++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:11:56 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: P21212_pse14 P21212_pse14_fa -i -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P21212_pse14_fa.res FA and alpha from P21212_pse14_fa.hkl Native data from P21212_pse14.hkl Listing output to P21212_pse14_i.lst Phases output to P21212_pse14_i.phs Revised heavy atom sites output to P21212_pse14_i.hat Revised heavy atom phases output to P21212_pse14_i.pha Poly-Ala trace output to P21212_pse14_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 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 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 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 2 Allowed origin shift code: 4 14 atoms read from file P21212_pse14_fa.res 11695 Reflections read from file P21212_pse14_fa.hkl 21043 Reflections read from file P21212_pse14.hkl 21016 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003948h^2 -0.000442k^2 -0.000489l^2 +0.000000kl +0.000000hl +0.000000hk 24 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 63 0.000 <= z <= 0.500 92 Point spherical net set up with radius 2.42A 24 Extra Fourier layers will be generated <|E^2-1|> = 0.781 ** Atom coordinates inverted ** 14 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 14 18.13% 0.234 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 17.84% = 0.118 for phases from phiT = phiA + alpha = 0.200 after including heavy atoms = 0.168, Contrast = 0.030, Connect. = 0.536 for dens.mod. cycle 1 = 0.188, Contrast = 0.083, Connect. = 0.593 for dens.mod. cycle 2 = 0.204, Contrast = 0.108, Connect. = 0.604 for dens.mod. cycle 3 = 0.216, Contrast = 0.134, Connect. = 0.614 for dens.mod. cycle 4 = 0.228, Contrast = 0.157, Connect. = 0.625 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 1891 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 250 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 2.504 1.402 0.023 0.347 0.800 0.400 O 1.152 B: 16 3.204 1.459 0.393 0.092 0.600 0.267 CB 1.145 C: 7 2.892 1.120 0.437 0.823 0.833 0.667 N 0.665 D: 7 3.336 1.484 0.548 0.348 0.667 0.500 CB 1.050 E: 9 2.242 1.349 -0.050 0.360 0.750 0.375 CB 0.959 F: 6 2.329 1.294 0.345 0.427 0.800 0.600 O 0.808 G: 6 2.512 1.566 0.649 0.100 0.800 0.200 CB 0.906 6 1.641 1.352 -0.006 0.364 0.800 0.400 CB 0.790 ? 6 1.037 1.241 0.167 0.614 1.000 0.600 CB 0.288 ? H: 9 2.946 1.273 0.713 0.437 0.625 0.500 N 0.816 I: 7 4.981 1.148 0.669 0.711 1.000 0.667 N 0.876 6 1.969 1.145 0.044 0.605 0.800 0.800 N 0.833 ? J: 6 2.534 1.179 0.657 0.379 1.000 0.800 CB 0.660 K: 6 3.495 1.104 0.467 0.727 1.000 0.800 CA 0.786 L: 6 4.051 1.336 0.969 0.444 0.800 0.400 N 0.912 6 1.652 1.149 0.395 0.350 0.800 0.400 CB 0.678 ? M: 6 2.787 1.355 0.461 0.562 0.800 0.600 CB 0.741 N: 7 2.211 1.232 0.601 0.411 0.833 0.667 CB 0.603 O: 7 2.100 1.302 0.542 0.272 0.667 0.333 CB 0.830 8 1.838 1.232 0.343 0.326 0.571 0.429 CB 0.890 ? 