Starting phenix.real_space_refine on Tue Mar 19 17:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/03_2024/8e00_27811_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 118 5.16 5 C 15867 2.51 5 N 4165 2.21 5 O 4633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1854": "OD1" <-> "OD2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2139": "OD1" <-> "OD2" Residue "A PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 465": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 19069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19069 Classifications: {'peptide': 2363} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 64, 'TRANS': 2298} Chain breaks: 10 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "C" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2832 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.57, per 1000 atoms: 0.51 Number of scatterers: 24794 At special positions: 0 Unit cell: (159.82, 113.97, 195.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 P 11 15.00 O 4633 8.00 N 4165 7.00 C 15867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.19 Conformation dependent library (CDL) restraints added in 4.1 seconds 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 29 sheets defined 45.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.65 Creating SS restraints... Processing helix chain 'A' and resid 1450 through 1458 Processing helix chain 'A' and resid 1465 through 1467 No H-bonds generated for 'chain 'A' and resid 1465 through 1467' Processing helix chain 'A' and resid 1470 through 1478 Processing helix chain 'A' and resid 1516 through 1522 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.638A pdb=" N GLN A1533 " --> pdb=" O ARG A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 Processing helix chain 'A' and resid 1542 through 1550 Processing helix chain 'A' and resid 1557 through 1565 removed outlier: 3.705A pdb=" N MET A1562 " --> pdb=" O VAL A1558 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1632 Processing helix chain 'A' and resid 1636 through 1638 No H-bonds generated for 'chain 'A' and resid 1636 through 1638' Processing helix chain 'A' and resid 1645 through 1664 Processing helix chain 'A' and resid 1670 through 1688 removed outlier: 4.080A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1717 Processing helix chain 'A' and resid 1721 through 1730 removed outlier: 3.798A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1788 removed outlier: 3.964A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1828 through 1841 Processing helix chain 'A' and resid 1850 through 1852 No H-bonds generated for 'chain 'A' and resid 1850 through 1852' Processing helix chain 'A' and resid 1855 through 1874 removed outlier: 3.867A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1915 removed outlier: 4.667A pdb=" N SER A1915 " --> pdb=" O ASN A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1936 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1970 through 1982 removed outlier: 3.588A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1984 through 1987 No H-bonds generated for 'chain 'A' and resid 1984 through 1987' Processing helix chain 'A' and resid 1991 through 2005 Proline residue: A2004 - end of helix Processing helix chain 'A' and resid 2008 through 2021 Processing helix chain 'A' and resid 2032 through 2045 Processing helix chain 'A' and resid 2051 through 2066 removed outlier: 3.686A pdb=" N LYS A2065 " --> pdb=" O TYR A2061 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2095 Processing helix chain 'A' and resid 2111 through 2114 No H-bonds generated for 'chain 'A' and resid 2111 through 2114' Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2160 through 2170 removed outlier: 3.702A pdb=" N GLU A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET A2166 " --> pdb=" O TYR A2162 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A2167 " --> pdb=" O VAL A2163 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 No H-bonds generated for 'chain 'A' and resid 2204 through 2207' Processing helix chain 'A' and resid 2222 through 2236 Processing helix chain 'A' and resid 2245 through 2256 Processing helix chain 'A' and resid 2259 through 2271 removed outlier: 4.231A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2280 through 2301 removed outlier: 5.223A pdb=" N GLU A2285 " --> pdb=" O PHE A2281 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR A2286 " --> pdb=" O ASN A2282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A2299 " --> pdb=" O ILE A2295 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2327 Processing helix chain 'A' and resid 2332 through 