++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:44:06 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: I4122_p9 I4122_p9_fa -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I4122_p9_fa.res FA and alpha from I4122_p9_fa.hkl Native data from I4122_p9.hkl Listing output to I4122_p9.lst Phases output to I4122_p9.phs Revised heavy atom sites output to I4122_p9.hat Revised heavy atom phases output to I4122_p9.pha Poly-Ala trace output to I4122_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 41 2 2 Allowed origin shift code:110 7 atoms read from file I4122_p9_fa.res Trimmed to 4 atoms with occupancy > 0.2 5593 Reflections read from file I4122_p9_fa.hkl 11203 Reflections read from file I4122_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 5 Reflections with d > 1.944 and 22507 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 8 0.000 <= z <= 0.125 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) = 6.53% = 0.055 for phases from phiT = phiA + alpha = 0.127 after including heavy atoms = 0.148, Contrast = 0.012, Connect. = 0.445 for dens.mod. cycle 1 = 0.215, Contrast = 0.030, Connect. = 0.514 for dens.mod. cycle 2 = 0.269, Contrast = 0.112, Connect. = 0.584 for dens.mod. cycle 3 = 0.276, Contrast = 0.269, Connect. = 0.705 for dens.mod. cycle 4 = 0.283, Contrast = 0.295, Connect. = 0.718 for dens.mod. cycle 5 = 0.289, Contrast = 0.286, Connect. = 0.710 for dens.mod. cycle 6 = 0.292, Contrast = 0.277, Connect. = 0.703 for dens.mod. cycle 7 = 0.296, Contrast = 0.268, Connect. = 0.696 for dens.mod. cycle 8 = 0.298, Contrast = 0.260, Connect. = 0.691 for dens.mod. cycle 9 = 0.299, Contrast = 0.254, Connect. = 0.686 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 990 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 48 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 2.591 1.352 0.177 0.280 1.000 0.429 N 0.789 B: 8 3.001 1.127 0.244 0.485 1.000 0.429 C 0.822 6 1.716 1.018 0.295 0.555 0.800 0.600 N 0.690 ? 6 1.503 0.948 0.678 0.279 0.800 0.600 CB 0.678 ? 16 residues left after pruning, divided into chains as follows: A: 8 B: 8 CC for partial structure against native data = 1.79 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.299, Contrast = 0.227, Connect. = 0.598 for dens.mod. cycle 1 = 0.299, Contrast = 0.238, Connect. = 0.598 for dens.mod. cycle 2 = 0.299, Contrast = 0.251, Connect. = 0.615 for dens.mod. cycle 3 = 0.299, Contrast = 0.256, Connect. = 0.625 for dens.mod. cycle 4 = 0.299, Contrast = 0.258, Connect. = 0.632 for dens.mod. cycle 5 = 0.299, Contrast = 0.258, Connect. = 0.637 for dens.mod. cycle 6 = 0.299, Contrast = 0.257, Connect. = 0.641 for dens.mod. cycle 7 = 0.299, Contrast = 0.257, Connect. = 0.644 for dens.mod. cycle 8 = 0.299, Contrast = 0.255, Connect. = 0.648 for dens.mod. cycle 9 = 0.299, Contrast = 0.254, Connect. = 0.651 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 976 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 69 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 18.346 2.444 0.356 0.485 1.000 0.667 CB 1.872 B: 10 10.706 2.498 0.143 0.274 0.778 0.444 CB 2.076 Using tripeptides from previous cycle as seeds 20 residues left after pruning, divided into chains as follows: A: 10 B: 10 CC for partial structure against native data = 4.55 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.299, Contrast = 0.305, Connect. = 0.599 for dens.mod. cycle 1 = 0.299, Contrast = 0.317, Connect. = 0.596 for dens.mod. cycle 2 = 0.299, Contrast = 0.329, Connect. = 0.614 for dens.mod. cycle 3 = 0.299, Contrast = 0.330, Connect. = 0.624 for dens.mod. cycle 4 = 0.299, Contrast = 0.328, Connect. = 0.632 for dens.mod. cycle 5 = 0.299, Contrast = 0.324, Connect. = 0.638 for dens.mod. cycle 6 = 0.299, Contrast = 0.320, Connect. = 0.641 for dens.mod. cycle 7 = 0.299, Contrast = 0.315, Connect. = 0.644 for dens.mod. cycle 8 = 0.299, Contrast = 0.309, Connect. = 0.647 for dens.mod. cycle 9 = 0.299, Contrast = 0.305, Connect. = 0.649 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 970 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 75 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 9.644 2.518 0.261 0.178 0.667 0.333 CB 1.942 B: 14 11.299 2.257 0.333 0.344 0.769 0.308 CB 1.604 C: 8 3.670 1.587 0.445 0.304 0.714 0.286 CA 1.053 Using tripeptides from previous cycle as seeds 24 residues left after pruning, divided into chains as follows: A: 6 B: 14 C: 4 CC for partial structure against native data = 1.95 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.299, Contrast = 0.262, Connect. = 0.596 for dens.mod. cycle 1 = 0.299, Contrast = 0.272, Connect. = 0.592 for dens.mod. cycle 2 = 0.299, Contrast = 0.289, Connect. = 0.610 for dens.mod. cycle 3 = 0.299, Contrast = 0.296, Connect. = 0.621 for dens.mod. cycle 4 = 0.299, Contrast = 0.299, Connect. = 0.628 for dens.mod. cycle 5 = 0.299, Contrast = 0.299, Connect. = 0.634 for dens.mod. cycle 6 = 0.299, Contrast = 0.299, Connect. = 0.638 for dens.mod. cycle 7 = 0.299, Contrast = 0.298, Connect. = 0.642 for dens.mod. cycle 8 = 0.299, Contrast = 0.296, Connect. = 0.645 for dens.mod. cycle 9 = 0.299, Contrast = 0.295, Connect. = 0.648 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 958 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 14.545 2.744 0.304 0.300 0.857 0.286 CB 2.239 B: 13 16.207 2.605 0.349 0.337 0.750 0.333 CB 2.120 C: 7 3.299 2.027 0.105 0.460 0.500 0.333 CB 1.253 D: 9 4.217 1.432 0.439 0.322 0.875 0.500 C 1.006 Using tripeptides from previous cycle as seeds 23 residues left after pruning, divided into chains as follows: A: 5 B: 13 C: 5 CC for partial structure against native data = 4.58 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.299, Contrast = 0.304, Connect. = 0.598 for dens.mod. cycle 1 = 0.299, Contrast = 0.317, Connect. = 0.598 for dens.mod. cycle 2 = 0.299, Contrast = 0.335, Connect. = 0.616 for dens.mod. cycle 3 = 0.299, Contrast = 0.339, Connect. = 0.628 for dens.mod. cycle 4 = 0.299, Contrast = 0.339, Connect. = 0.634 for dens.mod. cycle 5 = 0.299, Contrast = 0.336, Connect. = 0.638 for dens.mod. cycle 6 = 0.299, Contrast = 0.333, Connect. = 0.643 for dens.mod. cycle 7 = 0.299, Contrast = 0.329, Connect. = 0.646 for dens.mod. cycle 8 = 0.299, Contrast = 0.325, Connect. = 0.649 for dens.mod. cycle 9 = 0.299, Contrast = 0.321, Connect. = 0.651 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 4 heavy atoms with Occ*Z > 6.11 added to NOGO map 967 peaks > 0.5 sigma used to seed fragment search Space for about 83 unique residues taking solvent into account 79 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 7.291 1.854 0.291 0.327 0.786 0.357 CB 1.253 B: 10 6.323 2.303 0.190 0.321 0.556 0.444 CB 1.685 C: 17 13.757 2.370 0.201 0.279 0.812 0.312 CB 1.907 Using tripeptides from previous cycle as seeds 32 residues left after pruning, divided into chains as follows: A: 5 B: 10 C: 17 CC for partial structure against native data = 6.82 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.299, Contrast = 0.308, Connect. = 0.611 for dens.mod. cycle 1 = 0.300, Contrast = 0.320, Connect. = 0.606 for dens.mod. cycle 2 = 0.302, Contrast = 0.340, Connect. = 0.646 for dens.mod. cycle 3 = 0.302, Contrast = 0.377, Connect. = 0.656 for dens.mod. cycle 4 = 0.304, Contrast = 0.357, Connect. = 0.658 for dens.mod. cycle 5 = 0.303, Contrast = 0.342, Connect. = 0.649 for dens.mod. cycle 6 = 0.305, Contrast = 0.323, Connect. = 0.646 for dens.mod. cycle 7 = 0.305, Contrast = 0.306, Connect. = 0.637 for dens.mod. cycle 8 = 0.306, Contrast = 0.295, Connect. = 0.636 for dens.mod. cycle 9 = 0.305, Contrast = 0.283, Connect. = 0.633 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 0.364 0.354 0.280 0.248 0.272 0.250 0.285 0.334 0.330 0.371 0.554 0.521 0.418 0.341 0.374 0.336 0.379 0.457 0.441 0.483 N 1123 1119 1128 1124 1150 1079 1158 1148 1224 950 Estimated mean FOM = 0.308 Pseudo-free CC = 34.08 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.0311 0.0311 0.0000 17.0000 35.65 2 0.1656 -0.1430 -0.4720 20.3626 20.44 3 0.2112 -0.2365 -0.3437 19.5670 21.50 4 0.0716 -0.0460 -0.2190 18.9006 19.47 Site x y z h(sig) near old near new 1 0.0309 0.0309 0.0000 35.7 1/0.03 7/1.78 7/1.78 5/1.91 5/1.91 2 0.2113 -0.2361 -0.3438 21.7 3/0.05 2/10.48 2/10.48 2/10.48 3/12.56 3 0.1651 -0.1427 -0.4698 20.6 2/0.10 3/4.10 2/12.56 2/12.77 2/14.29 4 0.0722 -0.0453 -0.2161 19.8 4/0.14 7/10.36 5/11.30 1/12.12 1/12.12 5 0.0326 0.0305 0.0584 -5.3 1/1.90 7/1.67 1/1.91 1/1.91 7/3.30 6 0.2176 0.2088 0.1077 4.9 1/29.57 6/7.14 6/9.46 6/11.71 6/15.03 7 0.0377 0.0214 -0.0365 -4.8 1/1.78 5/1.67 1/1.78 1/1.78 5/3.30 Best trace (cycle 5 with CC 6.82%) was saved as I4122_p9.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.8 - Setup, data input and phasing 2.2 - FFTs and peak-searches 4.6 - Sphere of influence 0.2 - Rest of density modification 0.0 - Alpha-helix search 49.9 - Tripeptide search 12.7 - 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 13:45:17 Total time: 71.29 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++