++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:20:15 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: P212121_pse14 P212121_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P212121_pse14_fa.res FA and alpha from P212121_pse14_fa.hkl Native data from P212121_pse14.hkl Listing output to P212121_pse14.lst Phases output to P212121_pse14.phs Revised heavy atom sites output to P212121_pse14.hat Revised heavy atom phases output to P212121_pse14.pha Poly-Ala trace output to P212121_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 21 21 21 Allowed origin shift code: 4 14 atoms read from file P212121_pse14_fa.res Trimmed to 13 atoms with occupancy > 0.2 11695 Reflections read from file P212121_pse14_fa.hkl 21043 Reflections read from file P212121_pse14.hkl 20997 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.004009h^2 -0.000438k^2 -0.000495l^2 +0.000000kl +0.000000hl +0.000000hk 22 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|> = 0.780 13 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 13 25.92% 0.168 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 25.57% = 0.154 for phases from phiT = phiA + alpha = 0.220 after including heavy atoms = 0.194, Contrast = 0.057, Connect. = 0.545 for dens.mod. cycle 1 = 0.211, Contrast = 0.188, Connect. = 0.611 for dens.mod. cycle 2 = 0.226, Contrast = 0.287, Connect. = 0.656 for dens.mod. cycle 3 = 0.238, Contrast = 0.362, Connect. = 0.683 for dens.mod. cycle 4 = 0.250, Contrast = 0.412, Connect. = 0.699 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1841 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 220 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 23 24.174 1.800 0.812 0.856 1.000 0.727 CB 1.165 B: 20 18.527 1.706 0.744 0.848 0.947 0.895 CB 1.118 C: 17 26.804 1.870 0.565 0.899 1.000 0.938 CB 1.636 D: 16 15.049 1.730 0.764 0.829 0.867 0.733 CB 1.106 E: 10 12.025 1.643 0.590 0.788 1.000 0.556 CB 1.192 F: 10 13.452 1.781 0.652 0.856 1.000 0.889 CB 1.124 G: 7 3.041 1.540 0.711 0.386 0.500 0.333 CB 1.064 H: 23 27.409 1.668 0.943 0.878 1.000 0.682 CB 1.309 I: 14 14.884 1.597 0.654 0.882 0.846 0.692 CB 1.336 J: 6 3.722 1.531 0.696 0.369 0.600 0.600 CB 1.229 K: 6 4.111 1.490 0.663 0.720 0.800 0.400 CB 0.760 L: 12 4.638 1.419 0.676 0.259 0.727 0.455 CB 1.066 M: 7 2.627 1.353 0.399 0.304 0.667 0.500 CB 1.056 N: 7 2.809 1.200 0.465 0.428 0.833 0.500 CB 0.844 O: 11 3.152 1.451 0.456 0.353 0.500 0.400 N 1.106 7 residues pruned to eliminate duplicates P: 13 11.906 1.524 0.958 0.830 0.833 0.833 CB 1.039 Q: 7 4.790 1.387 0.619 0.770 1.000 0.500 CB 0.685 167 residues left after pruning, divided into chains as follows: A: 23 B: 20 C: 17 D: 16 E: 8 F: 10 G: 23 H: 14 I: 7 J: 9 K: 13 L: 7 CC for partial structure against native data = 25.94 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.407, Connect. = 0.654 for dens.mod. cycle 1 = 0.281, Contrast = 0.490, Connect. = 0.675 for dens.mod. cycle 2 = 0.281, Contrast = 0.630, Connect. = 0.734 for dens.mod. cycle 3 = 0.281, Contrast = 0.655, Connect. = 0.743 for dens.mod. cycle 4 = 