++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2014/4 + + Copyright (c) George M. Sheldrick 2001-14 + + Started at 16:50:50 on 30 Jan 2015 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please cite: G.M. Sheldrick (2010), "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification", Acta Cryst. D66, 479-485 (Open Access) if SHELXE proves useful. Command line parameters: shelxe-input.pda -a5 -q -s0.4771 -o -n -t4 -x Cell and symmetry from shelxe-input.pda Phases calculated using atoms from shelxe-input.pda Native data from shelxe-input.hkl Pruned PDB fragment output to shelxe-input.pdo Listing output to shelxe-input.lst Phases output to shelxe-input.phs Poly-Ala trace output to shelxe-input.pdb Summary of parameters to be employed: -a 5 global autotracing cycles -b 5.0 extra B for revised heavy atom sites -c 0.400 fraction of pixels in crossover region -d 0.000 high resolution limit to be applied to input data -e unset fill in missing data up to maximum resolution + 0.2 Ang. -f unset read intensity not F from native .hkl file -F 0.800 fractional weight for phases from previous global cycle -g 1.100 solvent gamma flipping factor -i unset no structure inversion -k 4.5 minimum height/sigma for revised heavy atom sites -l 2 space for 2000000 reflections -L 6 minimum number of residues per chain (if more than 3 chains) -m 20 cycles of density modification -G 0.700 FOM threshold for initial tripeptides and chain extension -n unset do not apply NCS in autotracing -o omit residues from fragment to optimize CC -q alpha-helix search -r 3.00 map resolution (multiplies maximum indices) -s 0.477 solvent fraction -t 4.00 time factor for peptide searches (increase if difficult) -u 500 MB allocatable memory for fragment optimization -U 0.00 abort if less than this % of fragment CA retained within 0.7A -v 0.000 density sharpening factor -w 0.200 weight for experimental phases after cycle 1 -x 2 read name.ent, generate phase and trace diagnostics -y 1.80 highest resolution in Ang. for starting phases from model -z unset do not optimize heavy atoms Space group: P 21 21 21 Allowed origin shift code: 4 3589 Reflections read from file shelxe-input.hkl 3589 Unique data, highest resolution = 2.201 Angstroms Anisotropic scaling: intensities multiplied by 0.000270h^2 +0.000039k^2 -0.001864l^2 +0.000000kl +0.000000hl +0.000000hk 69 Reflections with d > 2.401 and 0 in range 2.401 > d > 2.401 added 561 Atoms read from PDB format file shelxe-input.ent Fourier grid = 128 x 64 x 9 0.000 <= z <= 0.250 92 Point spherical net set up with radius 2.42A 24 Extra Fourier layers will be generated <|E^2-1|> = 0.792 384 Atoms read from PDB format file shelxe-input.pda 0 NCS groups defined in .pda input file 12 Residue blocks eliminated out of 59, increasing CC from 42.37 to 50.59% 47 residues written to shelxe-input.pdo Overall CC between native Eobs and Ecalc (from fragment) = 52.51% Statistics for fragment phases: 0.589 / 0.482 0.757 / 0.855 MPE 44.3 / 46.6 wMPE 38.6 / 40.2 Starting from fragment phases truncated to 1.800A 0.589 / 0.482 0.757 / 0.855 MPE 44.3 / 46.6 wMPE 38.6 / 40.2 = 0.757 for fragment phases 0.603 / 0.497 0.300 / 0.310 MPE 43.2 / 45.2 wMPE 37.4 / 38.5 = 0.300, Contrast = 0.324, Connect. = 0.625 for dens.mod. cycle 1 0.622 / 0.536 0.300 / 0.325 MPE 41.6 / 41.8 wMPE 33.3 / 30.8 = 0.300, Contrast = 0.389, Connect. = 0.660 for dens.mod. cycle 2 0.618 / 0.513 0.300 / 0.335 MPE 41.9 / 43.8 wMPE 32.8 / 31.1 = 0.300, Contrast = 0.462, Connect. = 0.692 for dens.mod. cycle 3 0.621 / 0.534 0.300 / 0.338 MPE 41.6 / 42.0 wMPE 33.0 / 31.6 = 0.300, Contrast = 0.477, Connect. = 0.696 for dens.mod. cycle 4 0.612 / 0.513 0.300 / 0.340 MPE 42.3 / 43.8 wMPE 33.9 / 32.9 = 0.300, Contrast = 0.493, Connect. = 0.704 for dens.mod. cycle 5 0.606 / 0.515 0.300 / 0.339 MPE 42.8 / 43.6 wMPE 34.8 / 33.8 = 0.300, Contrast = 0.498, Connect. = 0.706 for dens.mod. cycle 6 0.599 / 0.523 0.300 / 0.339 MPE 43.3 / 42.9 wMPE 35.6 / 34.4 = 0.300, Contrast = 0.506, Connect. = 0.710 for dens.mod. cycle 7 0.593 / 0.521 0.300 / 0.338 MPE 43.8 / 43.1 wMPE 36.4 / 35.2 = 0.300, Contrast = 0.510, Connect. = 0.711 for dens.mod. cycle 8 0.583 / 0.505 0.300 / 0.337 MPE 44.5 / 44.5 wMPE 36.8 / 35.2 = 0.300, Contrast = 0.513, Connect. = 0.714 for dens.mod. cycle 9 0.577 / 0.497 0.300 / 0.336 MPE 45.1 / 45.2 wMPE 37.5 / 36.0 = 0.300, Contrast = 0.513, Connect. = 0.715 for dens.mod. cycle 10 0.574 / 0.503 0.300 / 0.337 MPE 45.3 / 44.8 wMPE 38.0 / 36.2 = 0.300, Contrast = 0.515, Connect. = 0.717 for dens.mod. cycle 11 0.566 / 0.492 0.300 / 0.337 MPE 46.0 / 45.7 wMPE 38.6 / 36.9 = 0.300, Contrast = 0.514, Connect. = 0.715 for dens.mod. cycle 12 0.565 / 0.508 0.300 / 0.337 MPE 46.1 / 44.3 wMPE 39.0 / 37.2 = 0.300, Contrast = 0.515, Connect. = 0.717 for dens.mod. cycle 13 0.558 / 0.495 0.300 / 0.338 MPE 46.7 / 45.5 wMPE 39.6 / 37.9 = 0.300, Contrast = 0.513, Connect. = 0.716 for dens.mod. cycle 14 0.557 / 0.505 0.300 / 0.337 MPE 46.7 / 44.5 wMPE 39.9 / 38.0 = 0.300, Contrast = 0.514, Connect. = 0.718 for dens.mod. cycle 15 0.551 / 0.497 0.300 / 0.339 MPE 47.2 / 45.2 wMPE 40.3 / 38.6 = 0.300, Contrast = 0.512, Connect. = 0.715 for dens.mod. cycle 16 0.549 / 0.502 0.300 / 0.339 MPE 47.4 / 44.8 wMPE 40.6 / 38.8 = 0.300, Contrast = 0.513, Connect. = 0.718 for dens.mod. cycle 17 0.542 / 0.487 0.300 / 0.340 MPE 47.9 / 46.2 wMPE 41.0 / 39.3 = 0.300, Contrast = 0.510, Connect. = 0.715 for dens.mod. cycle 18 0.539 / 0.490 0.300 / 0.339 MPE 48.2 / 45.9 wMPE 41.3 / 39.3 = 0.300, Contrast = 0.511, Connect. = 0.718 for dens.mod. cycle 19 0.532 / 0.474 0.300 / 0.341 MPE 48.7 / 47.3 wMPE 41.6 / 39.8 = 0.300, Contrast = 0.509, Connect. = 0.715 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 338 peaks > 0.5 sigma used to seed fragment search 10 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) A: 32 16.439 1.779 0.537 0.494 0.935 0.645 CB 1.161 3.10 11.63 17.83 16.28 13.95 13.18 6.20 2.33 2.33 13.178 43.729 0.593 16 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) B: 26 13.116 1.633 0.852 0.358 0.840 0.640 CB 1.203 6.67 14.29 20.00 13.33 8.57 8.57 8.57 0.95 2.86 16.190 35.593 0.589 Global chain diagnostics: 5.24 14.29 19.52 14.76 12.38 11.90 7.62 1.43 1.90 10.952 71.186 0.520 84.7% of CA within 1.0A, 57.6% within 0.5A and 5.1% incorrect CA 52 residues left after pruning, divided into chains as follows: A: 32 B: 20 89.4% starting CA preserved within 1.0A, 78.7% / 0.7A and 68.1% / 0.5A CC for partial structure against native data = 47.16 % Phases from trace: 0.416 / 0.374 0.839 / 0.917 MPE 58.0 / 56.4 wMPE 54.7 / 53.9 Combined phases: 0.458 / 0.371 0.857 / 0.865 MPE 54.6 / 56.6 wMPE 49.1 / 49.0 ------------------------------------------------------------------------------ Global autotracing cycle 2 0.458 / 0.371 0.857 / 0.865 MPE 54.6 / 56.6 wMPE 49.1 / 49.0 = 0.857 for fragment phases 0.470 / 0.379 0.300 / 0.294 MPE 53.6 / 55.9 wMPE 48.2 / 47.0 = 0.300, Contrast = 0.329, Connect. = 0.635 for dens.mod. cycle 1 0.505 / 0.459 0.300 / 0.323 MPE 50.8 / 48.7 wMPE 42.9 / 38.9 = 0.300, Contrast = 0.381, Connect. = 0.667 for dens.mod. cycle 2 0.521 / 0.474 0.300 / 0.336 MPE 49.5 / 47.3 wMPE 40.9 / 37.4 = 0.300, Contrast = 0.449, Connect. = 0.695 for dens.mod. cycle 3 0.533 / 0.487 0.300 / 0.343 MPE 48.6 / 46.2 wMPE 40.2 / 37.5 = 0.300, Contrast = 0.456, Connect. = 0.696 for dens.mod. cycle 4 0.535 / 0.487 0.300 / 0.346 MPE 48.5 / 46.2 wMPE 40.1 / 37.8 = 0.300, Contrast = 0.465, Connect. = 0.700 for dens.mod. cycle 5 0.536 / 0.485 0.300 / 0.347 MPE 48.4 / 46.4 wMPE 40.4 / 38.8 = 0.300, Contrast = 0.471, Connect. = 0.703 for dens.mod. cycle 6 0.532 / 0.474 0.300 / 0.346 MPE 48.7 / 47.3 wMPE 40.6 / 39.1 = 0.300, Contrast = 0.476, Connect. = 0.706 for dens.mod. cycle 7 0.530 / 0.469 0.300 / 0.347 MPE 48.9 / 47.8 wMPE 41.0 / 40.0 = 0.300, Contrast = 0.481, Connect. = 0.710 for dens.mod. cycle 8 0.526 / 0.464 0.300 / 0.347 MPE 49.3 / 48.2 wMPE 41.3 / 40.4 = 0.300, Contrast = 0.484, Connect. = 0.711 for dens.mod. cycle 9 0.519 / 0.441 0.300 / 0.346 MPE 49.9 / 50.3 wMPE 41.7 / 41.1 = 0.300, Contrast = 0.487, Connect. = 0.712 for dens.mod. cycle 10 0.518 / 0.451 0.300 / 0.347 MPE 49.9 / 49.4 wMPE 42.1 / 41.5 = 0.300, Contrast = 0.489, Connect. = 0.712 for dens.mod. cycle 11 0.515 / 0.451 0.300 / 0.347 MPE 50.1 / 49.4 wMPE 42.4 / 41.9 = 0.300, Contrast = 0.491, Connect. = 0.714 for dens.mod. cycle 12 0.514 / 0.454 0.300 / 0.347 MPE 50.3 / 49.2 wMPE 42.8 / 42.4 = 0.300, Contrast = 0.492, Connect. = 0.713 for dens.mod. cycle 13 0.511 / 0.454 0.300 / 0.348 MPE 50.5 / 49.2 wMPE 43.1 / 42.6 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 14 0.509 / 0.454 0.300 / 0.349 MPE 50.7 / 49.2 wMPE 43.5 / 42.9 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 15 0.505 / 0.448 0.300 / 0.349 MPE 51.0 / 49.6 wMPE 43.8 / 43.1 = 0.300, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 16 0.503 / 0.448 0.300 / 0.349 MPE 51.1 / 49.6 wMPE 44.0 / 43.3 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 17 0.500 / 0.446 0.300 / 0.348 MPE 51.4 / 49.9 wMPE 44.3 / 43.4 = 0.300, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 18 0.500 / 0.459 0.300 / 0.349 MPE 51.3 / 48.7 wMPE 44.6 / 43.6 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 19 0.495 / 0.446 0.300 / 0.348 MPE 51.7 / 49.9 wMPE 44.8 / 43.7 = 0.300, Contrast = 0.495, Connect. = 0.714 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 361 peaks > 0.5 sigma used to seed fragment search 15 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) A: 22 17.159 1.688 0.936 0.441 0.905 0.667 CB 1.346 1.12 10.11 15.73 16.85 12.36 8.99 8.99 3.37 1.12 21.348 30.169 0.760 22 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) B: 12 8.177 1.930 0.602 0.489 1.000 0.727 CA 0.806 4.08 16.33 36.73 24.49 0.00 4.08 0.00 2.04 6.12 6.122 16.610 0.381 C: 16 12.389 1.654 0.716 0.389 