++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:38:09 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: I41_p9 I41_p9_fa -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I41_p9_fa.res FA and alpha from I41_p9_fa.hkl Native data from I41_p9.hkl Listing output to I41_p9.lst Phases output to I41_p9.phs Revised heavy atom sites output to I41_p9.hat Revised heavy atom phases output to I41_p9.pha Poly-Ala trace output to I41_p9.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 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/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 Allowed origin shift code:108 7 atoms read from file I41_p9_fa.res 16206 Reflections read from file I41_p9_fa.hkl 21557 Reflections read from file I41_p9.hkl 21557 Unique data, highest resolution = 1.744 Angstroms Anisotropic scaling: intensities multiplied by -0.000103h^2 -0.000103k^2 +0.003717l^2 +0.000000kl +0.000000hl +0.000000hk 7 Reflections with d > 1.944 and 44090 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|> = 0.746 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 30.95% = 0.230 for phases from phiT = phiA + alpha = 0.316 after including heavy atoms = 0.263, Contrast = 0.042, Connect. = 0.484 for dens.mod. cycle 1 = 0.274, Contrast = 0.167, Connect. = 0.573 for dens.mod. cycle 2 = 0.283, Contrast = 0.177, Connect. = 0.571 for dens.mod. cycle 3 = 0.288, Contrast = 0.178, Connect. = 0.564 for dens.mod. cycle 4 = 0.292, Contrast = 0.179, Connect. = 0.560 for dens.mod. cycle 5 = 0.294, Contrast = 0.180, Connect. = 0.557 for dens.mod. cycle 6 = 0.295, Contrast = 0.182, Connect. = 0.556 for dens.mod. cycle 7 = 0.295, Contrast = 0.184, Connect. = 0.555 for dens.mod. cycle 8 = 0.295, Contrast = 0.186, Connect. = 0.556 for dens.mod. cycle 9 = 0.295, Contrast = 0.188, Connect. = 0.556 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 2218 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 238 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 2.872 1.326 0.349 0.179 0.643 0.286 C 0.983 6 1.219 1.334 0.575 0.276 0.400 0.200 C 0.836 ? B: 8 2.173 1.358 0.431 0.273 0.714 0.286 N 0.765 7 1.701 1.284 0.630 0.250 0.833 0.500 CB 0.531 ? C: 7 2.813 1.247 0.668 0.568 0.833 0.667 CB 0.621 D: 10 5.160 1.437 0.397 0.389 0.778 0.333 CA 1.239 6 1.675 1.228 0.268 0.290 0.600 0.600 CB 1.015 ? 6 1.096 1.177 0.197 0.441 1.000 0.600 CB 0.370 ? E: 6 2.258 1.312 0.088 0.299 0.800 0.800 CA 1.108 6 1.124 1.442 -0.290 0.332 0.600 0.400 CB 0.984 ? F: 6 3.018 1.346 0.005 0.581 1.000 0.600 CB 0.924 6 1.571 1.312 -0.037 0.280 0.800 0.800 CB 0.891 ? G: 6 3.238 1.417 0.761 0.292 0.600 0.600 CA 1.222 6 1.186 1.319 -0.097 0.229 0.600 0.400 CB 1.019 ? H: 6 2.785 1.404 -0.133 0.469 1.000 0.400 CB 1.056 I: 10 4.411 1.353 0.644 0.338 0.778 0.444 CA 1.013 6 1.683 1.160 0.218 0.296 0.800 0.800 C 0.836 ? J: 11 4.329 1.354 0.169 0.348 0.900 0.500 N 1.133 K: 8 2.010 1.375 0.212 0.436 0.571 0.571 CA 0.852 L: 8 2.520 1.080 0.187 0.355 1.000 0.714 N 0.869 37 residues left after pruning, divided into chains as follows: A: 9 B: 10 C: 6 D: 6 E: 6 CC for partial structure against native data = 3.59 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.295, Contrast = 0.161, Connect. = 0.524 for dens.mod. cycle 1 = 0.295, Contrast = 0.164, Connect. = 0.516 for dens.mod. cycle 2 = 0.295, Contrast = 0.173, Connect. = 0.525 for dens.mod. cycle 3 = 0.295, Contrast = 0.179, Connect. = 0.532 for dens.mod. cycle 4 = 0.295, Contrast = 0.184, Connect. = 0.538 for dens.mod. cycle 5 = 0.295, Contrast = 0.187, Connect. = 0.542 for dens.mod. cycle 6 = 0.295, Contrast = 0.190, Connect. = 0.545 for dens.mod. cycle 7 = 0.295, Contrast = 0.198, Connect. = 0.549 for dens.mod. cycle 8 = 0.295, Contrast = 0.199, Connect. = 0.551 for dens.mod. cycle 9 = 0.295, Contrast = 0.207, Connect. = 0.555 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 2195 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 228 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 9.224 1.770 0.454 0.540 0.778 0.667 CB 1.477 B: 14 7.770 1.573 0.338 0.435 0.846 0.692 CB 1.295 C: 14 4.356 1.396 0.516 0.178 0.692 0.385 N 1.215 6 1.452 1.367 0.047 0.518 0.600 0.600 N 0.743 ? D: 7 3.661 1.525 0.345 0.247 0.833 0.500 CB 1.170 E: 7 3.937 1.564 0.181 0.517 0.833 0.333 CB 1.028 F: 6 2.802 1.479 -0.278 0.633 0.800 0.600 CA 1.295 G: 6 5.002 1.396 0.401 0.582 1.000 0.600 N 1.057 H: 13 2.950 1.189 0.454 0.215 0.833 0.250 N 0.826 I: 10 2.270 1.239 0.461 0.165 0.667 0.333 CA 0.943 J: 6 2.256 1.318 0.177 0.265 0.800 0.600 C 1.062 K: 14 4.463 1.451 0.125 0.302 0.846 0.538 CB 1.117 14 residues pruned to eliminate duplicates 6 1.810 1.206 0.754 0.537 0.800 0.400 N 0.461 ? L: 8 2.200 0.926 0.768 0.765 1.000 0.714 N 0.401 M: 8 2.900 1.446 0.514 0.280 0.714 0.429 CB 0.898 Using tripeptides from previous cycle as seeds 59 residues left after pruning, divided into chains as follows: A: 10 B: 9 C: 6 D: 7 E: 6 F: 9 G: 6 H: 6 CC for partial structure against native data = 4.68 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.295, Contrast = 0.171, Connect. = 0.530 for dens.mod. cycle 1 = 0.295, Contrast = 0.173, Connect. = 0.520 for dens.mod. cycle 2 = 0.295, Contrast = 0.181, Connect. = 0.529 for dens.mod. cycle 3 = 0.295, Contrast = 0.186, Connect. = 0.535 for dens.mod. cycle 4 = 0.295, Contrast = 0.190, Connect. = 0.539 for dens.mod. cycle 5 = 0.295, Contrast = 0.197, Connect. = 0.546 for dens.mod. cycle 6 = 0.295, Contrast = 0.199, Connect. = 0.547 for dens.mod. cycle 7 = 0.295, Contrast = 0.209, Connect. = 0.554 for dens.mod. cycle 8 = 0.295, Contrast = 0.208, Connect. = 0.554 for dens.mod. cycle 9 = 0.295, Contrast = 0.217, Connect. = 0.559 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 2219 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 237 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 5.778 1.764 0.330 0.388 0.727 0.273 CB 1.149 B: 15 6.570 1.570 0.447 0.482 0.643 0.357 CB 1.223 C: 9 3.589 1.998 -0.274 0.495 0.750 0.500 CB 1.172 D: 10 2.857 1.642 0.362 0.130 0.556 0.222 CB 1.217 E: 9 5.063 1.501 0.323 0.366 1.000 0.500 CB 1.040 F: 10 4.169 1.383 0.205 0.450 0.778 0.222 CB 1.128 G: 15 2.898 1.290 0.408 0.236 0.571 0.357 CB 1.015 H: 7 2.247 1.309 0.314 0.245 0.667 0.500 CA 1.074 Using tripeptides from previous cycle as seeds 7 1.352 1.373 0.280 0.408 0.667 0.500 CB 0.519 ? I: 7 3.212 1.463 0.296 0.302 0.833 0.500 CB 1.034 J: 7 4.372 1.591 0.354 0.443 0.833 0.667 CB 1.055 47 residues left after pruning, divided into chains as follows: A: 12 B: 7 C: 8 D: 10 E: 10 CC for partial structure against native data = 3.22 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.295, Contrast = 