++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + 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 -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.lst Phases output to P41_visc-standard.phs Revised heavy atom sites output to P41_visc-standard.hat Revised heavy atom phases output to P41_visc-standard.pha Poly-Ala trace output to P41_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 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 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 = 0.148, Contrast = 0.024, Connect. = 0.539 for dens.mod. cycle 1 = 0.165, Contrast = 0.084, Connect. = 0.581 for dens.mod. cycle 2 = 0.183, Contrast = 0.095, Connect. = 0.584 for dens.mod. cycle 3 = 0.199, Contrast = 0.099, Connect. = 0.577 for dens.mod. cycle 4 = 0.213, Contrast = 0.113, Connect. = 0.578 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 1788 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 150 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 3.169 1.287 -0.010 0.627 1.000 0.800 CB 0.988 B: 7 2.402 1.322 0.426 0.304 0.833 0.500 N 0.777 C: 6 4.219 1.378 0.196 0.505 1.000 0.600 CB 1.140 D: 8 3.180 1.473 0.522 0.317 0.571 0.429 O 1.148 6 1.549 1.056 0.150 0.445 1.000 0.400 CB 0.604 ? 6 1.590 1.292 0.143 0.445 0.600 0.400 CB 0.849 ? 6 1.774 1.338 0.445 0.193 0.600 0.200 CB 0.987 ? 6 1.210 1.029 0.775 0.300 0.600 0.400 CB 0.617 ? E: 7 3.183 1.287 0.075 0.438 1.000 0.500 CA 1.001 6 1.973 0.915 0.281 0.664 1.000 0.600 N 0.647 ? 9 1.647 1.054 0.110 0.270 0.875 0.250 CA 0.740 ? 6 1.847 1.251 0.864 0.100 0.600 0.400 C 0.984 ? 28 residues left after pruning, divided into chains as follows: A: 7 B: 6 C: 8 D: 7 CC for partial structure against native data = 2.99 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.287, Contrast = 0.185, Connect. = 0.527 for dens.mod. cycle 1 = 0.287, Contrast = 0.194, Connect. = 0.469 for dens.mod. cycle 2 = 0.287, Contrast = 0.199, Connect. = 0.484 for dens.mod. cycle 3 = 0.287, Contrast = 0.201, Connect. = 0.497 for dens.mod. cycle 4 = 0.287, Contrast = 0.204, Connect. = 0.508 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 2181 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 134 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 9.471 2.619 0.407 0.381 0.500 0.375 CB 2.062 B: 8 11.111 2.511 0.151 0.243 1.000 0.286 CB 1.955 C: 9 2.646 1.788 0.169 0.187 0.625 0.625 CB 1.043 D: 7 2.801 1.695 0.116 0.276 0.667 0.333 CA 1.168 E: 10 9.662 2.301 0.294 0.194 0.889 0.444 CB 1.754 8 residues pruned to eliminate duplicates F: 6 2.385 1.164 0.658 0.320 1.000 0.400 CA 0.674 G: 6 2.344 1.113 0.233 0.724 1.000 0.800 N 0.624 Using tripeptides from previous cycle as seeds 34 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 9 D: 8 CC for partial structure against native data = 1.89 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.217, Connect. = 0.510 for dens.mod. cycle 1 = 0.287, Contrast = 0.231, Connect. = 0.483 for dens.mod. cycle 2 = 0.287, Contrast = 0.234, Connect. = 0.497 for dens.mod. cycle 3 = 0.287, Contrast = 0.236, Connect. = 0.509 for dens.mod. cycle 4 = 0.287, Contrast = 0.241, Connect. = 0.519 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 2169 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 144 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 10.173 2.613 0.135 0.282 0.636 0.364 CB 2.079 B: 11 10.745 2.530 0.393 0.185 0.800 0.400 CB 1.759 C: 11 13.590 2.467 0.427 0.300 0.800 0.400 CB 1.908 D: 12 13.395 2.337 0.340 0.480 0.818 0.455 CB 1.609 Using tripeptides from previous cycle as seeds 43 residues left after pruning, divided into chains as follows: A: 12 B: 11 C: 8 D: 12 CC for partial structure against native data = 4.06 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.257, Connect. = 0.517 for dens.mod. cycle 1 = 0.287, Contrast = 0.267, Connect. = 0.496 for dens.mod. cycle 2 = 0.287, Contrast = 0.270, Connect. = 0.508 for dens.mod. cycle 3 = 0.287, Contrast = 0.268, Connect. = 0.519 for dens.mod. cycle 4 = 0.287, Contrast = 0.283, Connect. = 0.535 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 2127 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 146 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 12.709 2.327 0.332 0.369 0.750 0.500 CB 1.817 B: 8 8.436 2.420 0.016 0.566 0.714 0.429 CA 1.703 C: 10 7.666 2.293 0.206 0.207 0.667 0.444 CB 1.960 D: 7 3.514 1.528 -0.190 0.677 0.833 0.667 CB 1.182 E: 15 12.201 2.222 0.525 