1.000 0.400 CB 1.268 6.15 7.69 16.92 27.69 7.69 6.15 1.54 6.15 0.00 20.000 22.034 0.686 D: 6 3.692 1.404 0.591 0.561 0.800 0.600 CB 0.871 0.00 0.00 0.00 0.00 4.00 8.00 8.00 0.00 4.00 76.000 8.475 1.380 Using tripeptides from previous cycle as seeds Global chain diagnostics: 3.06 8.67 17.86 19.39 8.67 7.65 5.61 3.57 1.53 23.980 66.441 0.737 67.8% of CA within 1.0A, 47.5% within 0.5A and 6.8% incorrect CA 48 residues left after pruning, divided into chains as follows: A: 22 B: 5 C: 16 D: 5 70.2% starting CA preserved within 1.0A, 59.6% / 0.7A and 48.9% / 0.5A CC for partial structure against native data = 39.19 % Phases from trace: 0.345 / 0.348 0.775 / 0.886 MPE 63.5 / 58.7 wMPE 59.6 / 55.8 Combined phases: 0.390 / 0.358 0.808 / 0.842 MPE 60.1 / 57.8 wMPE 53.9 / 51.1 ------------------------------------------------------------------------------ Global autotracing cycle 3 0.390 / 0.358 0.808 / 0.842 MPE 60.1 / 57.8 wMPE 53.9 / 51.1 = 0.808 for fragment phases 0.400 / 0.366 0.300 / 0.300 MPE 59.2 / 57.1 wMPE 53.2 / 48.9 = 0.300, Contrast = 0.316, Connect. = 0.616 for dens.mod. cycle 1 0.435 / 0.448 0.300 / 0.329 MPE 56.3 / 49.6 wMPE 48.2 / 41.1 = 0.300, Contrast = 0.373, Connect. = 0.646 for dens.mod. cycle 2 0.446 / 0.423 0.300 / 0.344 MPE 55.6 / 52.0 wMPE 46.3 / 40.5 = 0.300, Contrast = 0.451, Connect. = 0.693 for dens.mod. cycle 3 0.464 / 0.456 0.300 / 0.350 MPE 54.1 / 48.9 wMPE 45.3 / 39.8 = 0.300, Contrast = 0.455, Connect. = 0.692 for dens.mod. cycle 4 0.467 / 0.438 0.300 / 0.353 MPE 54.0 / 50.6 wMPE 45.2 / 40.8 = 0.300, Contrast = 0.465, Connect. = 0.699 for dens.mod. cycle 5 0.468 / 0.446 0.300 / 0.353 MPE 53.8 / 49.9 wMPE 45.2 / 40.9 = 0.300, Contrast = 0.469, Connect. = 0.701 for dens.mod. cycle 6 0.467 / 0.443 0.300 / 0.354 MPE 53.9 / 50.1 wMPE 45.5 / 41.9 = 0.300, Contrast = 0.476, Connect. = 0.704 for dens.mod. cycle 7 0.469 / 0.454 0.300 / 0.353 MPE 53.8 / 49.2 wMPE 45.7 / 42.2 = 0.300, Contrast = 0.477, Connect. = 0.706 for dens.mod. cycle 8 0.468 / 0.451 0.300 / 0.353 MPE 53.8 / 49.4 wMPE 46.1 / 42.9 = 0.300, Contrast = 0.482, Connect. = 0.706 for dens.mod. cycle 9 0.464 / 0.441 0.300 / 0.353 MPE 54.1 / 50.3 wMPE 46.4 / 43.4 = 0.300, Contrast = 0.482, Connect. = 0.708 for dens.mod. cycle 10 0.465 / 0.446 0.300 / 0.352 MPE 54.1 / 49.9 wMPE 46.6 / 43.6 = 0.300, Contrast = 0.484, Connect. = 0.710 for dens.mod. cycle 11 0.460 / 0.432 0.300 / 0.353 MPE 54.5 / 51.1 wMPE 46.9 / 44.2 = 0.300, Contrast = 0.484, Connect. = 0.712 for dens.mod. cycle 12 0.459 / 0.438 0.300 / 0.351 MPE 54.5 / 50.6 wMPE 47.0 / 44.2 = 0.300, Contrast = 0.485, Connect. = 0.712 for dens.mod. cycle 13 0.456 / 0.430 0.300 / 0.352 MPE 54.7 / 51.3 wMPE 47.3 / 44.8 = 0.300, Contrast = 0.484, Connect. = 0.713 for dens.mod. cycle 14 0.456 / 0.433 0.300 / 0.351 MPE 54.7 / 51.0 wMPE 47.5 / 44.9 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 15 0.455 / 0.430 0.300 / 0.351 MPE 54.8 / 51.3 wMPE 47.7 / 45.3 = 0.300, Contrast = 0.484, Connect. = 0.715 for dens.mod. cycle 16 0.454 / 0.433 0.300 / 0.351 MPE 54.9 / 51.0 wMPE 47.9 / 45.6 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 17 0.452 / 0.428 0.300 / 0.351 MPE 55.1 / 51.5 wMPE 48.1 / 45.8 = 0.300, Contrast = 0.485, Connect. = 0.715 for dens.mod. cycle 18 0.450 / 0.420 0.300 / 0.350 MPE 