++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2014/4 + + Copyright (c) George M. Sheldrick 2001-14 + + Started at 18:15:03 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 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 unset no 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 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% Starting from fragment phases truncated to 1.800A = 0.757 for fragment phases = 0.300, Contrast = 0.324, Connect. = 0.625 for dens.mod. cycle 1 = 0.300, Contrast = 0.389, Connect. = 0.660 for dens.mod. cycle 2 = 0.300, Contrast = 0.462, Connect. = 0.692 for dens.mod. cycle 3 = 0.300, Contrast = 0.477, Connect. = 0.696 for dens.mod. cycle 4 = 0.300, Contrast = 0.493, Connect. = 0.704 for dens.mod. cycle 5 = 0.300, Contrast = 0.498, Connect. = 0.706 for dens.mod. cycle 6 = 0.300, Contrast = 0.506, Connect. = 0.710 for dens.mod. cycle 7 = 0.300, Contrast = 0.510, Connect. = 0.711 for dens.mod. cycle 8 = 0.300, Contrast = 0.513, Connect. = 0.714 for dens.mod. cycle 9 = 0.300, Contrast = 0.513, Connect. = 0.715 for dens.mod. cycle 10 = 0.300, Contrast = 0.515, Connect. = 0.717 for dens.mod. cycle 11 = 0.300, Contrast = 0.514, Connect. = 0.715 for dens.mod. cycle 12 = 0.300, Contrast = 0.515, Connect. = 0.717 for dens.mod. cycle 13 = 0.300, Contrast = 0.513, Connect. = 0.716 for dens.mod. cycle 14 = 0.300, Contrast = 0.514, Connect. = 0.718 for dens.mod. cycle 15 = 0.300, Contrast = 0.512, Connect. = 0.715 for dens.mod. cycle 16 = 0.300, Contrast = 0.513, Connect. = 0.718 for dens.mod. cycle 17 = 0.300, Contrast = 0.510, Connect. = 0.715 for dens.mod. cycle 18 = 0.300, Contrast = 0.511, Connect. = 0.718 for dens.mod. cycle 19 = 0.300, Contrast = 0.509, Connect. = 0.715 for dens.mod. cycle 20 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 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 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 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.857 for fragment phases = 0.300, Contrast = 0.329, Connect. = 0.635 for dens.mod. cycle 1 = 0.300, Contrast = 0.381, Connect. = 0.667 for dens.mod. cycle 2 = 0.300, Contrast = 0.449, Connect. = 0.695 for dens.mod. cycle 3 = 0.300, Contrast = 0.456, Connect. = 0.696 for dens.mod. cycle 4 = 0.300, Contrast = 0.465, Connect. = 0.700 for dens.mod. cycle 5 = 0.300, Contrast = 0.471, Connect. = 0.703 for dens.mod. cycle 6 = 0.300, Contrast = 0.476, Connect. = 0.706 for dens.mod. cycle 7 = 0.300, Contrast = 0.481, Connect. = 0.710 for dens.mod. cycle 8 = 0.300, Contrast = 0.484, Connect. = 0.711 for dens.mod. cycle 9 = 0.300, Contrast = 0.487, Connect. = 0.712 for dens.mod. cycle 10 = 0.300, Contrast = 0.489, Connect. = 0.712 for dens.mod. cycle 11 = 0.300, Contrast = 0.491, Connect. = 0.714 for dens.mod. cycle 12 = 0.300, Contrast = 0.492, Connect. = 0.713 for dens.mod. cycle 13 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 14 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 15 = 0.300, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 16 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 17 = 0.300, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 18 = 0.300, Contrast = 0.494, Connect. = 0.714 for dens.mod. cycle 19 = 0.300, Contrast = 0.495, Connect. = 0.714 for dens.mod. cycle 20 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 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 C: 16 12.389 1.654 0.716 0.389 1.000 0.400 CB 1.268 D: 6 3.692 1.404 0.591 0.561 0.800 0.600 CB 0.871 Using tripeptides from previous cycle as seeds 