++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:26:35 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: P41_visc-standard P41_visc-standard_fa -i -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P41_visc-standard_fa.res FA and alpha from P41_visc-standard_fa.hkl Native data from P41_visc-standard.hkl Listing output to P41_visc-standard_i.lst Phases output to P41_visc-standard_i.phs Revised heavy atom sites output to P41_visc-standard_i.hat Revised heavy atom phases output to P41_visc-standard_i.pha Poly-Ala trace output to P41_visc-standard_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 0.500 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 41 Allowed origin shift code: 7 21 atoms read from file P41_visc-standard_fa.res Trimmed to 18 atoms with occupancy > 0.2 14490 Reflections read from file P41_visc-standard_fa.hkl 22220 Reflections read from file P41_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 ** Space group converted to enantiomorph ** ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 13.36% = 0.102 for phases from phiT = phiA + alpha = 0.190 after including heavy atoms = 0.139, Contrast = 0.024, Connect. = 0.541 for dens.mod. cycle 1 = 0.157, Contrast = 0.092, Connect. = 0.595 for dens.mod. cycle 2 = 0.173, Contrast = 0.121, Connect. = 0.609 for dens.mod. cycle 3 = 0.188, Contrast = 0.139, Connect. = 0.609 for dens.mod. cycle 4 = 0.202, Contrast = 0.155, Connect. = 0.609 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 1664 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 89 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 6 1.262 1.331 0.382 0.291 0.600 0.400 N 0.646 ? A: 8 2.642 1.261 0.115 0.444 1.000 0.571 CA 0.753 B: 9 4.520 1.192 0.566 0.493 0.875 0.375 CB 0.985 C: 12 3.772 1.362 0.231 0.335 0.727 0.455 CA 1.117 D: 7 3.967 1.320 0.191 0.782 1.000 0.833 CB 0.804 E: 8 2.208 1.272 0.392 0.155 0.857 0.429 CA 0.840 36 residues left after pruning, divided into chains as follows: A: 8 B: 9 C: 12 D: 7 CC for partial structure against native data = 1.58 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.275, Contrast = 0.168, Connect. = 0.546 for dens.mod. cycle 1 = 0.279, Contrast = 0.170, Connect. = 0.474 for dens.mod. cycle 2 = 0.283, Contrast = 0.188, Connect. = 0.495 for dens.mod. cycle 3 = 0.287, Contrast = 0.204, Connect. = 0.512 for dens.mod. cycle 4 = 0.287, Contrast = 0.218, Connect. = 0.527 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2202 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 111 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 18.964 2.135 0.431 0.777 1.000 0.600 CB 1.538 B: 10 14.956 2.214 0.315 0.486 1.000 0.333 C 1.737 C: 13 12.168 2.222 0.348 0.303 0.750 0.333 N 1.947 D: 7 9.252 1.986 0.542 0.625 0.833 0.500 N 1.315 E: 12 6.865 1.892 0.216 0.333 0.818 0.455 CB 1.321 6 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 41 residues left after pruning, divided into chains as follows: A: 11 B: 10 C: 13 D: 7 CC for partial structure against native data = 2.23 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.230, Connect. = 0.530 for dens.mod. cycle 1 = 0.287, Contrast = 0.230, Connect. = 0.481 for dens.mod. cycle 2 = 0.287, Contrast = 0.239, Connect. = 0.499 for dens.mod. cycle 3 = 0.287, Contrast = 0.254, Connect. = 0.520 for dens.mod. cycle 4 = 0.287, Contrast = 0.266, Connect. = 0.536 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2220 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 119 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 31.989 2.606 0.421 0.736 0.917 0.583 CA 2.202 B: 16 10.255 2.474 -0.026 0.288 0.667 0.200 CA 2.091 C: 16 11.798 2.045 0.601 0.282 0.800 0.400 CB 1.487 14 residues pruned to eliminate duplicates D: 13 10.784 2.244 0.300 0.404 0.750 0.250 CA 1.575 E: 19 15.662 2.158 0.190 0.440 0.889 0.500 CB 1.720 15 residues pruned to eliminate duplicates F: 6 2.152 1.274 0.444 0.454 0.600 0.400 CB 0.913 9 1.540 1.187 0.289 0.295 0.500 0.500 CB 0.895 ? Using tripeptides from previous cycle as seeds 44 residues left after pruning, divided into chains as follows: A: 14 B: 11 C: 19 CC for partial structure against native data = 3.98 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.253, Connect. = 0.524 for dens.mod. cycle 1 = 0.287, Contrast = 0.259, Connect. = 0.494 for dens.mod. cycle 2 = 0.287, Contrast = 0.263, Connect. = 0.509 for dens.mod. cycle 3 = 0.287, Contrast = 0.267, Connect. = 0.522 for dens.mod. cycle 4 = 0.287, Contrast = 0.277, Connect. = 0.537 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2161 