55.3 / 52.2 wMPE 48.4 / 46.2 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 19 0.447 / 0.415 0.300 / 0.351 MPE 55.5 / 52.7 wMPE 48.5 / 46.3 = 0.300, Contrast = 0.484, Connect. = 0.715 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 350 peaks > 0.5 sigma used to seed fragment search 13 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) A: 19 13.140 1.758 0.631 0.478 0.833 0.556 CB 1.325 3.90 11.69 16.88 31.17 10.39 6.49 2.60 3.90 0.00 12.987 26.102 0.569 21 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) B: 11 4.316 1.761 0.082 0.483 0.900 0.700 CA 0.810 2.22 22.22 28.89 22.22 13.33 4.44 4.44 2.22 0.00 0.000 15.254 0.314 C: 15 15.356 1.659 1.063 0.469 1.000 0.643 CA 1.238 3.28 11.48 18.03 21.31 11.48 6.56 9.84 1.64 0.00 16.393 20.678 0.520 Using tripeptides from previous cycle as seeds D: 12 3.553 1.333 0.325 0.298 0.727 0.545 CB 1.045 0.00 0.00 0.00 0.00 0.00 4.08 4.08 2.04 4.08 85.714 16.610 1.593 Global chain diagnostics: 3.43 12.57 20.57 25.71 11.43 6.29 5.71 2.86 0.00 11.429 59.322 0.501 71.2% of CA within 1.0A, 55.9% within 0.5A and 1.7% incorrect CA 43 residues left after pruning, divided into chains as follows: A: 19 B: 9 C: 15 70.2% starting CA preserved within 1.0A, 61.7% / 0.7A and 46.8% / 0.5A CC for partial structure against native data = 36.62 % Phases from trace: 0.365 / 0.332 0.749 / 0.873 MPE 62.1 / 60.1 wMPE 58.1 / 58.3 Combined phases: 0.402 / 0.325 0.788 / 0.826 MPE 59.3 / 60.8 wMPE 53.0 / 53.7 ------------------------------------------------------------------------------ Global autotracing cycle 4 0.402 / 0.325 0.788 / 0.826 MPE 59.3 / 60.8 wMPE 53.0 / 53.7 = 0.788 for fragment phases 0.415 / 0.326 0.300 / 0.303 MPE 58.3 / 60.6 wMPE 52.1 / 51.9 = 0.300, Contrast = 0.337, Connect. = 0.623 for dens.mod. cycle 1 0.457 / 0.412 0.300 / 0.332 MPE 54.9 / 52.9 wMPE 47.2 / 43.8 = 0.300, Contrast = 0.397, Connect. = 0.649 for dens.mod. cycle 2 0.477 / 0.441 0.300 / 0.345 MPE 53.2 / 50.3 wMPE 45.1 / 41.8 = 0.300, Contrast = 0.464, Connect. = 0.688 for dens.mod. cycle 3 0.486 / 0.438 0.300 / 0.351 MPE 52.5 / 50.6 wMPE 44.1 / 41.4 = 0.300, Contrast = 0.466, Connect. = 0.691 for dens.mod. cycle 4 0.490 / 0.438 0.300 / 0.354 MPE 52.1 / 50.6 wMPE 44.0 / 41.7 = 0.300, Contrast = 0.474, Connect. = 0.695 for dens.mod. cycle 5 0.491 / 0.433 0.300 / 0.354 MPE 52.0 / 51.0 wMPE 44.0 / 42.1 = 0.300, Contrast = 0.479, Connect. = 0.697 for dens.mod. cycle 6 0.492 / 0.443 0.300 / 0.353 MPE 51.9 / 50.1 wMPE 44.3 / 42.9 = 0.300, Contrast = 0.485, Connect. = 0.700 for dens.mod. cycle 7 0.486 / 0.433 0.300 / 0.352 MPE 52.4 / 51.0 wMPE 44.6 / 43.2 = 0.300, Contrast = 0.488, Connect. = 0.700 for dens.mod. cycle 8 0.484 / 0.425 0.300 / 0.352 MPE 52.6 / 51.7 wMPE 45.1 / 44.1 = 0.300, Contrast = 0.491, Connect. = 0.704 for dens.mod. cycle 9 0.480 / 0.425 0.300 / 0.352 MPE 52.9 / 51.7 wMPE 45.4 / 44.5 = 0.300, Contrast = 0.492, Connect. = 0.704 for dens.mod. cycle 10 0.475 / 0.412 0.300 / 0.352 MPE 53.2 / 52.9 wMPE 45.8 / 45.3 = 0.300, Contrast = 0.493, Connect. = 0.706 for dens.mod. cycle 11 0.475 / 0.420 0.300 / 0.352 MPE 53.3 / 52.2 wMPE 46.1 / 45.3 = 0.300, Contrast = 0.493, Connect. = 0.707 for dens.mod. cycle 12 0.469 / 0.405 0.300 / 0.352 MPE 53.7 / 53.6 wMPE 46.4 / 45.9 = 0.300, Contrast = 0.494, Connect. = 