++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:34:24 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: I4_p9 I4_p9_fa -i -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I4_p9_fa.res FA and alpha from I4_p9_fa.hkl Native data from I4_p9.hkl Listing output to I4_p9_i.lst Phases output to I4_p9_i.phs Revised heavy atom sites output to I4_p9_i.hat Revised heavy atom phases output to I4_p9_i.pha Poly-Ala trace output to I4_p9_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 1.200 high resolution limit for data extrapolation -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 10 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 0.600 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: I 4 Allowed origin shift code: 8 7 atoms read from file I4_p9_fa.res Trimmed to 3 atoms with occupancy > 0.2 16206 Reflections read from file I4_p9_fa.hkl 21557 Reflections read from file I4_p9.hkl 21557 Unique data, highest resolution = 1.744 Angstroms Anisotropic scaling: intensities multiplied by -0.000103h^2 -0.000103k^2 +0.003717l^2 +0.000000kl +0.000000hl +0.000000hk 11 Reflections with d > 1.944 and 44093 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 28 0.000 <= z <= 0.500 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.746 ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 44.88% = 0.344 for phases from phiT = phiA + alpha = 0.442 after including heavy atoms = 0.287, Contrast = 0.070, Connect. = 0.510 for dens.mod. cycle 1 = 0.295, Contrast = 0.283, Connect. = 0.610 for dens.mod. cycle 2 = 0.295, Contrast = 0.538, Connect. = 0.723 for dens.mod. cycle 3 = 0.295, Contrast = 0.688, Connect. = 0.772 for dens.mod. cycle 4 = 0.295, Contrast = 0.776, Connect. = 0.796 for dens.mod. cycle 5 = 0.295, Contrast = 0.823, Connect. = 0.809 for dens.mod. cycle 6 = 0.295, Contrast = 0.850, Connect. = 0.816 for dens.mod. cycle 7 = 0.295, Contrast = 0.868, Connect. = 0.819 for dens.mod. cycle 8 = 0.295, Contrast = 0.880, Connect. = 0.822 for dens.mod. cycle 9 = 0.295, Contrast = 0.887, Connect. = 0.823 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 3 heavy atoms with Occ*Z > 10.20 added to NOGO map 1138 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 131 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 44 38.733 2.206 1.026 0.498 0.860 0.674 CB 1.539 B: 28 42.787 2.277 1.286 0.502 1.000 0.593 CB 1.579 C: 51 59.875 2.431 1.261 0.502 1.000 0.680 CB 1.537 11 residues pruned to eliminate duplicates D: 36 36.200 2.284 1.178 0.390 0.971 0.514 CB 1.423 19 residues pruned to eliminate duplicates 129 residues left after pruning, divided into chains as follows: A: 44 B: 85 CC for partial structure against native data = 42.98 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.295, Contrast = 0.497, Connect. = 0.702 for dens.mod. cycle 1 = 0.295, Contrast = 0.652, Connect. = 0.761 for dens.mod. cycle 2 = 0.295, Contrast = 0.871, Connect. = 0.818 for dens.mod. cycle 3 = 0.295, Contrast = 0.874, Connect. = 0.820 for dens.mod. cycle 4 = 0.295, Contrast = 0.896, Connect. = 0.824 for dens.mod. cycle 5 = 0.295, Contrast = 0.894, Connect. = 0.824 for dens.mod. cycle 6 = 0.295, Contrast = 0.904, Connect. = 0.826 for dens.mod. cycle 7 = 0.295, Contrast = 0.902, Connect. = 0.825 for dens.mod. cycle 8 = 0.295, Contrast = 0.908, Connect. = 0.827 for dens.mod. cycle 9 = 0.295, Contrast = 0.905, Connect. = 0.826 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 3 heavy atoms with Occ*Z > 10.20 added to NOGO map 1124 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 134 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 83 77.233 2.432 1.249 0.493 0.976 0.707 CB 1.609 B: 71 72.261 2.434 1.154 0.529 0.957 0.657 CB 1.672 47 residues pruned to eliminate duplicates C: 89 87.279 2.458 1.270 0.532 0.943 0.750 CB 1.712 68 