83 residues left after pruning, divided into chains as follows: A: 16 B: 7 C: 7 D: 9 E: 6 F: 7 G: 6 H: 6 I: 6 J: 6 K: 7 CC for partial structure against native data = 6.68 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.207, Connect. = 0.589 for dens.mod. cycle 1 = 0.281, Contrast = 0.217, Connect. = 0.557 for dens.mod. cycle 2 = 0.281, Contrast = 0.243, Connect. = 0.592 for dens.mod. cycle 3 = 0.281, Contrast = 0.262, Connect. = 0.615 for dens.mod. cycle 4 = 0.281, Contrast = 0.281, Connect. = 0.631 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2374 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 221 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 5.087 1.802 0.387 0.391 0.667 0.500 O 1.398 B: 6 9.826 1.917 1.105 0.447 0.800 0.600 CB 1.438 C: 6 7.343 2.047 0.462 0.408 1.000 0.800 CB 1.208 D: 8 9.065 1.665 0.331 0.877 0.857 0.714 CB 1.311 E: 6 3.363 1.539 0.553 0.459 0.800 0.600 CB 0.820 F: 6 3.693 1.650 0.343 0.484 0.800 0.400 CB 0.946 G: 7 4.546 1.704 0.094 0.461 0.833 0.333 CB 1.243 H: 7 3.759 1.631 0.077 0.386 0.833 0.667 N 1.183 6 1.921 1.578 -0.066 0.301 0.600 0.400 CB 1.213 ? 6 1.575 1.508 0.779 0.291 0.400 0.400 CB 0.830 ? I: 7 2.521 1.303 0.202 0.278 0.833 0.500 N 1.015 J: 7 2.744 1.329 0.288 0.389 0.833 0.500 N 0.883 6 1.705 1.241 0.110 0.473 0.800 0.400 N 0.712 ? K: 7 2.174 1.477 0.991 0.291 0.333 0.333 CB 1.146 L: 7 4.984 1.475 0.088 0.549 1.000 0.333 N 1.209 M: 11 6.918 1.839 0.570 0.315 0.600 0.400 C 1.550 11 residues pruned to eliminate duplicates N: 13 3.904 1.641 0.550 0.134 0.667 0.417 CB 1.048 6 1.955 1.184 0.266 0.549 1.000 0.600 CB 0.556 ? O: 11 3.881 1.519 0.490 0.241 0.700 0.600 CB 1.044 Using tripeptides from previous cycle as seeds P: 7 2.143 1.639 -0.011 0.089 0.833 0.500 CB 1.099 Q: 6 8.464 1.722 0.249 0.770 1.000 0.800 CA 1.386 73 residues left after pruning, divided into chains as follows: A: 7 B: 6 C: 8 D: 6 E: 6 F: 7 G: 7 H: 7 I: 7 J: 6 K: 6 CC for partial structure against native data = 6.94 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.261, Connect. = 0.596 for dens.mod. cycle 1 = 0.281, Contrast = 0.282, Connect. = 0.584 for dens.mod. cycle 2 = 0.281, Contrast = 0.312, Connect. = 0.622 for dens.mod. cycle 3 = 0.281, Contrast = 0.327, Connect. = 0.641 for dens.mod. cycle 4 = 0.281, Contrast = 0.341, Connect. = 0.657 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2271 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 9.898 2.612 0.338 0.454 0.600 0.600 CA 2.212 B: 11 5.293 1.842 0.399 0.272 0.600 0.400 CB 1.402 C: 6 8.183 2.271 0.303 0.481 0.800 0.400 CB 1.576 D: 8 4.668 1.809 0.329 0.415 0.714 0.571 CB 1.122 E: 6 10.782 1.993 0.381 0.687 1.000 1.000 CB 1.476 F: 8 12.417 1.899 0.866 0.794 0.714 0.714 N 1.433 G: 10 7.102 1.981 0.091 0.420 1.000 0.444 CB 1.190 H: 10 2.639 1.371 0.382 0.206 0.667 0.444 CB 0.986 7 1.695 1.316 0.194 0.228 0.500 0.333 O 1.210 ? I: 7 2.822 1.540 0.274 0.334 0.833 0.500 C 0.845 6 1.774 1.392 0.457 0.343 0.800 0.400 CB 0.580 ? J: 6 2.426 1.579 -0.021 0.312 0.800 0.400 CB 1.081 K: 8 4.643 1.217 0.602 0.717 0.714 0.571 CB 1.036 L: 12 3.436 1.423 0.194 0.180 0.818 0.273 CB 1.096 M: 9 3.390 1.509 0.235 0.515 0.750 0.500 CB 0.844 Using tripeptides from previous cycle as seeds 80 residues left after pruning, divided into chains as follows: A: 11 B: 6 C: 8 D: 6 E: 8 F: 10 G: 10 H: 6 I: 8 J: 7 CC for partial structure against