++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:44:06 on 15 Dec 2020 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features" Acta Cryst. D74, 106-116 (Open Access) if SHELXE proves useful. Command line parameters: I4122_p9 I4122_p9_fa -i -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I4122_p9_fa.res FA and alpha from I4122_p9_fa.hkl Native data from I4122_p9.hkl Listing output to I4122_p9_i.lst Phases output to I4122_p9_i.phs Revised heavy atom sites output to I4122_p9_i.hat Revised heavy atom phases output to I4122_p9_i.pha Poly-Ala trace output to I4122_p9_i.pdb Summary of parameters to be employed: -a 5 global autotracing cycles -b 5.0 extra B for revised heavy atom sites -B unset just build single beta-strands -c 0.400 fraction of pixels in crossover region -d 0.000 high resolution limit to be applied to input data -D unset do not fuse disulfides for NCS -e 1.200 high resolution limit for data extrapolation -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 -G 0.700 FOM threshold for initial tripeptides and chain building -h heavy atoms present in native - use all with occ > 0.2 -i invert structure (and space group) -k 4.5 minimum height/sigma for revised heavy atom sites -l 2 space for 2000000 reflections -L 6 minimum number of residues/chain (if more than 3 chains) -m 10 cycles of density modification -n unset do not apply NCS -p unset no phosphate search -q unset no alpha-helix search -r 3.00 map resolution (multiplies maximum indices) -s 0.600 solvent fraction -S 2.42 radius of sphere of influence -t 1.00 time for initial searches (-t6 or more if difficult) -u 500 MB allocatable memory for fragment optimization -v unset density sharpening factor dependent on resolution -w 0.200 weight for experimental phases after cycle 1 -x unset no phase and trace diagnostics -z unset do not optimize heavy atoms -z 0 read heavy atoms from .res Space group: I 41 2 2 Allowed origin shift code:110 7 atoms read from file I4122_p9_fa.res Trimmed to 4 atoms with occupancy > 0.2 5593 Reflections read from file I4122_p9_fa.hkl 11203 Reflections read from file I4122_p9.hkl 11203 Unique data, highest resolution = 1.744 Angstroms Anisotropic scaling: intensities multiplied by -0.000081h^2 -0.000081k^2 +0.002623l^2 +0.000000kl +0.000000hl +0.000000hk 5 Reflections with d > 1.944 and 22507 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 8 0.000 <= z <= 0.125 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.660 ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 6.53% = 0.055 for phases from phiT = phiA + alpha = 0.127 after including heavy atoms = 0.143, Contrast = 0.012, Connect. = 0.446 for dens.mod. cycle 1 = 0.212, Contrast = 0.025, Connect. = 0.503 for dens.mod. cycle 2 = 0.270, Contrast = 0.090, Connect. = 0.566 for dens.mod. cycle 3 = 0.276, Contrast = 0.258, Connect. = 0.698 for dens.mod. cycle 4 = 0.282, Contrast = 0.301, Connect. = 0.723 for dens.mod. cycle 5 = 0.288, Contrast = 0.295, Connect. = 0.718 for dens.mod. cycle 6 = 0.292, Contrast = 0.284, Connect. = 0.709 for dens.mod. cycle 7 = 0.295, Contrast = 0.276, Connect. = 0.702 for dens.mod. cycle 8 = 0.298, Contrast = 0.268, Connect. = 0.695 for dens.mod. cycle 9 = 0.299, Contrast = 0.262, Connect. = 0.691 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 989 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 58 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 3.148 1.476 0.929 0.296 0.600 0.400 CB 1.035 B: 8 3.266 1.496 0.581 