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 128 residues left after pruning, divided into chains as follows: A: 128 CC for partial structure against native data = 46.17 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.295, Contrast = 0.514, Connect. = 0.707 for dens.mod. cycle 1 = 0.295, Contrast = 0.671, Connect. = 0.766 for dens.mod. cycle 2 = 0.295, Contrast = 0.887, Connect. = 0.819 for dens.mod. cycle 3 = 0.295, Contrast = 0.886, Connect. = 0.821 for dens.mod. cycle 4 = 0.295, Contrast = 0.903, Connect. = 0.824 for dens.mod. cycle 5 = 0.295, Contrast = 0.901, Connect. = 0.824 for dens.mod. cycle 6 = 0.295, Contrast = 0.908, Connect. = 0.825 for dens.mod. cycle 7 = 0.295, Contrast = 0.906, Connect. = 0.826 for dens.mod. cycle 8 = 0.295, Contrast = 0.910, Connect. = 0.826 for dens.mod. cycle 9 = 0.295, Contrast = 0.908, Connect. = 0.826 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 3 heavy atoms with Occ*Z > 10.20 added to NOGO map 1114 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 134 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 92 90.019 2.451 1.269 0.537 0.945 0.703 CB 1.731 B: 84 70.983 2.416 1.183 0.485 0.952 0.699 CB 1.575 46 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 130 residues left after pruning, divided into chains as follows: A: 130 CC for partial structure against native data = 45.67 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.295, Contrast = 0.513, Connect. = 0.706 for dens.mod. cycle 1 = 0.295, Contrast = 0.671, Connect. = 0.765 for dens.mod. cycle 2 = 0.295, Contrast = 0.888, Connect. = 0.819 for dens.mod. cycle 3 = 0.295, Contrast = 0.886, Connect. = 0.820 for dens.mod. cycle 4 = 0.295, Contrast = 0.904, Connect. = 0.824 for dens.mod. cycle 5 = 0.295, Contrast = 0.901, Connect. = 0.824 for dens.mod. cycle 6 = 0.295, Contrast = 0.909, Connect. = 0.826 for dens.mod. cycle 7 = 0.295, Contrast = 0.906, Connect. = 0.825 for dens.mod. cycle 8 = 0.295, Contrast = 0.911, Connect. = 0.826 for dens.mod. cycle 9 = 0.295, Contrast = 0.908, Connect. = 0.826 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 3 heavy atoms with Occ*Z > 10.20 added to NOGO map 1121 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 126 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 49 62.086 2.426 1.293 0.518 0.979 0.688 CB 1.616 B: 109 84.134 2.359 1.276 0.499 0.944 0.667 CB 1.599 49 residues pruned to eliminate duplicates C: 45 34.988 2.219 0.898 0.419 0.909 0.591 CB 1.499 23 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 131 residues left after pruning, divided into chains as follows: A: 131 CC for partial structure against native data = 43.37 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.295, Contrast = 0.499, Connect. = 0.703 for dens.mod. cycle 1 = 0.295, Contrast = 0.658, Connect. = 0.760 for dens.mod. cycle 2 = 0.295, Contrast = 0.877, Connect. = 0.817 for dens.mod. cycle 3 = 0.295, Contrast = 0.879, Connect. = 0.819 for dens.mod. cycle 4 = 0.295, Contrast = 0.899, Connect. = 0.824 for dens.mod. cycle 5 = 0.295, Contrast = 0.897, Connect. = 0.824 for dens.mod. cycle 6 = 0.295, Contrast = 0.907, Connect. = 0.825 for dens.mod. cycle 7 = 0.295, Contrast = 0.905, Connect. = 0.825 for dens.mod. cycle 8 = 0.295, Contrast = 0.910, Connect. = 0.826 for dens.mod. cycle 9 = 0.295, Contrast = 0.907, Connect. = 0.826 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 3 heavy atoms with Occ*Z > 10.20 added to NOGO map 1114 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 137 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 86 73.413 2.391 1.176 0.489 0.941 0.706 CB 1.644 B: 21 29.273 2.409 1.108 0.419 0.900 0.550 CB 1.559 C: 25 32.115 2.201 1.258 0.424 0.875 0.625 CB 1.632 10 residues pruned to eliminate duplicates D: 49 75.636 2.528 1.378 0.583 1.000 0.812 CB 