2346 Processing helix chain 'A' and resid 2371 through 2373 No H-bonds generated for 'chain 'A' and resid 2371 through 2373' Processing helix chain 'A' and resid 2382 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2424 through 2433 Processing helix chain 'A' and resid 2451 through 2458 removed outlier: 3.777A pdb=" N LEU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2511 Processing helix chain 'A' and resid 2548 through 2553 removed outlier: 5.032A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2580 removed outlier: 3.778A pdb=" N LYS A2580 " --> pdb=" O LYS A2576 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2606 removed outlier: 5.163A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU A2590 " --> pdb=" O SER A2587 " (cutoff:3.500A) Proline residue: A2591 - end of helix Processing helix chain 'A' and resid 2619 through 2634 Processing helix chain 'A' and resid 2641 through 2656 Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2709 through 2726 Processing helix chain 'A' and resid 2736 through 2750 Processing helix chain 'A' and resid 2766 through 2776 Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2819 through 2821 No H-bonds generated for 'chain 'A' and resid 2819 through 2821' Processing helix chain 'A' and resid 2825 through 2836 removed outlier: 3.501A pdb=" N THR A2833 " --> pdb=" O GLU A2829 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2843 No H-bonds generated for 'chain 'A' and resid 2841 through 2843' Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.704A pdb=" N LYS A2851 " --> pdb=" O GLU A2848 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2897 through 2904 Processing helix chain 'A' and resid 2906 through 2909 No H-bonds generated for 'chain 'A' and resid 2906 through 2909' Processing helix chain 'A' and resid 2922 through 2935 removed outlier: 3.636A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2952 No H-bonds generated for 'chain 'A' and resid 2950 through 2952' Processing helix chain 'A' and resid 2961 through 2980 Processing helix chain 'A' and resid 2990 through 3057 removed outlier: 4.316A pdb=" N LYS A3036 " --> pdb=" O ASN A3032 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A3037 " --> pdb=" O GLU A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3318 removed outlier: 4.845A pdb=" N PHE A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3336 removed outlier: 4.604A pdb=" N GLY A3335 " --> pdb=" O GLU A3331 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS A3336 " --> pdb=" O THR A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3355 Processing helix chain 'A' and resid 3366 through 3370 Processing helix chain 'A' and resid 3373 through 3381 Processing helix chain 'A' and resid 3388 through 3398 Processing helix chain 'A' and resid 3413 through 3422 Processing helix chain 'A' and resid 3436 through 3446 Processing helix chain 'A' and resid 3455 through 3457 No H-bonds generated for 'chain 'A' and resid 3455 through 3457' Processing helix chain 'A' and resid 3460 through 3466 removed outlier: 5.244A pdb=" N ARG A3464 " --> pdb=" O ILE A3461 " (cutoff:3.500A) Processing helix chain 'A' and resid 3507 through 3512 removed outlier: 3.638A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3522 through 3537 Processing helix chain 'A' and resid 3539 through 3571 Processing helix chain 'A' and resid 3581 through 3638 removed outlier: 3.912A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A3607 " --> pdb=" O GLU A3603 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE A3608 " --> pdb=" O SER A3604 " (cutoff:3.500A) Proline residue: A3609 - end of helix removed outlier: 4.114A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A3619 " --> pdb=" O VAL A3615 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3658 removed outlier: 3.847A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3689 removed outlier: 4.577A pdb=" N THR A3688 " --> pdb=" O CYS A3684 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA A3689 " --> pdb=" O GLN A3685 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3710 removed outlier: 4.198A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3726 Processing helix chain 'A' and resid 3742 through 3752 Processing helix chain 'A' and resid 3756 through 3767 removed outlier: 4.227A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3779 Processing helix chain 'A' and resid 3797 through 3806 Processing helix chain 'A' and resid 3819 through 3834 removed outlier: 3.644A pdb=" N LYS A3833 " --> pdb=" O ILE A3829 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3851 removed outlier: 3.788A pdb=" N LEU A3848 " --> pdb=" O GLN A3845 