++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:42:09 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: I422_p9 I422_p9_fa -i -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I422_p9_fa.res FA and alpha from I422_p9_fa.hkl Native data from I422_p9.hkl Listing output to I422_p9_i.lst Phases output to I422_p9_i.phs Revised heavy atom sites output to I422_p9_i.hat Revised heavy atom phases output to I422_p9_i.pha Poly-Ala trace output to I422_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 4 2 2 Allowed origin shift code: 10 7 atoms read from file I422_p9_fa.res Trimmed to 6 atoms with occupancy > 0.2 5593 Reflections read from file I422_p9_fa.hkl 11203 Reflections read from file I422_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 9 Reflections with d > 1.944 and 22510 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 15 0.000 <= z <= 0.250 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) = 11.08% = 0.073 for phases from phiT = phiA + alpha = 0.177 after including heavy atoms = 0.146, Contrast = 0.013, Connect. = 0.486 for dens.mod. cycle 1 = 0.184, Contrast = 0.060, Connect. = 0.564 for dens.mod. cycle 2 = 0.211, Contrast = 0.130, Connect. = 0.649 for dens.mod. cycle 3 = 0.225, Contrast = 0.207, Connect. = 0.694 for dens.mod. cycle 4 = 0.238, Contrast = 0.210, Connect. = 0.689 for dens.mod. cycle 5 = 0.251, Contrast = 0.202, Connect. = 0.680 for dens.mod. cycle 6 = 0.261, Contrast = 0.194, Connect. = 0.670 for dens.mod. cycle 7 = 0.271, Contrast = 0.188, Connect. = 0.661 for dens.mod. cycle 8 = 0.280, Contrast = 0.184, Connect. = 0.654 for dens.mod. cycle 9 = 0.286, Contrast = 0.180, Connect. = 0.647 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1009 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 41 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 8 1.584 1.118 0.448 0.225 0.714 0.429 CB 0.714 ? A: 6 5.042 1.453 0.399 0.413 1.000 0.800 CA 1.214 6 0.930 1.207 0.180 0.310 0.600 0.400 N 0.601 ? 7 1.800 1.138 0.190 0.387 0.833 0.667 CB 0.734 ? 6 1.298 1.129 0.782 0.480 0.800 0.800 CB 0.368 ? 6 residues left after pruning, divided into chains as follows: A: 6 CC for partial structure against native data = 0.74 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.297, Contrast = 0.238, Connect. = 0.584 for dens.mod. cycle 1 = 0.298, Contrast = 0.234, Connect. = 0.569 for dens.mod. cycle 2 = 0.298, Contrast = 0.235, Connect. = 0.585 for dens.mod. cycle 3 = 0.299, Contrast = 0.232, Connect. = 0.595 for dens.mod. cycle 4 = 0.299, Contrast = 0.228, Connect. = 0.602 for dens.mod. cycle 5 = 0.299, Contrast = 0.223, Connect. = 0.609 for dens.mod. cycle 6 = 0.299, Contrast = 0.219, Connect. = 0.613 for dens.mod. cycle 7 = 0.299, Contrast = 0.215, Connect. = 0.616 for dens.mod. cycle 8 = 0.299, Contrast = 0.212, Connect. = 0.619 for dens.mod. cycle 9 = 0.299, Contrast = 0.209, Connect. = 0.621 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 991 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 37 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 5.597 2.062 0.214 0.490 0.600 0.600 C 1.683 B: 7 2.129 1.168 0.103 0.375 0.833 0.500 CA 0.925 Using tripeptides from previous cycle as seeds 13 residues left after pruning, divided into chains as follows: A: 6 B: 7 CC for partial structure against native data = 3.50 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.299, Contrast = 0.247, Connect. = 0.573 for dens.mod. cycle 1 = 0.299, Contrast = 0.255, Connect. = 0.567 for dens.mod. cycle 2 = 0.299, Contrast = 0.258, Connect. = 0.582 for dens.mod. cycle 3 = 0.299, Contrast = 0.254, Connect. = 0.592 for dens.mod. cycle 4 = 0.299, Contrast = 0.249, Connect. = 0.598 for dens.mod. cycle 5 = 0.299, Contrast = 0.243, Connect. = 0.604 for dens.mod. cycle 6 = 0.299, Contrast = 0.238, Connect. = 0.608 for dens.mod. cycle 7 = 0.299, Contrast = 0.233, Connect. = 0.612 for dens.mod. cycle 8 = 0.299, Contrast = 0.228, Connect. = 0.615 for dens.mod. cycle 9 = 0.299, Contrast = 0.224, Connect. = 0.617 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1001 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 53 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 6.575 2.159 0.009 0.309 0.833 0.500 CA 1.828 B: 8 11.193 2.462 0.006 0.478 0.857 0.714 CB 2.037 6 1.823 1.310 0.542 0.297 0.600 0.400 CB 0.844 ? C: 7 2.860 1.171 1.076 0.499 1.000 0.500 CB 0.481 Using tripeptides from previous cycle as seeds 19 residues left after pruning, divided into chains as follows: A: 7 B: 8 C: 4 CC for partial structure against native data = 2.33 