0.281, Contrast = 0.675, Connect. = 0.749 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1733 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 226 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 26 44.048 2.168 0.788 0.883 1.000 0.880 CB 1.644 B: 27 47.862 2.191 0.753 0.895 1.000 0.885 CA 1.752 C: 21 44.252 2.259 1.013 0.888 1.000 0.700 CB 1.568 D: 23 35.256 2.064 0.635 0.912 0.955 0.591 CB 1.653 E: 26 40.346 2.119 0.744 0.905 0.960 0.760 CB 1.620 F: 17 23.283 1.922 0.481 0.908 1.000 0.875 CB 1.452 G: 36 45.417 2.109 0.911 0.899 0.943 0.771 CB 1.444 21 residues pruned to eliminate duplicates H: 15 26.177 2.084 0.605 0.869 0.929 0.857 CA 1.645 I: 24 24.234 1.777 0.609 0.837 1.000 0.696 CB 1.321 J: 15 15.782 1.675 0.748 0.918 1.000 0.714 CB 1.016 K: 8 9.408 1.815 0.277 0.809 1.000 0.857 CB 1.173 L: 36 25.801 1.931 0.426 0.614 0.943 0.714 CB 1.508 36 residues pruned to eliminate duplicates M: 29 17.393 1.731 0.700 0.552 0.857 0.464 CB 1.239 22 residues pruned to eliminate duplicates N: 6 10.458 1.733 0.673 0.763 1.000 0.600 CB 1.277 Using tripeptides from previous cycle as seeds 221 residues left after pruning, divided into chains as follows: A: 26 B: 27 C: 23 D: 26 E: 14 F: 36 G: 15 H: 24 I: 30 CC for partial structure against native data = 36.90 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.483, Connect. = 0.688 for dens.mod. cycle 1 = 0.281, Contrast = 0.581, Connect. = 0.720 for dens.mod. cycle 2 = 0.281, Contrast = 0.721, Connect. = 0.760 for dens.mod. cycle 3 = 0.281, Contrast = 0.729, Connect. = 0.761 for dens.mod. cycle 4 = 0.281, Contrast = 0.739, Connect. = 0.763 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1628 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 26 47.849 2.309 0.670 0.905 1.000 0.920 CB 1.766 B: 21 52.151 2.258 1.059 0.908 1.000 0.800 CA 1.781 C: 27 38.349 2.171 0.831 0.864 0.923 0.615 CB 1.503 D: 26 53.815 2.294 1.069 0.892 0.960 0.760 CA 1.697 E: 27 40.334 2.098 0.827 0.933 0.923 0.692 CB 1.561 F: 18 31.647 2.089 0.809 0.916 0.941 0.824 CB 1.523 G: 21 35.049 2.045 0.839 0.925 1.000 0.950 CB 1.463 H: 37 37.297 2.017 0.831 0.798 0.944 0.694 CB 1.374 21 residues pruned to eliminate duplicates I: 14 32.445 2.256 0.748 0.857 0.923 0.923 CA 1.823 J: 11 6.487 1.970 0.209 0.346 0.700 0.400 CB 1.453 K: 13 9.326 1.900 0.694 0.547 0.750 0.583 CB 1.065 L: 10 7.642 1.513 0.523 0.596 0.778 0.333 CB 1.297 Using tripeptides from previous cycle as seeds M: 54 32.415 2.030 0.500 0.620 0.906 0.792 CB 1.442 46 residues pruned to eliminate duplicates 236 residues left after pruning, divided into chains as follows: A: 26 B: 21 C: 26 D: 27 E: 16 F: 37 G: 14 H: 10 I: 59 CC for partial structure against native data = 40.26 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.491, Connect. = 0.696 for dens.mod. cycle 1 = 0.281, Contrast = 0.592, Connect. = 0.731 for dens.mod. cycle 2 = 0.281, Contrast = 0.733, Connect. = 0.765 for dens.mod. cycle 3 = 0.281, Contrast = 0.738, Connect. = 0.765 for dens.mod. cycle 4 = 0.281, Contrast = 0.748, Connect. = 0.767 