++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:32:58 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: P43_visc-standard P43_visc-standard_fa -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P43_visc-standard_fa.res FA and alpha from P43_visc-standard_fa.hkl Native data from P43_visc-standard.hkl Listing output to P43_visc-standard.lst Phases output to P43_visc-standard.phs Revised heavy atom sites output to P43_visc-standard.hat Revised heavy atom phases output to P43_visc-standard.pha Poly-Ala trace output to P43_visc-standard.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 0.500 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: P 43 Allowed origin shift code: 7 21 atoms read from file P43_visc-standard_fa.res 14490 Reflections read from file P43_visc-standard_fa.hkl 22220 Reflections read from file P43_visc-standard.hkl 22199 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000221h^2 +0.000221k^2 -0.000681l^2 +0.000000kl +0.000000hl +0.000000hk 9 Reflections with d > 1.902 and 0 in range 1.902 > d > 1.702 added Density sharpening factor set to 1.20 Fourier grid = 128 x 128 x 21 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|> = 0.759 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 13.96% = 0.107 for phases from phiT = phiA + alpha = 0.195 after including heavy atoms = 0.146, Contrast = 0.024, Connect. = 0.530 for dens.mod. cycle 1 = 0.164, Contrast = 0.091, Connect. = 0.586 for dens.mod. cycle 2 = 0.181, Contrast = 0.118, Connect. = 0.601 for dens.mod. cycle 3 = 0.195, Contrast = 0.130, Connect. = 0.598 for dens.mod. cycle 4 = 0.207, Contrast = 0.143, Connect. = 0.597 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 1758 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 141 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 4.241 1.291 0.471 0.528 1.000 0.800 CB 0.971 B: 7 3.482 1.336 0.480 0.352 0.833 0.333 CB 1.012 C: 11 3.113 1.269 0.394 0.257 0.800 0.400 CB 0.919 D: 8 2.565 1.332 0.477 0.323 0.571 0.286 CB 1.048 E: 6 2.064 1.271 0.210 0.237 0.800 0.400 N 1.019 F: 9 2.310 1.356 0.710 0.302 0.625 0.250 CB 0.702 G: 6 2.905 1.233 0.624 0.595 0.800 0.400 N 0.740 H: 6 2.115 1.265 0.428 0.277 0.800 0.200 CB 0.843 38 residues left after pruning, divided into chains as follows: A: 7 B: 11 C: 8 D: 6 E: 6 CC for partial structure against native data = 1.14 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.284, Contrast = 0.154, Connect. = 0.537 for dens.mod. cycle 1 = 0.285, Contrast = 0.157, Connect. = 0.469 for dens.mod. cycle 2 = 0.286, Contrast = 0.169, Connect. = 0.487 for dens.mod. cycle 3 = 0.287, Contrast = 0.183, Connect. = 0.505 for dens.mod. cycle 4 = 0.287, Contrast = 0.197, Connect. = 0.520 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2244 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 152 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 9.242 2.390 0.218 0.425 0.625 0.375 CB 1.941 B: 9 7.819 2.104 0.008 0.372 0.875 0.250 CA 1.709 C: 7 4.258 2.255 0.066 0.234 0.667 0.500 CB 1.479 D: 15 11.276 2.088 0.417 0.262 0.786 0.357 CB 1.699 E: 9 9.674 2.186 0.456 0.260 0.750 0.500 CA 1.886 F: 10 3.616 1.397 0.464 0.332 0.778 0.333 CB 0.911 8 1.897 1.185 0.296 0.221 0.714 0.286 CB 0.906 ? Using tripeptides from previous cycle as seeds 53 residues left after pruning, divided into chains as follows: A: 9 B: 