0.392 0.643 0.286 CB 1.678 8 residues pruned to eliminate duplicates F: 6 2.954 1.325 0.731 0.362 0.600 0.600 N 1.113 6 1.645 1.165 0.008 0.588 1.000 0.600 CB 0.576 ? Using tripeptides from previous cycle as seeds G: 6 8.117 2.140 0.681 0.251 1.000 0.400 CB 1.343 47 residues left after pruning, divided into chains as follows: A: 13 B: 6 C: 7 D: 15 E: 6 CC for partial structure against native data = 5.05 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.246, Connect. = 0.514 for dens.mod. cycle 1 = 0.287, Contrast = 0.255, Connect. = 0.496 for dens.mod. cycle 2 = 0.287, Contrast = 0.258, Connect. = 0.508 for dens.mod. cycle 3 = 0.287, Contrast = 0.258, Connect. = 0.519 for dens.mod. cycle 4 = 0.287, Contrast = 0.265, Connect. = 0.531 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 2109 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 148 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 10.148 2.240 0.053 0.681 0.750 0.500 CB 1.717 B: 21 17.606 2.389 0.352 0.281 0.750 0.300 C 2.080 C: 12 8.897 2.244 0.110 0.263 0.818 0.364 CB 1.725 D: 7 5.800 1.902 0.310 0.518 0.667 0.500 CB 1.400 6 1.869 1.183 0.251 0.348 0.800 0.400 CB 0.833 ? E: 12 5.340 1.579 0.577 0.227 0.818 0.455 CB 1.087 Using tripeptides from previous cycle as seeds F: 6 6.161 1.637 0.274 0.531 1.000 0.200 N 1.281 53 residues left after pruning, divided into chains as follows: A: 9 B: 21 C: 11 D: 6 E: 6 CC for partial structure against native data = 4.41 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.287, Contrast = 0.241, Connect. = 0.521 for dens.mod. cycle 1 = 0.287, Contrast = 0.250, Connect. = 0.498 for dens.mod. cycle 2 = 0.287, Contrast = 0.254, Connect. = 0.510 for dens.mod. cycle 3 = 0.287, Contrast = 0.253, Connect. = 0.520 for dens.mod. cycle 4 = 0.287, Contrast = 0.252, Connect. = 0.527 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 0.222 0.342 0.292 0.300 0.261 0.284 0.320 0.325 0.304 0.290 0.286 0.440 0.386 0.393 0.357 0.417 0.480 0.507 0.499 0.504 N 2223 2221 2248 2276 2140 2248 2426 2133 2189 2095 Estimated mean FOM = 0.294 Pseudo-free CC = 34.64 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.1722 0.0525 0.1479 16.0000 29.76 2 0.3416 0.4225 0.0791 15.0608 29.07 3 0.1593 -0.0731 0.5142 14.3808 27.57 4 0.3801 0.2660 -0.1947 13.8864 25.34 5 0.3008 0.3455 -0.0391 13.5584 24.05 6 0.4499 0.3336 -0.2944 12.6400 24.10 7 0.3110 0.5705 0.1009 11.4048 21.90 8 0.2135 -0.1439 0.6309 11.0768 20.18 9 0.2195 0.1311 0.0280 10.9872 20.39 10 0.1801 0.0681 0.4892 10.5568 18.86 11 0.5928 0.3242 -0.3293 9.0352 16.45 12 0.0964 0.1602 0.4336 8.5312 14.66 13 0.0780 0.1020 0.5643 6.2848 12.22 14 0.1531 0.5162 0.0625 5.9072 10.44 15 0.2218 0.1048 0.1766 5.6576 10.78 16 0.2740 0.0091 0.4045 5.1632 10.55 17 0.4022 -0.1539 0.3482 5.1408 8.72 18 0.1666 0.5135 -0.0401 3.3280 6.50 Site x y z h(sig) near old near new 1 0.1722 0.0528 0.1474 29.8 1/0.03 14/4.85 8/8.18 12/9.95 13/12.56 2 0.3416 0.4221 0.0788 29.1 2/0.03 6/7.96 7/10.00 16/13.83 18/14.16 3 0.1594 -0.0737 0.5137 27.6 3/0.04 9/7.99 10/9.55 13/10.16 15/10.65 4 0.3808 0.2657 -0.1952 25.4 4/0.06 5/7.88 6/10.44 11/15.76 17/16.25 5 0.4491 0.3339 -0.2942 24.3 6/0.05 4/7.88 11/9.59 6/15.50 11/16.54 6 0.3011 0.3451 -0.0388 24.1 5/0.04 2/7.96 4/10.44 9/14.02 18/14.17 7 0.3112 0.5702 0.1016 21.9 7/0.04 11/9.97 2/10.00 16/11.04 18/12.26 8 0.2195 0.1307 0.0293 20.5 9/0.07 14/7.13 1/8.18 9/10.20 6/15.42 9 0.2134 -0.1439 0.6298 20.2 8/0.05 3/7.99 8/10.20 6/14.02 15/15.22 10 0.1807 0.0689 0.4889 18.9 10/0.07 13/7.92 15/8.34 12/8.62 3/9.55 11 0.5923 0.3236 -0.3302 16.5 11/0.07 5/9.59 7/9.97 17/14.00 4/15.76 12 0.0958 0.1610 0.4348 14.7 12/0.09 13/7.35 10/8.62 1/9.95 14/13.73 13 0.0781 0.1012 0.5642 12.2 13/0.06 12/7.35 10/7.92 3/10.16 1/12.56 14 0.2211 0.1041 0.1759 10.8 15/0.07 1/4.85 8/7.13 15/12.85 12/13.73 15 0.2736 0.0089 0.4023 10.6 16/0.11 10/8.34 3/10.65 14/12.85 13/13.36 16 0.1542 0.5171 0.0628 10.5 14/0.09 18/4.92 7/11.04 2/13.83 6/15.62 17 0.4012 -0.1533 0.3481 8.8 17/0.07 15/13.81 11/14.00 4/16.25 5/16.81 18 0.1657 0.5128 -0.0402 6.5 18/0.08 16/4.92 7/12.26 2/14.16 6/14.17 Best trace (cycle 4 with CC 5.05%) was saved as P41_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 125.3 - Tripeptide search 26.0 - Chain tracing 0.0 - NCS analysis 2.1 - B-value refinement for trace 0.0 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:29:13 Total time: 157.98 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++