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1596 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 239 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 22 48.409 2.250 0.944 0.902 1.000 0.762 CB 1.723 B: 25 57.884 2.373 1.029 0.908 0.917 0.750 CB 1.901 C: 27 43.565 2.160 0.930 0.920 0.962 0.692 CB 1.501 D: 28 39.474 2.122 0.871 0.859 0.926 0.593 CB 1.520 E: 26 51.307 2.279 0.823 0.914 0.960 0.680 CB 1.821 F: 19 27.447 2.069 0.455 0.865 1.000 0.833 CB 1.574 G: 35 57.032 2.233 1.002 0.917 0.941 0.824 CB 1.640 22 residues pruned to eliminate duplicates H: 15 29.108 2.191 0.708 0.834 0.929 0.786 CB 1.678 I: 18 22.814 2.046 0.438 0.821 1.000 0.765 CB 1.424 J: 14 24.013 2.014 0.571 0.876 1.000 0.846 CB 1.530 K: 7 10.644 1.859 0.698 0.842 1.000 0.833 CB 1.026 L: 61 34.346 2.068 0.267 0.631 0.967 0.733 CB 1.548 42 residues pruned to eliminate duplicates M: 8 2.803 1.479 0.284 0.335 0.857 0.571 CA 0.779 Using tripeptides from previous cycle as seeds N: 23 22.331 2.007 0.847 0.755 0.818 0.636 CB 1.251 18 residues pruned to eliminate duplicates 237 residues left after pruning, divided into chains as follows: A: 25 B: 27 C: 26 D: 19 E: 15 F: 16 G: 7 H: 43 I: 13 J: 6 K: 40 CC for partial structure against native data = 39.04 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.489, Connect. = 0.698 for dens.mod. cycle 1 = 0.281, Contrast = 0.591, Connect. = 0.730 for dens.mod. cycle 2 = 0.281, Contrast = 0.730, Connect. = 0.765 for dens.mod. cycle 3 = 0.281, Contrast = 0.736, Connect. = 0.766 for dens.mod. cycle 4 = 0.281, Contrast = 0.746, Connect. = 0.767 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1578 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 22 46.825 2.192 1.128 0.914 1.000 0.952 CB 1.549 B: 27 38.527 2.167 0.619 0.939 0.962 0.769 CB 1.557 C: 27 58.180 2.236 1.157 0.922 0.962 0.808 CA 1.730 D: 26 46.522 2.248 0.784 0.890 0.960 0.760 CB 1.738 E: 34 25.794 2.077 0.383 0.560 0.909 0.667 CB 1.622 F: 26 34.139 2.161 0.473 0.946 0.960 0.840 CB 1.545 G: 36 50.518 2.195 0.788 0.905 0.971 0.714 CB 1.594 21 residues pruned to eliminate duplicates H: 15 32.041 2.196 0.697 0.854 1.000 0.643 CB 1.696 I: 37 45.542 2.020 0.861 0.887 1.000 0.722 CB 1.456 J: 8 10.188 1.912 0.257 0.751 0.857 0.714 CB 1.495 K: 27 31.134 2.114 0.707 0.615 0.923 0.654 CB 1.644 24 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 239 residues left after pruning, divided into chains as follows: A: 27 B: 27 C: 26 D: 33 E: 26 F: 37 G: 37 H: 26 CC for partial structure against native data = 40.02 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 3 used as input for final density modification = 0.281, Contrast = 0.482, Connect. = 0.695 for dens.mod. cycle 1 = 0.282, Contrast = 0.586, Connect. = 0.731 for dens.mod. cycle 2 = 0.282, Contrast = 0.730, Connect. = 0.766 for dens.mod. cycle 3 = 0.282, Contrast = 0.737, Connect. = 0.767 for dens.mod. cycle 4 = 0.282, Contrast = 0.747, Connect. = 0.768 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.06 - 3.98 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.725 0.756 0.760 0.736 0.690 