0.708 for dens.mod. cycle 13 0.472 / 0.428 0.300 / 0.352 MPE 53.4 / 51.5 wMPE 46.7 / 45.8 = 0.300, Contrast = 0.494, Connect. = 0.707 for dens.mod. cycle 14 0.466 / 0.405 0.300 / 0.352 MPE 54.0 / 53.6 wMPE 47.0 / 46.4 = 0.300, Contrast = 0.495, Connect. = 0.709 for dens.mod. cycle 15 0.468 / 0.423 0.300 / 0.351 MPE 53.8 / 52.0 wMPE 47.2 / 46.2 = 0.300, Contrast = 0.495, Connect. = 0.709 for dens.mod. cycle 16 0.460 / 0.397 0.300 / 0.351 MPE 54.5 / 54.3 wMPE 47.5 / 46.7 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 17 0.461 / 0.415 0.300 / 0.351 MPE 54.4 / 52.7 wMPE 47.6 / 46.4 = 0.300, Contrast = 0.495, Connect. = 0.710 for dens.mod. cycle 18 0.456 / 0.399 0.300 / 0.351 MPE 54.8 / 54.0 wMPE 47.9 / 46.7 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 19 0.455 / 0.405 0.300 / 0.351 MPE 54.9 / 53.6 wMPE 48.0 / 46.5 = 0.300, Contrast = 0.496, Connect. = 0.709 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 365 peaks > 0.5 sigma used to seed fragment search 10 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) A: 17 7.898 1.688 0.187 0.443 1.000 0.688 CA 1.044 0.00 10.14 15.94 10.14 13.04 14.49 11.59 4.35 5.80 14.493 23.390 0.625 23 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) B: 28 23.573 1.821 0.774 0.584 1.000 0.741 CA 1.296 5.31 19.47 26.55 15.93 8.85 7.08 5.31 0.88 3.54 7.080 38.305 0.456 17 residues pruned to eliminate duplicates C: 7 4.988 1.614 0.317 0.542 0.833 0.833 CA 1.103 0.00 3.45 17.24 20.69 10.34 13.79 6.90 3.45 6.90 17.241 9.831 0.666 Using tripeptides from previous cycle as seeds D: 15 10.134 1.706 0.634 0.351 1.000 0.429 CA 1.141 0.00 9.84 21.31 14.75 8.20 8.20 13.11 3.28 8.20 13.115 20.678 0.559 7 residues pruned to eliminate duplicates Global chain diagnostics: 3.45 16.09 24.71 15.52 8.62 7.47 8.05 1.72 5.17 9.195 58.983 0.492 71.2% of CA within 1.0A, 52.5% within 0.5A and 1.7% incorrect CA 43 residues left after pruning, divided into chains as follows: A: 28 B: 15 63.8% starting CA preserved within 1.0A, 55.3% / 0.7A and 46.8% / 0.5A CC for partial structure against native data = 40.72 % Phases from trace: 0.372 / 0.363 0.784 / 0.885 MPE 61.2 / 57.3 wMPE 57.1 / 54.2 Combined phases: 0.409 / 0.371 0.821 / 0.849 MPE 58.3 / 56.6 wMPE 52.8 / 50.6 ------------------------------------------------------------------------------ Global autotracing cycle 5 0.409 / 0.371 0.821 / 0.849 MPE 58.3 / 56.6 wMPE 52.8 / 50.6 = 0.821 for fragment phases 0.420 / 0.371 0.300 / 0.298 MPE 57.6 / 56.6 wMPE 52.0 / 48.2 = 0.300, Contrast = 0.349, Connect. = 0.620 for dens.mod. cycle 1 0.449 / 0.423 0.300 / 0.328 MPE 55.2 / 52.0 wMPE 47.2 / 41.1 = 0.300, Contrast = 0.403, Connect. = 0.649 for dens.mod. cycle 2 0.469 / 0.454 0.300 / 0.344 MPE 53.6 / 49.2 wMPE 45.1 / 39.3 = 0.300, Contrast = 0.470, Connect. = 0.687 for dens.mod. cycle 3 0.475 / 0.446 0.300 / 0.349 MPE 53.1 / 49.9 wMPE 44.1 / 38.5 = 0.300, Contrast = 0.470, Connect. = 0.689 for dens.mod. cycle 4 0.478 / 0.456 0.300 / 0.350 MPE 52.9 / 48.9 wMPE 43.7 / 38.3 = 0.300, Contrast = 0.476, Connect. = 0.693 for dens.mod. cycle 5 0.477 / 0.446 0.300 / 0.349 MPE 53.0 / 49.9 wMPE 43.7 / 38.7 = 0.300, Contrast = 0.478, Connect. = 0.697 for dens.mod. cycle 6 0.478 / 0.448 0.300 / 0.348 MPE 52.9 / 49.6 wMPE 43.9 / 38.9 = 0.300, Contrast = 