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 113 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 25.384 2.408 0.324 0.764 0.909 0.636 C 2.088 B: 9 13.697 2.595 0.103 0.562 0.750 0.500 CA 2.123 C: 16 11.334 2.357 0.184 0.338 0.600 0.267 CB 2.086 D: 10 5.758 2.011 -0.219 0.407 0.889 0.556 CB 1.516 E: 6 2.124 1.163 0.589 0.337 0.800 0.400 CB 0.768 Using tripeptides from previous cycle as seeds 48 residues left after pruning, divided into chains as follows: A: 12 B: 7 C: 14 D: 9 E: 6 CC for partial structure against native data = 4.59 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.286, Connect. = 0.522 for dens.mod. cycle 1 = 0.287, Contrast = 0.295, Connect. = 0.501 for dens.mod. cycle 2 = 0.287, Contrast = 0.294, Connect. = 0.512 for dens.mod. cycle 3 = 0.287, Contrast = 0.294, Connect. = 0.524 for dens.mod. cycle 4 = 0.287, Contrast = 0.314, Connect. = 0.543 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2130 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 110 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 14 21.905 2.273 0.326 0.770 0.846 0.615 CB 1.876 B: 14 11.588 1.936 0.341 0.485 0.923 0.462 CA 1.362 C: 9 9.215 2.202 0.022 0.447 0.875 0.375 CA 1.746 D: 8 5.425 1.872 0.349 0.224 0.714 0.429 CA 1.568 E: 10 7.424 1.925 0.032 0.429 0.889 0.444 CA 1.508 F: 9 4.567 1.689 1.038 0.073 0.625 0.250 CB 1.311 G: 12 4.383 1.590 0.431 0.270 0.636 0.364 CB 1.185 Using tripeptides from previous cycle as seeds 60 residues left after pruning, divided into chains as follows: A: 13 B: 12 C: 9 D: 8 E: 10 F: 8 CC for partial structure against native data = 3.16 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.287, Contrast = 0.240, Connect. = 0.529 for dens.mod. cycle 1 = 0.287, Contrast = 0.250, Connect. = 0.494 for dens.mod. cycle 2 = 0.287, Contrast = 0.259, Connect. = 0.509 for dens.mod. cycle 3 = 0.287, Contrast = 0.269, Connect. = 0.523 for dens.mod. cycle 4 = 0.287, Contrast = 0.293, Connect. = 0.543 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 0.368 0.300 0.278 0.280 0.247 0.283 0.323 0.328 0.291 0.278 0.503 0.406 0.374 0.370 0.333 0.414 0.492 0.519 0.500 0.499 N 2223 2221 2248 2276 2140 2248 2426 2133 2189 2095 Estimated mean FOM = 0.298 Pseudo-free CC = 35.60 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.8278 0.9475 0.8521 16.0000 29.48 2 0.6584 0.5775 0.9209 15.0608 28.07 3 0.8407 1.0731 0.4858 14.3808 26.94 4 0.6199 0.7340 1.1947 13.8864 24.03 5 0.6992 0.6545 1.0391 13.5584 23.71 6 0.5501 0.6664 1.2944 12.6400 22.05 7 0.6890 0.4295 0.8991 11.4048 19.32 8 0.7865 1.1439 0.3691 11.0768 19.93 9 0.7805 0.8689 0.9720 10.9872 20.07 10 0.8199 0.9319 0.5108 10.5568 17.75 11 0.4072 0.6758 1.3293 9.0352 15.36 12 0.9036 0.8398 0.5664 8.5312 15.86 13 0.9220 0.8980 0.4357 6.2848 12.19 14 0.8469 0.4838 0.9375 5.9072 10.28 15 0.7782 0.8952 0.8234 5.6576 10.41 16 0.7260 0.9909 0.5955 5.1632 8.93 17 0.5978 1.1539 0.6518 5.1408 8.70 18 0.8334 0.4865 1.0401 3.3280 5.69 Site x y z h(sig) near old near new 1 0.8279 0.9472 0.8518 29.5 1/0.02 15/4.86 7/8.26 12/10.03 14/12.51 2 0.6580 0.5775 0.9208 28.1 2/0.03 5/7.98 10/9.97 16/13.88 19/14.10 3 0.8410 1.0733 0.4856 27.0 3/0.03 9/0.75 8/8.04 11/9.53 14/10.19 4 0.6195 0.7339 1.1952 24.1 4/0.04 6/7.92 5/10.47 13/15.76 18/16.25 5 0.6993 0.6547 1.0381 23.7 5/0.05 2/7.98 4/10.47 8/14.00 19/14.07 6 0.5507 0.6658 1.2951 22.1 6/0.06 4/7.92 13/9.58 5/15.59 13/16.46 7 0.7805 0.8689 0.9718 20.1 9/0.01 15/7.19 1/8.26 8/10.11 5/15.38 8 0.7866 1.1439 0.3690 19.9 8/0.01 3/8.04 9/8.57 7/10.11 5/14.00 9 0.8407 1.0730 0.5016 19.3 3/0.74 3/0.75 8/8.57 11/9.44 14/9.50 10 0.6892 0.4298 0.8991 19.3 7/0.02 2/9.97 13/10.00 16/11.10 19/12.18 11 0.8195 0.9312 0.5114 17.8 10/0.06 14/7.92 17/8.38 12/8.56 9/9.44 12 0.9028 0.8389 0.5652 16.0 12/0.10 14/7.36 11/8.56 1/10.03 15/13.80 13 0.4074 0.6765 1.3292 15.4 11/0.05 6/9.58 10/10.00 18/13.95 4/15.76 14 0.9222 0.8987 0.4360 12.2 13/0.05 12/7.36 11/7.92 9/9.50 3/10.19 15 0.7780 0.8964 0.8242 10.5 15/0.09 1/4.86 7/7.19 17/12.83 12/13.80 16 0.8468 0.4837 0.9377 10.3 14/0.01 19/4.88 10/11.10 2/13.88 5/15.58 17 0.7252 0.9904 0.5976 9.0 16/0.12 11/8.38 9/10.38 3/10.75 15/12.83 18 0.5985 1.1536 0.6521 8.7 17/0.05 17/13.82 13/13.95 4/16.25 6/16.81 19 0.8335 0.4880 1.0393 5.7 18/0.11 16/4.88 10/12.18 5/14.07 2/14.10 Best trace (cycle 4 with CC 4.59%) was saved as P41_visc-standard_i.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 123.9 - Tripeptide search 21.2 - 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 12:29:07 Total time: 152.12 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++