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A3849 " --> pdb=" O MET A3846 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3865 removed outlier: 4.236A pdb=" N GLU A3860 " --> pdb=" O HIS A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3886 through 3891 Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.841A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3958 through 3974 removed outlier: 3.836A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3991 Processing helix chain 'A' and resid 3995 through 3997 No H-bonds generated for 'chain 'A' and resid 3995 through 3997' Processing helix chain 'A' and resid 4001 through 4016 removed outlier: 3.871A pdb=" N CYS A4016 " --> pdb=" O ALA A4012 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4050 Processing helix chain 'A' and resid 4058 through 4061 No H-bonds generated for 'chain 'A' and resid 4058 through 4061' Processing helix chain 'A' and resid 4067 through 4090 removed outlier: 4.139A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'C' and resid 363 through 368 Processing sheet with id= A, first strand: chain 'A' and resid 1589 through 1591 Processing sheet with id= B, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id= C, first strand: chain 'A' and resid 1916 through 1920 removed outlier: 6.988A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id= E, first strand: chain 'A' and resid 2211 through 2215 removed outlier: 8.826A pdb=" N LEU A2070 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A2192 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A2072 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A2194 " --> pdb=" O LEU A2072 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY A2074 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR A2196 " --> pdb=" O GLY A2074 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2117 through 2119 Processing sheet with id= G, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id= H, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id= I, first strand: chain 'A' and resid 2554 through 2558 removed outlier: 6.713A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.191A pdb=" N ASN A2481 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A2441 " --> pdb=" O ASN A2481 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A2483 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A2443 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A2485 " --> pdb=" O ILE A2443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id= L, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 6.643A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A2913 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE A2759 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A2915 " --> pdb=" O ILE A2759 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3513 through 3517 removed outlier: 6.879A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id= O, first strand: chain 'A' and resid 3893 through 3896 removed outlier: 8.482A pdb=" N PHE A3786 " --> pdb=" O PHE A3871 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET A3873 " --> pdb=" O PHE A3786 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET A3788 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET A3875 " --> pdb=" O MET A3788 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER A3790 " --> pdb=" O MET A3875 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A3877 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.000A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.389A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 201 through 208 removed outlier: 7.166A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 256 through 264 removed outlier: 6.935A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN B 263 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 300 through 306 removed outlier: 7.045A pdb=" N GLY B 313 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE B 303 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 311 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL B 305 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS B 323 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY B 329 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 340 through 346 removed outlier: 6.882A pdb=" N ALA B 376 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 343 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 374 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE B 345 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR B 372 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU B 386 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N