0.484, Connect. = 0.699 for dens.mod. cycle 7 0.475 / 0.438 0.300 / 0.347 MPE 53.1 / 50.6 wMPE 44.2 / 39.6 = 0.300, Contrast = 0.484, Connect. = 0.703 for dens.mod. cycle 8 0.477 / 0.446 0.300 / 0.346 MPE 52.9 / 49.9 wMPE 44.5 / 39.9 = 0.300, Contrast = 0.488, Connect. = 0.704 for dens.mod. cycle 9 0.473 / 0.438 0.300 / 0.346 MPE 53.2 / 50.6 wMPE 44.8 / 40.6 = 0.300, Contrast = 0.489, Connect. = 0.706 for dens.mod. cycle 10 0.474 / 0.451 0.300 / 0.345 MPE 53.1 / 49.4 wMPE 45.1 / 40.7 = 0.300, Contrast = 0.492, Connect. = 0.708 for dens.mod. cycle 11 0.470 / 0.443 0.300 / 0.346 MPE 53.4 / 50.1 wMPE 45.5 / 41.5 = 0.300, Contrast = 0.492, Connect. = 0.709 for dens.mod. cycle 12 0.468 / 0.441 0.300 / 0.345 MPE 53.6 / 50.3 wMPE 45.7 / 41.5 = 0.300, Contrast = 0.493, Connect. = 0.710 for dens.mod. cycle 13 0.464 / 0.430 0.300 / 0.345 MPE 54.0 / 51.3 wMPE 46.1 / 42.2 = 0.300, Contrast = 0.494, Connect. = 0.711 for dens.mod. cycle 14 0.464 / 0.441 0.300 / 0.345 MPE 54.0 / 50.3 wMPE 46.3 / 42.2 = 0.300, Contrast = 0.495, Connect. = 0.711 for dens.mod. cycle 15 0.459 / 0.433 0.300 / 0.345 MPE 54.3 / 51.0 wMPE 46.6 / 42.8 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 16 0.460 / 0.443 0.300 / 0.345 MPE 54.3 / 50.1 wMPE 46.8 / 42.8 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 17 0.454 / 0.430 0.300 / 0.345 MPE 54.7 / 51.3 wMPE 47.1 / 43.3 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 18 0.454 / 0.438 0.300 / 0.346 MPE 54.7 / 50.6 wMPE 47.3 / 43.3 = 0.300, Contrast = 0.496, Connect. = 0.712 for dens.mod. cycle 19 0.448 / 0.420 0.300 / 0.345 MPE 55.2 / 52.2 wMPE 47.6 / 43.9 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 349 peaks > 0.5 sigma used to seed fragment search 16 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) A: 33 16.547 1.768 0.570 0.433 0.906 0.688 CB 1.246 1.50 6.77 15.04 21.05 21.05 11.28 6.02 3.76 3.01 10.526 45.085 0.581 9 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) B: 6 2.347 1.411 -0.133 0.461 1.000 0.800 CB 0.892 0.00 4.00 8.00 4.00 4.00 8.00 8.00 0.00 0.00 64.000 8.475 1.357 C: 14 5.571 1.570 0.662 0.230 0.769 0.385 CB 1.054 0.00 7.02 7.02 24.56 17.54 5.26 5.26 1.75 0.00 31.579 19.322 0.838 Using tripeptides from previous cycle as seeds D: 24 7.691 1.504 0.487 0.284 0.783 0.261 CB 1.168 0.00 4.12 7.22 11.34 9.28 12.37 4.12 7.22 3.09 41.237 32.881 1.049 14 residues pruned to eliminate duplicates Global chain diagnostics: 0.91 5.48 12.33 16.89 16.89 12.33 6.39 5.02 2.74 21.005 74.237 0.745 78.0% of CA within 1.0A, 45.8% within 0.5A and 8.5% incorrect CA 54 residues left after pruning, divided into chains as follows: A: 33 B: 4 C: 17 74.5% starting CA preserved within 1.0A, 66.0% / 0.7A and 44.7% / 0.5A CC for partial structure against native data = 44.19 % Phases from trace: 0.384 / 0.379 0.809 / 0.895 MPE 60.4 / 55.9 wMPE 56.2 / 51.9 Combined phases: 0.415 / 0.379 0.845 / 0.852 MPE 58.0 / 55.9 wMPE 52.7 / 48.4 ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 1 used as input for final density modification 0.415 / 0.379 0.845 / 0.852 MPE 58.0 / 55.9 wMPE 52.7 / 48.4 = 0.845 for fragment phases 0.428 / 0.387 0.300 / 0.294 MPE 56.9 / 55.2 wMPE 52.2 / 47.7 = 0.300, Contrast = 0.324, Connect. = 0.625 for dens.mod. cycle 1 0.450 / 0.410 0.303 / 0.327 MPE 55.1 / 53.1 