native data = 8.32 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.281, Connect. = 0.599 for dens.mod. cycle 1 = 0.281, Contrast = 0.309, Connect. = 0.594 for dens.mod. cycle 2 = 0.281, Contrast = 0.337, Connect. = 0.630 for dens.mod. cycle 3 = 0.281, Contrast = 0.352, Connect. = 0.651 for dens.mod. cycle 4 = 0.281, Contrast = 0.364, Connect. = 0.666 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2244 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 231 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 9.986 2.036 0.192 0.644 0.875 0.750 CA 1.454 B: 9 8.665 1.919 0.466 0.767 0.625 0.500 CB 1.376 C: 9 5.051 1.880 0.480 0.263 0.750 0.250 CB 1.122 D: 9 4.636 1.770 0.305 0.376 0.750 0.250 CB 1.079 E: 7 3.924 1.598 0.420 0.420 0.667 0.333 CB 1.151 F: 6 3.708 1.718 0.261 0.426 0.600 0.600 O 1.378 G: 10 5.516 1.874 0.312 0.266 0.889 0.333 CB 1.099 7 1.652 1.475 0.353 0.297 0.667 0.333 N 0.636 ? H: 8 3.180 1.305 0.466 0.323 0.714 0.429 CB 1.069 7 1.762 1.647 0.429 0.133 0.667 0.333 CB 0.724 ? I: 7 3.324 1.470 0.488 0.246 0.833 0.500 CB 0.999 J: 11 4.888 1.404 0.389 0.412 0.900 0.500 CB 0.966 K: 7 3.330 1.493 0.314 0.370 0.667 0.333 CB 1.194 L: 10 4.847 1.299 0.464 0.498 0.889 0.444 CB 0.957 7 1.940 1.279 0.001 0.405 0.667 0.667 N 1.026 ? M: 6 3.032 1.397 0.450 0.303 0.800 0.600 CB 1.042 N: 6 2.019 1.162 0.454 0.519 0.600 0.200 C 0.874 O: 9 3.618 1.504 0.590 0.367 0.625 0.250 CA 0.987 P: 9 8.365 1.834 0.616 0.265 0.875 0.375 CB 1.492 Using tripeptides from previous cycle as seeds Q: 19 13.434 2.145 0.258 0.290 0.944 0.556 CB 1.572 10 residues pruned to eliminate duplicates 66 residues left after pruning, divided into chains as follows: A: 7 B: 9 C: 6 D: 10 E: 6 F: 9 G: 19 CC for partial structure against native data = 7.43 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.307, Connect. = 0.603 for dens.mod. cycle 1 = 0.281, Contrast = 0.339, Connect. = 0.598 for dens.mod. cycle 2 = 0.281, Contrast = 0.370, Connect. = 0.638 for dens.mod. cycle 3 = 0.281, Contrast = 0.379, Connect. = 0.655 for dens.mod. cycle 4 = 0.281, Contrast = 0.387, Connect. = 0.668 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2280 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 223 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 7.298 1.879 0.210 0.766 0.714 0.714 N 1.341 B: 6 6.079 1.992 0.249 0.376 0.800 0.600 CB 1.559 C: 9 2.321 1.655 0.429 0.391 0.375 0.375 CB 1.038 D: 6 2.573 1.474 -0.070 0.423 0.800 0.400 CB 1.136 E: 6 3.980 1.563 0.581 0.329 0.800 0.400 CB 1.085 F: 9 3.752 1.348 0.641 0.336 0.625 0.250 C 1.148 G: 6 2.003 1.636 0.618 0.297 0.600 0.400 CB 0.708 8 1.493 1.494 0.021 0.294 0.571 0.429 CA 0.815 ? H: 6 3.352 1.230 0.662 0.444 0.800 0.400 CB 0.971 7 1.112 1.307 0.100 0.249 0.833 0.667 CB 0.506 ? I: 6 5.461 1.797 0.109 0.449 0.800 0.800 O 1.615 J: 9 4.241 1.505 0.290 0.442 1.000 0.375 CB 0.820 K: 6 2.829 1.233 0.943 0.362 0.800 0.400 CB 0.765 L: 6 4.094 1.566 0.385 0.441 1.000 0.600 CB 0.898 M: 7 3.041 1.483 0.551 0.294 0.833 0.333 CB 0.815 N: 7 2.359 1.389 0.074 0.469 0.667 0.500 C 0.998 6 1.295 1.132 0.307 0.100 0.800 0.400 CB 0.815 ? O: 7 2.288 1.088 0.261 0.388 1.000 0.333 