7 C: 7 D: 15 E: 9 F: 6 CC for partial structure against native data = 5.76 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.219, Connect. = 0.510 for dens.mod. cycle 1 = 0.287, Contrast = 0.227, Connect. = 0.497 for dens.mod. cycle 2 = 0.287, Contrast = 0.237, Connect. = 0.514 for dens.mod. cycle 3 = 0.287, Contrast = 0.244, Connect. = 0.527 for dens.mod. cycle 4 = 0.287, Contrast = 0.249, Connect. = 0.536 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2142 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 158 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 10.084 2.140 0.235 0.311 0.889 0.333 CB 1.765 B: 20 12.432 2.134 0.141 0.292 0.789 0.316 CB 1.874 C: 12 10.517 2.162 0.197 0.344 0.818 0.455 CB 1.774 D: 11 8.062 2.121 0.085 0.331 0.800 0.200 CB 1.666 E: 12 8.629 2.208 0.268 0.262 0.727 0.455 CB 1.677 F: 7 2.480 1.396 -0.002 0.353 1.000 0.833 CB 0.851 6 0.812 1.135 0.361 0.376 0.800 0.600 CB 0.335 ? Using tripeptides from previous cycle as seeds 65 residues left after pruning, divided into chains as follows: A: 10 B: 20 C: 12 D: 11 E: 12 CC for partial structure against native data = 4.10 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.219, Connect. = 0.523 for dens.mod. cycle 1 = 0.287, Contrast = 0.226, Connect. = 0.499 for dens.mod. cycle 2 = 0.287, Contrast = 0.232, Connect. = 0.512 for dens.mod. cycle 3 = 0.287, Contrast = 0.239, Connect. = 0.526 for dens.mod. cycle 4 = 0.287, Contrast = 0.250, Connect. = 0.538 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2146 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 173 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 9.196 2.519 0.047 0.201 0.778 0.222 C 2.131 B: 21 15.925 2.536 0.142 0.269 0.750 0.300 CB 2.131 C: 12 8.867 2.402 0.386 0.235 0.545 0.273 CA 2.004 D: 11 11.303 2.505 0.106 0.372 0.700 0.200 CB 2.114 E: 17 8.214 2.141 0.377 0.178 0.625 0.375 CB 1.643 Using tripeptides from previous cycle as seeds 70 residues left after pruning, divided into chains as follows: A: 10 B: 21 C: 12 D: 11 E: 16 CC for partial structure against native data = 5.48 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.228, Connect. = 0.519 for dens.mod. cycle 1 = 0.287, Contrast = 0.232, Connect. = 0.504 for dens.mod. cycle 2 = 0.287, Contrast = 0.237, Connect. = 0.518 for dens.mod. cycle 3 = 0.287, Contrast = 0.243, Connect. = 0.531 for dens.mod. cycle 4 = 0.287, Contrast = 0.250, Connect. = 0.541 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2131 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 178 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 23 16.394 2.565 0.132 0.228 0.773 0.227 CB 2.141 B: 12 8.337 2.334 0.163 0.154 0.727 0.364 C 1.946 C: 15 7.382 2.316 0.086 0.234 0.571 0.143 CA 1.870 D: 18 12.076 2.054 0.436 0.387 0.765 0.412 CB 1.463 E: 10 4.745 1.847 0.050 0.383 0.667 0.333 CB 1.384 F: 18 11.334 1.948 0.172 0.456 0.824 0.412 CB 1.530 15 residues pruned to eliminate duplicates G: 14 4.298 1.751 0.052 0.254 0.692 0.231 CB 1.240 14 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 79 residues left after pruning, divided into chains as follows: A: 12 B: 16 C: 10 D: 18 E: 23 CC for partial structure against native data = 7.20 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.287, Contrast = 0.222, Connect. = 0.520 for dens.mod. cycle 1 = 0.287, Contrast = 0.231, Connect. = 