0.170, Connect. = 0.535 for dens.mod. cycle 1 = 0.295, Contrast = 0.169, Connect. = 0.516 for dens.mod. cycle 2 = 0.295, Contrast = 0.178, Connect. = 0.525 for dens.mod. cycle 3 = 0.295, Contrast = 0.183, Connect. = 0.532 for dens.mod. cycle 4 = 0.295, Contrast = 0.187, Connect. = 0.536 for dens.mod. cycle 5 = 0.295, Contrast = 0.191, Connect. = 0.540 for dens.mod. cycle 6 = 0.295, Contrast = 0.201, Connect. = 0.547 for dens.mod. cycle 7 = 0.295, Contrast = 0.202, Connect. = 0.548 for dens.mod. cycle 8 = 0.295, Contrast = 0.208, Connect. = 0.553 for dens.mod. cycle 9 = 0.295, Contrast = 0.208, Connect. = 0.553 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 2240 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 227 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 6.694 1.848 0.265 0.355 0.636 0.364 CB 1.587 B: 10 6.262 1.907 -0.060 0.646 0.889 0.444 CB 1.143 C: 13 8.045 1.886 0.137 0.428 0.750 0.167 CB 1.556 D: 6 2.910 1.348 0.753 0.647 0.600 0.600 CB 0.800 E: 8 3.874 1.451 0.623 0.404 0.714 0.286 CB 0.963 F: 6 3.382 1.411 0.360 0.475 0.800 0.600 CB 1.011 6 0.617 1.119 0.275 0.302 0.600 0.600 N 0.402 ? G: 8 3.986 1.423 0.423 0.291 1.000 0.571 CB 0.941 6 1.216 1.373 0.296 0.298 0.800 0.400 CB 0.479 ? H: 12 2.592 1.235 0.605 0.283 0.636 0.364 CB 0.791 I: 14 5.138 1.214 0.472 0.314 0.923 0.538 CB 1.062 J: 6 3.965 1.291 0.405 0.603 0.800 0.400 CB 1.108 Using tripeptides from previous cycle as seeds K: 8 2.568 1.441 0.649 0.439 0.429 0.286 C 1.015 51 residues left after pruning, divided into chains as follows: A: 12 B: 13 C: 6 D: 6 E: 8 F: 6 CC for partial structure against native data = 4.83 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.295, Contrast = 0.180, Connect. = 0.535 for dens.mod. cycle 1 = 0.295, Contrast = 0.176, Connect. = 0.518 for dens.mod. cycle 2 = 0.295, Contrast = 0.186, Connect. = 0.526 for dens.mod. cycle 3 = 0.295, Contrast = 0.191, Connect. = 0.533 for dens.mod. cycle 4 = 0.295, Contrast = 0.194, Connect. = 0.538 for dens.mod. cycle 5 = 0.295, Contrast = 0.205, Connect. = 0.546 for dens.mod. cycle 6 = 0.295, Contrast = 0.206, Connect. = 0.548 for dens.mod. cycle 7 = 0.295, Contrast = 0.215, Connect. = 0.554 for dens.mod. cycle 8 = 0.295, Contrast = 0.214, Connect. = 0.554 for dens.mod. cycle 9 = 0.295, Contrast = 0.228, Connect. = 0.562 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 2224 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 225 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 8.388 1.965 0.439 0.529 0.625 0.375 CB 1.631 B: 6 6.125 1.759 0.507 0.640 0.600 0.400 CB 1.511 C: 13 5.641 1.707 0.283 0.334 0.750 0.333 CB 1.188 D: 14 6.013 1.679 0.535 0.241 0.692 0.308 CB 1.261 6 residues pruned to eliminate duplicates E: 6 2.788 1.558 0.467 0.355 1.000 0.400 CB 0.638 F: 8 2.625 1.433 0.353 0.275 0.571 0.429 N 1.154 9 1.533 1.336 0.308 0.370 0.750 0.375 CB 0.475 ? G: 8 3.399 1.631 0.211 0.261 0.714 0.571 CB 1.197 H: 6 2.029 1.250 -0.022 0.670 0.800 0.600 N 0.793 6 1.418 1.034 0.050 0.653 0.800 0.800 C 0.634 ? 