wMPE 47.3 / 42.0 = 0.303, Contrast = 0.382, Connect. = 0.662 for dens.mod. cycle 2 0.467 / 0.428 0.304 / 0.342 MPE 53.7 / 51.5 wMPE 45.4 / 41.3 = 0.304, Contrast = 0.460, Connect. = 0.702 for dens.mod. cycle 3 0.477 / 0.443 0.304 / 0.348 MPE 52.9 / 50.1 wMPE 44.6 / 41.2 = 0.304, Contrast = 0.464, Connect. = 0.702 for dens.mod. cycle 4 0.480 / 0.436 0.304 / 0.351 MPE 52.7 / 50.8 wMPE 44.6 / 42.2 = 0.304, Contrast = 0.475, Connect. = 0.706 for dens.mod. cycle 5 0.480 / 0.436 0.304 / 0.352 MPE 52.7 / 50.8 wMPE 44.7 / 42.6 = 0.304, Contrast = 0.478, Connect. = 0.706 for dens.mod. cycle 6 0.479 / 0.433 0.304 / 0.353 MPE 52.8 / 51.0 wMPE 45.1 / 43.8 = 0.304, Contrast = 0.483, Connect. = 0.707 for dens.mod. cycle 7 0.480 / 0.438 0.304 / 0.353 MPE 52.7 / 50.6 wMPE 45.3 / 44.1 = 0.304, Contrast = 0.487, Connect. = 0.708 for dens.mod. cycle 8 0.475 / 0.425 0.304 / 0.353 MPE 53.1 / 51.7 wMPE 45.8 / 45.2 = 0.304, Contrast = 0.489, Connect. = 0.710 for dens.mod. cycle 9 0.474 / 0.425 0.304 / 0.353 MPE 53.3 / 51.7 wMPE 46.1 / 45.4 = 0.304, Contrast = 0.491, Connect. = 0.710 for dens.mod. cycle 10 0.470 / 0.412 0.304 / 0.353 MPE 53.6 / 52.9 wMPE 46.5 / 46.2 = 0.304, Contrast = 0.493, Connect. = 0.711 for dens.mod. cycle 11 0.468 / 0.412 0.304 / 0.353 MPE 53.7 / 52.9 wMPE 46.7 / 46.4 = 0.304, Contrast = 0.493, Connect. = 0.712 for dens.mod. cycle 12 0.463 / 0.399 0.304 / 0.354 MPE 54.1 / 54.0 wMPE 47.0 / 47.0 = 0.304, Contrast = 0.494, Connect. = 0.713 for dens.mod. cycle 13 0.462 / 0.405 0.304 / 0.353 MPE 54.2 / 53.6 wMPE 47.3 / 47.2 = 0.304, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 14 0.460 / 0.399 0.304 / 0.354 MPE 54.4 / 54.0 wMPE 47.6 / 47.7 = 0.304, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 15 0.455 / 0.387 0.304 / 0.353 MPE 54.8 / 55.2 wMPE 47.8 / 47.8 = 0.304, Contrast = 0.496, Connect. = 0.715 for dens.mod. cycle 16 0.454 / 0.389 0.304 / 0.353 MPE 54.9 / 55.0 wMPE 48.0 / 48.2 = 0.304, Contrast = 0.496, Connect. = 0.714 for dens.mod. cycle 17 0.450 / 0.379 0.304 / 0.353 MPE 55.2 / 55.9 wMPE 48.2 / 48.3 = 0.304, Contrast = 0.497, Connect. = 0.715 for dens.mod. cycle 18 0.449 / 0.379 0.304 / 0.354 MPE 55.4 / 55.9 wMPE 48.5 / 48.7 = 0.304, Contrast = 0.498, Connect. = 0.714 for dens.mod. cycle 19 0.444 / 0.369 0.304 / 0.354 MPE 55.7 / 56.8 wMPE 48.7 / 48.8 = 0.304, Contrast = 0.498, Connect. = 0.715 for dens.mod. cycle 20 Shift from model in .ent: dx= 0.000 dy= 0.000 dz= 0.000 Estimated mean FOM and mapCC as a function of resolution d inf - 4.96 - 3.87 - 3.36 - 3.04 - 2.82 - 2.64 - 2.50 - 2.39 - 2.29 - 2.21 0.760 0.787 0.735 0.719 0.707 0.747 0.752 0.691 0.573 0.484 0.893 0.896 0.872 0.858 0.897 0.919 0.936 0.887 0.743 0.682 N 359 360 363 363 350 371 362 345 367 349 Estimated mean FOM = 0.696 Pseudo-free CC = 69.75 % Best trace (cycle 1 with CC 47.16%) was saved as shelxe-input.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 0.3 - FFTs and peak-searches 2.6 - Sphere of influence 0.1 - Rest of density modification 76.1 - Alpha-helix search 35.1 - Tripeptide search 44.6 - Chain tracing 0.0 - NCS analysis 1.1 - B-value refinement for trace 0.0 - Rest of tracing 0.1 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 16:53:30 Total time: 160.32 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++