C 0.767 Using tripeptides from previous cycle as seeds 70 residues left after pruning, divided into chains as follows: A: 8 B: 6 C: 9 D: 6 E: 8 F: 6 G: 6 H: 7 I: 7 J: 7 CC for partial structure against native data = 7.38 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 3 used as input for final density modification = 0.281, Contrast = 0.290, Connect. = 0.606 for dens.mod. cycle 1 = 0.282, Contrast = 0.329, Connect. = 0.602 for dens.mod. cycle 2 = 0.282, Contrast = 0.369, Connect. = 0.645 for dens.mod. cycle 3 = 0.282, Contrast = 0.383, Connect. = 0.664 for dens.mod. cycle 4 = 0.282, Contrast = 0.392, Connect. = 0.676 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.06 - 3.99 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.521 0.553 0.538 0.469 0.452 0.378 0.244 0.142 0.160 0.149 0.680 0.740 0.750 0.677 0.673 0.598 0.404 0.240 0.267 0.260 N 2112 2094 2121 2158 2095 2054 2101 2200 2180 1901 Estimated mean FOM = 0.361 Pseudo-free CC = 39.76 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.5501 0.4081 0.9955 1.0000 26.06 2 0.7960 0.3413 1.4806 0.8570 22.08 3 0.2992 0.2572 1.1267 0.8524 23.47 4 0.5543 0.4558 1.5004 0.7443 20.65 5 0.8012 0.2932 0.9804 0.7376 19.83 6 0.6461 0.3024 0.9543 0.6781 18.43 7 0.8081 0.3168 1.3667 0.5414 14.13 8 0.7799 0.4238 1.0328 0.4152 12.24 9 0.7828 0.5940 1.4756 0.3578 8.99 10 0.4535 0.2459 0.8198 0.3363 7.97 11 0.5488 0.3560 0.8873 0.3108 8.56 12 0.7257 0.5205 1.2488 0.2971 7.56 13 0.4532 0.1001 0.7668 0.2595 6.64 14 0.5473 0.4381 1.1160 0.2338 5.98 Site x y z h(sig) near old near new 1 0.5504 0.4080 0.9954 26.1 1/0.02 6/11.00 10/11.28 14/11.78 8/13.84 2 0.2991 0.2573 1.1266 23.5 3/0.02 16/9.08 5/11.02 6/12.78 10/17.19 3 0.7954 0.3402 1.4808 22.2 2/0.10 15/2.91 17/8.04 7/10.95 4/16.99 4 0.5538 0.4552 1.5006 20.7 4/0.06 4/9.68 3/16.99 9/17.53 15/19.01 5 0.8026 0.2934 0.9806 19.9 5/0.09 16/2.59 6/9.44 2/11.02 8/11.99 6 0.6452 0.3028 0.9547 18.5 6/0.07 16/9.11 5/9.44 10/9.60 1/11.00 7 0.8073 0.3174 1.3676 14.4 7/0.11 15/9.11 3/10.95 17/12.09 13/16.69 8 0.7813 0.4243 1.0325 12.3 8/0.10 5/11.99 16/12.71 1/13.84 6/14.76 9 0.7818 0.5920 1.4755 9.1 9/0.18 17/14.12 4/17.53 15/19.78 4/19.89 10 0.5502 0.3557 0.8858 8.7 11/0.17 6/9.60 1/11.28 11/12.21 16/16.60 11 0.4528 0.2480 0.8212 8.3 10/0.23 10/12.21 13/13.37 6/17.46 7/20.54 12 0.7288 0.5208 1.2482 7.7 12/0.19 13/16.31 14/17.75 13/19.63 14/20.4 13 0.4511 0.0996 0.7663 6.7 13/0.13 11/13.37 12/16.31 7/16.69 13/17.45 14 0.5450 0.4396 1.1162 6.1 14/0.18 14/11.29 1/11.78 8/15.83 12/17.75 15 0.8038 0.3121 1.4633 -5.6 2/2.96 3/2.91 17/5.85 7/9.11 4/19.01 16 0.8031 0.3011 0.9542 -5.1 5/2.58 5/2.59 2/9.08 6/9.11 8/12.71 17 0.7984 0.2434 1.4771 -4.6 2/8.13 15/5.85 3/8.04 7/12.09 9/14.12 Best trace (cycle 3 with CC 8.32%) was saved as P21212_pse14_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 10.5 - Setup, data input and phasing 2.4 - FFTs and peak-searches 5.1 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 54.2 - Tripeptide search 62.6 - Chain tracing 0.0 - NCS analysis 3.4 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:14:15 Total time: 138.30 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++