++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:03:42 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: P2221_pse14 P2221_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P2221_pse14_fa.res FA and alpha from P2221_pse14_fa.hkl Native data from P2221_pse14.hkl Listing output to P2221_pse14.lst Phases output to P2221_pse14.phs Revised heavy atom sites output to P2221_pse14.hat Revised heavy atom phases output to P2221_pse14.pha Poly-Ala trace output to P2221_pse14.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 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 -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 5 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 0.450 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 refine an unlimited number of heavy atoms Space group: P 2 2 21 Allowed origin shift code: 4 14 atoms read from file P2221_pse14_fa.res Trimmed to 13 atoms with occupancy > 0.2 11695 Reflections read from file P2221_pse14_fa.hkl 21043 Reflections read from file P2221_pse14.hkl 21024 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003997h^2 -0.000434k^2 -0.000496l^2 +0.000000kl +0.000000hl +0.000000hk 26 Reflections with d > 2.489 and 0 in range 2.489 > d > 2.289 added Density sharpening factor set to 0.32 Fourier grid = 128 x 128 x 32 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|> = 0.781 13 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 13 19.48% 0.294 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 19.41% = 0.125 for phases from phiT = phiA + alpha = 0.199 after including heavy atoms = 0.178, Contrast = 0.036, Connect. = 0.530 for dens.mod. cycle 1 = 0.198, Contrast = 0.113, Connect. = 0.596 for dens.mod. cycle 2 = 0.213, Contrast = 0.155, Connect. = 0.610 for dens.mod. cycle 3 = 0.225, Contrast = 0.196, Connect. = 0.627 for dens.mod. cycle 4 = 0.235, Contrast = 0.234, Connect. = 0.643 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 0.30 added to NOGO map 1965 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 4.073 1.542 0.255 0.383 1.000 0.333 CB 0.973 7 1.589 1.334 0.142 0.194 0.667 0.167 N 0.920 ? B: 7 8.487 1.428 0.956 0.815 0.833 0.667 CA 1.132 C: 8 3.083 1.389 0.472 0.355 0.571 0.429 N 1.166 D: 8 3.113 1.237 0.317 0.537 0.857 0.857 N 0.812 E: 6 2.843 1.503 0.378 0.369 0.800 0.600 CB 0.883 F: 6 5.020 1.209 0.875 0.832 1.000 0.800 CB 0.743 G: 6 3.230 1.410 0.416 0.467 0.600 0.600 CB 1.247 H: 7 4.847 1.553 0.728 0.285 0.833 0.167 O 1.128 I: 6 4.305 1.344 0.579 0.565 0.800 0.600 O 1.065 10 1.705 1.243 0.367 0.182 0.556 0.333 N 0.883 ? J: 8 5.154 1.495 0.268 0.532 1.000 0.429 CB 0.996 K: 6 4.832 1.245 0.877 0.719 0.800 0.800 CB 0.949 L: 6 2.668 1.366 0.568 0.475 0.600 0.600 CB 0.952 M: 8 3.986 1.326 0.298 0.408 1.000 0.714 N 0.964 N: 6 2.924 1.284 0.196 0.700 1.000 0.800 CB 0.709 6 1.892 1.254 0.836 0.297 0.600 0.400 CB 0.768 ? 6 1.453 1.122 0.122 0.353 1.000 0.600 CB 0.606 ? 