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.299, Contrast = 0.268, Connect. = 0.586 for dens.mod. cycle 1 = 0.299, Contrast = 0.275, Connect. = 0.582 for dens.mod. cycle 2 = 0.299, Contrast = 0.276, Connect. = 0.593 for dens.mod. cycle 3 = 0.299, Contrast = 0.271, Connect. = 0.602 for dens.mod. cycle 4 = 0.299, Contrast = 0.264, Connect. = 0.607 for dens.mod. cycle 5 = 0.299, Contrast = 0.257, Connect. = 0.611 for dens.mod. cycle 6 = 0.299, Contrast = 0.251, Connect. = 0.615 for dens.mod. cycle 7 = 0.299, Contrast = 0.245, Connect. = 0.617 for dens.mod. cycle 8 = 0.299, Contrast = 0.240, Connect. = 0.619 for dens.mod. cycle 9 = 0.299, Contrast = 0.235, Connect. = 0.621 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 971 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: 10 16.628 2.474 0.327 0.392 0.889 0.444 CA 2.130 B: 6 3.352 1.540 -0.066 0.392 1.000 0.400 CB 1.168 Using tripeptides from previous cycle as seeds C: 7 4.352 1.427 0.568 0.511 0.833 0.500 CB 0.942 21 residues left after pruning, divided into chains as follows: A: 10 B: 6 C: 5 CC for partial structure against native data = 4.11 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.299, Contrast = 0.291, Connect. = 0.590 for dens.mod. cycle 1 = 0.299, Contrast = 0.298, Connect. = 0.586 for dens.mod. cycle 2 = 0.299, Contrast = 0.299, Connect. = 0.600 for dens.mod. cycle 3 = 0.299, Contrast = 0.293, Connect. = 0.608 for dens.mod. cycle 4 = 0.299, Contrast = 0.284, Connect. = 0.613 for dens.mod. cycle 5 = 0.299, Contrast = 0.275, Connect. = 0.617 for dens.mod. cycle 6 = 0.299, Contrast = 0.267, Connect. = 0.620 for dens.mod. cycle 7 = 0.299, Contrast = 0.259, Connect. = 0.621 for dens.mod. cycle 8 = 0.299, Contrast = 0.253, Connect. = 0.623 for dens.mod. cycle 9 = 0.299, Contrast = 0.247, Connect. = 0.624 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 986 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 61 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 12.598 2.429 0.343 0.380 0.636 0.455 CB 2.079 B: 6 6.782 2.009 0.379 0.330 0.800 0.200 CB 1.649 C: 11 7.215 1.695 0.479 0.389 0.800 0.600 CB 1.280 6 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds D: 6 5.771 1.987 0.058 0.376 0.800 0.400 CB 1.752 21 residues left after pruning, divided into chains as follows: A: 12 B: 9 CC for partial structure against native data = 4.27 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.299, Contrast = 0.275, Connect. = 0.595 for dens.mod. cycle 1 = 0.300, Contrast = 0.283, Connect. = 0.589 for dens.mod. cycle 2 = 0.304, Contrast = 0.286, Connect. = 0.620 for dens.mod. cycle 3 = 0.303, Contrast = 0.313, Connect. = 0.630 for dens.mod. cycle 4 = 0.305, Contrast = 0.291, Connect. = 0.632 for dens.mod. cycle 5 = 0.304, Contrast = 0.276, Connect. = 0.630 for dens.mod. cycle 6 = 0.305, Contrast = 0.258, Connect. = 0.627 for dens.mod. cycle 7 = 0.305, Contrast = 0.247, Connect. = 0.625 for dens.mod. cycle 8 = 0.306, Contrast = 0.240, Connect. = 0.626 for dens.mod. cycle 9 = 0.306, Contrast = 0.234, Connect. = 0.624 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 0.397 0.403 0.325 0.200 0.251 0.260 0.221 0.220 0.300 0.384 0.599 0.590 0.504 0.292 0.362 0.355 0.303 0.298 0.403 0.502 N 1123 1119 1128 1124 1150 1079 1158 1148 1224 950 Estimated mean FOM = 0.294 Pseudo-free CC = 33.15 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.3198 0.6163 0.9157 34.0000 30.42 2 0.1645 0.6645 1.2500 12.7262 21.28 3 0.2375 0.6861 1.3622 22.6338 19.93 4 0.3347 0.6358 0.9174 19.0434 15.71 5 0.1311 0.5368 1.1323 17.9044 16.45 6 0.1746 0.7194 1.6931 15.2796 13.94 Site x y z h(sig) near old near new 1 0.3199 0.6164 0.9151 30.4 1/0.02 5/2.80 7/5.48 5/9.26 7/10.21 2 0.1643 0.6643 1.2500 21.3 2/0.02 3/9.45 3/9.45 4/15.41 4/15.41 3 0.2376 0.6862 1.3623 19.9 3/0.02 2/9.45 2/9.45 6/13.49 6/14.63 4 0.1310 0.5375 1.1333 16.5 5/0.10 4/12.17 2/15.41 2/15.41 4/16.86 5 0.3343 0.6362 0.9188 15.8 4/0.08 1/2.80 7/5.98 7/7.44 1/9.26 6 0.1744 0.7195 1.6937 14.0 6/0.03 8/6.77 8/6.77 6/8.13 3/13.49 7 0.3178 0.6193 1.0834 -6.1 1/5.46 1/5.48 5/5.98 5/7.44 1/10.21 8 0.1633 0.6633 1.7500 -4.6 6/6.77 6/6.77 6/6.77 3/15.39 3/15.39 Best trace (cycle 5 with CC 4.27%) was saved as I422_p9_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 1.1 - Setup, data input and phasing 3.7 - FFTs and peak-searches 5.3 - Sphere of influence 0.2 - Rest of density modification 0.0 - Alpha-helix search 52.4 - Tripeptide search 15.2 - Chain tracing 0.0 - NCS analysis 0.6 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:43:28 Total time: 78.74 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++