CYS B 409 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 420 through 426 removed outlier: 6.442A pdb=" N CYS B 433 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 423 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 431 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE B 425 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.049A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 192 through 195 removed outlier: 4.411A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.962A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 256 through 264 removed outlier: 6.794A pdb=" N CYS C 273 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 271 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 261 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N HIS C 269 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN C 263 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.741A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.844A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 420 through 426 removed outlier: 6.603A pdb=" N CYS C 433 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 423 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE C 431 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 425 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1161 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.18 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4063 1.29 - 1.43: 6559 1.43 - 1.56: 14506 1.56 - 1.70: 18 1.70 - 1.83: 181 Bond restraints: 25327 Sorted by residual: bond pdb=" C MET A2259 " pdb=" O MET A2259 " ideal model delta sigma weight residual 1.237 1.160 0.077 1.17e-02 7.31e+03 4.31e+01 bond pdb=" C VAL A3859 " pdb=" O VAL A3859 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.17e-02 7.31e+03 2.16e+01 bond pdb=" CA SER A3832 " pdb=" CB SER A3832 " ideal model delta sigma weight residual 1.530 1.466 0.065 1.69e-02 3.50e+03 1.46e+01 bond pdb=" C GLU A3860 " pdb=" O GLU A3860 " ideal model delta sigma weight residual 1.237 1.282 -0.045 1.19e-02 7.06e+03 1.43e+01 bond pdb=" CA ALA A3886 " pdb=" CB ALA A3886 " ideal model delta sigma weight residual 1.534 1.494 0.040 1.18e-02 7.18e+03 1.17e+01 ... (remaining 25322 not shown) Histogram of bond angle deviations from ideal: 97.22 - 106.06: 478 106.06 - 114.89: 15385 114.89 - 123.72: 17594 123.72 - 132.56: 762 132.56 - 141.39: 65 Bond angle restraints: 34284 Sorted by residual: angle pdb=" N LYS A3863 " pdb=" CA LYS A3863 " pdb=" C LYS A3863 " ideal model delta sigma weight residual 111.28 97.93 13.35 1.09e+00 8.42e-01 1.50e+02 angle pdb=" C THR A3862 " pdb=" CA THR A3862 " pdb=" CB THR A3862 " ideal model delta sigma weight residual 109.72 124.20 -14.48 1.92e+00 2.71e-01 5.69e+01 angle pdb=" CA ASP A1454 " pdb=" C ASP A1454 " pdb=" O ASP A1454 " ideal model delta sigma weight residual 120.82 113.82 7.00 1.05e+00 9.07e-01 4.44e+01 angle pdb=" C ILE A3834 " pdb=" N GLU A3835 " pdb=" CA GLU A3835 " ideal model delta sigma weight residual 122.36 111.38 10.98 1.72e+00 3.38e-01 4.08e+01 angle pdb=" N LYS A3833 " pdb=" CA LYS A3833 " pdb=" C LYS A3833 " ideal model delta sigma weight residual 112.72 104.56 8.16 1.28e+00 6.10e-01 4.07e+01 ... (remaining 34279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 14959 35.61 - 71.23: 242 71.23 - 106.84: 12 106.84 - 142.45: 1 142.45 - 178.06: 2 Dihedral angle restraints: 15216 sinusoidal: 6270 harmonic: 8946 Sorted by residual: dihedral pdb=" C THR A3862 " pdb=" N THR A3862 " pdb=" CA THR A3862 " pdb=" CB THR A3862 " ideal model delta harmonic sigma weight residual -122.00 -140.78 18.78 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" O1B ADP A4203 " pdb=" O3A ADP A4203 " pdb=" PB ADP A4203 " pdb=" PA ADP A4203 " ideal model delta sinusoidal sigma weight residual -60.00 118.06 -178.06 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A4203 " pdb=" O5' ADP A4203 " pdb=" PA ADP A4203 " pdb=" O2A ADP A4203 " ideal model delta sinusoidal sigma weight residual -60.00 100.40 -160.40 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 15213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3753 0.124 - 0.247: 113 0.247 - 0.371: 10 0.371 - 0.494: 0 0.494 - 0.618: 1 Chirality restraints: 3877 Sorted by residual: chirality pdb=" CA THR A3862 " pdb=" N THR A3862 " pdb=" C THR A3862 " pdb=" CB THR A3862 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" C3' ATP A4202 " pdb=" C2' ATP A4202 " pdb=" C4' ATP A4202 " pdb=" O3' ATP A4202 " both_signs ideal model delta sigma weight residual False -2.63 -2.98 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2' ATP A4204 " pdb=" C1' ATP A4204 " pdb=" C3' ATP