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 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.808 for fragment phases = 0.300, Contrast = 0.316, Connect. = 0.616 for dens.mod. cycle 1 = 0.300, Contrast = 0.373, Connect. = 0.646 for dens.mod. cycle 2 = 0.300, Contrast = 0.451, Connect. = 0.693 for dens.mod. cycle 3 = 0.300, Contrast = 0.455, Connect. = 0.692 for dens.mod. cycle 4 = 0.300, Contrast = 0.465, Connect. = 0.699 for dens.mod. cycle 5 = 0.300, Contrast = 0.469, Connect. = 0.701 for dens.mod. cycle 6 = 0.300, Contrast = 0.476, Connect. = 0.704 for dens.mod. cycle 7 = 0.300, Contrast = 0.477, Connect. = 0.706 for dens.mod. cycle 8 = 0.300, Contrast = 0.482, Connect. = 0.706 for dens.mod. cycle 9 = 0.300, Contrast = 0.482, Connect. = 0.708 for dens.mod. cycle 10 = 0.300, Contrast = 0.484, Connect. = 0.710 for dens.mod. cycle 11 = 0.300, Contrast = 0.484, Connect. = 0.712 for dens.mod. cycle 12 = 0.300, Contrast = 0.485, Connect. = 0.712 for dens.mod. cycle 13 = 0.300, Contrast = 0.484, Connect. = 0.713 for dens.mod. cycle 14 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 15 = 0.300, Contrast = 0.484, Connect. = 0.715 for dens.mod. cycle 16 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 17 = 0.300, Contrast = 0.485, Connect. = 0.715 for dens.mod. cycle 18 = 0.300, Contrast = 0.485, Connect. = 0.714 for dens.mod. cycle 19 = 0.300, Contrast = 0.484, Connect. = 0.715 for dens.mod. cycle 20 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 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 C: 15 15.356 1.659 1.063 0.469 1.000 0.643 CA 1.238 Using tripeptides from previous cycle as seeds D: 12 3.553 1.333 0.325 0.298 0.727 0.545 CB 1.045 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 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.788 for fragment phases = 0.300, Contrast = 0.337, Connect. = 0.623 for dens.mod. cycle 1 = 0.300, Contrast = 0.397, Connect. = 0.649 for dens.mod. cycle 2 = 0.300, Contrast = 0.464, Connect. = 0.688 for dens.mod. cycle 3 = 0.300, Contrast = 0.466, Connect. = 0.691 for dens.mod. cycle 4 = 0.300, Contrast = 0.474, Connect. = 0.695 for dens.mod. cycle 5 = 0.300, Contrast = 0.479, Connect. = 0.697 for dens.mod. cycle 6 = 0.300, Contrast = 0.485, Connect. = 0.700 for dens.mod. cycle 7 = 0.300, Contrast = 0.488, Connect. = 0.700 for dens.mod. cycle 8 = 0.300, Contrast = 0.491, Connect. = 0.704 for dens.mod. cycle 9 = 0.300, Contrast = 0.492, Connect. = 0.704 for dens.mod. cycle 10 = 0.300, Contrast = 0.493, Connect. = 0.706 for dens.mod. cycle 11 = 0.300, Contrast = 0.493, Connect. = 0.707 for dens.mod. cycle 12 = 0.300, Contrast = 0.494, Connect. = 0.708 for dens.mod. cycle 13 = 0.300, Contrast = 0.494, Connect. = 0.707 for dens.mod. cycle 14 = 0.300, Contrast = 0.495, Connect. = 0.709 for dens.mod. cycle 15 = 0.300, Contrast = 0.495, Connect. = 0.709 for dens.mod. cycle 16 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 17 = 0.300, Contrast = 0.495, Connect. = 0.710 for dens.mod. cycle 18 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 19 = 0.300, Contrast = 0.496, Connect. = 0.709 for dens.mod. cycle 20 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 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 17 residues pruned to eliminate duplicates C: 7 4.988 1.614 0.317 0.542 0.833 0.833 CA 1.103 Using tripeptides from previous cycle as seeds D: 15 10.134 1.706 0.634 0.351 1.000 0.429 CA 1.141 7 residues pruned to eliminate duplicates 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 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.821 