0.281 0.571 0.429 CB 1.170 13 residues left after pruning, divided into chains as follows: A: 5 B: 8 CC for partial structure against native data = 4.82 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.299, Contrast = 0.299, Connect. = 0.599 for dens.mod. cycle 1 = 0.299, Contrast = 0.312, Connect. = 0.609 for dens.mod. cycle 2 = 0.299, Contrast = 0.322, Connect. = 0.625 for dens.mod. cycle 3 = 0.299, Contrast = 0.324, Connect. = 0.633 for dens.mod. cycle 4 = 0.299, Contrast = 0.322, Connect. = 0.640 for dens.mod. cycle 5 = 0.299, Contrast = 0.318, Connect. = 0.644 for dens.mod. cycle 6 = 0.299, Contrast = 0.314, Connect. = 0.648 for dens.mod. cycle 7 = 0.299, Contrast = 0.310, Connect. = 0.651 for dens.mod. cycle 8 = 0.299, Contrast = 0.305, Connect. = 0.653 for dens.mod. cycle 9 = 0.299, Contrast = 0.301, Connect. = 0.655 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 972 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 52 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 7 1.846 2.131 -0.019 0.248 0.500 0.333 CB 0.963 ? A: 9 2.711 1.953 0.390 0.187 0.500 0.375 CB 1.027 B: 8 7.095 2.279 0.257 0.137 0.857 0.429 CA 1.715 Using tripeptides from previous cycle as seeds 13 residues left after pruning, divided into chains as follows: A: 9 B: 4 CC for partial structure against native data = 3.85 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.299, Contrast = 0.321, Connect. = 0.594 for dens.mod. cycle 1 = 0.299, Contrast = 0.331, Connect. = 0.595 for dens.mod. cycle 2 = 0.299, Contrast = 0.341, Connect. = 0.609 for dens.mod. cycle 3 = 0.299, Contrast = 0.343, Connect. = 0.619 for dens.mod. cycle 4 = 0.299, Contrast = 0.341, Connect. = 0.626 for dens.mod. cycle 5 = 0.299, Contrast = 0.337, Connect. = 0.632 for dens.mod. cycle 6 = 0.299, Contrast = 0.333, Connect. = 0.636 for dens.mod. cycle 7 = 0.299, Contrast = 0.328, Connect. = 0.641 for dens.mod. cycle 8 = 0.299, Contrast = 0.324, Connect. = 0.644 for dens.mod. cycle 9 = 0.299, Contrast = 0.320, Connect. = 0.646 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 988 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 62 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 5.697 2.613 -0.005 0.135 0.545 0.182 CB 1.907 B: 7 7.671 2.814 -0.064 0.323 0.667 0.500 CB 2.167 Using tripeptides from previous cycle as seeds 19 residues left after pruning, divided into chains as follows: A: 12 B: 7 CC for partial structure against native data = 6.14 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.299, Contrast = 0.374, Connect. = 0.605 for dens.mod. cycle 1 = 0.299, Contrast = 0.383, Connect. = 0.607 for dens.mod. cycle 2 = 0.299, Contrast = 0.395, Connect. = 0.622 for dens.mod. cycle 3 = 0.299, Contrast = 0.394, Connect. = 0.631 for dens.mod. cycle 4 = 0.299, Contrast = 0.388, Connect. = 0.637 for dens.mod. cycle 5 = 0.299, Contrast = 0.380, Connect. = 0.640 for dens.mod. cycle 6 = 0.299, Contrast = 0.373, Connect. = 0.644 for dens.mod. cycle 7 = 0.299, Contrast = 0.365, Connect. = 0.647 for dens.mod. cycle 8 = 0.299, Contrast = 0.358, Connect. = 0.650 for dens.mod. cycle 9 = 0.299, Contrast = 0.351, Connect. = 0.652 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 978 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 66 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 4.300 2.367 0.093 0.242 0.600 0.200 CA 1.669 B: 9 5.495 2.290 0.058 0.186 0.750 0.375 CB 1.559 C: 9 6.697 2.196 0.634 0.196 0.500 0.250 CA 1.895 Using tripeptides