A4204 " pdb=" O2' ATP A4204 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 3874 not shown) Planarity restraints: 4296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A3856 " -0.027 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C HIS A3856 " 0.091 2.00e-02 2.50e+03 pdb=" O HIS A3856 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS A3857 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A2257 " 0.026 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C PHE A2257 " -0.090 2.00e-02 2.50e+03 pdb=" O PHE A2257 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A2258 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 210 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C ASN C 210 " 0.075 2.00e-02 2.50e+03 pdb=" O ASN C 210 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR C 211 " -0.025 2.00e-02 2.50e+03 ... (remaining 4293 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2146 2.74 - 3.28: 24951 3.28 - 3.82: 41736 3.82 - 4.36: 50687 4.36 - 4.90: 85769 Nonbonded interactions: 205289 Sorted by model distance: nonbonded pdb=" NZ LYS A2225 " pdb=" O3' ATP A4201 " model vdw 2.201 2.520 nonbonded pdb=" N GLU A2112 " pdb=" OE1 GLU A2112 " model vdw 2.207 2.520 nonbonded pdb=" N GLU C 253 " pdb=" OE1 GLU C 253 " model vdw 2.223 2.520 nonbonded pdb=" O GLY A3643 " pdb=" NH2 ARG A3894 " model vdw 2.242 2.520 nonbonded pdb=" OD2 ASP A2839 " pdb=" OH TYR A2874 " model vdw 2.244 2.440 ... (remaining 205284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 139 through 213 or resid 216 through 350 or resid 355 thro \ ugh 400 or resid 405 through 494)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.300 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 68.630 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25327 Z= 0.286 Angle : 0.792 14.480 34284 Z= 0.460 Chirality : 0.052 0.618 3877 Planarity : 0.005 0.100 4296 Dihedral : 12.790 178.064 9398 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 0.47 % Allowed : 4.55 % Favored : 94.98 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3017 helix: 1.69 (0.13), residues: 1387 sheet: 0.69 (0.22), residues: 504 loop : -0.31 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 442 HIS 0.016 0.001 HIS A2400 PHE 0.025 0.002 PHE A1561 TYR 0.027 0.002 TYR C 219 ARG 0.013 0.001 ARG A2387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2049 MET cc_start: 0.6982 (tpp) cc_final: 0.6471 (tpp) REVERT: A 2259 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (tpp) REVERT: B 304 ASP cc_start: 0.7618 (t0) cc_final: 0.7353 (t0) REVERT: C 365 TYR cc_start: 0.7600 (m-80) cc_final: 0.7363 (m-10) outliers start: 13 outliers final: 5 residues processed: 159 average time/residue: 0.3632 time to fit residues: 93.3575 Evaluate side-chains 116 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2868 ASP Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3856 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 177 optimal weight: 0.3980 chunk 276 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25327 Z= 0.168 Angle : 0.489 6.623 34284 Z= 0.264 Chirality : 0.041 0.153 3877 Planarity : 0.004 0.043 4296 Dihedral : 9.134 169.957 3384 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.90 % Allowed : 4.80 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3017 helix: 2.24 (0.14), residues: 1387 sheet: 0.59 (0.22), residues: 508 loop : -0.21 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.007 0.001 HIS A2400 PHE 0.017 0.001 PHE A2972 TYR 0.016 0.001 TYR B 309 ARG 0.005 0.000 ARG A2387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2043 GLN cc_start: 0.8115 (tp40) cc_final: 0.7499 (mt0) REVERT: A 2259 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: A 2272 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 2638 ARG cc_start: 0.7191 (tmm-80) cc_final: 0.6807 (ttp80) REVERT: B 300 VAL cc_start: 0.8233 (t) cc_final: 0.7984 (t) REVERT: B 304 ASP cc_start: 0.7827 (t0) cc_final: 0.7420 (t70) REVERT: B 311 ILE cc_start: 0.8966 (mt) cc_final: 0.8762 (tt) REVERT: C 342 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8243 (mptt) outliers start: 25 outliers final: 7 residues processed: 144 average time/residue: 0.3295 time to fit residues: 80.8302 Evaluate side-chains 111 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1712 ILE Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1864 ASN A1867 GLN A2201 HIS A2228 HIS A2553 HIS A3517 HIS B 176 HIS C 176 HIS C 328 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25327 Z= 0.319 Angle : 0.580 6.648 34284 Z= 0.307 Chirality : 0.044 0.156 3877 Planarity : 0.004 0.047 4296 Dihedral : 8.810 171.347 3375 