0.508 for dens.mod. cycle 2 = 0.287, Contrast = 0.241, Connect. = 0.522 for dens.mod. cycle 3 = 0.287, Contrast = 0.250, Connect. = 0.535 for dens.mod. cycle 4 = 0.287, Contrast = 0.273, Connect. = 0.554 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 3.71 - 2.94 - 2.56 - 2.32 - 2.16 - 2.03 - 1.92 - 1.84 - 1.77 - 1.71 0.379 0.341 0.273 0.269 0.280 0.289 0.308 0.299 0.268 0.242 0.519 0.456 0.358 0.347 0.369 0.411 0.448 0.452 0.418 0.401 N 2223 2221 2248 2276 2140 2248 2426 2133 2189 2095 Estimated mean FOM = 0.295 Pseudo-free CC = 34.54 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.5762 0.3409 0.1824 16.0000 31.47 2 0.4450 0.3338 -0.1903 14.1584 27.78 3 0.6558 0.3031 0.3062 13.9968 27.04 4 0.9500 0.1732 0.1199 12.9648 25.37 5 0.3747 0.2749 -0.3026 12.1072 22.43 6 0.5920 0.3194 -0.1647 11.8768 24.53 7 0.8851 0.2438 0.2136 10.3536 19.74 8 0.8416 0.0731 0.5150 9.5328 19.37 9 0.8093 -0.0693 0.5189 8.9392 17.48 10 0.4304 0.3060 0.1703 8.6464 16.40 11 0.6013 0.3427 -0.1181 7.6592 15.14 12 0.7909 0.1475 0.3839 7.6112 13.46 13 0.5545 0.2233 -0.3716 6.5536 12.13 14 0.9007 -0.1577 0.5746 5.7856 11.01 15 0.4458 0.4303 -0.1011 5.7760 10.81 16 0.9530 0.3158 0.3894 5.2032 9.64 17 0.4348 0.1276 -0.0583 4.1696 7.66 18 0.4904 0.0548 0.1763 4.0064 6.44 19 0.5100 0.1126 -0.1093 3.9152 6.92 20 0.7270 -0.0073 0.6042 3.7920 7.26 21 0.4713 0.0647 0.0918 3.3888 6.20 Site x y z h(sig) near old near new 1 0.5768 0.3412 0.1836 31.6 1/0.07 22/2.21 3/8.16 10/9.86 11/14.40 2 0.4453 0.3346 -0.1897 27.9 2/0.06 15/7.56 6/8.08 5/9.76 11/10.72 3 0.6562 0.3034 0.3059 27.1 3/0.04 1/8.16 22/9.23 6/9.37 12/14.06 4 0.9499 0.1730 0.1208 25.4 4/0.04 7/7.68 14/10.03 18/14.38 16/15.81 5 0.5917 0.3192 -0.1638 24.6 6/0.05 11/2.63 2/9.76 10/10.76 13/11.89 6 0.3750 0.2742 -0.3023 22.5 5/0.05 2/8.08 3/9.37 13/12.69 15/14.71 7 0.8853 0.2437 0.2143 19.8 7/0.04 4/7.68 16/10.53 12/12.00 3/16.16 8 0.8416 0.0740 0.5146 19.4 8/0.06 12/8.46 9/9.58 18/10.18 14/14.74 9 0.8098 -0.0682 0.5199 17.6 9/0.10 18/7.86 14/8.92 8/9.58 8/15.44 10 0.4315 0.3055 0.1700 16.5 10/0.08 11/8.72 1/9.86 22/10.60 5/10.76 11 0.6003 0.3425 -0.1200 15.3 11/0.11 5/2.63 10/8.72 2/10.72 15/11.76 12 0.7905 0.1470 0.3851 13.5 12/0.07 8/8.46 7/12.00 3/14.06 18/15.12 13 0.5547 0.2249 -0.3727 12.3 13/0.12 5/11.89 6/12.69 2/13.35 11/14.52 14 0.9016 -0.1600 0.5751 11.2 14/0.16 9/8.92 4/10.03 18/14.50 8/14.74 15 0.4451 0.4307 -0.1017 10.8 15/0.06 2/7.56 11/11.76 5/12.21 5/12.46 16 0.9526 0.3164 0.3898 9.7 16/0.05 7/10.53 20/14.44 12/15.42 6/15.64 17 0.4354 0.1273 -0.0608 7.7 17/0.12 19/5.49 21/8.61 20/12.57 2/14.93 18 0.7273 -0.0075 0.6059 7.3 20/0.09 9/7.86 8/10.18 21/13.48 4/14.38 19 0.5093 0.1120 -0.1109 7.0 19/0.10 17/5.49 21/10.43 20/13.98 13/14.72 20 0.4910 0.0556 0.1738 6.5 18/0.13 21/4.12 17/12.57 19/13.98 16/14.44 21 0.4692 0.0654 0.0930 6.3 21/0.15 20/4.12 17/8.61 19/10.43 18/13.48 22 0.5771 0.3746 0.1782 -4.6 1/2.23 1/2.21 3/9.23 10/10.60 11/14.30 Best trace (cycle 5 with CC 7.20%) was saved as P43_visc-standard.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 1.1 - FFTs and peak-searches 3.1 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 124.0 - Tripeptide search 29.4 - Chain tracing 0.0 - NCS analysis 3.0 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:35:39 Total time: 160.93 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++