1.677 49 residues pruned to eliminate duplicates E: 7 6.853 1.707 0.454 0.710 0.667 0.667 N 1.397 Using tripeptides from previous cycle as seeds 128 residues left after pruning, divided into chains as follows: A: 122 B: 6 CC for partial structure against native data = 43.78 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 2 used as input for final density modification = 0.295, Contrast = 0.503, Connect. = 0.700 for dens.mod. cycle 1 = 0.308, Contrast = 0.661, Connect. = 0.761 for dens.mod. cycle 2 = 0.317, Contrast = 0.954, Connect. = 0.840 for dens.mod. cycle 3 = 0.318, Contrast = 0.926, Connect. = 0.843 for dens.mod. cycle 4 = 0.319, Contrast = 0.939, Connect. = 0.845 for dens.mod. cycle 5 = 0.320, Contrast = 0.891, Connect. = 0.843 for dens.mod. cycle 6 = 0.320, Contrast = 0.869, Connect. = 0.839 for dens.mod. cycle 7 = 0.321, Contrast = 0.814, Connect. = 0.829 for dens.mod. cycle 8 = 0.321, Contrast = 0.789, Connect. = 0.823 for dens.mod. cycle 9 = 0.322, Contrast = 0.744, Connect. = 0.807 for dens.mod. cycle 10 Estimated mean FOM and mapCC as a function of resolution d inf - 3.82 - 3.02 - 2.63 - 2.39 - 2.21 - 2.08 - 1.98 - 1.89 - 1.81 - 1.75 0.777 0.790 0.813 0.815 0.822 0.796 0.774 0.775 0.834 0.870 0.902 0.906 0.917 0.925 0.930 0.908 0.900 0.909 0.975 0.986 N 2172 2153 2174 2129 2262 2141 2064 2233 2385 1844 Estimated mean FOM = 0.806 Pseudo-free CC = 84.16 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.6797 0.3872 0.8063 34.0000 70.17 2 0.7619 0.3136 1.2791 29.0564 59.56 3 0.7939 0.3352 1.2122 26.1970 54.32 Site x y z h(sig) near old near new 1 0.6799 0.3873 0.8068 70.2 1/0.03 8/1.92 19/1.93 7/2.27 6/2.28 2 0.7622 0.3141 1.2765 60.1 2/0.10 17/1.56 15/1.85 26/1.88 5/1.99 3 0.7934 0.3353 1.2134 53.8 3/0.07 21/1.98 12/2.26 23/4.05 18/4.56 4 0.7412 0.5280 0.3934 8.9 1/22.06 14/18.01 10/18.91 20/19.87 22/19.9 5 0.7639 0.3102 1.3361 -7.6 2/1.90 15/1.95 2/1.99 26/2.33 17/2.97 6 0.6801 0.3880 0.8769 -7.6 1/2.29 9/1.62 1/2.28 19/2.86 8/2.99 7 0.6799 0.3865 0.7370 -6.9 1/2.25 20/1.83 1/2.27 8/2.96 19/3.10 8 0.6706 0.3733 0.8084 -6.8 1/1.89 1/1.92 7/2.96 6/2.99 19/3.81 9 0.6806 0.3867 0.9265 -6.6 1/3.91 6/1.62 1/3.89 19/4.27 8/4.28 10 0.6816 0.3876 1.1640 -6.5 1/11.62 22/2.12 9/7.71 6/9.33 17/11.41 11 0.7946 0.3336 0.7327 -6.5 1/14.64 13/4.40 24/4.42 25/8.82 16/12.22 12 0.7929 0.3331 1.2825 -6.1 3/2.30 3/2.26 16/2.44 21/2.82 2/4.12 13 0.7635 0.3156 1.6826 -6.0 2/13.11 24/2.86 11/4.40 25/9.26 5/11.27 14 0.6790 0.3875 0.5231 -5.9 1/9.20 20/5.12 7/6.95 1/9.21 8/9.45 15 0.7569 0.2997 1.2954 -5.8 2/1.77 26/1.65 2/1.85 5/1.95 17/2.82 16 0.7927 0.3367 1.3565 -5.8 3/4.69 12/2.44 5/4.51 3/4.65 21/5.04 17 0.7518 0.3226 1.2677 -5.7 2/1.59 2/1.56 23/2.00 15/2.82 5/2.97 18 0.7657 0.3147 1.1425 -5.5 2/4.46 23/2.54 2/4.37 17/4.46 3/4.56 19 0.6853 0.4033 0.8096 -5.4 1/1.95 1/1.93 6/2.86 7/3.10 8/3.81 20 0.6794 0.3870 0.6808 -5.3 1/4.08 7/1.83 1/4.09 8/4.54 19/4.62 21 0.8043 0.3218 1.2164 -5.1 3/1.95 3/1.98 12/2.82 23/4.90 26/5.01 22 0.6802 0.3870 1.0989 -5.1 1/9.50 10/2.12 9/5.60 6/7.21 1/9.49 23 0.7614 0.3198 1.2172 -5.0 2/2.13 17/2.00 2/2.03 18/2.54 26/3.20 24 0.7618 0.3158 0.7706 -4.9 1/12.45 13/2.86 11/4.42 25/6.40 18/12.08 25 0.7615 0.3130 0.9675 -4.8 3/9.12 18/5.70 24/6.40 23/8.14 11/8.82 26 0.7706 0.2999 1.2788 -4.8 2/1.85 15/1.65 2/1.88 5/2.33 23/3.20 Best trace (cycle 2 with CC 46.17%) was saved as I4_p9_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.9 - Setup, data input and phasing 6.3 - FFTs and peak-searches 10.1 - Sphere of influence 0.4 - Rest of density modification 0.0 - Alpha-helix search 40.0 - Tripeptide search 44.2 - Chain tracing 0.0 - NCS analysis 5.4 - B-value refinement for trace 0.2 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:36:11 Total time: 107.39 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++