 32.81 26.98 5.82 0.981 0.019 trans PRO 40: 32.29 27.95 4.34 1.000 0.000 trans PRO 58: 33.13 27.95 5.18 0.998 0.002 trans PRO 75: 32.40 27.63 4.76 0.999 0.001 trans PRO 97: 31.19 28.28 2.91 1.000 0.000 trans PRO 98: 32.61 28.20 4.41 1.000 0.000 trans PRO 109: 32.18 28.28 3.91 1.000 0.000 trans PRO 112: 32.80 28.60 4.20 1.000 0.000 trans PRO 126: 32.16 27.63 4.53 1.000 0.000 trans PRO 338: 32.81 26.98 5.82 0.981 0.019 trans PRO 340: 32.29 27.95 4.34 1.000 0.000 trans PRO 358: 33.13 27.95 5.18 0.998 0.002 trans PRO 375: 32.40 27.63 4.76 0.999 0.001 trans PRO 397: 31.19 28.28 2.91 1.000 0.000 trans PRO 398: 32.61 28.20 4.41 1.000 0.000 trans PRO 409: 32.18 28.28 3.91 1.000 0.000 trans PRO 412: 32.80 28.60 4.20 1.000 0.000 trans PRO 426: 32.16 27.63 4.53 1.000 0.000 trans =================== NOE assignment cycle 1 =================== - noeassign: ./init - init: read lib /s/src/cyana-2.0/lib/cyana.lib Library file "/s/src/cyana-2.0/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 - noeassign: calibration prot=znf42 peaks=n15no,c13no,c13ar,fc12no format= consta nt= dref=4.0 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1976 chemical shifts. - calibration: read peaks n15no format= Peak list "n15no.peaks" read, 1293 peaks, 99 assignments. - calibration: peaks select "** list=1" 1293 of 1293 peaks, 1293 of 1293 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1293 peaks set. - calibration: peaks simplecal dref=4.0 Calibration constant for peak list 1: 6.09E+06 Upper limit set for 1293 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 141 10.9% 3.00-3.99 A: 552 42.7% 4.00-4.99 A: 480 37.1% 5.00-5.99 A: 117 9.0% 6.00- A: 0 0.0% All: 1293 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1976 chemical shifts. - calibration: read peaks c13no format= append Peak list "c13no.peaks" read, 3513 peaks, 1018 assignments. - calibration: peaks select "** list=2" 3513 of 4806 peaks, 3513 of 4806 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3513 peaks set. - calibration: peaks simplecal dref=4.0 Calibration constant for peak list 2: 1.40E+07 Upper limit set for 3513 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 549 15.6% 3.00-3.99 A: 1392 39.6% 4.00-4.99 A: 1230 35.0% 5.00-5.99 A: 339 9.6% 6.00- A: 0 0.0% All: 3513 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1976 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 17 assignments. - calibration: peaks select "** list=3" 281 of 5087 peaks, 281 of 5087 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal dref=4.0 Calibration constant for peak list 3: 1.06E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 31 11.0% 3.00-3.99 A: 118 42.0% 4.00-4.99 A: 129 45.9% 5.00-5.99 A: 2 0.7% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1976 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 332 peaks, 156 assignments. - calibration: peaks select "** list=4" 332 of 5419 peaks, 332 of 5419 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 332 peaks set. - calibration: peaks simplecal dref=4.0 Calibration constant for peak list 4: 5.04E+06 Upper limit set for 332 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 12 3.6% 3.00-3.99 A: 175 52.7% 4.00-4.99 A: 134 40.4% 5.00-5.99 A: 10 3.0% 6.00- A: 0 0.0% All: 332 100.0% - calibration: peaks select ** 5419 of 5419 peaks, 5419 of 5419 assignments selected. - NOEASSIGN:KEEP: peaks select "*,* levels=175..400" 52 of 5419 peaks, 52 of 5419 assignments selected. - noeassign: peak unassign "! / **" Assignment of 5367 peaks deleted. - noeassign: peaks select "! *, *" 5367 of 5419 peaks, 5367 of 5419 assignments selected. - noeassign: read upl cycle0.upl append Distance constraint file "cycle0.upl" read, 31549 upper limits, 31549 assignments. - noeassign: assign probability=p quality=0.45 violation=v elasticity=1.0..1.0 ma tchfactor=matchfactor alignfactor=alignfactor confidence=0.5 - noeassign: peaks calibrate ** simple 4644 upper limits added, 36/44 at lower/upper bound, average 4.02 A. - noeassign: distance unique 116 duplicate distance constraints deleted. - noeassign: distance select "*, * levels=2.. multiple=ifall" 1651 of 4528 distance constraints, 7432 of 15923 assignments selected. - noeassign: distance combine sort=individual equal 1651 constraints: 3 unchanged, 1648 combined, 0 deleted. - noeassign: distance select "*, *" 4528 of 4528 distance constraints, 23335 of 23335 assignments selected. - noeassign: distance multiple 1111 distance constraints deleted. - noeassign: molecules symmetrize 20807 symmetric dimer distance constraints added. - noeassign: distance multiple 0 distance constraints deleted. - noeassign: write upl cycle1.upl Distance constraint file "cycle1.upl" written, 6834 upper limits, 41614 assignments. - noeassign: caltab Distance bounds: -2.99 A: 348 5.1% 3.00-3.99 A: 4150 60.7% 4.00-4.99 A: 2092 30.6% 5.00-5.99 A: 238 3.5% 6.00- A: 0 0.0% All: 6834 100.0% - noeassign: structcalc constraints=cycle1.upl,znf42.aco prefix=cycle1 - structcalc: ./init - init: read lib /s/src/cyana-2.0/lib/cyana.lib Library file "/s/src/cyana-2.0/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 - structcalc: readdata cycle1.upl Distance constraint file "cycle1.upl" read, 6834 upper limits, 41614 assignments. Angle constraint file "znf42.aco" read, 270 constraints for 270 angles. 100 structures selected. 100 random structures created (seed 434726). Terminated