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.61 % Allowed : 4.88 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3017 helix: 2.19 (0.14), residues: 1375 sheet: 0.48 (0.22), residues: 505 loop : -0.43 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 299 HIS 0.007 0.001 HIS C 164 PHE 0.021 0.002 PHE B 338 TYR 0.019 0.002 TYR A2571 ARG 0.004 0.001 ARG A1815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 109 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 2043 GLN cc_start: 0.8161 (tp40) cc_final: 0.7592 (mt0) REVERT: A 2259 MET cc_start: 0.8644 (mmm) cc_final: 0.8384 (tpp) REVERT: A 2272 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8593 (mm) REVERT: A 2302 PHE cc_start: 0.8127 (m-10) cc_final: 0.7824 (m-80) REVERT: A 2638 ARG cc_start: 0.7333 (tmm-80) cc_final: 0.7032 (ttp80) REVERT: A 2938 MET cc_start: 0.8433 (mtt) cc_final: 0.8196 (mtm) REVERT: A 3631 MET cc_start: 0.8510 (tmm) cc_final: 0.8238 (tmm) REVERT: B 304 ASP cc_start: 0.7584 (t0) cc_final: 0.7192 (t70) REVERT: B 311 ILE cc_start: 0.8982 (mt) cc_final: 0.8711 (tt) REVERT: B 480 MET cc_start: 0.7686 (tmm) cc_final: 0.7416 (tmm) REVERT: C 342 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8240 (mptt) REVERT: C 422 ASP cc_start: 0.8380 (t0) cc_final: 0.8031 (t0) outliers start: 45 outliers final: 22 residues processed: 143 average time/residue: 0.3358 time to fit residues: 81.5252 Evaluate side-chains 123 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2868 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3408 LEU Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 132 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 278 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1864 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25327 Z= 0.136 Angle : 0.445 6.958 34284 Z= 0.236 Chirality : 0.040 0.138 3877 Planarity : 0.003 0.044 4296 Dihedral : 7.957 173.189 3372 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.72 % Allowed : 5.84 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.15), residues: 3017 helix: 2.52 (0.14), residues: 1373 sheet: 0.56 (0.22), residues: 503 loop : -0.42 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS C 164 PHE 0.017 0.001 PHE A2244 TYR 0.013 0.001 TYR A2571 ARG 0.003 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8039 (m-30) cc_final: 0.7756 (m-30) REVERT: A 2043 GLN cc_start: 0.7897 (tp40) cc_final: 0.7433 (mt0) REVERT: A 2259 MET cc_start: 0.8603 (mmm) cc_final: 0.8303 (tpp) REVERT: A 2272 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8505 (mm) REVERT: A 2518 THR cc_start: 0.7696 (p) cc_final: 0.7114 (t) REVERT: A 2638 ARG cc_start: 0.7345 (tmm-80) cc_final: 0.7050 (ttp80) REVERT: A 2938 MET cc_start: 0.8479 (mtt) cc_final: 0.8204 (mtm) REVERT: A 3608 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: A 3722 MET cc_start: 0.8870 (mmm) cc_final: 0.8638 (mmm) REVERT: B 300 VAL cc_start: 0.8197 (t) cc_final: 0.7942 (t) REVERT: B 304 ASP cc_start: 0.7442 (t0) cc_final: 0.7140 (t70) REVERT: B 385 TRP cc_start: 0.7863 (OUTLIER) cc_final: 0.6585 (m100) REVERT: C 422 ASP cc_start: 0.8353 (t0) cc_final: 0.8124 (t0) outliers start: 20 outliers final: 9 residues processed: 124 average time/residue: 0.3321 time to fit residues: 71.7714 Evaluate side-chains 107 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3608 PHE Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 203 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25327 Z= 0.232 Angle : 0.479 7.025 34284 Z= 0.252 Chirality : 0.041 0.170 3877 Planarity : 0.003 0.043 4296 Dihedral : 7.626 176.375 3372 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.22 % Allowed : 5.99 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 3017 helix: 2.53 (0.14), residues: 1382 sheet: 0.51 (0.23), residues: 510 loop : -0.46 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS C 164 PHE 0.018 0.001 PHE B 345 TYR 0.016 0.001 TYR A2571 ARG 0.002 0.000 ARG A2460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 2.997 Fit side-chains REVERT: A 1544 ASP cc_start: 0.8098 (m-30) cc_final: 0.7847 (m-30) REVERT: A 2043 GLN cc_start: 0.7925 (tp40) cc_final: 0.7453 (mt0) REVERT: A 2259 MET cc_start: 0.8630 (mmm) cc_final: 0.8364 (tpp) REVERT: A 2272 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 2871 GLN cc_start: 0.8336 (tp40) cc_final: 0.7546 (tm-30) REVERT: A 2938 MET cc_start: 0.8502 (mtt) cc_final: 0.8216 (mtm) REVERT: A 3345 MET cc_start: 0.8532 (mmt) cc_final: 0.8247 (mmp) REVERT: A 3608 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: A 3846 MET cc_start: 0.9061 (mmt) cc_final: 0.8772 (mmm) REVERT: B 300 VAL cc_start: 0.8275 (t) cc_final: 0.8026 (t) REVERT: B 304 ASP