from previous cycle as seeds 20 residues left after pruning, divided into chains as follows: A: 5 B: 7 C: 8 CC for partial structure against native data = 5.39 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.299, Contrast = 0.359, Connect. = 0.602 for dens.mod. cycle 1 = 0.299, Contrast = 0.372, Connect. = 0.605 for dens.mod. cycle 2 = 0.299, Contrast = 0.384, Connect. = 0.620 for dens.mod. cycle 3 = 0.299, Contrast = 0.383, Connect. = 0.627 for dens.mod. cycle 4 = 0.299, Contrast = 0.377, Connect. = 0.634 for dens.mod. cycle 5 = 0.299, Contrast = 0.371, Connect. = 0.638 for dens.mod. cycle 6 = 0.299, Contrast = 0.364, Connect. = 0.642 for dens.mod. cycle 7 = 0.299, Contrast = 0.358, Connect. = 0.645 for dens.mod. cycle 8 = 0.299, Contrast = 0.352, Connect. = 0.647 for dens.mod. cycle 9 = 0.299, Contrast = 0.346, Connect. = 0.649 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 980 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 75 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 7.921 2.637 0.190 0.200 0.500 0.286 CB 1.927 B: 11 7.796 2.220 0.167 0.211 0.900 0.200 CB 1.487 Using tripeptides from previous cycle as seeds 24 residues left after pruning, divided into chains as follows: A: 15 B: 9 CC for partial structure against native data = 5.72 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 3 used as input for final density modification = 0.299, Contrast = 0.350, Connect. = 0.609 for dens.mod. cycle 1 = 0.300, Contrast = 0.361, Connect. = 0.610 for dens.mod. cycle 2 = 0.305, Contrast = 0.367, Connect. = 0.641 for dens.mod. cycle 3 = 0.304, Contrast = 0.407, Connect. = 0.654 for dens.mod. cycle 4 = 0.306, Contrast = 0.382, Connect. = 0.656 for dens.mod. cycle 5 = 0.305, Contrast = 0.366, Connect. = 0.651 for dens.mod. cycle 6 = 0.307, Contrast = 0.345, Connect. = 0.647 for dens.mod. cycle 7 = 0.306, Contrast = 0.331, Connect. = 0.643 for dens.mod. cycle 8 = 0.307, Contrast = 0.321, Connect. = 0.644 for dens.mod. cycle 9 = 0.307, Contrast = 0.309, Connect. = 0.639 for dens.mod. cycle 10 Estimated mean FOM and mapCC as a function of resolution d inf - 3.88 - 3.05 - 2.65 - 2.40 - 2.22 - 2.09 - 1.98 - 1.89 - 1.81 - 1.75 0.454 0.364 0.288 0.309 0.297 0.186 0.163 0.204 0.227 0.255 0.668 0.537 0.427 0.426 0.411 0.255 0.215 0.269 0.298 0.328 N 1123 1119 1128 1124 1150 1079 1158 1148 1224 950 Estimated mean FOM = 0.274 Pseudo-free CC = 32.08 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.9689 0.4689 0.2500 17.0000 32.12 2 0.8344 0.6430 0.7220 20.3626 20.07 3 0.7888 0.7365 0.5937 19.5670 19.86 4 0.9284 0.5460 0.4690 18.9006 18.17 Site x y z h(sig) near old near new 1 0.9688 0.4688 0.2500 32.1 1/0.03 5/1.92 5/1.92 6/3.80 6/3.80 2 0.8351 0.6431 0.7192 20.3 2/0.13 3/12.56 3/12.80 3/14.23 3/14.83 3 0.7888 0.7365 0.5932 19.9 3/0.02 3/3.70 3/10.38 3/10.48 3/10.97 4 0.9281 0.5457 0.4656 18.4 4/0.12 6/9.13 5/10.78 6/11.58 1/12.13 5 0.9682 0.4727 0.3075 -6.0 1/1.92 1/1.92 1/1.92 6/3.72 5/3.81 6 0.9470 0.4939 0.2614 4.9 1/3.80 5/3.72 1/3.80 1/3.80 5/4.71 Best trace (cycle 3 with CC 6.14%) was saved as I4122_p9_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.7 - Setup, data input and phasing 2.2 - FFTs and peak-searches 4.5 - Sphere of influence 0.2 - Rest of density modification 0.0 - Alpha-helix search 50.4 - Tripeptide search 11.1 - Chain tracing 0.0 - NCS analysis 0.7 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:45:16 Total time: 70.04 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++