++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:42:09 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: I422_p9 I422_p9_fa -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I422_p9_fa.res FA and alpha from I422_p9_fa.hkl Native data from I422_p9.hkl Listing output to I422_p9.lst Phases output to I422_p9.phs Revised heavy atom sites output to I422_p9.hat Revised heavy atom phases output to I422_p9.pha Poly-Ala trace output to I422_p9.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 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 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 2 2 Allowed origin shift code: 10 7 atoms read from file I422_p9_fa.res Trimmed to 6 atoms with occupancy > 0.2 5593 Reflections read from file I422_p9_fa.hkl 11203 Reflections read from file I422_p9.hkl 11203 Unique data, highest resolution = 1.744 Angstroms Anisotropic scaling: intensities multiplied by -0.000081h^2 -0.000081k^2 +0.002623l^2 +0.000000kl +0.000000hl +0.000000hk 9 Reflections with d > 1.944 and 22510 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 15 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|> = 0.660 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 11.08% = 0.073 for phases from phiT = phiA + alpha = 0.177 after including heavy atoms = 0.150, Contrast = 0.013, Connect. = 0.488 for dens.mod. cycle 1 = 0.194, Contrast = 0.061, Connect. = 0.564 for dens.mod. cycle 2 = 0.222, Contrast = 0.134, Connect. = 0.651 for dens.mod. cycle 3 = 0.237, Contrast = 0.205, Connect. = 0.696 for dens.mod. cycle 4 = 0.252, Contrast = 0.202, Connect. = 0.688 for dens.mod. cycle 5 = 0.263, Contrast = 0.194, Connect. = 0.676 for dens.mod. cycle 6 = 0.272, Contrast = 0.188, Connect. = 0.667 for dens.mod. cycle 7 = 0.280, Contrast = 0.184, Connect. = 0.659 for dens.mod. cycle 8 = 0.286, Contrast = 0.180, Connect. = 0.653 for dens.mod. cycle 9 = 0.290, Contrast = 0.177, Connect. = 0.648 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1004 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 58 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 2.090 1.410 -0.102 0.493 0.800 0.800 CA 0.929 7 1.439 1.160 0.421 0.247 0.833 0.333 C 0.572 ? B: 6 2.694 1.201 0.135 0.437 1.000 0.400 CA 0.942 12 residues left after pruning, divided into chains as follows: A: 6 B: 6 CC for partial structure against native data = 3.01 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.299, Contrast = 0.214, Connect. = 0.591 for dens.mod. cycle 1 = 0.298, Contrast = 0.217, Connect. = 0.573 for dens.mod. cycle 2 = 0.299, Contrast = 0.221, Connect. = 0.588 for dens.mod. cycle 3 = 0.299, Contrast = 0.219, Connect. = 0.598 for dens.mod. cycle 4 = 0.299, Contrast = 0.215, Connect. = 0.605 for dens.mod. cycle 5 = 0.299, Contrast = 0.211, Connect. = 0.611 for dens.mod. cycle 6 = 0.299, Contrast = 0.207, Connect. = 0.615 for dens.mod. cycle 7 = 0.299, Contrast = 0.204, Connect. = 0.620 for dens.mod. cycle 8 = 0.299, Contrast = 0.200, Connect. = 0.623 for dens.mod. cycle 9 = 0.299, Contrast = 0.197, Connect. = 0.626 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 990 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 67 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 9.928 2.189 0.169 0.354 0.889 0.222 CB 1.703 B: 9 5.475 2.149 -0.012 0.307 0.625 0.375 CB 1.806 Using tripeptides from previous cycle as seeds 18 residues left after pruning, divided into chains as follows: A: 9 B: 9 CC for partial structure against native data = 1.54 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.299, Contrast = 0.229, Connect. = 0.595 for dens.mod. cycle 1 = 0.299, Contrast = 0.231, Connect. = 0.567 for dens.mod. cycle 2 = 0.299, Contrast = 0.235, Connect. = 0.582 for dens.mod. cycle 3 = 0.299, Contrast = 0.233, Connect. = 0.593 for dens.mod. cycle 4 = 0.299, Contrast = 0.229, Connect. = 0.601 for dens.mod. cycle 5 = 0.299, Contrast = 0.225, Connect. = 0.607 for dens.mod. cycle 6 = 0.299, Contrast = 0.220, Connect. = 0.612 for dens.mod. cycle 7 = 0.299, Contrast = 0.216, Connect. = 0.615 for dens.mod. cycle 8 = 0.299, Contrast = 0.213, Connect. = 0.619 for dens.mod. cycle 9 = 0.299, Contrast = 0.209, Connect. = 0.622 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1002 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 67 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 13.124 2.514 0.477 0.167 0.875 0.250 CB 2.141 B: 13 6.666 2.104 0.171 0.218 0.750 0.417 CB 1.450 C: 10 2.858 1.347 0.689 0.242 0.778 0.556 CA 0.726 Using tripeptides from previous cycle as seeds 26 residues left after pruning, divided into chains as follows: A: 9 B: 13 C: 4 CC for partial structure against native data = 5.32 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.299, Contrast = 0.257, Connect. = 0.590 for dens.mod. cycle 1 = 0.299, Contrast = 0.263, Connect. = 0.584 for dens.mod. cycle 2 = 0.299, Contrast = 0.268, Connect. = 0.598 for dens.mod. cycle 3 = 0.299, Contrast = 0.263, Connect. = 0.607 for dens.mod. cycle 4 = 0.299, Contrast = 0.257, Connect. = 0.613 for dens.mod. cycle 5 = 0.299, Contrast = 0.250, Connect. = 0.618 for dens.mod. cycle 6 = 0.299, Contrast = 0.243, Connect. = 0.621 for dens.mod. cycle 7 = 0.299, Contrast = 0.237, Connect. = 0.623 for dens.mod. cycle 8 = 0.299, Contrast = 0.231, Connect. = 0.625 for dens.mod. cycle 9 = 0.299, Contrast = 0.226, Connect. = 0.626 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 970 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 66 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 10.867 2.549 0.295 0.144 0.778 0.222 CB 2.189 B: 10 8.331 2.141 0.228 0.300 0.778 0.444 CB 1.698 C: 6 4.263 2.190 -0.115 0.284 0.800 0.600 CB 1.568 Using tripeptides from previous cycle as seeds 25 residues left after pruning, divided into chains as follows: A: 10 B: 10 C: 5 CC for partial structure against native data = 5.45 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.299, Contrast = 0.287, Connect. = 0.595 for dens.mod. cycle 1 = 0.299, Contrast = 0.292, Connect. = 0.587 for dens.mod. cycle 2 = 0.299, Contrast = 0.294, Connect. = 0.600 for dens.mod. cycle 3 = 0.299, Contrast = 0.287, Connect. = 0.608 for dens.mod. cycle 4 = 0.299, Contrast = 0.278, Connect. = 0.614 for dens.mod. cycle 5 = 0.299, Contrast = 0.269, Connect. = 0.618 for dens.mod. cycle 6 = 0.299, Contrast = 0.260, Connect. = 0.620 for dens.mod. cycle 7 = 0.299, Contrast = 0.252, Connect. = 0.623 for dens.mod. cycle 8 = 0.299, Contrast = 0.245, Connect. = 0.624 for dens.mod. cycle 9 = 0.299, Contrast = 0.239, Connect. = 0.626 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 