6 1.553 1.091 0.737 0.298 0.800 0.400 C 0.574 ? I: 10 3.734 1.426 0.203 0.384 0.778 0.444 CB 1.056 Using tripeptides from previous cycle as seeds 55 residues left after pruning, divided into chains as follows: A: 9 B: 12 C: 14 D: 8 E: 6 F: 6 CC for partial structure against native data = 6.05 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.295, Contrast = 0.180, Connect. = 0.533 for dens.mod. cycle 1 = 0.297, Contrast = 0.179, Connect. = 0.524 for dens.mod. cycle 2 = 0.303, Contrast = 0.188, Connect. = 0.552 for dens.mod. cycle 3 = 0.302, Contrast = 0.252, Connect. = 0.589 for dens.mod. cycle 4 = 0.306, Contrast = 0.235, Connect. = 0.586 for dens.mod. cycle 5 = 0.304, Contrast = 0.249, Connect. = 0.592 for dens.mod. cycle 6 = 0.308, Contrast = 0.248, Connect. = 0.593 for dens.mod. cycle 7 = 0.307, Contrast = 0.262, Connect. = 0.603 for dens.mod. cycle 8 = 0.310, Contrast = 0.271, Connect. = 0.610 for dens.mod. cycle 9 = 0.310, Contrast = 0.284, Connect. = 0.619 for dens.mod. cycle 10 Estimated mean FOM and mapCC as a function of resolution d inf - 3.82 - 3.02 - 2.63 - 2.39 - 2.21 - 2.08 - 1.98 - 1.89 - 1.81 - 1.75 0.444 0.358 0.253 0.380 0.470 0.373 0.303 0.321 0.472 0.565 0.655 0.512 0.321 0.497 0.639 0.529 0.440 0.493 0.706 0.809 N 2172 2153 2174 2129 2262 2141 2064 2233 2385 1844 Estimated mean FOM = 0.393 Pseudo-free CC = 42.47 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.8875 0.8208 0.0011 34.0000 50.24 2 1.1862 0.7610 -0.2236 33.1840 51.61 3 1.1809 0.8866 0.0021 29.5188 42.50 4 1.1648 0.7934 -0.1538 29.1958 46.24 5 0.7628 0.8137 0.2848 22.8990 33.32 6 0.7950 0.8348 0.3488 18.4756 25.37 7 0.7507 0.9673 0.2804 8.5918 13.21 Site x y z h(sig) near old near new 1 1.1859 0.7610 -0.2238 51.7 2/0.03 18/1.81 20/2.01 13/2.23 15/4.07 2 0.8876 0.8210 0.0013 50.3 1/0.03 17/4.09 8/12.05 7/12.53 8/14.61 3 1.1647 0.7930 -0.1553 46.4 4/0.07 15/2.21 20/3.66 18/3.67 13/4.06 4 1.1813 0.8866 0.0018 42.6 3/0.04 3/11.97 19/12.06 21/12.40 12/12.69 5 0.7636 0.8139 0.2879 33.8 5/0.14 6/4.71 11/12.43 6/12.94 7/13.18 6 0.7952 0.8344 0.3475 25.8 6/0.07 5/4.71 11/11.71 17/12.75 5/12.94 7 0.8141 0.7394 0.0232 -15.6 1/12.51 8/4.97 2/12.53 8/12.63 17/13.03 8 0.7931 0.8354 -0.1572 -13.5 1/12.03 7/4.97 2/12.05 7/12.63 17/14.21 9 0.7506 0.9671 0.2790 13.2 7/0.05 14/11.09 19/11.14 11/12.09 6/16.11 10 1.1120 0.6782 -0.2502 -12.2 2/12.70 16/11.70 14/12.11 18/12.42 1/12.67 11 0.8861 0.8176 0.5048 -9.4 6/11.71 6/11.71 9/12.09 17/12.28 5/12.43 12 1.2352 0.6862 -0.4571 -8.6 2/12.70 16/4.63 21/5.29 21/12.49 13/12.60 13 1.1844 0.7633 -0.1558 -5.7 2/2.22 1/2.23 20/2.46 18/2.72 3/4.06 14 0.7515 1.0328 0.5313 -5.7 7/11.04 9/11.09 10/12.11 3/16.00 18/16.05 15 1.1690 0.7925 -0.2217 -5.6 4/2.26 3/2.21 18/2.72 20/2.79 1/4.07 16 1.2045 0.6652 -0.3999 -5.4 2/12.51 12/4.63 21/5.39 10/11.70 1/12.51 17 0.8870 0.8224 0.1271 -5.3 1/4.10 2/4.09 11/12.28 6/12.75 7/13.03 18 1.1721 0.7688 -0.2250 -5.1 2/1.83 1/1.81 20/2.19 13/2.72 15/2.72 19 0.7490 1.0341 0.0295 -4.8 7/11.15 9/11.14 4/12.06 16/15.93 21/15.96 20 1.1885 0.7780 -0.2096 -4.7 2/2.00 1/2.01 18/2.19 13/2.46 15/2.79 21 1.1651 0.7924 0.1844 -4.6 4/10.98 12/5.29 16/5.39 3/11.03 13/11.74 Best trace (cycle 5 with CC 6.05%) was saved as I41_p9.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.7 - Setup, data input and phasing 4.5 - FFTs and peak-searches 9.0 - Sphere of influence 0.4 - Rest of density modification 0.0 - Alpha-helix search 131.8 - Tripeptide search 47.9 - Chain tracing 0.0 - NCS analysis 2.4 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:41:26 Total time: 196.75 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++