74 residues left after pruning, divided into chains as follows: A: 7 B: 7 C: 8 D: 6 E: 6 F: 7 G: 6 H: 7 I: 6 J: 8 K: 6 CC for partial structure against native data = 7.23 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.248, Connect. = 0.589 for dens.mod. cycle 1 = 0.281, Contrast = 0.278, Connect. = 0.579 for dens.mod. cycle 2 = 0.281, Contrast = 0.332, Connect. = 0.624 for dens.mod. cycle 3 = 0.281, Contrast = 0.357, Connect. = 0.645 for dens.mod. cycle 4 = 0.281, Contrast = 0.379, Connect. = 0.663 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 0.30 added to NOGO map 2346 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 216 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 13.573 2.068 0.506 0.859 0.889 0.667 CA 1.203 B: 8 9.656 1.918 0.195 0.698 1.000 0.571 CB 1.330 C: 9 6.406 1.861 0.302 0.396 0.625 0.375 O 1.670 D: 11 5.985 1.720 0.029 0.326 0.900 0.700 CB 1.439 E: 7 5.851 1.643 0.429 0.432 0.833 0.500 CB 1.310 F: 6 6.857 1.558 0.423 0.733 1.000 0.600 CB 1.122 G: 10 6.378 1.554 0.207 0.705 0.778 0.444 CB 1.209 H: 7 2.903 1.506 0.352 0.307 0.667 0.333 N 1.082 I: 6 4.858 1.789 0.156 0.615 0.800 0.600 CB 1.178 J: 7 2.335 1.368 0.495 0.249 0.667 0.333 O 0.933 7 1.354 1.398 -0.219 0.454 1.000 0.833 CB 0.531 ? 7 1.525 1.235 0.553 0.271 0.667 0.333 CB 0.631 ? 9 1.577 1.213 0.752 0.158 0.625 0.250 CB 0.638 ? K: 6 2.180 1.242 0.376 0.309 0.800 0.400 CB 0.881 L: 6 4.508 1.212 0.482 0.808 1.000 0.600 N 0.859 6 1.435 1.362 0.526 0.287 0.600 0.400 CB 0.654 ? M: 8 2.979 1.194 1.193 0.591 0.857 0.429 CB 0.460 N: 12 5.941 1.680 0.329 0.319 0.727 0.273 N 1.347 O: 8 2.515 1.261 0.304 0.252 0.857 0.714 CB 0.897 Using tripeptides from previous cycle as seeds P: 8 3.535 1.506 0.393 0.257 0.857 0.286 N 0.982 101 residues left after pruning, divided into chains as follows: A: 10 B: 8 C: 9 D: 11 E: 7 F: 6 G: 10 H: 6 I: 6 J: 6 K: 6 L: 8 M: 8 CC for partial structure against native data = 9.30 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.302, Connect. = 0.608 for dens.mod. cycle 1 = 0.281, Contrast = 0.347, Connect. = 0.614 for dens.mod. cycle 2 = 0.281, Contrast = 0.406, Connect. = 0.658 for dens.mod. cycle 3 = 0.281, Contrast = 0.429, Connect. = 0.679 for dens.mod. cycle 4 = 0.281, Contrast = 0.446, Connect. = 0.692 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 0.30 added to NOGO map 2077 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 213 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 16.710 2.035 0.311 0.903 1.000 0.900 CA 1.412 B: 11 4.701 1.655 0.227 0.320 0.700 0.400 CA 1.275 C: 6 6.566 1.914 0.745 0.701 1.000 0.600 CB 0.732 D: 10 5.877 1.976 0.017 0.362 0.778 0.556 CB 1.453 E: 6 4.906 1.861 0.695 0.394 0.800 0.400 CB 0.972 F: 20 4.323 1.725 0.344 0.151 0.579 0.421 CB 1.134 G: 8 5.133 1.731 0.356 0.400 0.714 0.286 CB 1.284 H: 6 11.775 1.875 0.600 0.815 1.000 0.800 N 1.335 I: 10 2.861 1.350 0.458 0.279 0.667 0.444 CB 0.934 6 1.762 1.611 0.073 0.414 0.800 0.600 CB 0.624 ? J: 7 3.477 1.771 0.156 0.483 0.667 0.500 CB 1.058 K: 8 8.729 1.701 0.276 0.607 1.000 0.571 CA 1.372 L: 15 4.592 1.541 0.281 0.223 0.714 0.357 CB 1.205 M: 13 5.544 1.524 0.443 0.387 0.750 0.500 CB 1.093 N: 9 3.325 1.432 0.368 0.302 0.625 0.375 N 1.197 O: 6 5.365 1.691 0.407 0.299 1.000 0.400 N 1.261 6 residues pruned to eliminate duplicates P: 7 2.703 1.577 0.360 0.387 0.500 0.333 CB 1.160 Q: 6 2.739 1.441 -0.124 0.567 0.800 0.400 CB 1.136 Using tripeptides from previous cycle as seeds R: 7 8.143 1.591 0.348 0.824 1.000 0.667 CA 1.171 102 residues left after