cc_start: 0.7513 (t0) cc_final: 0.7147 (t70) REVERT: B 385 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.6729 (m100) outliers start: 34 outliers final: 23 residues processed: 127 average time/residue: 0.3232 time to fit residues: 72.0205 Evaluate side-chains 122 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2738 MET Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3608 PHE Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 295 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25327 Z= 0.160 Angle : 0.440 7.326 34284 Z= 0.231 Chirality : 0.040 0.141 3877 Planarity : 0.003 0.042 4296 Dihedral : 6.956 142.536 3372 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.00 % Allowed : 6.31 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 3017 helix: 2.65 (0.14), residues: 1377 sheet: 0.57 (0.23), residues: 509 loop : -0.50 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.004 0.001 HIS C 164 PHE 0.013 0.001 PHE B 345 TYR 0.016 0.001 TYR A3268 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 3.047 Fit side-chains REVERT: A 1544 ASP cc_start: 0.8105 (m-30) cc_final: 0.7854 (m-30) REVERT: A 2043 GLN cc_start: 0.7913 (tp40) cc_final: 0.7329 (mt0) REVERT: A 2259 MET cc_start: 0.8558 (mmm) cc_final: 0.8299 (tpp) REVERT: A 2272 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 2938 MET cc_start: 0.8549 (mtt) cc_final: 0.8248 (mtm) REVERT: A 3345 MET cc_start: 0.8511 (mmt) cc_final: 0.8220 (mmp) REVERT: A 3608 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: A 3846 MET cc_start: 0.9067 (mmt) cc_final: 0.8791 (mmm) REVERT: B 300 VAL cc_start: 0.8238 (t) cc_final: 0.8014 (t) REVERT: B 304 ASP cc_start: 0.7314 (t0) cc_final: 0.6985 (t70) REVERT: B 385 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.6515 (m100) REVERT: C 211 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7146 (p90) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.3410 time to fit residues: 74.6443 Evaluate side-chains 118 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3608 PHE Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 0.0570 chunk 164 optimal weight: 0.6980 chunk 293 optimal weight: 0.0670 chunk 183 optimal weight: 3.9990 chunk 179 optimal weight: 0.0470 chunk 135 optimal weight: 0.0770 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2741 HIS A2931 ASN C 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25327 Z= 0.104 Angle : 0.420 9.136 34284 Z= 0.219 Chirality : 0.039 0.137 3877 Planarity : 0.003 0.042 4296 Dihedral : 6.445 104.527 3372 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.72 % Allowed : 6.85 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 3017 helix: 2.74 (0.14), residues: 1380 sheet: 0.74 (0.23), residues: 507 loop : -0.46 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 324 HIS 0.004 0.000 HIS B 323 PHE 0.010 0.001 PHE A2972 TYR 0.016 0.001 TYR A3268 ARG 0.002 0.000 ARG A3942 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8038 (m-30) cc_final: 0.7756 (m-30) REVERT: A 2043 GLN cc_start: 0.7789 (tp40) cc_final: 0.7198 (mt0) REVERT: A 2259 MET cc_start: 0.8472 (mmm) cc_final: 0.8248 (tpp) REVERT: A 2272 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 3291 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.6999 (mmm160) REVERT: A 3700 MET cc_start: 0.8300 (ttp) cc_final: 0.8072 (ttm) REVERT: A 3846 MET cc_start: 0.9105 (mmt) cc_final: 0.8800 (mmm) REVERT: B 304 ASP cc_start: 0.7454 (t0) cc_final: 0.7121 (t70) REVERT: C 211 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6982 (p90) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.3271 time to fit residues: 72.1910 Evaluate side-chains 113 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 25327 Z= 0.142 Angle : 0.430 9.340 34284 Z= 0.223 Chirality : 0.040 0.217 3877 Planarity : 0.003 0.041 4296 Dihedral : 6.218 79.874 3372 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.04 % Allowed : 6.78 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.16), residues: 3017 helix: 2.74 (0.14), residues: 1383 sheet: 0.76 (0.23), residues: 501 loop : -0.47 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.004 0.001 HIS C 164 PHE 0.012 0.001 PHE C 234 TYR 0.018 0.001 TYR A3268 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8153 (m-30) cc_final: 0.7907 (m-30) REVERT: A 2043 GLN cc_start: 0.7819 (tp40) cc_final: 0.7229 (mt0) REVERT: A 2259 MET cc_start: 0.8520 (mmm) cc_final: 0.8290 (tpp) REVERT: A 2272 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 2792 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 3345 MET cc_start: 0.8452 (mmt) cc_final: 0.8198 (mmp) REVERT: A 3846 MET cc_start: 0.9151 (mmt) cc_final: 0.8833 (mmm) REVERT: B 304 ASP cc_start: 0.7619 (t0) cc_final: 0.7270 (t70) REVERT: B 385 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.6744 (m100) REVERT: C 211 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6980 (p90) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.3301 time to fit residues: 70.1208 Evaluate side-chains 118 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 0.0030 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25327 Z= 0.166 Angle : 0.442 9.833 34284 Z= 0.229 Chirality : 0.040 0.201 3877 Planarity : 0.003 0.041 4296 Dihedral : 6.124 79.988 3372 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.90 % Allowed : 6.96 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 3017 helix: 2.72 (0.14), residues: 1388 sheet: 0.73 (0.23), residues: 501 loop : -0.49 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.004 0.001 HIS A3413 PHE 0.012 0.001 PHE C 234 TYR 0.018 0.001 TYR A3268 ARG 0.001 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 3.012 Fit side-chains revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8091 (m-30) cc_final: 0.7849 (m-30) REVERT: A 2043 GLN cc_start: 0.7835 (tp40) cc_final: 0.7244 (mt0) REVERT: A 2259 MET cc_start: 0.8402 (mmm) cc_final: 0.8151 (tpp) REVERT: A 2272 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8463 (mm) REVERT: A 2792 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 3700 MET cc_start: 0.8356 (ttp) cc_final: 0.8057 (ttm) REVERT: A 3722 MET cc_start: 0.9149 (tpp) cc_final: 0.8637 (mmt) REVERT: A 3846 MET cc_start: 0.9163 (mmt) cc_final: 0.8850 (mmm) REVERT: B 304 ASP cc_start: 0.7630 (t0) cc_final: 0.7308 (t70) REVERT: B 385 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.6743 (m100) REVERT: C 211 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6939 (p90) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.3321 time to fit residues: 67.9828 Evaluate side-chains 118 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 0.0870 chunk 289 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 186 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25327 Z= 0.269 Angle : 0.514 9.409 34284 Z= 0.267 Chirality : 0.042 0.180 3877 Planarity : 0.003 0.040 4296 Dihedral : 6.414 85.390 3372 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.97 % Allowed : 6.99 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 3017 helix: 2.59 (0.14), residues: 1388 sheet: 0.50 (0.23), residues: 508 loop : -0.59 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 299 HIS 0.007 0.001 HIS A3413 PHE 0.016 0.002 PHE C 234 TYR 0.018 0.001 TYR A3268 ARG 0.003 0.000 ARG A1815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 2.926 Fit side-chains revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8238 (m-30) cc_final: 0.8030 (m-30) REVERT: A 2043 GLN cc_start: 0.7911 (tp40) cc_final: 0.7272 (mt0) REVERT: A 2259 MET cc_start: 0.8333 (mmm) cc_final: 0.8130 (tpp) REVERT: A 2272 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8572 (mm) REVERT: A 3700 MET cc_start: 0.8502 (ttp) cc_final: 0.8225 (ttm) REVERT: A 3722 MET cc_start: 0.9363 (tpp) cc_final: 0.8751 (mmt) REVERT: A 3846 MET cc_start: 0.9073 (mmt) cc_final: 0.8819 (mmm) REVERT: B 304 ASP cc_start: 0.7776 (t0) cc_final: 0.7441 (t70) REVERT: B 385 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.6937 (m100) REVERT: C 211 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.6804 (p90) outliers start: 27 outliers final: 22 residues processed: 118 average time/residue: 0.3429 time to fit residues: 70.2762 Evaluate side-chains 119 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 385 TRP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 248 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3890 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062222 restraints weight = 84098.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064275 restraints weight = 41082.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065609 restraints weight = 26097.231| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 25327 Z= 0.133 Angle : 0.436 8.008 34284 Z= 0.227 Chirality : 0.040 0.210 3877 Planarity : 0.003 0.041 4296 Dihedral : 6.193 83.346 3372 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.79 % Allowed : 7.24 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.16), residues: 3017 helix: 2.72 (0.14), residues: 1385 sheet: 0.59 (0.23), residues: 504 loop : -0.56 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.003 0.001 HIS C 164 PHE 0.012 0.001 PHE A2972 TYR 0.017 0.001 TYR A3268 ARG 0.002 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.75 seconds wall clock time: 67 minutes 36.13 seconds (4056.13 seconds total)