970 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 73 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 6.724 2.374 0.087 0.273 0.714 0.286 CB 1.783 B: 13 8.339 2.024 0.314 0.304 0.667 0.333 CB 1.689 C: 6 4.642 2.371 0.298 0.298 0.600 0.400 CB 1.409 Using tripeptides from previous cycle as seeds D: 10 3.124 1.812 0.356 0.167 0.667 0.111 CB 0.953 27 residues left after pruning, divided into chains as follows: A: 8 B: 13 C: 6 CC for partial structure against native data = 3.41 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.299, Contrast = 0.251, Connect. = 0.596 for dens.mod. cycle 1 = 0.299, Contrast = 0.259, Connect. = 0.584 for dens.mod. cycle 2 = 0.304, Contrast = 0.266, Connect. = 0.616 for dens.mod. cycle 3 = 0.304, Contrast = 0.291, Connect. = 0.629 for dens.mod. cycle 4 = 0.305, Contrast = 0.272, Connect. = 0.631 for dens.mod. cycle 5 = 0.304, Contrast = 0.259, Connect. = 0.627 for dens.mod. cycle 6 = 0.306, Contrast = 0.243, Connect. = 0.624 for dens.mod. cycle 7 = 0.305, Contrast = 0.230, Connect. = 0.620 for dens.mod. cycle 8 = 0.306, Contrast = 0.221, Connect. = 0.621 for dens.mod. cycle 9 = 0.306, Contrast = 0.214, Connect. = 0.618 for dens.mod. cycle 10 Estimated mean FOM and mapCC as a function of resolution d inf - 3.88 - 3.05 - 2.65 - 2.40 - 2.22 - 2.09 - 1.98 - 1.89 - 1.81 - 1.75 0.316 0.346 0.364 0.323 0.360 0.291 0.262 0.232 0.120 0.127 0.480 0.502 0.562 0.465 0.512 0.401 0.360 0.328 0.165 0.170 N 1123 1119 1128 1124 1150 1079 1158 1148 1224 950 Estimated mean FOM = 0.275 Pseudo-free CC = 30.84 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.6802 0.3837 0.0843 34.0000 32.29 2 0.8355 0.3355 -0.2500 12.7262 22.81 3 0.7625 0.3139 -0.3622 22.6338 21.92 4 0.6653 0.3642 0.0826 19.0434 17.83 5 0.8689 0.4632 -0.1323 17.9044 15.95 6 0.8254 0.2806 -0.6931 15.2796 15.09 Site x y z h(sig) near old near new 1 0.6800 0.3838 0.0845 32.3 1/0.02 9/1.92 11/2.00 10/2.13 4/2.83 2 0.8356 0.3356 -0.2500 22.8 2/0.01 13/7.91 13/7.91 3/9.42 3/9.42 3 0.7625 0.3140 -0.3620 21.9 3/0.01 13/2.11 2/9.42 2/9.42 13/10.32 4 0.6656 0.3636 0.0822 17.9 4/0.07 9/2.09 11/2.19 1/2.83 10/3.57 5 0.8686 0.4627 -0.1334 16.0 5/0.08 2/15.43 2/15.43 8/19.45 8/19.45 6 0.8253 0.2805 -0.6936 15.1 6/0.03 8/6.67 8/6.67 13/12.09 10/13.30 7 0.6818 0.3813 -0.0820 -6.1 1/5.41 12/2.44 9/4.14 1/5.42 11/5.68 8 0.8357 0.3357 -0.7500 -5.4 6/6.65 6/6.67 6/6.67 13/13.94 13/13.94 9 0.6731 0.3752 0.0399 -5.2 1/1.91 1/1.92 11/1.95 4/2.09 10/3.79 10 0.6801 0.3836 0.1502 -5.2 1/2.14 1/2.13 11/3.04 4/3.57 9/3.79 11 0.6626 0.3826 0.0794 -4.9 1/2.01 9/1.95 1/2.00 4/2.19 10/3.04 12 0.6330 0.3341 0.0847 -4.9 4/5.03 7/2.44 9/4.23 4/5.01 4/5.43 13 0.7806 0.3127 -0.3752 -4.5 3/2.12 3/2.11 2/7.91 2/7.91 13/9.63 Best trace (cycle 4 with CC 5.45%) was saved as I422_p9.pdb ============================================================================== CPU times required in seconds ----------------------------- 1.0 - Setup, data input and phasing 3.7 - FFTs and peak-searches 5.3 - Sphere of influence 0.2 - Rest of density modification 0.0 - Alpha-helix search 52.4 - Tripeptide search 14.4 - Chain tracing 0.0 - NCS analysis 0.8 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:43:27 Total time: 77.92 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++