for fragment phases = 0.300, Contrast = 0.349, Connect. = 0.620 for dens.mod. cycle 1 = 0.300, Contrast = 0.403, Connect. = 0.649 for dens.mod. cycle 2 = 0.300, Contrast = 0.470, Connect. = 0.687 for dens.mod. cycle 3 = 0.300, Contrast = 0.470, Connect. = 0.689 for dens.mod. cycle 4 = 0.300, Contrast = 0.476, Connect. = 0.693 for dens.mod. cycle 5 = 0.300, Contrast = 0.478, Connect. = 0.697 for dens.mod. cycle 6 = 0.300, Contrast = 0.484, Connect. = 0.699 for dens.mod. cycle 7 = 0.300, Contrast = 0.484, Connect. = 0.703 for dens.mod. cycle 8 = 0.300, Contrast = 0.488, Connect. = 0.704 for dens.mod. cycle 9 = 0.300, Contrast = 0.489, Connect. = 0.706 for dens.mod. cycle 10 = 0.300, Contrast = 0.492, Connect. = 0.708 for dens.mod. cycle 11 = 0.300, Contrast = 0.492, Connect. = 0.709 for dens.mod. cycle 12 = 0.300, Contrast = 0.493, Connect. = 0.710 for dens.mod. cycle 13 = 0.300, Contrast = 0.494, Connect. = 0.711 for dens.mod. cycle 14 = 0.300, Contrast = 0.495, Connect. = 0.711 for dens.mod. cycle 15 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 16 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 17 = 0.300, Contrast = 0.495, Connect. = 0.712 for dens.mod. cycle 18 = 0.300, Contrast = 0.496, Connect. = 0.712 for dens.mod. cycle 19 = 0.300, Contrast = 0.496, Connect. = 0.711 for dens.mod. cycle 20 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 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 C: 14 5.571 1.570 0.662 0.230 0.769 0.385 CB 1.054 Using tripeptides from previous cycle as seeds D: 24 7.691 1.504 0.487 0.284 0.783 0.261 CB 1.168 14 residues pruned to eliminate duplicates 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 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 1 used as input for final density modification = 0.845 for fragment phases = 0.300, Contrast = 0.324, Connect. = 0.625 for dens.mod. cycle 1 = 0.303, Contrast = 0.382, Connect. = 0.662 for dens.mod. cycle 2 = 0.304, Contrast = 0.460, Connect. = 0.702 for dens.mod. cycle 3 = 0.304, Contrast = 0.464, Connect. = 0.702 for dens.mod. cycle 4 = 0.304, Contrast = 0.475, Connect. = 0.706 for dens.mod. cycle 5 = 0.304, Contrast = 0.478, Connect. = 0.706 for dens.mod. cycle 6 = 0.304, Contrast = 0.483, Connect. = 0.707 for dens.mod. cycle 7 = 0.304, Contrast = 0.487, Connect. = 0.708 for dens.mod. cycle 8 = 0.304, Contrast = 0.489, Connect. = 0.710 for dens.mod. cycle 9 = 0.304, Contrast = 0.491, Connect. = 0.710 for dens.mod. cycle 10 = 0.304, Contrast = 0.493, Connect. = 0.711 for dens.mod. cycle 11 = 0.304, Contrast = 0.493, Connect. = 0.712 for dens.mod. cycle 12 = 0.304, Contrast = 0.494, Connect. = 0.713 for dens.mod. cycle 13 = 0.304, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 14 = 0.304, Contrast = 0.495, Connect. = 0.713 for dens.mod. cycle 15 = 0.304, Contrast = 0.496, Connect. = 0.715 for dens.mod. cycle 16 = 0.304, Contrast = 0.496, Connect. = 0.714 for dens.mod. cycle 17 = 0.304, Contrast = 0.497, Connect. = 0.715 for dens.mod. cycle 18 = 0.304, Contrast = 0.498, Connect. = 0.714 for dens.mod. cycle 19 = 0.304, Contrast = 0.498, Connect. = 0.715 for dens.mod. cycle 20 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 0.2 - FFTs and peak-searches 2.6 - Sphere of influence 0.1 - Rest of density modification 76.4 - Alpha-helix search 35.1 - Tripeptide search 44.8 - Chain tracing 0.0 - NCS analysis 1.1 - B-value refinement for trace 0.0 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 18:17:46 Total time: 160.65 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++