0.636 0.599 0.561 0.516 0.447 0.807 0.874 0.885 0.881 0.868 0.836 0.818 0.818 0.788 0.711 N 2105 2122 2088 2157 2094 2053 2100 2199 2179 1900 Estimated mean FOM = 0.644 Pseudo-free CC = 69.50 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.1984 0.0677 0.2469 1.0000 41.07 2 -0.0483 0.1818 0.2308 0.9329 38.12 3 0.1072 0.1718 0.2047 0.5439 24.70 4 -0.0470 0.2326 0.1251 0.5436 20.58 5 -0.2304 0.2497 0.0895 0.3537 15.80 6 -0.0303 0.0522 0.2846 0.3151 11.90 7 -0.2203 0.2057 0.1929 0.3086 12.82 8 0.0088 0.3120 0.1207 0.2904 9.77 9 -0.2327 0.0103 0.2585 0.2567 9.74 10 0.0245 0.0971 0.2991 0.2409 7.98 11 -0.0355 -0.0692 0.2309 0.2377 8.57 12 0.1770 -0.0912 0.1920 0.2308 8.88 13 -0.1408 0.0728 0.3245 0.1681 4.92 Site x y z h(sig) near old near new 1 0.1977 0.0679 0.2476 41.2 1/0.08 22/2.42 21/2.56 17/2.60 23/10.47 2 -0.0488 0.1811 0.2305 38.2 2/0.07 27/2.60 19/2.67 14/2.68 25/6.24 3 0.1066 0.1715 0.2043 24.7 3/0.06 23/2.90 25/3.49 14/8.50 21/9.02 4 -0.0478 0.2337 0.1259 20.7 4/0.13 9/7.37 14/8.93 19/9.34 2/10.86 5 -0.2297 0.2504 0.0901 15.9 5/0.09 16/8.56 15/9.46 6/10.48 4/11.11 6 -0.2210 0.2053 0.1930 12.8 7/0.05 16/5.19 19/10.19 5/10.48 2/10.74 7 -0.0304 0.0521 0.2843 11.9 6/0.03 12/4.73 18/7.32 27/9.73 20/10.46 8 -0.2278 0.0114 0.2561 10.4 9/0.37 26/5.03 18/9.80 7/12.17 11/12.98 9 0.0067 0.3138 0.1208 9.9 8/0.20 4/7.37 19/13.26 15/13.40 14/14.32 10 0.1805 -0.0896 0.1907 9.0 12/0.27 24/9.22 11/13.29 22/13.63 1/14.18 11 -0.0388 -0.0679 0.2292 8.7 11/0.27 7/11.26 8/12.98 10/13.29 26/14.96 12 0.0167 0.0959 0.2985 8.5 10/0.47 7/4.73 27/7.74 18/9.24 2/10.30 13 -0.1920 0.3895 0.0413 7.8 5/12.67 15/9.09 5/12.63 9/15.09 4/17.34 14 -0.0408 0.1735 0.2036 -6.6 2/2.71 2/2.68 19/3.70 27/4.60 25/6.14 15 -0.1412 0.2906 0.0140 6.5 5/9.46 13/9.09 5/9.46 4/12.82 9/13.40 16 -0.2522 0.1743 0.1494 6.4 7/5.22 6/5.19 5/8.56 4/12.97 26/13.17 17 0.1931 0.0622 0.2744 -5.4 1/2.68 22/1.30 1/2.60 21/4.63 12/10.80 18 -0.1354 0.0746 0.3228 5.4 13/0.38 20/4.32 7/7.32 26/8.07 12/9.24 19 -0.0513 0.2119 0.2223 -5.3 2/2.63 2/2.67 14/3.70 27/4.99 25/6.79 20 -0.1446 0.1173 0.3481 5.3 13/4.33 18/4.32 7/10.46 12/10.58 26/10.79 21 0.2051 0.0951 0.2358 -5.3 1/2.54 1/2.56 17/4.63 22/4.87 23/8.60 22 0.1894 0.0496 0.2667 -5.2 1/2.47 17/1.30 1/2.42 21/4.87 12/11.09 23 0.1231 0.1816 0.2317 -4.9 3/2.84 3/2.90 25/3.77 21/8.60 27/9.35 24 0.3349 -0.0709 0.1714 4.8 12/9.46 10/9.22 1/15.74 22/15.89 21/16.83 25 0.0589 0.1832 0.2245 -4.8 3/3.49 3/3.49 23/3.77 27/6.13 14/6.14 26 -0.2042 0.0692 0.2491 -4.8 9/5.23 8/5.03 18/8.07 7/10.66 20/10.79 27 -0.0336 0.1629 0.2508 -4.6 2/2.61 2/2.60 14/4.60 19/4.99 25/6.13 Best trace (cycle 3 with CC 40.26%) was saved as P212121_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 10.1 - Setup, data input and phasing 1.0 - FFTs and peak-searches 4.7 - Sphere of influence 1.4 - Rest of density modification 0.0 - Alpha-helix search 36.9 - Tripeptide search 20.9 - Chain tracing 0.0 - NCS analysis 9.2 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:21:40 Total time: 84.39 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++