pruning, divided into chains as follows: A: 11 B: 9 C: 10 D: 6 E: 13 F: 6 G: 10 H: 7 I: 8 J: 8 K: 7 L: 7 CC for partial structure against native data = 10.24 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.324, Connect. = 0.616 for dens.mod. cycle 1 = 0.281, Contrast = 0.376, Connect. = 0.626 for dens.mod. cycle 2 = 0.281, Contrast = 0.436, Connect. = 0.671 for dens.mod. cycle 3 = 0.281, Contrast = 0.455, Connect. = 0.687 for dens.mod. cycle 4 = 0.281, Contrast = 0.468, Connect. = 0.699 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 0.30 added to NOGO map 2001 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 228 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 12.521 1.935 0.143 0.843 0.818 0.727 CA 1.553 B: 23 9.690 1.961 0.348 0.171 0.818 0.318 CB 1.424 C: 7 9.130 1.800 0.229 0.686 1.000 0.500 CA 1.422 D: 7 5.303 1.901 -0.045 0.399 1.000 0.667 CA 1.326 E: 10 6.061 1.822 0.143 0.360 0.889 0.444 CB 1.269 F: 6 12.252 1.914 0.765 0.810 1.000 0.600 CB 1.238 G: 6 7.834 1.727 0.744 0.738 0.800 0.400 CB 1.174 H: 8 7.802 1.806 0.644 0.328 0.857 0.429 CB 1.398 I: 12 4.297 1.649 0.299 0.221 0.727 0.364 CB 1.154 J: 11 7.836 1.822 0.318 0.442 0.800 0.400 CB 1.371 K: 9 5.240 1.528 0.387 0.423 0.875 0.625 CB 1.082 L: 6 3.379 1.287 0.976 0.733 1.000 0.800 CB 0.482 M: 10 14.571 1.882 0.493 0.656 1.000 0.778 CB 1.495 6 1.141 1.323 -0.407 0.414 1.000 0.400 CB 0.712 ? N: 7 3.782 1.238 0.441 0.530 0.833 0.500 C 1.008 O: 8 4.714 1.536 -0.090 0.592 1.000 0.714 N 1.167 10 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds P: 10 3.261 1.560 0.403 0.200 0.889 0.222 CB 0.797 93 residues left after pruning, divided into chains as follows: A: 12 B: 18 C: 7 D: 7 E: 10 F: 6 G: 9 H: 10 I: 7 J: 7 CC for partial structure against native data = 10.72 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.319, Connect. = 0.618 for dens.mod. cycle 1 = 0.281, Contrast = 0.381, Connect. = 0.637 for dens.mod. cycle 2 = 0.281, Contrast = 0.452, Connect. = 0.685 for dens.mod. cycle 3 = 0.281, Contrast = 0.468, Connect. = 0.699 for dens.mod. cycle 4 = 0.281, Contrast = 0.478, Connect. = 0.708 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 0.30 added to NOGO map 1963 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 217 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 22.699 2.117 0.469 0.808 0.917 0.583 CB 1.759 B: 11 18.685 2.019 0.550 0.643 1.000 0.500 N 1.652 C: 8 6.230 2.070 0.248 0.578 0.714 0.429 CB 1.184 D: 25 10.549 2.170 0.249 0.196 0.750 0.417 CB 1.522 E: 9 10.610 2.184 0.291 0.489 0.875 0.500 N 1.537 F: 9 7.237 1.612 0.347 0.699 0.875 0.625 N 1.123 G: 10 7.438 2.114 0.245 0.411 0.778 0.444 CB 1.329 H: 8 8.262 2.081 0.202 0.445 1.000 0.714 CB 1.320 I: 6 6.205 1.718 0.708 0.548 0.800 0.600 CB 1.128 J: 7 4.735 1.607 0.384 0.307 0.833 0.500 CB 1.292 K: 6 6.716 1.915 0.170 0.577 1.000 0.400 CA 1.245 L: 7 2.911 1.518 0.786 0.287 0.833 0.333 CB 0.668 M: 10 4.526 1.712 0.396 0.368 0.556 0.556 CB 1.310 10 residues pruned to eliminate duplicates N: 7 3.042 1.460 0.341 0.561 0.833 0.500 CB 0.717 Using tripeptides from previous cycle as seeds 103 residues left after pruning, divided into chains as follows: A: 13 B: 11 C: 8 D: 18 E: 9 F: 7 G: 10 H: 8 I: 6 J: 7 K: 6 CC for partial structure against native data = 10.30 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.281, Contrast = 0.329, Connect. = 0.627 for dens.mod. cycle 1 = 0.282, Contrast = 0.384, Connect. = 0.641 for dens.mod. cycle 2 = 0.282, Contrast = 0.453, Connect. = 0.688 for dens.mod. cycle 3 = 0.282, Contrast = 0.468, Connect. = 0.701 for dens.mod. cycle 4 = 0.282, Contrast = 0.477, Connect. = 0.710 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.07 - 3.99 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.476 0.619 0.647 0.616 0.471 0.410 0.406 0.423 0.407 0.354 0.610 0.802 0.854 0.830 0.682 0.603 0.614 0.688 0.676 0.624 N 2104 2106 2122 2159 2095 2055 2101 2201 2179 1902 Estimated mean FOM = 0.484 Pseudo-free CC = 54.00 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.4457 0.5661 0.1018 1.0000 32.05 2 0.3045 0.8187 -0.1241 0.8513 27.86 3 0.2062 0.6843 0.0824 0.5997 18.55 4 0.0423 0.9275 -0.1061 0.5820 20.01 5 0.3659 0.6744 0.0598 0.4257 15.23 6 0.2019 0.7354 -0.0200 0.4212 13.39 7 0.1521 0.8290 -0.1483 0.3922 12.30 8 0.5676 0.5712 -0.0209 0.3805 10.82 9 0.2978 0.7651 -0.2315 0.3770 10.13 10 0.0152 0.7507 -0.0606 0.3633 11.20 11 0.4764 0.9851 -0.1012 0.3618 10.42 12 0.1531 0.5444 0.0863 0.3060 8.04 13 0.4381 0.7583 -0.1216 0.2942 8.81 Site x y z h(sig) near old near new 1 0.4449 0.5661 0.1016 32.1 1/0.05 17/2.44 14/2.55 20/2.65 5/10.90 2 0.3053 0.8187 -0.1231 28.0 2/0.11 18/2.66 16/2.80 12/9.02 7/9.43 3 0.0447 0.9286 -0.1051 20.2 4/0.19 7/11.00 15/15.36 8/15.47 2/17.66 4 0.2083 0.6839 0.0825 18.6 3/0.13 5/9.27 6/10.68 13/12.08 19/13.70 5 0.3638 0.6744 0.0593 15.3 5/0.13 14/8.73 4/9.27 17/10.52 1/10.90 6 0.2013 0.7347 -0.0206 13.4 6/0.09 19/4.40 4/10.68 8/11.37 16/11.40 7 0.1478 0.8287 -0.1483 12.6 7/0.25 18/8.62 2/9.43 16/10.49 3/11.00 8 0.0164 0.7506 -0.0596 11.4 10/0.11 6/11.37 7/13.06 19/14.11 3/15.47 9 0.5710 0.5719 -0.0210 11.0 8/0.21 14/12.88 1/13.75 20/13.85 20/13.99 10 0.4760 0.9860 -0.1020 10.5 11/0.11 2/17.13 16/19.03 12/19.19 18/19.56 11 0.2990 0.7670 -0.2308 10.3 9/0.18 18/9.17 2/11.11 16/11.65 7/12.79 12 0.4346 0.7576 -0.1218 8.9 13/0.21 16/7.82 2/9.02 18/9.12 19/12.28 13 0.1518 0.5438 0.0877 8.0 12/0.16 4/12.08 20/16.05 5/16.56 1/17.06 14 0.4468 0.5937 0.0899 -6.0 1/2.55 1/2.55 17/3.08 20/4.76 5/8.73 15 -0.0513 1.0691 -0.1927 -5.2 4/15.33 3/15.36 3/22.48 7/23.39 7/25.63 16 0.3082 0.7887 -0.1098 -5.0 2/2.84 2/2.80 18/2.92 19/7.60 12/7.82 17 0.4428 0.5849 0.1213 -5.0 1/2.43 1/2.44 14/3.08 20/4.81 5/10.52 18 0.2876 0.7941 -0.1375 -4.9 2/2.60 2/2.66 16/2.92 7/8.62 12/9.12 19 0.2598 0.7379 -0.0501 4.9 6/4.40 6/4.40 16/7.60 18/9.66 2/10.00 20 0.4298 0.5376 0.0930 -4.7 1/2.67 1/2.65 14/4.76 17/4.81 5/12.39 21 0.1955 0.6785 -0.3287 -4.7 9/13.11 11/13.27 8/17.25 18/21.22 7/21.37 Best trace (cycle 4 with CC 10.72%) was saved as P2221_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 9.9 - Setup, data input and phasing 1.1 - FFTs and peak-searches 4.7 - Sphere of influence 1.1 - Rest of density modification 0.0 - Alpha-helix search 49.7 - Tripeptide search 43.9 - Chain tracing 0.0 - NCS analysis 4.3 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:05:37 Total time: 114.90 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++